#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
HPSE2	60495	broad.mit.edu	37	10	100401682	100401682	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:100401682G>A	ENST00000370552.3	-	7	1079	c.1020C>T	c.(1018-1020)ggC>ggT	p.G340G	HPSE2_ENST00000404542.1_Silent_p.G228G|HPSE2_ENST00000370549.1_Silent_p.G282G|HPSE2_ENST00000370546.1_Silent_p.G340G	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	340					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)	p.G340G(2)		NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		TGACCACCCGGCCATCAATGT	0.403																																					p.G340G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1020T	10						.						143.0	153.0	150.0					10																	100401682		2203	4300	6503	100391672	SO:0001819	synonymous_variant	60495	exon7			AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"""urofacial syndrome"", ""heparanase 2"""	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.1020C>T	10.37:g.100401682G>A		Somatic		Capture	Illumina HiSeq	Phase_I	100391672	NM_001166246	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Silent	SNP	ENST00000370552.3	37	CCDS7477.1																																																																																				0.403	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828	
CNNM1	26507	broad.mit.edu	37	10	101120636	101120636	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:101120636C>T	ENST00000356713.4	+	3	2051	c.1762C>T	c.(1762-1764)Cgg>Tgg	p.R588W	CNNM1_ENST00000370534.4_Missense_Mutation_p.R223W|CNNM1_ENST00000370528.3_Missense_Mutation_p.R517W|CNNM1_ENST00000446890.1_Missense_Mutation_p.R517W	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	588					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)	p.R223W(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		GGAGCGGAAGCGGCATGACTT	0.532																																					p.R588W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1762T	10						.						145.0	146.0	145.0					10																	101120636		2203	4300	6503	101110626	SO:0001583	missense	26507	exon3			AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"""cyclin M1"""	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.1762C>T	10.37:g.101120636C>T	ENSP00000349147:p.Arg588Trp	Somatic		Capture	Illumina HiSeq	Phase_I	101110626	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Missense_Mutation	SNP	ENST00000356713.4	37	CCDS7478.2	.	.	.	.	.	.	.	.	.	.	C	25.5	4.641878	0.87859	.	.	ENSG00000119946	ENST00000356713;ENST00000446890;ENST00000370528;ENST00000370534;ENST00000545665	D;D;D;T	0.84298	-1.83;-1.79;-1.78;-0.78	5.5	4.51	0.55191	.	0.135630	0.51477	D	0.000088	D	0.88952	0.6577	L	0.46819	1.47	0.37308	D	0.908982	D;D;D;D	0.76494	0.992;0.976;0.96;0.999	P;D;P;P	0.63283	0.72;0.913;0.586;0.735	D	0.91413	0.5152	10	0.72032	D	0.01	-19.095	16.9982	0.86373	0.136:0.8639:0.0:0.0	.	223;588;223;588	F5H5J0;Q9NRU3-2;B7Z5S3;Q9NRU3	.;.;.;CNNM1_HUMAN	W	588;517;517;223;41	ENSP00000349147:R588W;ENSP00000406492:R517W;ENSP00000359559:R517W;ENSP00000359565:R223W	ENSP00000349147:R588W	R	+	1	2	CNNM1	101110626	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.854000	0.48325	2.593000	0.87608	0.655000	0.94253	CGG		0.532	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348	
ENTPD7	57089	broad.mit.edu	37	10	101455842	101455842	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:101455842G>A	ENST00000370489.4	+	9	1151	c.973G>A	c.(973-975)Gaa>Aaa	p.E325K		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	325						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.E325K(2)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		GCAGCGCTACGAAGACCTTGT	0.438																																					p.E325K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G973A	10						.						99.0	94.0	95.0					10																	101455842		2203	4300	6503	101445832	SO:0001583	missense	57089	exon9			AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.973G>A	10.37:g.101455842G>A	ENSP00000359520:p.Glu325Lys	Somatic		Capture	Illumina HiSeq	Phase_I	101445832	NM_020354	B2RB83|B3KP21|D3DR64	Missense_Mutation	SNP	ENST00000370489.4	37	CCDS7480.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.021976	0.54576	.	.	ENSG00000198018	ENST00000370489	T	0.11930	2.73	4.75	3.84	0.44239	.	0.000000	0.85682	D	0.000000	T	0.29028	0.0721	M	0.73598	2.24	0.58432	D	0.999998	D	0.57257	0.979	P	0.55112	0.769	T	0.07597	-1.0764	10	0.29301	T	0.29	-19.207	14.6583	0.68850	0.0:0.0:0.8533:0.1467	.	325	Q9NQZ7	ENTP7_HUMAN	K	325	ENSP00000359520:E325K	ENSP00000359520:E325K	E	+	1	0	ENTPD7	101445832	1.000000	0.71417	1.000000	0.80357	0.137000	0.21094	7.771000	0.85420	1.339000	0.45563	-0.282000	0.10007	GAA		0.438	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354	
ABCC2	1244	broad.mit.edu	37	10	101577122	101577122	+	Missense_Mutation	SNP	A	A	C	rs376403595		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:101577122A>C	ENST00000370449.4	+	17	2265	c.2152A>C	c.(2152-2154)Aac>Cac	p.N718H		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	718	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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.N718H(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)	CATAAAGGACAACATCCTTTT	0.483																																					p.N718H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2152C	10						.						93.0	80.0	84.0					10																	101577122		2203	4300	6503	101567112	SO:0001583	missense	1244	exon17			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.2152A>C	10.37:g.101577122A>C	ENSP00000359478:p.Asn718His	Somatic		Capture	Illumina HiSeq	Phase_I	101567112	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.410672	0.83340	.	.	ENSG00000023839	ENST00000370449	D	0.94650	-3.48	5.41	5.41	0.78517	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.98381	0.9462	H	0.97852	4.09	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99774	1.1025	10	0.87932	D	0	-22.1244	15.4285	0.75072	1.0:0.0:0.0:0.0	.	718	Q92887	MRP2_HUMAN	H	718	ENSP00000359478:N718H	ENSP00000359478:N718H	N	+	1	0	ABCC2	101567112	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	9.317000	0.96327	2.049000	0.60858	0.533000	0.62120	AAC		0.483	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
ABCC2	1244	broad.mit.edu	37	10	101590128	101590128	+	Silent	SNP	C	C	T	rs201553035		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:101590128C>T	ENST00000370449.4	+	20	2798	c.2685C>T	c.(2683-2685)ccC>ccT	p.P895P		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	895					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.P895P(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)	AAGAGATCCCCGAAGATGCAG	0.512													C|||	1	0.000199681	0.0	0.0	5008	,	,		19960	0.001		0.0	False		,,,				2504	0.0				p.P895P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2685T	10						.						134.0	129.0	131.0					10																	101590128		2203	4300	6503	101580118	SO:0001819	synonymous_variant	1244	exon20			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.2685C>T	10.37:g.101590128C>T		Somatic		Capture	Illumina HiSeq	Phase_I	101580118	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Silent	SNP	ENST00000370449.4	37	CCDS7484.1																																																																																				0.512	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
CHUK	1147	broad.mit.edu	37	10	101967042	101967042	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:101967042A>G	ENST00000370397.7	-	11	1262	c.1176T>C	c.(1174-1176)acT>acC	p.T392T		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	392					anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|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)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)	p.T392T(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	CTTCATATACAGTTTTACTTT	0.318																																					p.T392T	Ovarian(159;52 1904 10536 35305 37148)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1176C	10						.						69.0	69.0	69.0					10																	101967042		2202	4295	6497	101957032	SO:0001819	synonymous_variant	1147	exon11			AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.1176T>C	10.37:g.101967042A>G		Somatic		Capture	Illumina HiSeq	Phase_I	101957032	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Silent	SNP	ENST00000370397.7	37	CCDS7488.1																																																																																				0.318	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278	
CWF19L1	55280	broad.mit.edu	37	10	102013244	102013244	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:102013244G>A	ENST00000354105.4	-	6	643	c.557C>T	c.(556-558)aCg>aTg	p.T186M	CWF19L1_ENST00000478047.1_5'UTR	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	186							catalytic activity (GO:0003824)	p.T186M(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		TTTCAAGCCCGTGGCAAGACT	0.393																																					p.T186M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C557T	10						.						132.0	130.0	131.0					10																	102013244		2203	4300	6503	102003234	SO:0001583	missense	55280	exon6			AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485			25613	protein-coding gene	gene with protein product						14702039	Standard	NM_018294		Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000354105.4:c.557C>T	10.37:g.102013244G>A	ENSP00000326411:p.Thr186Met	Somatic		Capture	Illumina HiSeq	Phase_I	102003234	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	De_novo_Start_OutOfFrame	SNP	ENST00000354105.4	37	CCDS7489.1	.	.	.	.	.	.	.	.	.	.	g	0.997	-0.692170	0.03303	.	.	ENSG00000095485	ENST00000354105	T	0.30448	1.53	5.55	0.0123	0.14091	.	0.823199	0.11797	N	0.528513	T	0.16685	0.0401	N	0.12569	0.235	0.09310	N	1	B;B	0.18461	0.028;0.009	B;B	0.10450	0.005;0.003	T	0.23261	-1.0193	10	0.31617	T	0.26	4.5702	11.113	0.48243	0.4369:0.0:0.5631:0.0	.	49;186	Q69YN2-3;Q69YN2	.;C19L1_HUMAN	M	186	ENSP00000326411:T186M	ENSP00000326411:T186M	T	-	2	0	CWF19L1	102003234	0.000000	0.05858	0.020000	0.16555	0.011000	0.07611	0.896000	0.28377	-0.105000	0.12132	-2.409000	0.00222	ACG		0.393	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294	
CWF19L1	55280	broad.mit.edu	37	10	102020068	102020068	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:102020068G>C	ENST00000354105.4	-	4	282	c.196C>G	c.(196-198)Cag>Gag	p.Q66E	RNU6-422P_ENST00000384632.1_RNA	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	66							catalytic activity (GO:0003824)	p.Q66E(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		ACATATGTCTGAATAGGAGCT	0.353																																					p.Q66E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C196G	10						.						126.0	118.0	121.0					10																	102020068		2203	4300	6503	102010058	SO:0001583	missense	55280	exon4			AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485			25613	protein-coding gene	gene with protein product						14702039	Standard	NM_018294		Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000354105.4:c.196C>G	10.37:g.102020068G>C	ENSP00000326411:p.Gln66Glu	Somatic		Capture	Illumina HiSeq	Phase_I	102010058	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Missense_Mutation	SNP	ENST00000354105.4	37	CCDS7489.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.337981	0.41398	.	.	ENSG00000095485	ENST00000354105	T	0.35048	1.33	5.56	5.56	0.83823	.	0.149534	0.64402	D	0.000009	T	0.29850	0.0746	L	0.28274	0.84	0.48901	D	0.999725	B	0.25235	0.121	B	0.23150	0.044	T	0.06041	-1.0849	10	0.56958	D	0.05	-3.7195	17.0229	0.86438	0.0:0.0:1.0:0.0	.	66	Q69YN2	C19L1_HUMAN	E	66	ENSP00000326411:Q66E	ENSP00000326411:Q66E	Q	-	1	0	CWF19L1	102010058	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	9.220000	0.95180	2.613000	0.88420	0.585000	0.79938	CAG		0.353	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294	
NPM3	10360	broad.mit.edu	37	10	103541576	103541576	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:103541576C>T	ENST00000370110.5	-	5	476	c.454G>A	c.(454-456)Gag>Aag	p.E152K	NPM3_ENST00000474993.1_5'UTR	NM_006993.2	NP_008924.1	O75607	NPM3_HUMAN	nucleophosmin/nucleoplasmin 3	152	Asp/Glu-rich (highly acidic).|Poly-Glu.				rRNA processing (GO:0006364)|rRNA transcription (GO:0009303)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.E152K(1)		large_intestine(3)|lung(1)|skin(1)	5		Colorectal(252;0.122)		Epithelial(162;3.94e-09)|all cancers(201;2.13e-07)		TCCTCTTCCTCGCTCTCCTCC	0.542																																					p.E152K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G454A	10						.						319.0	279.0	293.0					10																	103541576		2203	4300	6503	103531566	SO:0001583	missense	10360	exon5			AY049737	CCDS7519.1	10q24.31	2009-08-27	2009-08-27		ENSG00000107833	ENSG00000107833			7931	protein-coding gene	gene with protein product		606456				11722795	Standard	NM_006993		Approved		uc001ktt.3	O75607	OTTHUMG00000018942	ENST00000370110.5:c.454G>A	10.37:g.103541576C>T	ENSP00000359128:p.Glu152Lys	Somatic		Capture	Illumina HiSeq	Phase_I	103531566	NM_006993	Q9UNY6	Missense_Mutation	SNP	ENST00000370110.5	37	CCDS7519.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.330008	0.60743	.	.	ENSG00000107833	ENST00000370110	T	0.52295	0.67	3.93	3.93	0.45458	.	3.275200	0.02395	U	0.080052	T	0.59636	0.2208	N	0.19112	0.55	0.28526	N	0.912832	D	0.76494	0.999	D	0.77004	0.989	T	0.59375	-0.7466	10	0.62326	D	0.03	-14.5721	13.6199	0.62130	0.0:1.0:0.0:0.0	.	152	O75607	NPM3_HUMAN	K	152	ENSP00000359128:E152K	ENSP00000359128:E152K	E	-	1	0	NPM3	103531566	0.917000	0.31117	0.542000	0.28115	0.624000	0.37722	3.883000	0.56168	2.211000	0.71520	0.561000	0.74099	GAG		0.542	NPM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050003.2	NM_006993	
KCNIP2	30819	broad.mit.edu	37	10	103587984	103587984	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:103587984C>T	ENST00000356640.2	-	7	796	c.521G>A	c.(520-522)cGg>cAg	p.R174Q	KCNIP2_ENST00000353068.3_Missense_Mutation_p.R131Q|KCNIP2_ENST00000343195.4_Missense_Mutation_p.R124Q|KCNIP2_ENST00000358038.3_Missense_Mutation_p.R156Q|KCNIP2_ENST00000370046.1_Intron|KCNIP2-AS1_ENST00000412353.1_RNA|KCNIP2_ENST00000355657.2_5'UTR|KCNIP2_ENST00000461105.1_Missense_Mutation_p.R189Q|KCNIP2_ENST00000348850.5_Missense_Mutation_p.R129Q	NM_014591.4|NM_173191.2	NP_055406.2|NP_775283.1	Q9NS61	KCIP2_HUMAN	Kv channel interacting protein 2	174	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				clustering of voltage-gated potassium channels (GO:0045163)|detection of calcium ion (GO:0005513)|membrane repolarization (GO:0086009)|muscle contraction (GO:0006936)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of cation channel activity (GO:2001257)|regulation of heart contraction (GO:0008016)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|calcium ion binding (GO:0005509)|ER retention sequence binding (GO:0046923)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein N-terminus binding (GO:0047485)	p.R189Q(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	11		Colorectal(252;0.122)		Epithelial(162;4.93e-09)|all cancers(201;2.63e-07)		TACAGTTCCCCGAAGAATCAC	0.557																																					p.R156Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G467A	10						.						101.0	96.0	98.0					10																	103587984		2203	4300	6503	103577974	SO:0001583	missense	30819	exon6				CCDS7521.1, CCDS7522.1, CCDS7523.1, CCDS7524.1, CCDS7525.1, CCDS7526.1, CCDS41562.1	10q24.32	2013-09-20	2001-11-29		ENSG00000120049	ENSG00000120049		"""EF-hand domain containing"""	15522	protein-coding gene	gene with protein product		604661	"""Kv channel-interacting protein 2"""			10676964	Standard	NM_173192		Approved	KCHIP2	uc001kuc.3	Q9NS61	OTTHUMG00000018937	ENST00000356640.2:c.521G>A	10.37:g.103587984C>T	ENSP00000349055:p.Arg174Gln	Somatic		Capture	Illumina HiSeq	Phase_I	103577974	NM_173192	A6NJE5|A8MQ75|Q3YAC6|Q3YAC8|Q3YAC9|Q7Z6F1|Q96K86|Q96T41|Q96T42|Q96T43|Q96T44|Q9H0N4|Q9HD10|Q9HD11|Q9NS60|Q9NY10|Q9NZI1	Missense_Mutation	SNP	ENST00000356640.2	37	CCDS7522.1	.	.	.	.	.	.	.	.	.	.	C	34	5.294879	0.95546	.	.	ENSG00000120049	ENST00000348850;ENST00000358038;ENST00000359877;ENST00000370059;ENST00000356640;ENST00000434163;ENST00000353068;ENST00000461105;ENST00000343195	T;T;T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;0.93;-0.29;-0.29;-0.29	5.11	5.11	0.69529	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.86033	0.5836	M	0.91717	3.235	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;P	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.952	D;D;D;D;D;D;D;D;D;D;D;P	0.91635	0.972;0.996;0.999;0.997;0.999;0.999;0.999;0.999;0.981;0.999;0.979;0.615	D	0.88983	0.3409	10	0.87932	D	0	.	18.7219	0.91698	0.0:1.0:0.0:0.0	.	129;118;120;124;124;156;131;189;174;105;129;81	B4DW99;B4DHY9;Q9NS61-5;Q3YAC7;Q9NS61-3;Q9NS61-2;Q9NS61-7;Q9NS61-6;Q9NS61;B3KSZ5;Q3YAC6;Q9NS61-8	.;.;.;.;.;.;.;.;KCIP2_HUMAN;.;.;.	Q	129;156;105;156;174;81;131;189;124	ENSP00000239118:R129Q;ENSP00000350733:R156Q;ENSP00000349055:R174Q;ENSP00000411679:R81Q;ENSP00000341624:R131Q;ENSP00000420040:R189Q;ENSP00000344169:R124Q	ENSP00000344169:R124Q	R	-	2	0	KCNIP2	103577974	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.903000	0.69877	2.663000	0.90544	0.561000	0.74099	CGG		0.557	KCNIP2-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049973.1		
KCNIP2	30819	broad.mit.edu	37	10	103588871	103588871	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:103588871C>T	ENST00000356640.2	-	4	584	c.309G>A	c.(307-309)acG>acA	p.T103T	KCNIP2_ENST00000353068.3_Silent_p.T53T|KCNIP2_ENST00000343195.4_Silent_p.T53T|KCNIP2_ENST00000358038.3_Silent_p.T85T|KCNIP2_ENST00000370046.1_Silent_p.T53T|KCNIP2-AS1_ENST00000412353.1_RNA|KCNIP2_ENST00000355657.2_5'UTR|KCNIP2_ENST00000461105.1_Silent_p.T118T|KCNIP2_ENST00000348850.5_Silent_p.T58T	NM_014591.4|NM_173191.2	NP_055406.2|NP_775283.1	Q9NS61	KCIP2_HUMAN	Kv channel interacting protein 2	103	EF-hand 1; degenerate. {ECO:0000255|PROSITE-ProRule:PRU00448}.				clustering of voltage-gated potassium channels (GO:0045163)|detection of calcium ion (GO:0005513)|membrane repolarization (GO:0086009)|muscle contraction (GO:0006936)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of cation channel activity (GO:2001257)|regulation of heart contraction (GO:0008016)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|calcium ion binding (GO:0005509)|ER retention sequence binding (GO:0046923)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein N-terminus binding (GO:0047485)	p.T118T(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	11		Colorectal(252;0.122)		Epithelial(162;4.93e-09)|all cancers(201;2.63e-07)		ACTCCTTGCGCGTGAATTTGG	0.602																																					p.T85T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G255A	10						.						91.0	74.0	80.0					10																	103588871		2203	4300	6503	103578861	SO:0001819	synonymous_variant	30819	exon3				CCDS7521.1, CCDS7522.1, CCDS7523.1, CCDS7524.1, CCDS7525.1, CCDS7526.1, CCDS41562.1	10q24.32	2013-09-20	2001-11-29		ENSG00000120049	ENSG00000120049		"""EF-hand domain containing"""	15522	protein-coding gene	gene with protein product		604661	"""Kv channel-interacting protein 2"""			10676964	Standard	NM_173192		Approved	KCHIP2	uc001kuc.3	Q9NS61	OTTHUMG00000018937	ENST00000356640.2:c.309G>A	10.37:g.103588871C>T		Somatic		Capture	Illumina HiSeq	Phase_I	103578861	NM_173192	A6NJE5|A8MQ75|Q3YAC6|Q3YAC8|Q3YAC9|Q7Z6F1|Q96K86|Q96T41|Q96T42|Q96T43|Q96T44|Q9H0N4|Q9HD10|Q9HD11|Q9NS60|Q9NY10|Q9NZI1	Missense_Mutation	SNP	ENST00000356640.2	37	CCDS7522.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.374458	0.42105	.	.	ENSG00000120049	ENST00000359877;ENST00000434163	T	0.70631	-0.5	5.1	-10.2	0.00374	.	.	.	.	.	T	0.51278	0.1665	.	.	.	0.44643	D	0.997624	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35126	-0.9801	8	0.87932	D	0	.	4.0124	0.09629	0.1261:0.1062:0.3241:0.4436	.	25;34	B3KSZ5;Q9NS61-8	.;.	H	25;34	ENSP00000411679:R34H	ENSP00000352940:R25H	R	-	2	0	KCNIP2	103578861	0.007000	0.16637	0.018000	0.16275	0.946000	0.59487	-1.407000	0.02488	-3.236000	0.00208	-1.492000	0.00969	CGC		0.602	KCNIP2-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049973.1		
CYP17A1	1586	broad.mit.edu	37	10	104595121	104595121	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:104595121C>T	ENST00000369887.3	-	2	497	c.326G>A	c.(325-327)cGt>cAt	p.R109H	CYP17A1-AS1_ENST00000369884.4_RNA|CYP17A1_ENST00000489268.1_5'UTR	NM_000102.3	NP_000093.1	P05093	CP17A_HUMAN	cytochrome P450, family 17, subfamily A, polypeptide 1	109					adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|biphenyl metabolic process (GO:0018879)|cellular response to antibiotic (GO:0071236)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to lipopolysaccharide (GO:0071222)|dibenzo-p-dioxin metabolic process (GO:0018894)|glucocorticoid biosynthetic process (GO:0006704)|hippocampus development (GO:0021766)|hormone biosynthetic process (GO:0042446)|Leydig cell differentiation (GO:0033327)|ovulation (GO:0030728)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|progesterone metabolic process (GO:0042448)|response to acetate (GO:0010034)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to insecticide (GO:0017085)|response to ionizing radiation (GO:0010212)|response to methylmercury (GO:0051597)|response to nutrient levels (GO:0031667)|response to retinoic acid (GO:0032526)|response to steroid hormone (GO:0048545)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	axon (GO:0030424)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)	17-alpha-hydroxyprogesterone aldolase activity (GO:0047442)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|steroid 17-alpha-monooxygenase activity (GO:0004508)	p.R109H(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	Abiraterone(DB05812)|Aminophenazone(DB01424)|Dexamethasone(DB01234)|Metoclopramide(DB01233)|Progesterone(DB00396)	GATACCCTTACGGTTGTTGGA	0.572											OREG0020487	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R109H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G326A	10						.						169.0	129.0	143.0					10																	104595121		2203	4300	6503	104585111	SO:0001583	missense	1586	exon2			M19489	CCDS7541.1	10q24.3	2010-05-04	2003-02-14	2003-02-28	ENSG00000148795	ENSG00000148795	1.14.99.9	"""Cytochrome P450s"""	2593	protein-coding gene	gene with protein product	"""Steroid 17-alpha-monooxygenase"""	609300	"""cytochrome P450, subfamily XVII (steroid 17-alpha-hydroxylase), adrenal hyperplasia"""	CYP17		1347802	Standard	NM_000102		Approved	P450C17, CPT7, S17AH	uc001kwg.3	P05093	OTTHUMG00000018969	ENST00000369887.3:c.326G>A	10.37:g.104595121C>T	ENSP00000358903:p.Arg109His	Somatic	172	Capture	Illumina HiSeq	Phase_I	104585111	NM_000102	Q5TZV7	Missense_Mutation	SNP	ENST00000369887.3	37	CCDS7541.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.616829	0.46736	.	.	ENSG00000148795	ENST00000369887	T	0.68479	-0.33	5.76	1.6	0.23607	.	0.711700	0.13726	N	0.367035	T	0.52322	0.1727	N	0.17082	0.46	0.09310	N	1	P	0.48089	0.905	P	0.48368	0.575	T	0.40664	-0.9551	10	0.49607	T	0.09	.	5.6917	0.17833	0.0:0.4843:0.3018:0.2139	.	109	P05093	CP17A_HUMAN	H	109	ENSP00000358903:R109H	ENSP00000358903:R109H	R	-	2	0	CYP17A1	104585111	0.210000	0.23517	0.002000	0.10522	0.002000	0.02628	1.736000	0.38187	0.317000	0.23160	0.456000	0.33151	CGT		0.572	CYP17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050101.1	NM_000102	
CNNM2	54805	broad.mit.edu	37	10	104814119	104814119	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:104814119G>A	ENST00000369878.4	+	3	1987	c.1799G>A	c.(1798-1800)cGg>cAg	p.R600Q	CNNM2_ENST00000433628.2_Missense_Mutation_p.R600Q	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	600					magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)	p.R600Q(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GTGGCTCACCGGGAACGAAAG	0.428											OREG0020489	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R600Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1799A	10						.						65.0	64.0	64.0					10																	104814119		1913	4130	6043	104804109	SO:0001583	missense	54805	exon3			AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"""cyclin M2"""	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.1799G>A	10.37:g.104814119G>A	ENSP00000358894:p.Arg600Gln	Somatic	1384	Capture	Illumina HiSeq	Phase_I	104804109	NM_199076	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Missense_Mutation	SNP	ENST00000369878.4	37	CCDS44474.1	.	.	.	.	.	.	.	.	.	.	G	16.86	3.239564	0.58995	.	.	ENSG00000148842	ENST00000457502;ENST00000433628;ENST00000369878;ENST00000345419	T;T	0.74421	-0.84;-0.84	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.80470	0.4629	L	0.37850	1.14	0.80722	D	1	D;D	0.65815	0.995;0.989	P;P	0.61275	0.886;0.691	T	0.77593	-0.2530	10	0.39692	T	0.17	.	20.5568	0.99304	0.0:0.0:1.0:0.0	.	600;600	Q9H8M5-2;Q9H8M5	.;CNNM2_HUMAN	Q	600	ENSP00000392875:R600Q;ENSP00000358894:R600Q	ENSP00000286899:R600Q	R	+	2	0	CNNM2	104804109	1.000000	0.71417	0.997000	0.53966	0.197000	0.23852	8.004000	0.88535	2.861000	0.98227	0.655000	0.94253	CGG		0.428	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649	
PDCD11	22984	broad.mit.edu	37	10	105185268	105185268	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:105185268C>T	ENST00000369797.3	+	20	3385	c.3291C>T	c.(3289-3291)gaC>gaT	p.D1097D		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1097	S1 motif 9. {ECO:0000255|PROSITE- ProRule:PRU00180}.				mRNA processing (GO:0006397)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)	p.D1097D(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	64		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;7.21e-09)|all cancers(201;1.17e-08)|BRCA - Breast invasive adenocarcinoma(275;0.208)		GCGGGCGAGACATGAAGACAT	0.542																																					p.D1097D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3291T	10						.						55.0	57.0	56.0					10																	105185268		2203	4300	6503	105175258	SO:0001819	synonymous_variant	22984	exon20			D80007	CCDS31276.1	10q24.32	2010-07-06			ENSG00000148843	ENSG00000148843			13408	protein-coding gene	gene with protein product		612333				10229231	Standard	XM_005269647		Approved	KIAA0185, ALG-4, RRP5	uc001kwy.1	Q14690	OTTHUMG00000018988	ENST00000369797.3:c.3291C>T	10.37:g.105185268C>T		Somatic		Capture	Illumina HiSeq	Phase_I	105175258	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Silent	SNP	ENST00000369797.3	37	CCDS31276.1																																																																																				0.542	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
COL17A1	1308	broad.mit.edu	37	10	105797420	105797420	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:105797420G>A	ENST00000353479.5	-	46	3472	c.3182C>T	c.(3181-3183)gCa>gTa	p.A1061V	COL17A1_ENST00000369733.3_Missense_Mutation_p.A1016V	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	1061	Triple-helical region.				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.A1061V(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		AACGTGGCTTGCCAGCTCTGA	0.597																																					p.A1061V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3182T	10						.						111.0	105.0	107.0					10																	105797420		2203	4300	6503	105787410	SO:0001583	missense	1308	exon46			M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"""Collagens"""	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.3182C>T	10.37:g.105797420G>A	ENSP00000340937:p.Ala1061Val	Somatic		Capture	Illumina HiSeq	Phase_I	105787410	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Missense_Mutation	SNP	ENST00000353479.5	37	CCDS7554.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.955048	0.53293	.	.	ENSG00000065618	ENST00000353479;ENST00000369733	D;D	0.93547	-3.24;-3.2	5.27	5.27	0.74061	.	0.000000	0.46442	D	0.000287	D	0.94739	0.8302	L	0.59436	1.845	0.80722	D	1	D	0.67145	0.996	P	0.60609	0.877	D	0.92808	0.6262	10	0.19147	T	0.46	-11.1245	16.6671	0.85255	0.0:0.0:1.0:0.0	.	1061	Q9UMD9	COHA1_HUMAN	V	1061;1016	ENSP00000340937:A1061V;ENSP00000358748:A1016V	ENSP00000340937:A1061V	A	-	2	0	COL17A1	105787410	1.000000	0.71417	0.937000	0.37676	0.024000	0.10985	5.810000	0.69179	2.445000	0.82738	0.561000	0.74099	GCA		0.597	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494	
CFAP43	80217	broad.mit.edu	37	10	105891110	105891110	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:105891110T>C	ENST00000357060.3	-	37	4925	c.4810A>G	c.(4810-4812)Aaa>Gaa	p.K1604E	WDR96_ENST00000479392.1_5'Flank|WDR96_ENST00000428666.1_Missense_Mutation_p.K1576E	NM_025145.5	NP_079421.5												p.K1604E(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CAGATGTCTTTTCTCTCTGAG	0.338																																					p.K1604E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4810G	10						.						123.0	110.0	115.0					10																	105891110		2203	4300	6503	105881100	SO:0001583	missense	80217	exon37																														ENST00000357060.3:c.4810A>G	10.37:g.105891110T>C	ENSP00000349568:p.Lys1604Glu	Somatic		Capture	Illumina HiSeq	Phase_I	105881100	NM_025145		Missense_Mutation	SNP	ENST00000357060.3	37	CCDS31281.1	.	.	.	.	.	.	.	.	.	.	T	15.54	2.863700	0.51482	.	.	ENSG00000197748	ENST00000357060;ENST00000428666	T;T	0.14516	2.5;2.5	5.73	1.93	0.25924	.	0.409622	0.26635	N	0.023281	T	0.17365	0.0417	M	0.61703	1.905	0.21627	N	0.999615	B;P	0.36974	0.046;0.576	B;B	0.40066	0.041;0.318	T	0.07809	-1.0753	10	0.29301	T	0.29	.	13.5204	0.61563	0.0:0.0:0.5352:0.4648	.	1576;1604	G5E9L1;Q8NDM7	.;WDR96_HUMAN	E	1604;1576	ENSP00000349568:K1604E;ENSP00000400289:K1576E	ENSP00000349568:K1604E	K	-	1	0	WDR96	105881100	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	0.603000	0.24149	0.079000	0.16929	0.533000	0.62120	AAA		0.338	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SORCS1	114815	broad.mit.edu	37	10	108357185	108357185	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:108357185C>T	ENST00000263054.6	-	24	3196	c.3189G>A	c.(3187-3189)acG>acA	p.T1063T	SORCS1_ENST00000344440.6_Silent_p.T1063T|SORCS1_ENST00000369698.1_Silent_p.T598T|SORCS1_ENST00000478809.2_5'Flank	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	1063					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.T1063T(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		TTTGGTTGAGCGTGTGGATCA	0.433																																					p.T1063T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3189A	10						.						150.0	139.0	143.0					10																	108357185		2203	4300	6503	108347175	SO:0001819	synonymous_variant	114815	exon24			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.3189G>A	10.37:g.108357185C>T		Somatic		Capture	Illumina HiSeq	Phase_I	108347175	NM_052918	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	C	9.235	1.036802	0.19669	.	.	ENSG00000108018	ENST00000452214	.	.	.	5.71	-0.0738	0.13733	.	.	.	.	.	T	0.40196	0.1107	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27468	-1.0073	4	.	.	.	-12.778	0.9283	0.01329	0.2442:0.3528:0.1199:0.283	.	.	.	.	H	78	.	.	R	-	2	0	SORCS1	108347175	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	0.675000	0.25232	0.323000	0.23307	-0.181000	0.13052	CGC		0.433	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
USP6NL	9712	broad.mit.edu	37	10	11505387	11505387	+	Missense_Mutation	SNP	C	C	T	rs372185786		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:11505387C>T	ENST00000609104.1	-	15	1934	c.1540G>A	c.(1540-1542)Gcg>Acg	p.A514T	USP6NL_ENST00000277575.5_Missense_Mutation_p.A531T|USP6NL_ENST00000379237.2_Missense_Mutation_p.A537T	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	514					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)	p.A531T(1)		endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						ACTGCGAGCGCGGGGTGCGCT	0.592																																					p.A514T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1540A	10						.						126.0	128.0	127.0					10																	11505387		2043	4182	6225	11545393	SO:0001583	missense	9712	exon15			BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"""related to the N terminus of tre"""	605405	"""USP6NL intronic transcript 1 (non-protein coding)"""	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.1540G>A	10.37:g.11505387C>T	ENSP00000476462:p.Ala514Thr	Somatic		Capture	Illumina HiSeq	Phase_I	11545393	NM_014688	A8KA79|Q15400|Q5VV10|Q7L0K9	Missense_Mutation	SNP	ENST00000609104.1	37	CCDS53492.1	.	.	.	.	.	.	.	.	.	.	T	4.424	0.078488	0.08533	.	.	ENSG00000148429	ENST00000535316;ENST00000277575;ENST00000379237	T;T	0.03717	3.83;3.83	5.91	-0.567	0.11763	.	0.413195	0.25848	N	0.027904	T	0.01189	0.0039	N	0.04880	-0.145	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.43114	-0.9411	10	0.02654	T	1	.	1.0385	0.01554	0.2217:0.2553:0.1046:0.4184	.	514;531	Q92738;Q92738-2	US6NL_HUMAN;.	T	514;531;514	ENSP00000277575:A531T;ENSP00000368539:A514T	ENSP00000277575:A531T	A	-	1	0	USP6NL	11545393	0.014000	0.17966	0.033000	0.17914	0.037000	0.13140	-0.269000	0.08596	-0.644000	0.05465	-0.521000	0.04368	GCG		0.592	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688	
HABP2	3026	broad.mit.edu	37	10	115343959	115343959	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:115343959C>T	ENST00000351270.3	+	11	1386	c.1290C>T	c.(1288-1290)taC>taT	p.Y430Y	HABP2_ENST00000542051.1_Silent_p.Y404Y	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2	430	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)	p.Y430Y(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	AATCCAAATACGTGAAGACTG	0.507																																					p.Y404Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1212T	10						.						261.0	210.0	227.0					10																	115343959		2203	4300	6503	115333949	SO:0001819	synonymous_variant	3026	exon11				CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"""plasma hyaluronan binding protein"", ""factor VII activating protein"""	603924	"""hyaluronan-binding protein 2"""			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073	ENST00000351270.3:c.1290C>T	10.37:g.115343959C>T		Somatic		Capture	Illumina HiSeq	Phase_I	115333949	NM_001177660	A8K467|B7Z8U5|F5H5M6|O00663	Silent	SNP	ENST00000351270.3	37	CCDS7577.1																																																																																				0.507	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132	
CCDC186	55088	broad.mit.edu	37	10	115922730	115922730	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:115922730T>C	ENST00000369287.3	-	2	564	c.298A>G	c.(298-300)Aat>Gat	p.N100D	C10orf118_ENST00000369286.1_Missense_Mutation_p.N100D|C10orf118_ENST00000369285.3_Missense_Mutation_p.N100D	NM_018017.2	NP_060487.2	Q7Z3E2	CC186_HUMAN		100								p.N100D(1)		NS(1)|autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(2)	24		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0161)|all cancers(201;0.0397)		TTAGCAAAATTTCCACTAGGA	0.338																																					p.N100D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A298G	10						.						78.0	82.0	81.0					10																	115922730		2203	4300	6503	115912720	SO:0001583	missense	55088	exon2																														ENST00000369287.3:c.298A>G	10.37:g.115922730T>C	ENSP00000358293:p.Asn100Asp	Somatic		Capture	Illumina HiSeq	Phase_I	115912720	NM_018017	Q2M2V6|Q3ZB81|Q6NS91|Q7RTP1|Q8N117|Q8N3G3|Q8N6C2|Q9NWA3	Missense_Mutation	SNP	ENST00000369287.3	37	CCDS7587.1	.	.	.	.	.	.	.	.	.	.	T	0.093	-1.163986	0.01673	.	.	ENSG00000165813	ENST00000369287;ENST00000430353;ENST00000369286;ENST00000369285	T;T;T	0.22945	2.26;1.93;1.93	5.65	3.77	0.43336	.	0.387514	0.29087	N	0.013193	T	0.10337	0.0253	N	0.10874	0.06	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16689	-1.0394	10	0.02654	T	1	.	7.6387	0.28282	0.0:0.7161:0.1336:0.1504	.	100	Q7Z3E2	CJ118_HUMAN	D	100;206;100;100	ENSP00000358293:N100D;ENSP00000358292:N100D;ENSP00000358291:N100D	ENSP00000358291:N100D	N	-	1	0	C10orf118	115912720	0.995000	0.38212	0.990000	0.47175	0.491000	0.33493	0.938000	0.28965	0.720000	0.32209	-0.248000	0.11899	AAT		0.338	C10orf118-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050455.1		
AFAP1L2	84632	broad.mit.edu	37	10	116068256	116068256	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:116068256G>A	ENST00000304129.4	-	9	932	c.903C>T	c.(901-903)taC>taT	p.Y301Y	AFAP1L2_ENST00000545353.1_Silent_p.Y354Y|AFAP1L2_ENST00000369271.3_Silent_p.Y301Y			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	301					inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)	p.Y301Y(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		AAGCCGACAGGTACTTCTCAG	0.502																																					p.Y301Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C903T	10						.						117.0	112.0	114.0					10																	116068256		2203	4300	6503	116058246	SO:0001819	synonymous_variant	84632	exon9			BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"""Pleckstrin homology (PH) domain containing"""	25901	protein-coding gene	gene with protein product		612420	"""KIAA1914"""	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.903C>T	10.37:g.116068256G>A		Somatic		Capture	Illumina HiSeq	Phase_I	116058246	NM_001001936	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	37	CCDS31286.1																																																																																				0.502	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
PNLIPRP3	119548	broad.mit.edu	37	10	118202578	118202578	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:118202578G>A	ENST00000369230.3	+	3	362	c.216G>A	c.(214-216)gcG>gcA	p.A72A		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	72					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)	p.A72A(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		AGATCAGTGCGGTTAATTCTT	0.363																																					p.A72A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G216A	10						.						77.0	70.0	72.0					10																	118202578		2203	4300	6503	118192568	SO:0001819	synonymous_variant	119548	exon3			BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.216G>A	10.37:g.118202578G>A		Somatic		Capture	Illumina HiSeq	Phase_I	118192568	NM_001011709		Silent	SNP	ENST00000369230.3	37	CCDS31292.1																																																																																				0.363	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
PNLIPRP3	119548	broad.mit.edu	37	10	118236293	118236293	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:118236293A>G	ENST00000369230.3	+	11	1448	c.1302A>G	c.(1300-1302)gcA>gcG	p.A434A		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	434	PLAT.				lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)	p.A434A(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(29)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50				all cancers(201;0.0131)		AGTTGGGAGCAGAAATGGTGA	0.308																																					p.A434A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1302G	10						.						93.0	98.0	96.0					10																	118236293		2203	4300	6503	118226283	SO:0001819	synonymous_variant	119548	exon11			BC015840	CCDS31292.1	10q26.12	2014-03-14			ENSG00000203837	ENSG00000203837	3.1.1.3		23492	protein-coding gene	gene with protein product							Standard	NM_001011709		Approved		uc001lcl.4	Q17RR3	OTTHUMG00000019100	ENST00000369230.3:c.1302A>G	10.37:g.118236293A>G		Somatic		Capture	Illumina HiSeq	Phase_I	118226283	NM_001011709		Silent	SNP	ENST00000369230.3	37	CCDS31292.1																																																																																				0.308	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
SLC18A2	6571	broad.mit.edu	37	10	119003705	119003705	+	Silent	SNP	C	C	T	rs200945841		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:119003705C>T	ENST00000298472.5	+	3	488	c.345C>T	c.(343-345)tcC>tcT	p.S115S	RP11-501J20.5_ENST00000425264.1_RNA|SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	115					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)	p.S115S(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	CTGTTCCTTCCGACTGTCCCA	0.522													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20609	0.0		0.0	False		,,,				2504	0.0				p.S115S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C345T	10						.						106.0	92.0	97.0					10																	119003705		2203	4300	6503	118993695	SO:0001819	synonymous_variant	6571	exon3			L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"""Solute carriers"""	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.345C>T	10.37:g.119003705C>T		Somatic		Capture	Illumina HiSeq	Phase_I	118993695	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Silent	SNP	ENST00000298472.5	37	CCDS7599.1																																																																																				0.522	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054	
SLC18A2	6571	broad.mit.edu	37	10	119017337	119017337	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:119017337G>A	ENST00000298472.5	+	10	1068	c.925G>A	c.(925-927)Gcc>Acc	p.A309T	SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	309					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)	p.A309T(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	CATGGGCATCGCCATGCTGGA	0.547																																					p.A309T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G925A	10						.						86.0	75.0	79.0					10																	119017337		2203	4300	6503	119007327	SO:0001583	missense	6571	exon10			L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"""Solute carriers"""	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.925G>A	10.37:g.119017337G>A	ENSP00000298472:p.Ala309Thr	Somatic		Capture	Illumina HiSeq	Phase_I	119007327	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Missense_Mutation	SNP	ENST00000298472.5	37	CCDS7599.1	.	.	.	.	.	.	.	.	.	.	G	36	5.842433	0.97016	.	.	ENSG00000165646	ENST00000298472	T	0.81078	-1.45	5.94	5.94	0.96194	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.107759	0.64402	D	0.000006	D	0.87873	0.6287	M	0.86740	2.835	0.80722	D	1	P	0.35077	0.483	B	0.43194	0.411	D	0.87659	0.2533	10	0.66056	D	0.02	-11.9647	20.4384	0.99098	0.0:0.0:1.0:0.0	.	309	Q05940	VMAT2_HUMAN	T	309	ENSP00000298472:A309T	ENSP00000298472:A309T	A	+	1	0	SLC18A2	119007327	1.000000	0.71417	0.998000	0.56505	0.963000	0.63663	9.868000	0.99621	2.831000	0.97527	0.644000	0.83932	GCC		0.547	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054	
SLC18A2	6571	broad.mit.edu	37	10	119029637	119029637	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:119029637C>T	ENST00000298472.5	+	14	1385	c.1242C>T	c.(1240-1242)caC>caT	p.H414H	SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	414					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)	p.H414H(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	ACCTGCGGCACGTGTCCGTCT	0.468																																					p.H414H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1242T	10						.						270.0	219.0	237.0					10																	119029637		2203	4300	6503	119019627	SO:0001819	synonymous_variant	6571	exon14			L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"""Solute carriers"""	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.1242C>T	10.37:g.119029637C>T		Somatic		Capture	Illumina HiSeq	Phase_I	119019627	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Silent	SNP	ENST00000298472.5	37	CCDS7599.1																																																																																				0.468	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054	
PRLHR	2834	broad.mit.edu	37	10	120353878	120353878	+	Silent	SNP	C	C	T	rs146851098		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:120353878C>T	ENST00000369169.1	-	1	878	c.879G>A	c.(877-879)ccG>ccA	p.P293P	PRLHR_ENST00000239032.2_Silent_p.P293P			P49683	PRLHR_HUMAN	prolactin releasing hormone receptor	293					feeding behavior (GO:0007631)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|hormone metabolic process (GO:0042445)|neuropeptide signaling pathway (GO:0007218)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)|neuropeptide Y receptor activity (GO:0004983)	p.P293P(1)		large_intestine(2)|lung(8)|ovary(1)|skin(1)	12		Colorectal(252;0.0429)|Lung NSC(174;0.142)|all_lung(145;0.175)		all cancers(201;0.0166)		AGACGTGCAGCGGCAGCCAGC	0.677																																					p.P293P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G879A	10						.						35.0	38.0	37.0					10																	120353878		2202	4298	6500	120343868	SO:0001819	synonymous_variant	2834	exon2			AB048946	CCDS7606.1	10q25.3-q26	2014-02-21	2005-11-24	2005-11-24	ENSG00000119973	ENSG00000119973		"""GPCR / Class A : RF amide peptide receptors"""	4464	protein-coding gene	gene with protein product		600895	"""G protein-coupled receptor 10"""	GPR10		8666380, 15885496	Standard	NM_004248		Approved	PrRPR	uc001ldp.1	P49683	OTTHUMG00000019136	ENST00000369169.1:c.879G>A	10.37:g.120353878C>T		Somatic		Capture	Illumina HiSeq	Phase_I	120343868	NM_004248	O75194|Q502U8|Q5VXR9	Silent	SNP	ENST00000369169.1	37	CCDS7606.1																																																																																				0.677	PRLHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050610.1	NM_004248	
TIAL1	7073	broad.mit.edu	37	10	121339497	121339497	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:121339497C>T	ENST00000436547.2	-	6	441	c.397G>A	c.(397-399)Gca>Aca	p.A133T	TIAL1_ENST00000369093.2_Missense_Mutation_p.A150T|TIAL1_ENST00000369092.4_Missense_Mutation_p.A10T|TIAL1_ENST00000463089.2_5'Flank	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1	133	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|defense response (GO:0006952)|germ cell development (GO:0007281)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell division (GO:0017145)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A150T(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		TTTCCAGTTGCCATGTCTTTA	0.353																																					p.A150T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G448A	10						.						61.0	63.0	62.0					10																	121339497		2203	4300	6503	121329487	SO:0001583	missense	7073	exon6			AL833106	CCDS7613.1, CCDS31295.1	10q	2013-02-12	2001-11-28		ENSG00000151923	ENSG00000151923		"""RNA binding motif (RRM) containing"""	11804	protein-coding gene	gene with protein product		603413	"""TIA1 cytotoxic granule-associated RNA-binding protein-like 1"""			1326761	Standard	XM_005270108		Approved	TIAR	uc001lej.1	Q01085	OTTHUMG00000019156	ENST00000436547.2:c.397G>A	10.37:g.121339497C>T	ENSP00000394902:p.Ala133Thr	Somatic		Capture	Illumina HiSeq	Phase_I	121329487	NM_001033925	A8K3T0|A8K4L9	Missense_Mutation	SNP	ENST00000436547.2	37	CCDS7613.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.702955	0.48412	.	.	ENSG00000151923	ENST00000369093;ENST00000369092;ENST00000436547;ENST00000412524	D;T;D;D	0.85773	-2.03;2.34;-2.03;-2.03	5.8	4.9	0.64082	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.101254	0.64402	D	0.000002	T	0.77558	0.4148	N	0.25031	0.7	0.58432	D	0.99999	B;B;B;B	0.17465	0.006;0.022;0.0;0.001	B;B;B;B	0.26969	0.009;0.075;0.005;0.012	T	0.71297	-0.4635	10	0.27785	T	0.31	-19.0231	14.7214	0.69308	0.0:0.9307:0.0:0.0693	.	10;10;150;133	B4DHS3;Q49AS9;A8K4L9;Q01085	.;.;.;TIAR_HUMAN	T	150;10;133;94	ENSP00000358089:A150T;ENSP00000358088:A10T;ENSP00000394902:A133T;ENSP00000403573:A94T	ENSP00000358088:A10T	A	-	1	0	TIAL1	121329487	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.471000	0.60182	1.457000	0.47850	0.563000	0.77884	GCA		0.353	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252	
DMBT1	1755	broad.mit.edu	37	10	124390574	124390574	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:124390574T>C	ENST00000338354.3	+	46	5842	c.5736T>C	c.(5734-5736)gaT>gaC	p.D1912D	DMBT1_ENST00000330163.4_Silent_p.D1284D|DMBT1_ENST00000368955.3_Silent_p.D1902D|DMBT1_ENST00000368956.2_Silent_p.D1284D|DMBT1_ENST00000344338.3_Silent_p.D1902D|DMBT1_ENST00000368909.3_Silent_p.D1912D|DMBT1_ENST00000359586.6_Silent_p.D632D			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1912	SRCR 14. {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)	p.D1912D(1)		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)				CAGTTTGTGATGACTCCTGGA	0.507																																					p.D1912D	Ovarian(182;93 2026 18125 22222 38972)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T5736C	10						.						119.0	118.0	118.0					10																	124390574		2041	4197	6238	124380564	SO:0001819	synonymous_variant	1755	exon46				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.5736T>C	10.37:g.124390574T>C		Somatic		Capture	Illumina HiSeq	Phase_I	124380564	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	37																																																																																					0.507	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
ADARB2	105	broad.mit.edu	37	10	1262976	1262976	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:1262976G>A	ENST00000381312.1	-	7	1922	c.1597C>T	c.(1597-1599)Cgt>Tgt	p.R533C	ADARB2_ENST00000469464.1_5'UTR	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	533	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.R533C(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		CTGGGGCCACGCACGGGGACC	0.652																																					p.R533C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1597T	10						.						51.0	43.0	46.0					10																	1262976		2203	4299	6502	1252976	SO:0001583	missense	105	exon7			AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"""RED2 homolog (rat)"""	602065	"""adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)"", ""adenosine deaminase, RNA-specific, B2"""			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.1597C>T	10.37:g.1262976G>A	ENSP00000370713:p.Arg533Cys	Somatic		Capture	Illumina HiSeq	Phase_I	1252976	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	37	CCDS7058.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.014434	0.54468	.	.	ENSG00000185736	ENST00000381312	D	0.94046	-3.34	5.48	3.56	0.40772	Adenosine deaminase/editase (3);	0.000000	0.85682	D	0.000000	D	0.95169	0.8434	L	0.58354	1.805	0.80722	D	1	D	0.76494	0.999	D	0.65233	0.933	D	0.94879	0.8037	10	0.87932	D	0	-33.2574	14.4667	0.67490	0.0:0.0:0.7315:0.2685	.	533	Q9NS39	RED2_HUMAN	C	533	ENSP00000370713:R533C	ENSP00000370713:R533C	R	-	1	0	ADARB2	1252976	1.000000	0.71417	0.120000	0.21714	0.806000	0.45545	5.372000	0.66156	0.630000	0.30394	0.491000	0.48974	CGT		0.652	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702	
ACADSB	36	broad.mit.edu	37	10	124812593	124812593	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:124812593C>T	ENST00000358776.4	+	10	1159	c.1145C>T	c.(1144-1146)aCg>aTg	p.T382M	ACADSB_ENST00000368869.4_Missense_Mutation_p.T280M	NM_001609.3	NP_001600.1	P45954	ACDSB_HUMAN	acyl-CoA dehydrogenase, short/branched chain	382					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)	p.T382M(2)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.0811)|COAD - Colon adenocarcinoma(40;0.0835)	L-Isoleucine(DB00167)|Valproic Acid(DB00313)	GGACAAACAACGAGTAAATGT	0.383																																					p.T382M												.	.	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	c.C1145T	10						.						126.0	113.0	117.0					10																	124812593		2203	4300	6503	124802583	SO:0001583	missense	36	exon10			U12778	CCDS7634.1	10q25-q26	2014-09-17	2010-04-30		ENSG00000196177	ENSG00000196177	1.3.99.-		91	protein-coding gene	gene with protein product		600301	"""acyl-Coenzyme A dehydrogenase, short/branched chain"""			7698750, 7759115	Standard	NM_001609		Approved	SBCAD, ACAD7	uc001lhb.3	P45954	OTTHUMG00000019200	ENST00000358776.4:c.1145C>T	10.37:g.124812593C>T	ENSP00000357873:p.Thr382Met	Somatic		Capture	Illumina HiSeq	Phase_I	124802583	NM_001609	B4DQ51|Q5SQN6|Q96CX7	Missense_Mutation	SNP	ENST00000358776.4	37	CCDS7634.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.310257	0.81358	.	.	ENSG00000196177	ENST00000368869;ENST00000358776	D;D	0.96168	-3.93;-3.93	5.27	5.27	0.74061	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.97936	0.9321	M	0.85099	2.735	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.98792	1.0736	10	0.87932	D	0	.	18.5241	0.90965	0.0:1.0:0.0:0.0	.	382	P45954	ACDSB_HUMAN	M	280;382	ENSP00000357862:T280M;ENSP00000357873:T382M	ENSP00000357873:T382M	T	+	2	0	ACADSB	124802583	1.000000	0.71417	0.009000	0.14445	0.032000	0.12392	7.551000	0.82182	2.474000	0.83562	0.650000	0.86243	ACG		0.383	ACADSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050843.1	NM_001609	
GPR26	2849	broad.mit.edu	37	10	125426431	125426431	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:125426431G>A	ENST00000284674.1	+	1	561	c.508G>A	c.(508-510)Gcc>Acc	p.A170T		NM_153442.3	NP_703143.1	Q8NDV2	GPR26_HUMAN	G protein-coupled receptor 26	170					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A170T(1)		breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	20		Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)				CCTGCGCTTCGCCGTCTTCAC	0.672																																					p.A170T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G508A	10						.						29.0	23.0	25.0					10																	125426431		2202	4298	6500	125416421	SO:0001583	missense	2849	exon1				CCDS7636.1	10q26.2-q26.3	2012-08-21			ENSG00000154478	ENSG00000154478		"""GPCR / Class A : Orphans"""	4481	protein-coding gene	gene with protein product		604847					Standard	NM_153442		Approved		uc001lhh.3	Q8NDV2	OTTHUMG00000019204	ENST00000284674.1:c.508G>A	10.37:g.125426431G>A	ENSP00000284674:p.Ala170Thr	Somatic		Capture	Illumina HiSeq	Phase_I	125416421	NM_153442	Q2M2E2	Missense_Mutation	SNP	ENST00000284674.1	37	CCDS7636.1	.	.	.	.	.	.	.	.	.	.	G	0.990	-0.694252	0.03303	.	.	ENSG00000154478	ENST00000284674	T	0.37058	1.22	4.02	3.08	0.35506	GPCR, rhodopsin-like superfamily (1);	0.315462	0.29133	N	0.013042	T	0.14313	0.0346	N	0.10645	0.015	0.09310	N	0.999997	B	0.25904	0.137	B	0.21360	0.034	T	0.16719	-1.0393	10	0.14656	T	0.56	-15.7008	5.9754	0.19375	0.1696:0.1614:0.6689:0.0	.	170	Q8NDV2	GPR26_HUMAN	T	170	ENSP00000284674:A170T	ENSP00000284674:A170T	A	+	1	0	GPR26	125416421	1.000000	0.71417	0.827000	0.32855	0.145000	0.21501	2.295000	0.43576	2.067000	0.61834	0.655000	0.94253	GCC		0.672	GPR26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050850.1		
ADARB2	105	broad.mit.edu	37	10	1279726	1279726	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:1279726G>A	ENST00000381312.1	-	6	1748	c.1423C>T	c.(1423-1425)Ctg>Ttg	p.L475L	ADARB2_ENST00000469464.1_5'UTR	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	475	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.L475L(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		TTCTCTCGCAGCCGGTAGCCA	0.542																																					p.L475L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1423T	10						.						148.0	126.0	134.0					10																	1279726		2203	4300	6503	1269726	SO:0001819	synonymous_variant	105	exon6			AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"""RED2 homolog (rat)"""	602065	"""adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)"", ""adenosine deaminase, RNA-specific, B2"""			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.1423C>T	10.37:g.1279726G>A		Somatic		Capture	Illumina HiSeq	Phase_I	1269726	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Silent	SNP	ENST00000381312.1	37	CCDS7058.1																																																																																				0.542	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702	
CHST15	51363	broad.mit.edu	37	10	125780805	125780805	+	Silent	SNP	G	G	A	rs149508585		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:125780805G>A	ENST00000346248.5	-	6	1956	c.1314C>T	c.(1312-1314)tgC>tgT	p.C438C	CHST15_ENST00000421115.1_Silent_p.C438C|CHST15_ENST00000435907.1_Silent_p.C438C	NM_015892.4	NP_056976.2	Q7LFX5	CHSTF_HUMAN	carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15	438					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hexose biosynthetic process (GO:0019319)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)	p.C438C(1)		endometrium(4)|kidney(1)|large_intestine(11)|lung(6)|ovary(3)|stomach(1)	26						TGTTGTAGACGCAGGCGCGCA	0.532																																					p.C438C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1314T	10						.	G	,	0,4406		0,0,2203	72.0	65.0	67.0		1314,1314	-4.8	0.9	10	dbSNP_134	67	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CHST15	NM_014863.2,NM_015892.3	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	438/507,438/562	125780805	1,13005	2203	4300	6503	125770795	SO:0001819	synonymous_variant	51363	exon6			AB011170	CCDS7638.1	10q26	2009-07-09			ENSG00000182022	ENSG00000182022	2.8.2.33	"""Sulfotransferases, membrane-bound"""	18137	protein-coding gene	gene with protein product	"""B cell RAG associated protein"", ""N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase"""	608277				9628581, 9754571, 11572857	Standard	NM_014863		Approved	GALNAC4S-6ST, BRAG, KIAA0598	uc001lhm.4	Q7LFX5	OTTHUMG00000019208	ENST00000346248.5:c.1314C>T	10.37:g.125780805G>A		Somatic		Capture	Illumina HiSeq	Phase_I	125770795	NM_015892	O60338|O60474|Q86VM4	Silent	SNP	ENST00000346248.5	37	CCDS7638.1																																																																																				0.532	CHST15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050856.1	NM_015892	
FAM196A	642938	broad.mit.edu	37	10	128974365	128974365	+	Missense_Mutation	SNP	C	C	T	rs139369079		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:128974365C>T	ENST00000522781.1	-	4	850	c.295G>A	c.(295-297)Gtc>Atc	p.V99I	DOCK1_ENST00000280333.6_Intron|FAM196A_ENST00000424811.2_Missense_Mutation_p.V99I	NM_001039762.2	NP_001034851.1	Q6ZSG2	F196A_HUMAN	family with sequence similarity 196, member A	99								p.V99I(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CTCTTGGTGACGTTGGGGATG	0.617													C|||	1	0.000199681	0.0	0.0	5008	,	,		16601	0.0		0.001	False		,,,				2504	0.0				p.V99I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G295A	10						.	C	ILE/VAL,	0,4406		0,0,2203	124.0	110.0	115.0		295,	5.0	1.0	10	dbSNP_134	115	2,8598	2.2+/-6.3	0,2,4298	yes	missense,intron	DOCK1,FAM196A	NM_001039762.2,NM_001380.3	29,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,	99/480,	128974365	2,13004	2203	4300	6503	128864355	SO:0001583	missense	642938	exon4				CCDS31312.1	10q26.2	2009-09-11	2009-09-11	2009-09-11		ENSG00000188916			33859	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 141"""	C10orf141			Standard	NM_001039762		Approved	FLJ45557	uc001ljv.1	Q6ZSG2		ENST00000522781.1:c.295G>A	10.37:g.128974365C>T	ENSP00000429763:p.Val99Ile	Somatic		Capture	Illumina HiSeq	Phase_I	128864355	NM_001039762	B2RNT4|B7ZME7	Missense_Mutation	SNP	ENST00000522781.1	37	CCDS31312.1	.	.	.	.	.	.	.	.	.	.	C	32	5.171158	0.94807	0.0	2.33E-4	ENSG00000188916	ENST00000522781;ENST00000424811	T;T	0.53857	0.6;0.6	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.64427	0.2597	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.66097	-0.6008	10	0.52906	T	0.07	.	18.6775	0.91534	0.0:1.0:0.0:0.0	.	99;99	B7ZME7;Q6ZSG2	.;F196A_HUMAN	I	99	ENSP00000429763:V99I;ENSP00000428730:V99I	ENSP00000428730:V99I	V	-	1	0	FAM196A	128864355	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.424000	0.80242	2.492000	0.84095	0.563000	0.77884	GTC		0.617	FAM196A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050978.2	NM_001039762	
EBF3	253738	broad.mit.edu	37	10	131639173	131639173	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:131639173G>A	ENST00000355311.5	-	14	1568	c.1496C>T	c.(1495-1497)gCc>gTc	p.A499V	MIR4297_ENST00000579857.1_RNA|EBF3_ENST00000368648.3_Missense_Mutation_p.A490V			Q9H4W6	COE3_HUMAN	early B-cell factor 3	499	Pro/Ser/Thr-rich.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A490V(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		CCCTAGACTGGCCATGGCGCC	0.557																																					p.A490V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1469T	10						.						148.0	137.0	141.0					10																	131639173		2203	4300	6503	131529163	SO:0001583	missense	253738	exon14				CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.1496C>T	10.37:g.131639173G>A	ENSP00000347463:p.Ala499Val	Somatic		Capture	Illumina HiSeq	Phase_I	131529163	NM_001005463	A0AUY1|Q5T6H9|Q9H4W5	Missense_Mutation	SNP	ENST00000355311.5	37		.	.	.	.	.	.	.	.	.	.	G	15.65	2.897739	0.52227	.	.	ENSG00000108001	ENST00000355311;ENST00000368648	T;T	0.47177	0.85;0.85	4.7	4.7	0.59300	.	0.141118	0.45606	D	0.000344	T	0.48314	0.1493	L	0.46157	1.445	0.40700	D	0.982473	B	0.21821	0.061	B	0.31290	0.127	T	0.52624	-0.8551	10	0.66056	D	0.02	-21.123	17.8561	0.88764	0.0:0.0:1.0:0.0	.	490	Q9H4W6-2	.	V	499;490	ENSP00000347463:A499V;ENSP00000357637:A490V	ENSP00000347463:A499V	A	-	2	0	EBF3	131529163	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.416000	0.66417	2.421000	0.82119	0.655000	0.94253	GCC		0.557	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463	
MCM10	55388	broad.mit.edu	37	10	13233388	13233388	+	Missense_Mutation	SNP	G	G	A	rs368268628		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:13233388G>A	ENST00000484800.2	+	11	1611	c.1508G>A	c.(1507-1509)cGg>cAg	p.R503Q	MCM10_ENST00000378714.3_Missense_Mutation_p.R502Q|MCM10_ENST00000378694.1_Missense_Mutation_p.R502Q			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	503					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.R503Q(1)		central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						CAGGAAACACGGCAAAAACTC	0.403																																					p.R502Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1505A	10						.						96.0	95.0	95.0					10																	13233388		2203	4300	6503	13273394	SO:0001583	missense	55388	exon11			AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"""MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"""			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.1508G>A	10.37:g.13233388G>A	ENSP00000418268:p.Arg503Gln	Somatic		Capture	Illumina HiSeq	Phase_I	13273394	NM_018518	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	G	1.785	-0.480839	0.04383	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.14516	2.51;2.51;2.5	5.16	-2.47	0.06442	.	0.580923	0.19518	N	0.112349	T	0.06508	0.0167	N	0.24115	0.695	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.08055	0.002;0.003;0.002	T	0.42310	-0.9459	10	0.12103	T	0.63	-0.2138	8.069	0.30678	0.3818:0.1296:0.4886:0.0	.	502;502;503	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	Q	502;503;503;502	ENSP00000367986:R502Q;ENSP00000418268:R503Q;ENSP00000367966:R502Q	ENSP00000354945:R503Q	R	+	2	0	MCM10	13273394	0.000000	0.05858	0.001000	0.08648	0.249000	0.25844	-0.370000	0.07523	-0.306000	0.08818	-0.294000	0.09567	CGG		0.403	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
EBF3	253738	broad.mit.edu	37	10	131671763	131671763	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:131671763C>T	ENST00000355311.5	-	8	806	c.734G>A	c.(733-735)cGc>cAc	p.R245H	EBF3_ENST00000368648.3_Missense_Mutation_p.R245H			Q9H4W6	COE3_HUMAN	early B-cell factor 3	245					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R245H(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	44		all_cancers(35;1.8e-08)|all_epithelial(44;8.26e-08)|Lung NSC(174;0.0091)|all_lung(145;0.0123)|Breast(234;0.039)|all_neural(114;0.0722)|Colorectal(57;0.0764)		OV - Ovarian serous cystadenocarcinoma(35;0.00513)		GTCTAGGCGGCGGGCCCGCCT	0.502																																					p.R245H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G734A	10						.						56.0	56.0	56.0					10																	131671763		2203	4300	6503	131561753	SO:0001583	missense	253738	exon8				CCDS31314.1	10q26.3	2007-03-30			ENSG00000108001	ENSG00000108001			19087	protein-coding gene	gene with protein product		607407				12355068	Standard	NM_001005463		Approved	COE3, DKFZp667B0210	uc001lki.2	Q9H4W6	OTTHUMG00000019265	ENST00000355311.5:c.734G>A	10.37:g.131671763C>T	ENSP00000347463:p.Arg245His	Somatic		Capture	Illumina HiSeq	Phase_I	131561753	NM_001005463	A0AUY1|Q5T6H9|Q9H4W5	Missense_Mutation	SNP	ENST00000355311.5	37		.	.	.	.	.	.	.	.	.	.	C	32	5.180349	0.94846	.	.	ENSG00000108001	ENST00000355311;ENST00000368648	T;T	0.52295	0.67;0.69	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.68796	0.3040	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.67900	0.954	T	0.73639	-0.3919	10	0.87932	D	0	-17.531	18.4262	0.90610	0.0:1.0:0.0:0.0	.	245	Q9H4W6-2	.	H	245	ENSP00000347463:R245H;ENSP00000357637:R245H	ENSP00000347463:R245H	R	-	2	0	EBF3	131561753	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.717000	0.84732	2.435000	0.82474	0.655000	0.94253	CGC		0.502	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463	
DPYSL4	10570	broad.mit.edu	37	10	134012377	134012377	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:134012377G>A	ENST00000338492.4	+	8	877	c.713G>A	c.(712-714)cGa>cAa	p.R238Q	DPYSL4_ENST00000368627.1_Missense_Mutation_p.R138Q|DPYSL4_ENST00000368629.1_Missense_Mutation_p.R138Q	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	238					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)	cytosol (GO:0005829)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.R238Q(1)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		GCGGTGTACCGAGCTGTCACC	0.657																																					p.R238Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G713A	10						.						77.0	65.0	69.0					10																	134012377		2203	4299	6502	133862367	SO:0001583	missense	10570	exon8			AB006713	CCDS7665.1	10q25.2-q26	2008-05-14			ENSG00000151640	ENSG00000151640			3016	protein-coding gene	gene with protein product		608407				8973361, 9652388	Standard	NM_006426		Approved	ULIP4, DRP-4	uc009ybb.3	O14531	OTTHUMG00000019283	ENST00000338492.4:c.713G>A	10.37:g.134012377G>A	ENSP00000339850:p.Arg238Gln	Somatic		Capture	Illumina HiSeq	Phase_I	133862367	NM_006426	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Missense_Mutation	SNP	ENST00000338492.4	37	CCDS7665.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.048998	0.93740	.	.	ENSG00000151640	ENST00000338492;ENST00000368629;ENST00000368627	D;D;D	0.90444	-2.67;-2.67;-2.67	3.66	3.66	0.41972	Amidohydrolase 1 (1);	0.000000	0.85682	D	0.000000	D	0.96231	0.8771	M	0.92555	3.32	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97461	1.0034	10	0.87932	D	0	-25.2453	16.0148	0.80430	0.0:0.0:1.0:0.0	.	238	O14531	DPYL4_HUMAN	Q	238;138;138	ENSP00000339850:R238Q;ENSP00000357618:R138Q;ENSP00000357616:R138Q	ENSP00000339850:R238Q	R	+	2	0	DPYSL4	133862367	1.000000	0.71417	0.957000	0.39632	0.749000	0.42624	9.118000	0.94355	2.065000	0.61736	0.555000	0.69702	CGA		0.657	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2		
TUBB8	347688	broad.mit.edu	37	10	95127	95127	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:95127C>T	ENST00000309812.4	-	1	114	c.52G>A	c.(52-54)Gcc>Acc	p.A18T	TUBB8_ENST00000413237.3_Intron|TUBB8_ENST00000332708.5_Missense_Mutation_p.A18T|TUBB8_ENST00000447903.2_Intron	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	18					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.A18T(1)		NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		CCAACCTTGGCGCCGATCTGA	0.682																																					p.A18T	Pancreas(192;2041 3010 9013 18103)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G52A	10						.						14.0	13.0	13.0					10																	95127		2190	4281	6471	85127	SO:0001583	missense	347688	exon1			AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"""Tubulins"""	20773	protein-coding gene	gene with protein product	"""class VIII beta-tubulin"""						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.52G>A	10.37:g.95127C>T	ENSP00000311042:p.Ala18Thr	Somatic		Capture	Illumina HiSeq	Phase_I	85127	NM_177987	Q5SQX9|Q8WZ78	Missense_Mutation	SNP	ENST00000309812.4	37	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	C	9.214	1.031684	0.19590	.	.	ENSG00000173876	ENST00000440680;ENST00000328974;ENST00000309812;ENST00000332708	T;T	0.69561	-0.41;-0.27	0.109	0.109	0.14578	Tubulin/FtsZ, GTPase domain (3);	0.093235	0.40728	U	0.001035	T	0.44498	0.1296	N	0.19112	0.55	0.80722	D	1	B;B	0.24426	0.015;0.103	B;B	0.17433	0.007;0.018	T	0.25152	-1.0140	10	0.87932	D	0	.	5.9913	0.19465	0.0:0.9994:0.0:6.0E-4	.	18;18	C9JAA5;Q3ZCM7	.;TBB8_HUMAN	T	18	ENSP00000311042:A18T;ENSP00000371071:A18T	ENSP00000311042:A18T	A	-	1	0	RP11-631M21.2	85127	0.223000	0.23663	0.006000	0.13384	0.006000	0.05464	1.205000	0.32308	0.181000	0.19994	0.184000	0.17185	GCC		0.682	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
ZMYND11	10771	broad.mit.edu	37	10	255931	255931	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:255931C>T	ENST00000397962.3	+	3	647	c.219C>T	c.(217-219)tgC>tgT	p.C73C	ZMYND11_ENST00000381584.1_Silent_p.C56C|ZMYND11_ENST00000402736.1_Silent_p.C73C|ZMYND11_ENST00000509513.2_Silent_p.C73C|ZMYND11_ENST00000535374.1_5'UTR|ZMYND11_ENST00000397959.3_Silent_p.C73C|ZMYND11_ENST00000381607.4_Silent_p.C33C|ZMYND11_ENST00000545619.1_Silent_p.C33C|ZMYND11_ENST00000602682.1_Silent_p.C73C|ZMYND11_ENST00000403354.1_Silent_p.C73C|ZMYND11_ENST00000309776.4_Silent_p.C33C|ZMYND11_ENST00000381591.1_Silent_p.C73C|ZMYND11_ENST00000381604.4_Silent_p.C33C|ZMYND11_ENST00000558098.2_Silent_p.C73C|ZMYND11_ENST00000381602.4_Silent_p.C33C			Q15326	ZMY11_HUMAN	zinc finger, MYND-type containing 11	73					cell cycle (GO:0007049)|cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|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)|regulation of transcription elongation from RNA polymerase II promoter (GO:0034243)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.C33C(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	24		all_cancers(4;1.32e-05)|all_lung(4;3.67e-05)|Lung NSC(4;0.000301)|all_epithelial(10;0.000416)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.132)	Epithelial(11;0.00289)|all cancers(11;0.0108)|Lung(33;0.0689)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CAGTGGGCTGCAAAGGTTCAA	0.408																																					p.C73C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C219T	10						.						146.0	142.0	144.0					10																	255931		2203	4300	6503	245931	SO:0001819	synonymous_variant	10771	exon3			X86098	CCDS7052.1, CCDS7053.1, CCDS7052.2, CCDS55696.1, CCDS55697.1, CCDS7053.2, CCDS73060.1, CCDS73061.1	10p14	2011-01-26	2011-01-26		ENSG00000015171	ENSG00000015171		"""Zinc fingers, MYND-type"""	16966	protein-coding gene	gene with protein product		608668	"""zinc finger, MYND domain containing 11"""			7621829, 10734313	Standard	NM_006624		Approved	BS69	uc010pzx.2	Q15326	OTTHUMG00000017526	ENST00000397962.3:c.219C>T	10.37:g.255931C>T		Somatic		Capture	Illumina HiSeq	Phase_I	245931	NM_212479	B2R6G8|B7Z293|F6UH50|Q2LD45|Q2LD46|Q2LD47|Q2LD48|Q5VUI1|Q8N4B3	Silent	SNP	ENST00000397962.3	37	CCDS7052.2																																																																																				0.408	ZMYND11-206	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046382.4	NM_006624	
ANKRD16	54522	broad.mit.edu	37	10	5925099	5925099	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:5925099G>A	ENST00000380094.5	-	5	1262	c.719C>T	c.(718-720)gCc>gTc	p.A240V	ANKRD16_ENST00000380092.4_Missense_Mutation_p.A240V|ANKRD16_ENST00000191063.8_Missense_Mutation_p.A240V	NM_019046.2	NP_061919.1	Q6P6B7	ANR16_HUMAN	ankyrin repeat domain 16	240								p.A240V(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(3)|stomach(2)	12						CAGAGCCTGGGCACCCAGGCT	0.542																																					p.A240V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C719T	10						.						76.0	60.0	65.0					10																	5925099		2203	4300	6503	5965105	SO:0001583	missense	54522	exon5			AL137614	CCDS31136.1, CCDS31137.1	10p15.1	2013-01-10			ENSG00000134461	ENSG00000134461		"""Ankyrin repeat domain containing"""	23471	protein-coding gene	gene with protein product							Standard	NM_019046		Approved	DKFZP434N1511	uc010qat.2	Q6P6B7	OTTHUMG00000017610	ENST00000380094.5:c.719C>T	10.37:g.5925099G>A	ENSP00000369436:p.Ala240Val	Somatic		Capture	Illumina HiSeq	Phase_I	5965105	NM_001009943	A6NEF0|F8WEI4|Q9NT01	Missense_Mutation	SNP	ENST00000380094.5	37	CCDS31136.1	.	.	.	.	.	.	.	.	.	.	G	18.78	3.697811	0.68386	.	.	ENSG00000134461	ENST00000380094;ENST00000380092;ENST00000191063	T;T;T	0.60548	2.47;2.47;0.18	5.03	5.03	0.67393	Ankyrin repeat-containing domain (3);	0.106709	0.64402	D	0.000006	T	0.56731	0.2005	N	0.13299	0.325	0.58432	D	0.999999	P;P;D	0.65815	0.913;0.912;0.995	P;P;P	0.60286	0.548;0.773;0.872	T	0.53265	-0.8463	10	0.18710	T	0.47	-1.9265	18.3598	0.90371	0.0:0.0:1.0:0.0	.	240;240;240	Q6P6B7;C9JP28;F8WEI4	ANR16_HUMAN;.;.	V	240	ENSP00000369436:A240V;ENSP00000369434:A240V;ENSP00000352361:A240V	ENSP00000352361:A240V	A	-	2	0	ANKRD16	5965105	1.000000	0.71417	0.999000	0.59377	0.864000	0.49448	5.421000	0.66447	2.513000	0.84729	0.558000	0.71614	GCC		0.542	ANKRD16-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046611.2	XM_166138	
FBXO18	84893	broad.mit.edu	37	10	5963484	5963484	+	Silent	SNP	C	C	T	rs141613808		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:5963484C>T	ENST00000362091.4	+	15	2389	c.2274C>T	c.(2272-2274)gcC>gcT	p.A758A	FBXO18_ENST00000397269.3_Silent_p.A245A|FBXO18_ENST00000379999.5_Silent_p.A809A	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	758					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.A809A(1)		NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						TTGATGAGGCCGTACGGGTGA	0.498																																					p.A809A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2427T	10						.	C	,	1,4405	2.1+/-5.4	0,1,2202	114.0	93.0	100.0		2427,2274	-11.7	0.1	10	dbSNP_134	100	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FBXO18	NM_032807.3,NM_178150.1	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	809/1095,758/1044	5963484	1,13005	2203	4300	6503	6003490	SO:0001819	synonymous_variant	84893	exon16			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.2274C>T	10.37:g.5963484C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6003490	NM_032807	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Silent	SNP	ENST00000362091.4	37	CCDS7072.1																																																																																				0.498	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1	NM_032807	
IL2RA	3559	broad.mit.edu	37	10	6067832	6067832	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:6067832G>A	ENST00000379959.3	-	2	394	c.221C>T	c.(220-222)tCg>tTg	p.S74L	IL2RA_ENST00000379954.1_Missense_Mutation_p.S74L|RP11-536K7.5_ENST00000440436.1_RNA|IL2RA_ENST00000256876.6_Missense_Mutation_p.S74L	NM_000417.2	NP_000408.1	P01589	IL2RA_HUMAN	interleukin 2 receptor, alpha	74	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				activation-induced cell death of T cells (GO:0006924)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of defense response to virus (GO:0050687)|negative regulation of immune response (GO:0050777)|negative regulation of inflammatory response (GO:0050728)|negative regulation of T cell proliferation (GO:0042130)|Notch signaling pathway (GO:0007219)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of T cell differentiation (GO:0045582)|regulation of T cell homeostatic proliferation (GO:0046013)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|interleukin-2 receptor activity (GO:0004911)	p.S74L(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	17					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	GTCCCAGGACGAGTGGCTAGA	0.468																																					p.S74L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C221T	10						.						113.0	106.0	108.0					10																	6067832		2203	4300	6503	6107838	SO:0001583	missense	3559	exon2			X01057	CCDS7076.1	10p15-p14	2014-09-17			ENSG00000134460	ENSG00000134460		"""Interleukins and interleukin receptors"", ""CD molecules"""	6008	protein-coding gene	gene with protein product		147730	"""insulin-dependent diabetes mellitus 10"""	IL2R, IDDM10		3925551, 17676041	Standard	NM_000417		Approved	CD25	uc001iiz.2	P01589	OTTHUMG00000017616	ENST00000379959.3:c.221C>T	10.37:g.6067832G>A	ENSP00000369293:p.Ser74Leu	Somatic		Capture	Illumina HiSeq	Phase_I	6107838	NM_000417	Q5W007	Missense_Mutation	SNP	ENST00000379959.3	37	CCDS7076.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.35|12.35	1.912982|1.912982	0.33815|0.33815	.|.	.|.	ENSG00000134460|ENSG00000134460	ENST00000447847|ENST00000379959;ENST00000397240;ENST00000379954;ENST00000256876	.|T;T;T	.|0.64991	.|-0.13;-0.13;-0.13	3.71|3.71	0.684|0.684	0.18003|0.18003	.|Complement control module (2);Sushi/SCR/CCP (3);	.|1.052940	.|0.07517	.|N	.|0.909914	T|T	0.43010|0.43010	0.1228|0.1228	L|L	0.38838|0.38838	1.175|1.175	0.09310|0.09310	N|N	1|1	.|B;P;P	.|0.49696	.|0.397;0.836;0.927	.|B;B;B	.|0.35655	.|0.042;0.167;0.207	T|T	0.37686|0.37686	-0.9695|-0.9695	5|10	.|0.42905	.|T	.|0.14	-37.6983|-37.6983	2.9386|2.9386	0.05823|0.05823	0.2403:0.0:0.5426:0.2171|0.2403:0.0:0.5426:0.2171	.|.	.|74;60;74	.|Q5W005;E9PF94;P01589	.|.;.;IL2RA_HUMAN	C|L	45|74;60;74;74	.|ENSP00000369293:S74L;ENSP00000369287:S74L;ENSP00000256876:S74L	.|ENSP00000256876:S74L	R|S	-|-	1|2	0|0	IL2RA|IL2RA	6107838|6107838	0.002000|0.002000	0.14202|0.14202	0.000000|0.000000	0.03702|0.03702	0.037000|0.037000	0.13140|0.13140	0.586000|0.586000	0.23894|0.23894	0.327000|0.327000	0.23409|0.23409	0.585000|0.585000	0.79938|0.79938	CGT|TCG		0.468	IL2RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046627.1	NM_000417	
SFMBT2	57713	broad.mit.edu	37	10	7213903	7213903	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:7213903G>A	ENST00000361972.4	-	19	2459	c.2369C>T	c.(2368-2370)gCa>gTa	p.A790V	SFMBT2_ENST00000397167.1_Missense_Mutation_p.A790V	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	790					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)	p.A790V(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						CCCTTCCTCTGCTGAGGAGGC	0.731																																					p.A790V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2369T	10						.						8.0	10.0	9.0					10																	7213903		2093	4120	6213	7253909	SO:0001583	missense	57713	exon19			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.2369C>T	10.37:g.7213903G>A	ENSP00000355109:p.Ala790Val	Somatic		Capture	Illumina HiSeq	Phase_I	7253909	NM_001029880	A7MD09|Q9HCF5	Missense_Mutation	SNP	ENST00000361972.4	37	CCDS31138.1	.	.	.	.	.	.	.	.	.	.	G	10.42	1.345665	0.24426	.	.	ENSG00000198879	ENST00000361972;ENST00000397167	T;T	0.14391	2.51;2.51	4.98	3.13	0.36017	.	0.857190	0.10584	N	0.657532	T	0.12561	0.0305	L	0.44542	1.39	0.48696	D	0.999691	B	0.02656	0.0	B	0.04013	0.001	T	0.07252	-1.0782	10	0.15499	T	0.54	.	11.1342	0.48365	0.1502:0.0:0.8498:0.0	.	790	Q5VUG0	SMBT2_HUMAN	V	790	ENSP00000355109:A790V;ENSP00000380353:A790V	ENSP00000355109:A790V	A	-	2	0	SFMBT2	7253909	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.480000	0.22244	0.514000	0.28300	-0.254000	0.11334	GCA		0.731	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880	
SFMBT2	57713	broad.mit.edu	37	10	7290522	7290522	+	Silent	SNP	C	C	T	rs537921590		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:7290522C>T	ENST00000361972.4	-	8	1050	c.960G>A	c.(958-960)gcG>gcA	p.A320A	SFMBT2_ENST00000397167.1_Silent_p.A320A	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	320					negative regulation of gene expression (GO:0010629)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	histone binding (GO:0042393)	p.A320A(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						TAGTCACCGACGCAGGAGAGA	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		19628	0.001		0.0	False		,,,				2504	0.0				p.A320A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G960A	10						.						122.0	99.0	107.0					10																	7290522		2203	4300	6503	7330528	SO:0001819	synonymous_variant	57713	exon8			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.960G>A	10.37:g.7290522C>T		Somatic		Capture	Illumina HiSeq	Phase_I	7330528	NM_001029880	A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	37	CCDS31138.1																																																																																				0.493	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880	
ATP5C1	509	broad.mit.edu	37	10	7844756	7844756	+	Missense_Mutation	SNP	C	C	T	rs200847831		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:7844756C>T	ENST00000356708.7	+	8	908	c.829C>T	c.(829-831)Cgt>Tgt	p.R277C	ATP5C1_ENST00000541227.1_Missense_Mutation_p.R230C|ATP5C1_ENST00000493053.1_3'UTR|ATP5C1_ENST00000335698.4_Missense_Mutation_p.R277C	NM_001001973.1	NP_001001973.1	P36542	ATPG_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	277					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) (GO:0000275)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transmembrane transporter activity (GO:0022857)	p.R277C(1)		breast(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	16						GACATTCAACCGTACCCGCCA	0.348													C|||	1	0.000199681	0.0	0.0	5008	,	,		16600	0.001		0.0	False		,,,				2504	0.0				p.R277C	Melanoma(143;1012 1820 16249 30920 33158)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C829T	10						.	C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	90.0	88.0	89.0		829,829	5.5	1.0	10	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ATP5C1	NM_001001973.1,NM_005174.2	180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	277/299,277/298	7844756	1,13005	2203	4300	6503	7884762	SO:0001583	missense	509	exon8			D16561	CCDS7081.1, CCDS31142.1	10p14	2012-10-12			ENSG00000165629	ENSG00000165629		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	833	protein-coding gene	gene with protein product		108729		ATP5CL1, ATP5C		8168843, 8227057	Standard	NM_005174		Approved		uc001iju.3	P36542	OTTHUMG00000017639	ENST00000356708.7:c.829C>T	10.37:g.7844756C>T	ENSP00000349142:p.Arg277Cys	Somatic		Capture	Illumina HiSeq	Phase_I	7884762	NM_001001973	A8KA31|Q5VYP3|Q6I9V2|Q96AS8	Missense_Mutation	SNP	ENST00000356708.7	37	CCDS31142.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	31	5.103144	0.94245	0.0	1.16E-4	ENSG00000165629	ENST00000356708;ENST00000335698;ENST00000541227	.	.	.	5.49	5.49	0.81192	ATPase, F1 complex, gamma subunit domain (1);	0.000000	0.85682	D	0.000000	T	0.76506	0.3997	M	0.88979	2.995	0.80722	D	1	P	0.52463	0.953	P	0.48770	0.589	T	0.82133	-0.0608	9	0.87932	D	0	-6.9791	19.3571	0.94420	0.0:1.0:0.0:0.0	.	277	P36542	ATPG_HUMAN	C	277;277;230	.	ENSP00000338568:R277C	R	+	1	0	ATP5C1	7884762	1.000000	0.71417	0.997000	0.53966	0.964000	0.63967	7.675000	0.84002	2.731000	0.93534	0.650000	0.86243	CGT		0.348	ATP5C1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046708.1	NM_005174	
BEND7	222389	broad.mit.edu	37	10	13523009	13523009	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:13523009G>A	ENST00000396900.2	-	6	952	c.953C>T	c.(952-954)gCg>gTg	p.A318V	BEND7_ENST00000341083.3_Missense_Mutation_p.A266V|BEND7_ENST00000396898.2_Missense_Mutation_p.A331V|BEND7_ENST00000378605.3_Missense_Mutation_p.A279V			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	318	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.					extracellular vesicular exosome (GO:0070062)		p.A266V(1)|p.A279V(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						ATCAAAAAACGCACACACCAG	0.433																																					p.A266V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C797T	10						.						161.0	155.0	157.0					10																	13523009		2203	4300	6503	13563015	SO:0001583	missense	222389	exon6			BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"""BEN domain containing"""	23514	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 30"""	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.953C>T	10.37:g.13523009G>A	ENSP00000380108:p.Ala318Val	Somatic		Capture	Illumina HiSeq	Phase_I	13563015	NM_152751	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Missense_Mutation	SNP	ENST00000396900.2	37		.	.	.	.	.	.	.	.	.	.	G	33	5.262434	0.95368	.	.	ENSG00000165626	ENST00000396900;ENST00000341083;ENST00000440282;ENST00000396898;ENST00000378605	T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95	5.82	5.82	0.92795	BEN domain (2);	0.000000	0.85682	D	0.000000	T	0.48642	0.1511	N	0.08118	0	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.994	T	0.60105	-0.7328	10	0.87932	D	0	-17.6755	20.1001	0.97870	0.0:0.0:1.0:0.0	.	331;318;266	E5RFC0;Q8N7W2;Q8N7W2-3	.;BEND7_HUMAN;.	V	318;266;22;331;279	ENSP00000380108:A318V;ENSP00000345773:A266V;ENSP00000401256:A22V;ENSP00000380107:A331V;ENSP00000367868:A279V	ENSP00000345773:A266V	A	-	2	0	BEND7	13563015	1.000000	0.71417	0.993000	0.49108	0.992000	0.81027	9.709000	0.98729	2.760000	0.94817	0.655000	0.94253	GCG		0.433	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751	
FAM171A1	221061	broad.mit.edu	37	10	15326047	15326047	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:15326047G>A	ENST00000378116.4	-	2	161	c.155C>T	c.(154-156)gCg>gTg	p.A52V		NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	52						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.A52V(1)		breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						CTCGATGAGCGCATCTGCTAC	0.552																																					p.A52V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C155T	10						.						77.0	70.0	72.0					10																	15326047		2203	4300	6503	15366053	SO:0001583	missense	221061	exon2			AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468			23522	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 38"""	C10orf38			Standard	NM_001010924		Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.155C>T	10.37:g.15326047G>A	ENSP00000367356:p.Ala52Val	Somatic		Capture	Illumina HiSeq	Phase_I	15366053	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Missense_Mutation	SNP	ENST00000378116.4	37	CCDS31154.1	.	.	.	.	.	.	.	.	.	.	G	11.42	1.633691	0.29068	.	.	ENSG00000148468	ENST00000378116;ENST00000378114;ENST00000396781;ENST00000455654	T;T	0.38560	1.13;1.13	5.25	3.4	0.38934	.	0.160101	0.53938	N	0.000043	T	0.32971	0.0847	L	0.38175	1.15	0.47153	D	0.99933	B	0.15473	0.013	B	0.14578	0.011	T	0.11060	-1.0603	10	0.54805	T	0.06	-12.3515	11.3426	0.49541	0.1467:0.0:0.8533:0.0	.	52	Q5VUB5	F1711_HUMAN	V	52;52;53;52	ENSP00000367356:A52V;ENSP00000407796:A52V	ENSP00000367354:A52V	A	-	2	0	FAM171A1	15366053	1.000000	0.71417	0.415000	0.26534	0.278000	0.26855	4.243000	0.58721	0.718000	0.32166	0.591000	0.81541	GCG		0.552	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709	
CUBN	8029	broad.mit.edu	37	10	17026159	17026159	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:17026159G>A	ENST00000377833.4	-	30	4535	c.4470C>T	c.(4468-4470)acC>acT	p.T1490T		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1490	CUB 9. {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.T1490T(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)	TGGACAAGTCGGTCTTGAATC	0.502																																					p.T1490T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4470T	10						.						186.0	166.0	172.0					10																	17026159		2203	4300	6503	17066165	SO:0001819	synonymous_variant	8029	exon30			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.4470C>T	10.37:g.17026159G>A		Somatic		Capture	Illumina HiSeq	Phase_I	17066165	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																				0.502	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
CUBN	8029	broad.mit.edu	37	10	17147547	17147547	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:17147547G>A	ENST00000377833.4	-	11	1204	c.1139C>T	c.(1138-1140)cCg>cTg	p.P380L		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	380	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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.P380L(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)	AGTATAACCCGGGAGACACGT	0.443																																					p.P380L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1139T	10						.						108.0	94.0	99.0					10																	17147547		2203	4300	6503	17187553	SO:0001583	missense	8029	exon11			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.1139C>T	10.37:g.17147547G>A	ENSP00000367064:p.Pro380Leu	Somatic		Capture	Illumina HiSeq	Phase_I	17187553	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	.	.	.	.	.	.	.	.	.	.	G	19.02	3.745626	0.69418	.	.	ENSG00000107611	ENST00000377833	D	0.90676	-2.71	5.6	4.66	0.58398	EGF domain, merozoite surface protein 1-like (1);Growth factor, receptor (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.165157	0.29053	N	0.013283	D	0.92476	0.7611	M	0.78049	2.395	0.32090	N	0.591957	D	0.64830	0.994	P	0.52514	0.701	D	0.92265	0.5820	10	0.30078	T	0.28	.	14.3601	0.66766	0.0:0.0:0.7366:0.2634	.	380	O60494	CUBN_HUMAN	L	380	ENSP00000367064:P380L	ENSP00000367064:P380L	P	-	2	0	CUBN	17187553	0.099000	0.21834	0.714000	0.30535	0.821000	0.46438	1.130000	0.31393	2.636000	0.89361	0.655000	0.94253	CCG		0.443	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
STAM	8027	broad.mit.edu	37	10	17756585	17756585	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:17756585G>A	ENST00000377524.3	+	14	1644	c.1429G>A	c.(1429-1431)Gcg>Acg	p.A477T	STAM_ENST00000540523.1_Missense_Mutation_p.A366T	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	477					endosomal transport (GO:0016197)|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)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)	p.A477T(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						TCCCAGCCAGGCGCCAGTATA	0.478																																					p.A477T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1429A	10						.						74.0	74.0	74.0					10																	17756585		2203	4300	6503	17796591	SO:0001583	missense	8027	exon14			U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"""HSE1 homolog (S. cerevisiae)"""	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	ENST00000377524.3:c.1429G>A	10.37:g.17756585G>A	ENSP00000366746:p.Ala477Thr	Somatic		Capture	Illumina HiSeq	Phase_I	17796591	NM_003473	B0YJ99|D3DRU5|Q8N6D9	Missense_Mutation	SNP	ENST00000377524.3	37	CCDS7122.1	.	.	.	.	.	.	.	.	.	.	G	3.004	-0.205427	0.06180	.	.	ENSG00000136738	ENST00000377524;ENST00000540523	T;T	0.39056	1.38;1.1	5.4	3.55	0.40652	.	0.407543	0.28533	N	0.015013	T	0.23014	0.0556	N	0.17082	0.46	0.40524	D	0.980867	B;B	0.12630	0.006;0.001	B;B	0.10450	0.005;0.001	T	0.06552	-1.0820	10	0.15499	T	0.54	-13.928	8.4537	0.32886	0.1423:0.128:0.7297:0.0	.	366;477	B4DZT2;Q92783	.;STAM1_HUMAN	T	477;366	ENSP00000366746:A477T;ENSP00000438073:A366T	ENSP00000366746:A477T	A	+	1	0	STAM	17796591	1.000000	0.71417	0.972000	0.41901	0.021000	0.10359	2.623000	0.46435	1.280000	0.44463	0.467000	0.42956	GCG		0.478	STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047039.1	NM_003473	
SLC39A12	221074	broad.mit.edu	37	10	18276535	18276535	+	Silent	SNP	C	C	T	rs373860855		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:18276535C>T	ENST00000377369.2	+	7	1497	c.1224C>T	c.(1222-1224)gcC>gcT	p.A408A	SLC39A12_ENST00000539911.1_Silent_p.A274A|SLC39A12_ENST00000377374.4_Silent_p.A408A|SLC39A12_ENST00000377371.3_Silent_p.A408A	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	408					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)	p.A408A(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						TGGGCTTGGCCGTCGGGACAC	0.507																																					p.A408A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1224T	10						.	C	,	0,4406		0,0,2203	175.0	152.0	160.0		1224,1224	-10.6	0.1	10		160	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SLC39A12	NM_001145195.1,NM_152725.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	408/692,408/655	18276535	1,13005	2203	4300	6503	18316541	SO:0001819	synonymous_variant	221074	exon7				CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"""Solute carriers"""	20860	protein-coding gene	gene with protein product		608734	"""solute carrier family 39 (metal ion transporter), member 12"""			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.1224C>T	10.37:g.18276535C>T		Somatic		Capture	Illumina HiSeq	Phase_I	18316541	NM_001145195	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Silent	SNP	ENST00000377369.2	37	CCDS44362.1																																																																																				0.507	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725	
BMI1	648	broad.mit.edu	37	10	22615392	22615392	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:22615392C>T	ENST00000376663.3	+	2	519	c.14C>T	c.(13-15)aCg>aTg	p.T5M	COMMD3-BMI1_ENST00000602390.1_Missense_Mutation_p.T148M|COMMD3-BMI1_ENST00000463409.2_3'UTR	NM_005180.8	NP_005171.4	P35226	BMI1_HUMAN	BMI1 proto-oncogene, polycomb ring finger	5					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|regulation of gene expression (GO:0010468)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|ubiquitin ligase complex (GO:0000151)	RING-like zinc finger domain binding (GO:0071535)|zinc ion binding (GO:0008270)	p.T5M(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|urinary_tract(1)	12						CATCGAACAACGAGAATCAAG	0.393																																					p.T5M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C14T	10						.						207.0	183.0	191.0					10																	22615392		2203	4300	6503	22655398	SO:0001583	missense	648	exon2			BC011652	CCDS7138.1	10p13	2014-06-26	2014-06-26	2006-04-26	ENSG00000168283	ENSG00000168283		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	1066	protein-coding gene	gene with protein product		164831	"""polycomb group ring finger 4"", ""B lymphoma Mo-MLV insertion region 1 homolog (mouse)"""	PCGF4		8268912	Standard	NM_005180		Approved	RNF51		P35226	OTTHUMG00000017807	ENST00000376663.3:c.14C>T	10.37:g.22615392C>T	ENSP00000365851:p.Thr5Met	Somatic		Capture	Illumina HiSeq	Phase_I	22655398	NM_005180	Q16030|Q5T8Z3|Q96F37	Missense_Mutation	SNP	ENST00000376663.3	37	CCDS7138.1	.	.	.	.	.	.	.	.	.	.	C	16.62	3.172653	0.57584	.	.	ENSG00000168283	ENST00000417470;ENST00000376663;ENST00000442508;ENST00000456675;ENST00000416820	T;T;T	0.32988	1.43;1.9;2.23	5.71	5.71	0.89125	Zinc finger, RING/FYVE/PHD-type (1);	0.046795	0.85682	N	0.000000	T	0.27967	0.0689	N	0.19112	0.55	0.80722	D	1	D;D	0.61697	0.99;0.979	P;B	0.45610	0.487;0.406	T	0.02512	-1.1148	10	0.49607	T	0.09	-3.5622	18.6272	0.91344	0.0:1.0:0.0:0.0	.	5;5	Q5U0M5;P35226	.;BMI1_HUMAN	M	5	ENSP00000365851:T5M;ENSP00000397912:T5M;ENSP00000399220:T5M	ENSP00000365851:T5M	T	+	2	0	BMI1	22655398	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.721000	0.84768	2.706000	0.92434	0.650000	0.86243	ACG		0.393	BMI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047176.1	NM_005180	
KIAA1217	56243	broad.mit.edu	37	10	24669876	24669876	+	Missense_Mutation	SNP	G	G	A	rs369848932		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:24669876G>A	ENST00000376454.3	+	3	463	c.433G>A	c.(433-435)Gct>Act	p.A145T	KIAA1217_ENST00000376462.1_Missense_Mutation_p.A65T|KIAA1217_ENST00000458595.1_Missense_Mutation_p.A145T|KIAA1217_ENST00000430453.2_Missense_Mutation_p.A66T|KIAA1217_ENST00000376452.3_Missense_Mutation_p.A145T	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	145			A -> G (in dbSNP:rs17506606).		embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)		p.A145T(1)		breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						AGAGACGTCCGCTGATTCTTT	0.542																																					p.A145T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G433A	10						.	G	THR/ALA,THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	67.0	70.0	69.0		193,433,433	5.5	0.0	10		69	0,8600		0,0,4300	no	missense,missense,missense	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	58,58,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign	65/1265,145/1310,145/1944	24669876	1,13005	2203	4300	6503	24709882	SO:0001583	missense	56243	exon3			BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.433G>A	10.37:g.24669876G>A	ENSP00000365637:p.Ala145Thr	Somatic		Capture	Illumina HiSeq	Phase_I	24709882	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	37	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.886260	0.51908	2.27E-4	0.0	ENSG00000120549	ENST00000376462;ENST00000376456;ENST00000458595;ENST00000376454;ENST00000376452;ENST00000430453	T;D;T;T;T;T	0.94687	-0.15;-3.49;-0.15;-0.15;-0.15;-0.15	5.54	5.54	0.83059	.	0.377421	0.29932	N	0.010838	D	0.90885	0.7136	L	0.45137	1.4	0.34375	D	0.69245	P;P;P;P	0.49253	0.921;0.898;0.846;0.683	B;B;B;B	0.34242	0.162;0.178;0.163;0.084	D	0.93494	0.6838	10	0.42905	T	0.14	.	19.4705	0.94961	0.0:0.0:1.0:0.0	.	145;145;145;145	Q5T5P2-7;A6NLF3;Q5T5P2;Q5T5P2-2	.;.;SKT_HUMAN;.	T	65;145;145;145;145;66	ENSP00000365645:A65T;ENSP00000365639:A145T;ENSP00000392625:A145T;ENSP00000365637:A145T;ENSP00000365635:A145T;ENSP00000389680:A66T	ENSP00000365635:A145T	A	+	1	0	KIAA1217	24709882	0.976000	0.34144	0.015000	0.15790	0.477000	0.33069	5.724000	0.68500	2.616000	0.88540	0.591000	0.81541	GCT		0.542	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
KIAA1217	56243	broad.mit.edu	37	10	24835061	24835061	+	Silent	SNP	G	G	A	rs570245552		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:24835061G>A	ENST00000376454.3	+	21	5670	c.5640G>A	c.(5638-5640)ccG>ccA	p.P1880P	KIAA1217_ENST00000376462.1_Silent_p.P1201P|KIAA1217_ENST00000458595.1_Silent_p.P1286P|KIAA1217_ENST00000396445.1_3'UTR|KIAA1217_ENST00000376451.2_3'UTR|KIAA1217_ENST00000376452.3_Silent_p.P1311P	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1880	Ser-rich. {ECO:0000255}.				embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)		p.P1880P(1)		breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						CATTCTCACCGCAGAGTCAAA	0.527																																					p.P1880P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G5640A	10						.						158.0	135.0	143.0					10																	24835061		2203	4300	6503	24875067	SO:0001819	synonymous_variant	56243	exon21			BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.5640G>A	10.37:g.24835061G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24875067	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																				0.527	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
GAD2	2572	broad.mit.edu	37	10	26507982	26507982	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:26507982G>A	ENST00000376261.3	+	4	800	c.297G>A	c.(295-297)ccG>ccA	p.P99P	GAD2_ENST00000376248.1_5'UTR|GAD2_ENST00000259271.3_Silent_p.P99P	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	99					glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|cell junction (GO:0030054)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)	p.P99P(1)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(26)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						ACCTGCTGCCGGCGTGTGATG	0.358																																					p.P99P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G297A	10						.						80.0	77.0	78.0					10																	26507982		2203	4300	6503	26547988	SO:0001819	synonymous_variant	2572	exon4			AJ251501	CCDS7149.1	10p13-p11.2	2003-11-11	2002-08-29		ENSG00000136750	ENSG00000136750	4.1.1.15		4093	protein-coding gene	gene with protein product		138275	"""glutamate decarboxylase 2 (pancreatic islets and brain, 65kD)"""			2039509	Standard	NM_000818		Approved	GAD65	uc001isp.2	Q05329	OTTHUMG00000017836	ENST00000376261.3:c.297G>A	10.37:g.26507982G>A		Somatic		Capture	Illumina HiSeq	Phase_I	26547988	NM_001134366	Q9UD87	Silent	SNP	ENST00000376261.3	37	CCDS7149.1																																																																																				0.358	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818	
PDSS1	23590	broad.mit.edu	37	10	27031460	27031460	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:27031460T>C	ENST00000376215.5	+	11	1114	c.1061T>C	c.(1060-1062)tTc>tCc	p.F354S	PDSS1_ENST00000470978.1_3'UTR|PDSS1_ENST00000376203.5_Silent_p.V290V	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 1	354					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)	p.F354S(1)		autonomic_ganglia(1)|endometrium(1)|kidney(7)|large_intestine(6)|lung(5)|prostate(1)	21						ATGCGACGGTTCAGTTTGCCT	0.383																																					p.F354S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1061C	10						.						89.0	85.0	86.0					10																	27031460		2203	4300	6503	27071466	SO:0001583	missense	23590	exon11			AF118395	CCDS31168.1	10p12.2	2006-04-12	2006-02-14	2006-02-14	ENSG00000148459	ENSG00000148459			17759	protein-coding gene	gene with protein product	"""coenzyme Q1 homolog (yeast)"""	607429	"""trans-prenyltransferase"""	TPRT		10972372	Standard	NM_014317		Approved	TPT, COQ1	uc001isv.3	Q5T2R2	OTTHUMG00000017844	ENST00000376215.5:c.1061T>C	10.37:g.27031460T>C	ENSP00000365388:p.Phe354Ser	Somatic		Capture	Illumina HiSeq	Phase_I	27071466	NM_014317	Q53F75|Q6P473|Q86WQ8|Q9Y2W5	Missense_Mutation	SNP	ENST00000376215.5	37	CCDS31168.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.356671	0.82243	.	.	ENSG00000148459	ENST00000376215;ENST00000396343	T	0.63744	-0.06	4.94	4.94	0.65067	Terpenoid synthase (2);	0.000000	0.85682	D	0.000000	T	0.79741	0.4498	M	0.82132	2.575	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.83001	-0.0177	10	0.72032	D	0.01	-19.2	14.8713	0.70459	0.0:0.0:0.0:1.0	.	92;354	B4DJY1;Q5T2R2	.;DPS1_HUMAN	S	354;315	ENSP00000365388:F354S	ENSP00000365388:F354S	F	+	2	0	PDSS1	27071466	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	7.736000	0.84948	1.977000	0.57605	0.528000	0.53228	TTC		0.383	PDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047276.1		
MASTL	84930	broad.mit.edu	37	10	27454405	27454405	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:27454405G>A	ENST00000375940.4	+	6	805	c.748G>A	c.(748-750)Gta>Ata	p.V250I	MASTL_ENST00000375946.4_Missense_Mutation_p.V250I|MASTL_ENST00000342386.6_Missense_Mutation_p.V250I			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	250	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of protein phosphatase type 2A activity (GO:0034048)|regulation of cell cycle (GO:0051726)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein phosphatase 2A binding (GO:0051721)|protein serine/threonine kinase activity (GO:0004674)	p.V250I(1)		breast(3)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TCAAGGACTCGTATGCCCTAT	0.408																																					p.V250I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G748A	10						.						138.0	128.0	132.0					10																	27454405		2203	4300	6503	27494411	SO:0001583	missense	84930	exon6			BC009107	CCDS7153.1, CCDS53502.1, CCDS53503.1	10p12.1	2005-11-03			ENSG00000120539	ENSG00000120539			19042	protein-coding gene	gene with protein product		608221					Standard	NM_001172303		Approved	FLJ14813, THC2	uc001itm.3	Q96GX5	OTTHUMG00000017855	ENST00000375940.4:c.748G>A	10.37:g.27454405G>A	ENSP00000365107:p.Val250Ile	Somatic		Capture	Illumina HiSeq	Phase_I	27494411	NM_001172303	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	37	CCDS53502.1	.	.	.	.	.	.	.	.	.	.	G	0.037	-1.301333	0.01364	.	.	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	D;D;D	0.85955	-2.05;-2.05;-2.05	5.82	-2.62	0.06152	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.570780	0.02904	N	0.135769	T	0.62405	0.2425	N	0.03115	-0.41	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.56141	-0.8028	10	0.11794	T	0.64	-0.0061	2.0965	0.03669	0.4126:0.1983:0.283:0.1062	.	250;250;250	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	I	250	ENSP00000365113:V250I;ENSP00000343446:V250I;ENSP00000365107:V250I	ENSP00000343446:V250I	V	+	1	0	MASTL	27494411	0.000000	0.05858	0.016000	0.15963	0.037000	0.13140	-0.989000	0.03736	-0.100000	0.12241	-0.350000	0.07774	GTA		0.408	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844	
SVIL	6840	broad.mit.edu	37	10	29754657	29754657	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:29754657C>T	ENST00000355867.4	-	34	6752	c.6000G>A	c.(5998-6000)gcG>gcA	p.A2000A	PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000375400.3_Silent_p.A1574A|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000535393.1_Silent_p.A914A|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000455774.1_RNA|PTCHD3P1_ENST00000413405.1_RNA|SVIL_ENST00000375398.2_Silent_p.A2000A|PTCHD3P1_ENST00000445521.1_RNA	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	2000					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.A2000A(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				ACAGGCGGGGCGCGAAGTTAA	0.468																																					p.A1574A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4722A	10						.						23.0	26.0	25.0					10																	29754657		2203	4299	6502	29794663	SO:0001819	synonymous_variant	6840	exon32			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.6000G>A	10.37:g.29754657C>T		Somatic		Capture	Illumina HiSeq	Phase_I	29794663	NM_003174	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																				0.468	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
SVIL	6840	broad.mit.edu	37	10	29762863	29762863	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:29762863G>A	ENST00000355867.4	-	30	6185	c.5433C>T	c.(5431-5433)tgC>tgT	p.C1811C	PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000375400.3_Silent_p.C1385C|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000535393.1_Silent_p.C725C|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000413405.1_RNA|SVIL_ENST00000460007.1_5'UTR|SVIL_ENST00000375398.2_Silent_p.C1811C	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1811					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.C1811C(2)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				AGAAGTAGACGCACTTCTCTT	0.617																																					p.C1385C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C4155T	10						.						68.0	51.0	57.0					10																	29762863		2203	4300	6503	29802869	SO:0001819	synonymous_variant	6840	exon28			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.5433C>T	10.37:g.29762863G>A		Somatic		Capture	Illumina HiSeq	Phase_I	29802869	NM_003174	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																				0.617	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
SVIL	6840	broad.mit.edu	37	10	29769658	29769658	+	Missense_Mutation	SNP	C	C	T	rs150279349		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:29769658C>T	ENST00000355867.4	-	29	5937	c.5185G>A	c.(5185-5187)Gga>Aga	p.G1729R	SVIL_ENST00000538146.1_Missense_Mutation_p.G521R|PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000375400.3_Missense_Mutation_p.G1303R|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000535393.1_Missense_Mutation_p.G643R|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000413405.1_RNA|SVIL_ENST00000460007.1_5'UTR|SVIL_ENST00000375398.2_Missense_Mutation_p.G1729R	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1729					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.G1729R(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				ACGTTCACTCCGTCCAGGATG	0.572													C|||	1	0.000199681	0.0	0.0	5008	,	,		17031	0.001		0.0	False		,,,				2504	0.0				p.G1303R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3907A	10						.	C	ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	191.0	160.0	170.0		3907,5185	4.4	0.9	10	dbSNP_134	170	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SVIL	NM_003174.3,NM_021738.2	125,125	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	1303/1789,1729/2215	29769658	2,13004	2203	4300	6503	29809664	SO:0001583	missense	6840	exon27			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.5185G>A	10.37:g.29769658C>T	ENSP00000348128:p.Gly1729Arg	Somatic		Capture	Illumina HiSeq	Phase_I	29809664	NM_003174	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	C	18.43	3.623069	0.66901	2.27E-4	1.16E-4	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994;ENST00000538146	T;T;T;T;T	0.30714	2.55;2.55;2.55;2.45;1.52	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.59676	0.2211	M	0.83384	2.64	0.80722	D	1	D;D;D;D	0.89917	1.0;0.997;0.998;0.99	D;D;D;P	0.78314	0.991;0.937;0.924;0.743	T	0.68014	-0.5521	10	0.87932	D	0	-26.814	17.212	0.86932	0.0:1.0:0.0:0.0	.	643;521;1303;1729	F5H2Q5;F5GXV0;O95425-2;O95425	.;.;.;SVIL_HUMAN	R	1303;1729;1729;643;683;521	ENSP00000364549:G1303R;ENSP00000364547:G1729R;ENSP00000348128:G1729R;ENSP00000445472:G643R;ENSP00000440343:G521R	ENSP00000348128:G1729R	G	-	1	0	SVIL	29809664	1.000000	0.71417	0.885000	0.34714	0.090000	0.18270	7.559000	0.82265	2.277000	0.76020	0.561000	0.74099	GGA		0.572	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
SVIL	6840	broad.mit.edu	37	10	29779942	29779942	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:29779942C>T	ENST00000355867.4	-	22	4778	c.4026G>A	c.(4024-4026)acG>acA	p.T1342T	SVIL_ENST00000538146.1_Silent_p.T134T|SVIL_ENST00000375400.3_Silent_p.T916T|SVIL_ENST00000535393.1_Silent_p.T256T|SVIL_ENST00000375398.2_Silent_p.T1342T	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1342					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.T1342T(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				CCACGGAAGACGTCAATCTGC	0.582																																					p.T916T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2748A	10						.						26.0	26.0	26.0					10																	29779942		2203	4300	6503	29819948	SO:0001819	synonymous_variant	6840	exon20			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.4026G>A	10.37:g.29779942C>T		Somatic		Capture	Illumina HiSeq	Phase_I	29819948	NM_003174	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Silent	SNP	ENST00000355867.4	37	CCDS7164.1																																																																																				0.582	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
SVIL	6840	broad.mit.edu	37	10	29822292	29822292	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:29822292G>A	ENST00000355867.4	-	8	1756	c.1004C>T	c.(1003-1005)gCg>gTg	p.A335V	SVIL_ENST00000375400.3_Intron|SVIL_ENST00000375398.2_Missense_Mutation_p.A335V	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	335					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.A335V(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				ATGGACTGGCGCTGGCTGGTG	0.507																																					p.A335V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1004T	10						.						88.0	76.0	80.0					10																	29822292		2203	4300	6503	29862298	SO:0001583	missense	6840	exon8			AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.1004C>T	10.37:g.29822292G>A	ENSP00000348128:p.Ala335Val	Somatic		Capture	Illumina HiSeq	Phase_I	29862298	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	G	2.239	-0.374342	0.05034	.	.	ENSG00000197321	ENST00000375398;ENST00000355867	T;T	0.38722	1.12;1.12	5.62	-2.92	0.05615	.	1.158180	0.06338	N	0.707391	T	0.25382	0.0617	N	0.21448	0.665	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.23511	-1.0186	9	.	.	.	-2.404	7.5813	0.27965	0.3685:0.2308:0.4007:0.0	.	335	O95425	SVIL_HUMAN	V	335	ENSP00000364547:A335V;ENSP00000348128:A335V	.	A	-	2	0	SVIL	29862298	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.170000	0.09897	-0.383000	0.07858	0.655000	0.94253	GCG		0.507	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
MAP3K8	1326	broad.mit.edu	37	10	30747087	30747087	+	Silent	SNP	G	G	A	rs114464695	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:30747087G>A	ENST00000263056.1	+	7	1644	c.948G>A	c.(946-948)acG>acA	p.T316T	MAP3K8_ENST00000375321.1_Silent_p.T316T|MAP3K8_ENST00000542547.1_Silent_p.T316T	NM_001244134.1|NM_005204.3	NP_001231063.1|NP_005195.2	P41279	M3K8_HUMAN	mitogen-activated protein kinase kinase kinase 8	316	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|protein phosphorylation (GO:0006468)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein serine/threonine kinase activity (GO:0004674)	p.T316T(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Prostate(175;0.151)				TGGGGGCCACGCTCATCCACA	0.557													g|||	17	0.00339457	0.0121	0.0014	5008	,	,		15800	0.0		0.0	False		,,,				2504	0.0				p.T316T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G948A	10						.	A		45,4361	47.5+/-82.1	0,45,2158	81.0	79.0	80.0		948	-10.1	0.2	10	dbSNP_132	80	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	MAP3K8	NM_005204.3		0,48,6455	AA,AG,GG		0.0349,1.0213,0.3691		316/468	30747087	48,12958	2203	4300	6503	30787093	SO:0001819	synonymous_variant	1326	exon7			D14497	CCDS7166.1	10p11.2	2011-06-09			ENSG00000107968	ENSG00000107968		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6860	protein-coding gene	gene with protein product		191195		COT, ESTF		2072910, 8479752	Standard	NM_005204		Approved	Tpl-2, EST, c-COT, MEKK8	uc009xlf.2	P41279	OTTHUMG00000017889	ENST00000263056.1:c.948G>A	10.37:g.30747087G>A		Somatic		Capture	Illumina HiSeq	Phase_I	30787093	NM_005204	A8K2Q5|D3DRX1|Q14275|Q5T855|Q9HC81	Silent	SNP	ENST00000263056.1	37	CCDS7166.1																																																																																				0.557	MAP3K8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047416.2	NM_005204	
KIF5B	3799	broad.mit.edu	37	10	32306158	32306158	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:32306158G>A	ENST00000302418.4	-	24	3131	c.2674C>T	c.(2674-2676)Cgc>Tgc	p.R892C	KIF5B_ENST00000493889.1_5'UTR	NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	892					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cellular protein metabolic process (GO:0044267)|cytoplasm organization (GO:0007028)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane potential (GO:0042391)|stress granule disassembly (GO:0035617)|vesicle transport along microtubule (GO:0047496)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.R892C(1)	KIF5B/ALK(8)|KIF5B/RET(79)	NS(2)|breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)	35		Prostate(175;0.0137)				TAGCGTTTGCGATCACGAGAT	0.438			T	"""RET, ALK"""	NSCLC																																p.R892C			Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2674T	10						.						302.0	264.0	277.0					10																	32306158		2203	4300	6503	32346164	SO:0001583	missense	3799	exon24			X65873	CCDS7171.1	10p11.22	2007-02-13			ENSG00000170759	ENSG00000170759		"""Kinesins"""	6324	protein-coding gene	gene with protein product		602809		KNS1		1607388	Standard	NM_004521		Approved	KNS	uc001iwe.4	P33176	OTTHUMG00000017913	ENST00000302418.4:c.2674C>T	10.37:g.32306158G>A	ENSP00000307078:p.Arg892Cys	Somatic		Capture	Illumina HiSeq	Phase_I	32346164	NM_004521	A0AVB2|Q5VZ85	Missense_Mutation	SNP	ENST00000302418.4	37	CCDS7171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.369683	0.95900	.	.	ENSG00000170759	ENST00000302418	T	0.80994	-1.44	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.91683	0.7371	M	0.88979	2.995	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.92750	0.6215	10	0.87932	D	0	.	19.5519	0.95324	0.0:0.0:1.0:0.0	.	892	P33176	KINH_HUMAN	C	892	ENSP00000307078:R892C	ENSP00000307078:R892C	R	-	1	0	KIF5B	32346164	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.776000	0.99001	2.623000	0.88846	0.467000	0.42956	CGC		0.438	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521	
BMS1	9790	broad.mit.edu	37	10	43289388	43289388	+	Missense_Mutation	SNP	C	C	T	rs139699494		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:43289388C>T	ENST00000374518.5	+	9	1241	c.1178C>T	c.(1177-1179)aCg>aTg	p.T393M		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	393					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.T393M(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						AGTCGAGTGACGCTGTTTTCT	0.433																																					p.T393M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1178T	10						.	C	MET/THR	0,4406		0,0,2203	85.0	80.0	82.0		1178	3.8	1.0	10	dbSNP_134	82	1,8599	1.2+/-3.3	0,1,4299	no	missense	BMS1	NM_014753.3	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	393/1283	43289388	1,13005	2203	4300	6503	42609394	SO:0001583	missense	9790	exon9			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.1178C>T	10.37:g.43289388C>T	ENSP00000363642:p.Thr393Met	Somatic		Capture	Illumina HiSeq	Phase_I	42609394	NM_014753	Q5QPT5|Q86XJ9	Missense_Mutation	SNP	ENST00000374518.5	37	CCDS7199.1	.	.	.	.	.	.	.	.	.	.	c	12.57	1.976541	0.34848	0.0	1.16E-4	ENSG00000165733	ENST00000374518	T	0.08458	3.09	5.66	3.83	0.44106	.	0.162882	0.56097	N	0.000025	T	0.05868	0.0153	N	0.17474	0.49	0.30221	N	0.79686	B	0.27013	0.166	B	0.13407	0.009	T	0.07868	-1.0750	10	0.54805	T	0.06	.	12.8371	0.57780	0.0:0.8703:0.0:0.1297	.	393	Q14692	BMS1_HUMAN	M	393	ENSP00000363642:T393M	ENSP00000363642:T393M	T	+	2	0	BMS1	42609394	1.000000	0.71417	0.988000	0.46212	0.753000	0.42808	4.540000	0.60664	0.773000	0.33404	-0.788000	0.03338	ACG		0.433	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753	
ZNF485	220992	broad.mit.edu	37	10	44111740	44111740	+	Splice_Site	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:44111740C>T	ENST00000361807.3	+	5	443	c.249C>T	c.(247-249)gtC>gtT	p.V83V	ZNF485_ENST00000374435.3_Splice_Site_p.V83V|ZNF485_ENST00000374437.2_5'UTR	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	83					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.V44V(1)|p.V83V(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						TTCTTTCAGTCGAGGATTACT	0.353																																					p.V83V												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C249T	10						.						40.0	44.0	42.0					10																	44111740		2203	4300	6503	43431746	SO:0001630	splice_region_variant	220992	exon5			AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"""Zinc fingers, C2H2-type"", ""-"""	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.248-1C>T	10.37:g.44111740C>T		Somatic		Capture	Illumina HiSeq	Phase_I	43431746	NM_145312	B4DSE6|Q96CL0	Silent	SNP	ENST00000361807.3	37	CCDS7205.2																																																																																				0.353	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312	Silent
RASSF4	83937	broad.mit.edu	37	10	45486467	45486467	+	Missense_Mutation	SNP	G	G	A	rs201005781		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:45486467G>A	ENST00000340258.5	+	9	870	c.757G>A	c.(757-759)Gcc>Acc	p.A253T	RASSF4_ENST00000334940.6_Missense_Mutation_p.A262T|RASSF4_ENST00000472561.1_3'UTR|RASSF4_ENST00000374417.2_3'UTR	NM_032023.3	NP_114412.2	Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	0					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)	p.A253T(1)		NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						TGAGAAGATCGCCAGGATCTT	0.522																																					p.A253T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G757A	10						.						64.0	70.0	68.0					10																	45486467		2203	4300	6503	44806473	SO:0001583	missense	83937	exon9			BC032593	CCDS7208.1	10q11.1	2008-02-22	2008-02-22		ENSG00000107551	ENSG00000107551			20793	protein-coding gene	gene with protein product		610559					Standard	NM_032023		Approved	AD037, MGC44914	uc001jbo.3	Q9H2L5	OTTHUMG00000018060	ENST00000340258.5:c.757G>A	10.37:g.45486467G>A	ENSP00000339692:p.Ala253Thr	Somatic		Capture	Illumina HiSeq	Phase_I	44806473	NM_032023	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000340258.5	37	CCDS7208.1	.	.	.	.	.	.	.	.	.	.	G	32	5.152658	0.94645	.	.	ENSG00000107551	ENST00000334940;ENST00000340258;ENST00000374411	T;T	0.28895	1.59;1.59	5.82	5.82	0.92795	Ras-association (3);	0.104329	0.64402	D	0.000005	T	0.48040	0.1478	L	0.59436	1.845	0.80722	D	1	D;D;P	0.69078	0.991;0.997;0.92	P;P;P	0.58780	0.462;0.845;0.474	T	0.19647	-1.0299	10	0.35671	T	0.21	-19.9602	17.5789	0.87960	0.0:0.0:1.0:0.0	.	262;344;253	Q9H2L5-2;Q59FL4;Q9H2L5	.;.;RASF4_HUMAN	T	262;253;344	ENSP00000334543:A262T;ENSP00000339692:A253T	ENSP00000334543:A262T	A	+	1	0	RASSF4	44806473	1.000000	0.71417	0.812000	0.32479	0.897000	0.52465	4.003000	0.57061	2.758000	0.94735	0.650000	0.86243	GCC		0.522	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047745.2	NM_032023	
ALOX5	240	broad.mit.edu	37	10	45877942	45877942	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:45877942C>T	ENST00000374391.2	+	2	215	c.162C>T	c.(160-162)taC>taT	p.Y54Y	ALOX5_ENST00000542434.1_Silent_p.Y54Y	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	54	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)	p.Y54Y(1)		breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	TGGATTCATACGACGTGACTG	0.527																																					p.Y54Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C162T	10						.						130.0	101.0	111.0					10																	45877942		2203	4300	6503	45197948	SO:0001819	synonymous_variant	240	exon2			J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"""Arachidonate lipoxygenases"""	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.162C>T	10.37:g.45877942C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45197948	NM_000698	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Silent	SNP	ENST00000374391.2	37	CCDS7212.1																																																																																				0.527	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1		
SYT15	83849	broad.mit.edu	37	10	46968644	46968644	+	Missense_Mutation	SNP	C	C	T	rs530419005	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:46968644C>T	ENST00000374321.4	-	3	358	c.292G>A	c.(292-294)Gat>Aat	p.D98N	SYT15_ENST00000374325.3_Missense_Mutation_p.D98N|SYT15_ENST00000503753.1_Missense_Mutation_p.D98N|RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374323.4_Missense_Mutation_p.D151N	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D98N(1)		cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						CATGGGGCATCGGCCCACTCT	0.662													C|||	4	0.000798722	0.0023	0.0	5008	,	,		34690	0.0		0.0	False		,,,				2504	0.001				p.D98N	Ovarian(57;1152 1428 19651 37745)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G292A	10						.						43.0	53.0	50.0					10																	46968644		2114	4231	6345	46388650	SO:0001583	missense	83849	exon3			AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"""Synaptotagmins"""	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.292G>A	10.37:g.46968644C>T	ENSP00000363441:p.Asp98Asn	Somatic		Capture	Illumina HiSeq	Phase_I	46388650	NM_181519	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	37	CCDS44376.1	.	.	.	.	.	.	.	.	.	.	.	11.47	1.647056	0.29246	.	.	ENSG00000204176	ENST00000416127;ENST00000374325;ENST00000503753;ENST00000374323;ENST00000374321	T;T;T;T	0.13901	2.55;2.55;2.84;2.78	4.59	0.207	0.15214	.	0.942260	0.09012	N	0.861451	T	0.06416	0.0165	N	0.08118	0	0.09310	N	1	B;B	0.18610	0.017;0.029	B;B	0.15870	0.004;0.014	T	0.45086	-0.9285	10	0.17832	T	0.49	.	8.1778	0.31292	0.0:0.2909:0.4293:0.2799	.	98;98	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	N	98;98;98;151;98	ENSP00000363445:D98N;ENSP00000427607:D98N;ENSP00000363443:D151N;ENSP00000363441:D98N	ENSP00000363441:D98N	D	-	1	0	SYT15	46388650	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.610000	0.24253	-0.032000	0.13758	-0.235000	0.12190	GAT		0.662	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912	
GPRIN2	9721	broad.mit.edu	37	10	46999936	46999936	+	Silent	SNP	G	G	A	rs541094119	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:46999936G>A	ENST00000374317.1	+	3	1329	c.1056G>A	c.(1054-1056)ccG>ccA	p.P352P	GPRIN2_ENST00000374314.4_Silent_p.P352P	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	352								p.P352P(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						CCACCAGTCCGTCCCTGGAAG	0.672													G|||	8	0.00159744	0.0008	0.0	5008	,	,		29966	0.005		0.0	False		,,,				2504	0.002				p.P352P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1056A	10						.																																			46419942	SO:0001819	synonymous_variant	9721	exon3			BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.1056G>A	10.37:g.46999936G>A		Somatic		Capture	Illumina HiSeq	Phase_I	46419942	NM_014696	Q5SVF0	Silent	SNP	ENST00000374317.1	37	CCDS31192.1																																																																																				0.672	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
RBP3	5949	broad.mit.edu	37	10	48390167	48390167	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:48390167G>A	ENST00000224600.4	-	1	824	c.711C>T	c.(709-711)ggC>ggT	p.G237G	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	237	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)	p.G237G(1)		central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	CCTCGGCCACGCCCCTGGTCT	0.657																																					p.G237G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C711T	10						.						72.0	63.0	67.0					10																	48390167		2203	4300	6503	48010173	SO:0001819	synonymous_variant	5949	exon1			M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"""retinol-binding protein 3, interstitial"""				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.711C>T	10.37:g.48390167G>A		Somatic		Capture	Illumina HiSeq	Phase_I	48010173	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Silent	SNP	ENST00000224600.4	37	CCDS7218.1																																																																																				0.657	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900	
PRKG1	5592	broad.mit.edu	37	10	53667330	53667330	+	Splice_Site	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:53667330G>T	ENST00000401604.2	+	5	911	c.717G>T	c.(715-717)gaG>gaT	p.E239D	PRKG1_ENST00000373985.1_Splice_Site_p.E227D|PRKG1_ENST00000373980.4_Splice_Site_p.E254D			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	239	cGMP-binding, low affinity.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)	p.E254D(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TCCTTGAAGAGGTAATTGTTT	0.443																																					p.E254D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G762T	10						.						189.0	170.0	177.0					10																	53667330		2203	4300	6503	53337336	SO:0001630	splice_region_variant	5592	exon5				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.717+1G>T	10.37:g.53667330G>T		Somatic		Capture	Illumina HiSeq	Phase_I	53337336	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	G	16.61	3.171929	0.57584	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000373976	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.14	5.14	0.70334	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.058438	0.64402	D	0.000002	T	0.47544	0.1451	M	0.84156	2.68	0.58432	D	0.999999	P;D	0.53312	0.95;0.959	P;P	0.51777	0.679;0.634	T	0.48151	-0.9060	10	0.16896	T	0.51	-14.5246	16.0812	0.81005	0.0:0.0:1.0:0.0	.	254;239	Q13976-2;Q13976	.;KGP1_HUMAN	D	239;227;254;112	ENSP00000384200:E239D;ENSP00000363097:E227D;ENSP00000363092:E254D;ENSP00000363087:E112D	ENSP00000363087:E112D	E	+	3	2	PRKG1	53337336	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.719000	0.84751	2.403000	0.81681	0.491000	0.48974	GAG		0.443	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Missense_Mutation
EGR2	1959	broad.mit.edu	37	10	64574078	64574078	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:64574078C>T	ENST00000242480.3	-	2	645	c.320G>A	c.(319-321)tGc>tAc	p.C107Y	EGR2_ENST00000493899.2_5'Flank|EGR2_ENST00000439032.1_Missense_Mutation_p.C107Y|EGR2_ENST00000411732.1_Missense_Mutation_p.C57Y	NM_000399.3|NM_001136177.1	NP_000390.2|NP_001129649.1	P11161	EGR2_HUMAN	early growth response 2	107					brain development (GO:0007420)|brain segmentation (GO:0035284)|cell death (GO:0008219)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|facial nerve structural organization (GO:0021612)|fat cell differentiation (GO:0045444)|learning or memory (GO:0007611)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of apoptotic process (GO:0043066)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein export from nucleus (GO:0006611)|protein sumoylation (GO:0016925)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ossification (GO:0030278)|response to insulin (GO:0032868)|rhombomere 3 formation (GO:0021660)|rhombomere 5 formation (GO:0021666)|rhythmic behavior (GO:0007622)|Schwann cell differentiation (GO:0014037)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)	p.C107Y(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)	36	Prostate(12;0.0297)|all_hematologic(501;0.228)					TTCTGGGTAGCAGCTGGCACC	0.542																																					p.C107Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G320A	10						.						159.0	141.0	147.0					10																	64574078		2203	4300	6503	64244084	SO:0001583	missense	1959	exon2			BC035625	CCDS7267.1, CCDS44409.1	10q21.1	2014-09-17	2009-04-23		ENSG00000122877	ENSG00000122877		"""Zinc fingers, C2H2-type"""	3239	protein-coding gene	gene with protein product	"""Krox-20 homolog, Drosophila"""	129010	"""early growth response 2 (Krox-20 homolog, Drosophila)"""	KROX20			Standard	NM_000399		Approved		uc001jmi.3	P11161	OTTHUMG00000018308	ENST00000242480.3:c.320G>A	10.37:g.64574078C>T	ENSP00000242480:p.Cys107Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	64244084	NM_000399	B2R724|B3KRD7|Q68CZ5|Q8IV26|Q9UNA6	Missense_Mutation	SNP	ENST00000242480.3	37	CCDS7267.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168482	0.78339	.	.	ENSG00000122877	ENST00000242480;ENST00000439032;ENST00000411732;ENST00000432380	T;T;T	0.22539	1.95;1.95;1.95	5.54	5.54	0.83059	.	0.054136	0.85682	D	0.000000	T	0.15176	0.0366	L	0.34521	1.04	0.49051	D	0.99974	P;P	0.39282	0.615;0.666	B;B	0.33042	0.097;0.157	T	0.07673	-1.0760	10	0.16896	T	0.51	-20.8125	15.4889	0.75590	0.0:0.8611:0.1388:0.0	.	57;107	P11161-2;P11161	.;EGR2_HUMAN	Y	107;107;57;120	ENSP00000242480:C107Y;ENSP00000402040:C107Y;ENSP00000387634:C57Y	ENSP00000242480:C107Y	C	-	2	0	EGR2	64244084	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.885000	0.63142	2.592000	0.87571	0.563000	0.77884	TGC		0.542	EGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048245.2	NM_000399	
REEP3	221035	broad.mit.edu	37	10	65380581	65380581	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:65380581C>T	ENST00000373758.4	+	8	903	c.720C>T	c.(718-720)taC>taT	p.Y240Y	REEP3_ENST00000298249.4_Silent_p.Y225Y	NM_001001330.2	NP_001001330.1	Q6NUK4	REEP3_HUMAN	receptor accessory protein 3	240					mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|nuclear envelope organization (GO:0006998)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)		p.Y240Y(1)		endometrium(1)|large_intestine(2)|lung(3)	6	Prostate(12;0.0119)|all_hematologic(501;0.191)					AGGTGCGGTACGGGTCACTAA	0.294																																					p.Y240Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C720T	10						.						71.0	63.0	65.0					10																	65380581		1814	4072	5886	65050587	SO:0001819	synonymous_variant	221035	exon8			BC057832	CCDS44411.1	10q21.3	2011-01-05	2006-02-07	2006-02-07	ENSG00000165476	ENSG00000165476		"""Receptor accessory proteins"""	23711	protein-coding gene	gene with protein product		609348	"""chromosome 10 open reading frame 74"""	C10orf74		16271481, 15550249	Standard	NM_001001330		Approved		uc001jmt.3	Q6NUK4	OTTHUMG00000018318	ENST00000373758.4:c.720C>T	10.37:g.65380581C>T		Somatic		Capture	Illumina HiSeq	Phase_I	65050587	NM_001001330	Q5JQR5|Q5QGT2|Q6PEW8|Q6PJY4	Silent	SNP	ENST00000373758.4	37	CCDS44411.1																																																																																				0.294	REEP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001001330	
CTNNA3	29119	broad.mit.edu	37	10	68940233	68940233	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:68940233G>A	ENST00000433211.2	-	7	1063	c.889C>T	c.(889-891)Cga>Tga	p.R297*	CTNNA3_ENST00000373744.4_Nonsense_Mutation_p.R297*|CTNNA3_ENST00000545309.1_Nonsense_Mutation_p.R297*	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3									p.R297*(3)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						AGTGATGGTCGTATTTCCTCC	0.448																																					p.R297X												.	.	3	Substitution - Nonsense(3)	large_intestine(2)|ovary(1)	c.C889T	10						.						143.0	130.0	134.0					10																	68940233		2203	4300	6503	68610239	SO:0001587	stop_gained	29119	exon7			AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.889C>T	10.37:g.68940233G>A	ENSP00000389714:p.Arg297*	Somatic		Capture	Illumina HiSeq	Phase_I	68610239	NM_013266		Nonsense_Mutation	SNP	ENST00000433211.2	37	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	G	39	7.874806	0.98537	.	.	ENSG00000183230	ENST00000433211;ENST00000373744;ENST00000545309	.	.	.	5.83	1.89	0.25635	.	0.107942	0.39985	N	0.001208	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.0289	14.0978	0.65034	0.0:0.0:0.3637:0.6363	.	.	.	.	X	297	.	ENSP00000362849:R297X	R	-	1	2	CTNNA3	68610239	0.984000	0.35163	0.997000	0.53966	0.990000	0.78478	1.218000	0.32467	0.456000	0.26937	-0.347000	0.07816	CGA		0.448	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266	
DNA2	1763	broad.mit.edu	37	10	70179641	70179641	+	Silent	SNP	C	C	T	rs371684850		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:70179641C>T	ENST00000358410.3	-	18	2756	c.2706G>A	c.(2704-2706)gcG>gcA	p.A902A	DNA2_ENST00000399180.2_Silent_p.A988A|DNA2_ENST00000399179.2_Silent_p.A664A	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	902	Helicase activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)	p.A902A(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						CTTGTTCTGGCGCTGGAACCT	0.373																																					p.A988A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2964A	10						.	C		1,3649		0,1,1824	112.0	112.0	112.0		2706	0.6	1.0	10		112	2,8158		0,2,4078	no	coding-synonymous	DNA2	NM_001080449.2		0,3,5902	TT,TC,CC		0.0245,0.0274,0.0254		902/1061	70179641	3,11807	1825	4080	5905	69849647	SO:0001819	synonymous_variant	1763	exon18			D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"""DNA2 DNA replication helicase 2-like (yeast)"", ""DNA replication helicase 2 homolog (yeast)"""	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.2706G>A	10.37:g.70179641C>T		Somatic		Capture	Illumina HiSeq	Phase_I	69849647	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37		.	.	.	.	.	.	.	.	.	.	C	9.775	1.173678	0.21704	2.74E-4	2.45E-4	ENSG00000138346	ENST00000440722	D	0.82433	-1.61	5.92	0.63	0.17693	.	0.000000	0.85682	D	0.000000	T	0.81009	0.4734	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74241	-0.3729	7	0.59425	D	0.04	.	2.8047	0.05424	0.2348:0.0663:0.3451:0.3537	.	.	.	.	T	224	ENSP00000389713:A224T	ENSP00000389713:A224T	A	-	1	0	DNA2	69849647	0.998000	0.40836	0.998000	0.56505	0.947000	0.59692	0.327000	0.19663	-0.118000	0.11851	-0.324000	0.08512	GCC		0.373	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2		
TET1	80312	broad.mit.edu	37	10	70333060	70333060	+	Missense_Mutation	SNP	C	C	A	rs377638565		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:70333060C>A	ENST00000373644.4	+	2	1174	c.965C>A	c.(964-966)tCt>tAt	p.S322Y		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	322					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)	p.S322Y(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						GGGTCTACGTCTCCTACCTCT	0.448																																					p.S322Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C965A	10						.	C	TYR/SER	0,4406		0,0,2203	100.0	106.0	104.0		965	2.9	1.0	10		104	1,8599	1.2+/-3.3	0,1,4299	no	missense	TET1	NM_030625.2	144	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign	322/2137	70333060	1,13005	2203	4300	6503	70003066	SO:0001583	missense	80312	exon2			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.965C>A	10.37:g.70333060C>A	ENSP00000362748:p.Ser322Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	70003066	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	C	0.015	-1.546136	0.00926	0.0	1.16E-4	ENSG00000138336	ENST00000373644	T	0.04360	3.64	5.46	2.86	0.33363	.	0.689675	0.12697	N	0.446694	T	0.01320	0.0043	N	0.01352	-0.895	0.23346	N	0.997867	B	0.02656	0.0	B	0.01281	0.0	T	0.46965	-0.9153	10	0.02654	T	1	.	2.647	0.04987	0.5148:0.2665:0.0836:0.1351	.	322	Q8NFU7	TET1_HUMAN	Y	322	ENSP00000362748:S322Y	ENSP00000362748:S322Y	S	+	2	0	TET1	70003066	0.933000	0.31639	0.965000	0.40720	0.905000	0.53344	0.146000	0.16180	0.913000	0.36797	-0.457000	0.05445	TCT		0.448	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
TET1	80312	broad.mit.edu	37	10	70411651	70411651	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:70411651C>T	ENST00000373644.4	+	5	4534	c.4325C>T	c.(4324-4326)gCa>gTa	p.A1442V		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1442					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)	p.A1442V(2)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						CACCTTGGGGCAGGACCAAGT	0.423																																					p.A1442V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C4325T	10						.						150.0	156.0	154.0					10																	70411651		2203	4300	6503	70081657	SO:0001583	missense	80312	exon5			AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.4325C>T	10.37:g.70411651C>T	ENSP00000362748:p.Ala1442Val	Somatic		Capture	Illumina HiSeq	Phase_I	70081657	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	.	.	.	.	.	.	.	.	.	.	C	35	5.470375	0.96274	.	.	ENSG00000138336	ENST00000373644	T	0.39056	1.1	5.83	5.83	0.93111	TET cysteine-rich domain (1);	0.258725	0.38663	N	0.001611	T	0.55878	0.1948	L	0.52573	1.65	0.46901	D	0.999245	D	0.55800	0.973	P	0.55055	0.767	T	0.54997	-0.8209	10	0.66056	D	0.02	.	20.1356	0.98028	0.0:1.0:0.0:0.0	.	1442	Q8NFU7	TET1_HUMAN	V	1442	ENSP00000362748:A1442V	ENSP00000362748:A1442V	A	+	2	0	TET1	70081657	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.294000	0.78760	2.755000	0.94549	0.650000	0.86243	GCA		0.423	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
STOX1	219736	broad.mit.edu	37	10	70645270	70645270	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:70645270C>A	ENST00000298596.6	+	3	1801	c.1718C>A	c.(1717-1719)cCc>cAc	p.P573H	STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399169.4_Missense_Mutation_p.P573H|STOX1_ENST00000421961.2_Missense_Mutation_p.P463H|STOX1_ENST00000399165.4_Intron	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	573						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P573H(1)		breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						ACTGTCAAACCCATCAATGAT	0.398																																					p.P573H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1718A	10						.						109.0	98.0	101.0					10																	70645270		1900	4097	5997	70315276	SO:0001583	missense	219736	exon3			AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"""chromosome 10 open reading frame 24"""	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.1718C>A	10.37:g.70645270C>A	ENSP00000298596:p.Pro573His	Somatic		Capture	Illumina HiSeq	Phase_I	70315276	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	37	CCDS41535.1	.	.	.	.	.	.	.	.	.	.	C	7.688	0.690374	0.15039	.	.	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000421961	T;T;T	0.75938	-0.98;-0.98;-0.66	5.76	4.87	0.63330	.	0.630452	0.15964	N	0.236133	T	0.76026	0.3930	L	0.53249	1.67	0.09310	N	1	D	0.53151	0.958	P	0.50791	0.65	T	0.68484	-0.5396	10	0.72032	D	0.01	.	10.4405	0.44462	0.0:0.8359:0.0:0.1641	.	573	Q6ZVD7	STOX1_HUMAN	H	573;573;463	ENSP00000382121:P573H;ENSP00000298596:P573H;ENSP00000394509:P463H	ENSP00000298596:P573H	P	+	2	0	STOX1	70315276	0.005000	0.15991	0.002000	0.10522	0.005000	0.04900	2.069000	0.41481	1.452000	0.47756	-0.216000	0.12614	CCC		0.398	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709	
HKDC1	80201	broad.mit.edu	37	10	71005973	71005973	+	Silent	SNP	C	C	T	rs144489141	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:71005973C>T	ENST00000354624.5	+	8	1147	c.1014C>T	c.(1012-1014)caC>caT	p.H338H	HKDC1_ENST00000395086.2_Silent_p.H338H	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	338	Hexokinase type-2 1.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)	p.H338H(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						AAACACGGCACGTGGCTGCCA	0.567													C|||	2	0.000399361	0.0	0.0	5008	,	,		21668	0.002		0.0	False		,,,				2504	0.0				p.H338H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1014T	10						.						109.0	94.0	99.0					10																	71005973		2203	4300	6503	70675979	SO:0001819	synonymous_variant	80201	exon8				CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.1014C>T	10.37:g.71005973C>T		Somatic		Capture	Illumina HiSeq	Phase_I	70675979	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Silent	SNP	ENST00000354624.5	37	CCDS7288.1																																																																																				0.567	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130	
HK1	3098	broad.mit.edu	37	10	71142451	71142451	+	Missense_Mutation	SNP	C	C	T	rs373626952		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:71142451C>T	ENST00000359426.6	+	10	1578	c.1474C>T	c.(1474-1476)Cgg>Tgg	p.R492W	HK1_ENST00000404387.2_Missense_Mutation_p.R496W|HK1_ENST00000360289.2_Missense_Mutation_p.R480W|HK1_ENST00000448642.2_Missense_Mutation_p.R527W|HK1_ENST00000298649.3_Missense_Mutation_p.R491W|HK1_ENST00000494253.1_3'UTR	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	492	Catalytic.|Hexokinase type-1 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|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)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)	p.R496W(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						GAAGAGGATGCGGGCCGAGAT	0.617																																					p.R496W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1486T	10						.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83.0	65.0	71.0		1474,1471,1486,1486,1438	2.5	0.9	10		71	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	HK1	NM_000188.2,NM_033496.2,NM_033497.2,NM_033498.2,NM_033500.2	101,101,101,101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	492/918,491/917,496/922,496/922,480/906	71142451	1,13005	2203	4300	6503	70812457	SO:0001583	missense	3098	exon13			M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.1474C>T	10.37:g.71142451C>T	ENSP00000352398:p.Arg492Trp	Somatic		Capture	Illumina HiSeq	Phase_I	70812457	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Missense_Mutation	SNP	ENST00000359426.6	37	CCDS7292.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.377403	0.61735	0.0	1.16E-4	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	D;D;D;D;D	0.99023	-5.34;-5.34;-5.34;-5.34;-5.34	5.53	2.55	0.30701	Hexokinase, N-terminal (1);	0.096544	0.64402	D	0.000002	D	0.99348	0.9771	M	0.91920	3.255	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.78314	0.946;0.951;0.918;0.991;0.96;0.982	D	0.99184	1.0868	10	0.59425	D	0.04	-13.209	15.2153	0.73261	0.5008:0.4992:0.0:0.0	.	492;492;491;527;496;480	A8K7J7;P19367;P19367-2;E7ENR4;P19367-3;P19367-4	.;HXK1_HUMAN;.;.;.;.	W	480;527;496;491;492;492	ENSP00000353433:R480W;ENSP00000402103:R527W;ENSP00000384774:R496W;ENSP00000298649:R491W;ENSP00000352398:R492W	ENSP00000298649:R491W	R	+	1	2	HK1	70812457	0.995000	0.38212	0.947000	0.38551	0.673000	0.39480	0.791000	0.26915	0.337000	0.23665	0.655000	0.94253	CGG		0.617	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188	
NEUROG3	50674	broad.mit.edu	37	10	71332424	71332424	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:71332424G>A	ENST00000242462.4	-	2	405	c.376C>T	c.(376-378)Cgc>Tgc	p.R126C		NM_020999.3	NP_066279.2	Q9Y4Z2	NGN3_HUMAN	neurogenin 3	126	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				central nervous system development (GO:0007417)|endocrine pancreas development (GO:0031018)|epithelial cell differentiation (GO:0030855)|forebrain development (GO:0030900)|hindbrain development (GO:0030902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|peripheral nervous system development (GO:0007422)|positive regulation of neuron differentiation (GO:0045666)|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 dendrite morphogenesis (GO:0048814)|spinal cord development (GO:0021510)|transdifferentiation (GO:0060290)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|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 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)|transcription coactivator activity (GO:0003713)	p.R126C(1)		endometrium(4)|large_intestine(2)|lung(6)|prostate(1)	13						TGGGCGAAGCGCAGCGTCTCG	0.652																																					p.R126C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C376T	10						.						86.0	72.0	77.0					10																	71332424		2203	4300	6503	71002430	SO:0001583	missense	50674	exon2			AJ133776	CCDS31212.1	10q21.3	2013-05-21			ENSG00000122859	ENSG00000122859		"""Basic helix-loop-helix proteins"""	13806	protein-coding gene	gene with protein product		604882				9000438, 10677506	Standard	NM_020999		Approved	Atoh5, Math4B, ngn3, bHLHa7	uc001jpp.3	Q9Y4Z2	OTTHUMG00000018391	ENST00000242462.4:c.376C>T	10.37:g.71332424G>A	ENSP00000242462:p.Arg126Cys	Somatic		Capture	Illumina HiSeq	Phase_I	71002430	NM_020999	Q5VVI0|Q6DJX6|Q9BY24	Missense_Mutation	SNP	ENST00000242462.4	37	CCDS31212.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.257390	0.80246	.	.	ENSG00000122859	ENST00000242462	D	0.98280	-4.84	4.62	4.62	0.57501	Helix-loop-helix DNA-binding (5);	0.000000	0.41712	D	0.000825	D	0.99290	0.9752	H	0.97806	4.08	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98574	1.0647	10	0.87932	D	0	-20.2816	11.441	0.50096	0.0:0.0:0.8197:0.1803	.	126	Q9Y4Z2	NGN3_HUMAN	C	126	ENSP00000242462:R126C	ENSP00000242462:R126C	R	-	1	0	NEUROG3	71002430	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	4.236000	0.58675	2.355000	0.79922	0.655000	0.94253	CGC		0.652	NEUROG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048464.1	NM_020999	
H2AFY2	55506	broad.mit.edu	37	10	71868935	71868935	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:71868935G>A	ENST00000373255.4	+	8	1189	c.925G>A	c.(925-927)Gtc>Atc	p.V309I	AIFM2_ENST00000373248.1_Intron	NM_018649.2	NP_061119.1	Q9P0M6	H2AW_HUMAN	H2A histone family, member Y2	309	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				brain development (GO:0007420)|chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|transcription regulatory region DNA binding (GO:0044212)	p.V309I(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(4)|skin(1)	15						GCTAAAGTCCGTCGCGTTCCC	0.547																																					p.V309I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G925A	10						.						66.0	62.0	63.0					10																	71868935		2203	4300	6503	71538941	SO:0001583	missense	55506	exon8			AF336304	CCDS7296.1	10q22.1	2011-01-27			ENSG00000099284	ENSG00000099284		"""Histones / Replication-independent"""	14453	protein-coding gene	gene with protein product						11331621, 11262398	Standard	NM_018649		Approved	macroH2A2	uc001jqm.3	Q9P0M6	OTTHUMG00000018396	ENST00000373255.4:c.925G>A	10.37:g.71868935G>A	ENSP00000362352:p.Val309Ile	Somatic		Capture	Illumina HiSeq	Phase_I	71538941	NM_018649	Q5SQT2	Missense_Mutation	SNP	ENST00000373255.4	37	CCDS7296.1	.	.	.	.	.	.	.	.	.	.	G	13.79	2.341422	0.41498	.	.	ENSG00000099284	ENST00000373255;ENST00000395046	T	0.22336	1.96	5.93	5.93	0.95920	Appr-1-p processing (2);	0.118515	0.56097	D	0.000032	T	0.24774	0.0601	N	0.05414	-0.055	0.80722	D	1	D	0.67145	0.996	D	0.68192	0.956	T	0.05971	-1.0853	10	0.06891	T	0.86	.	19.9415	0.97165	0.0:0.0:1.0:0.0	.	309	Q9P0M6	H2AW_HUMAN	I	309;243	ENSP00000362352:V309I	ENSP00000362352:V309I	V	+	1	0	H2AFY2	71538941	1.000000	0.71417	0.564000	0.28396	0.620000	0.37586	6.710000	0.74670	2.797000	0.96272	0.655000	0.94253	GTC		0.547	H2AFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048480.2	NM_018649	
LRRC20	55222	broad.mit.edu	37	10	72061241	72061241	+	Missense_Mutation	SNP	C	C	T	rs116808853	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:72061241C>T	ENST00000355790.4	-	5	901	c.424G>A	c.(424-426)Gcc>Acc	p.A142T	LRRC20_ENST00000395010.1_Missense_Mutation_p.A86T|LRRC20_ENST00000373224.1_Missense_Mutation_p.A142T|LRRC20_ENST00000395011.1_Missense_Mutation_p.A92T|LRRC20_ENST00000358141.2_Missense_Mutation_p.A92T	NM_001278212.1|NM_001278214.1|NM_207119.1	NP_001265141.1|NP_001265143.1|NP_997002.1	Q8TCA0	LRC20_HUMAN	leucine rich repeat containing 20	142								p.A142T(1)		endometrium(2)|large_intestine(4)|lung(2)|urinary_tract(1)	9						GCTGGCATGGCGGCCAGCTTC	0.582													C|||	3	0.000599042	0.0	0.0	5008	,	,		16110	0.003		0.0	False		,,,				2504	0.0				p.A142T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G424A	10						.	C	THR/ALA,THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	116.0	115.0	115.0		256,274,424	1.5	1.0	10	dbSNP_132	115	0,8600		0,0,4300	no	missense,missense,missense	LRRC20	NM_018205.2,NM_018239.2,NM_207119.1	58,58,58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign	86/129,92/135,142/185	72061241	1,13005	2203	4300	6503	71731247	SO:0001583	missense	55222	exon5			BC024001	CCDS7300.1, CCDS7301.1, CCDS7302.1, CCDS73145.1	10q22.2	2004-04-15			ENSG00000172731	ENSG00000172731			23421	protein-coding gene	gene with protein product							Standard	NM_207119		Approved	FLJ10751, FLJ10844	uc031pvr.1	Q8TCA0	OTTHUMG00000018407	ENST00000355790.4:c.424G>A	10.37:g.72061241C>T	ENSP00000348043:p.Ala142Thr	Somatic		Capture	Illumina HiSeq	Phase_I	71731247	NM_207119	Q5T6D4|Q5T6D6|Q9NVA6|Q9NVG3	Missense_Mutation	SNP	ENST00000355790.4	37	CCDS7302.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	10.36	1.328362	0.24080	2.27E-4	0.0	ENSG00000172731	ENST00000373224;ENST00000355790;ENST00000395011;ENST00000395010;ENST00000358141;ENST00000357631;ENST00000446961	T;T;T;T;T;T;T	0.57107	0.42;0.42;0.42;0.68;0.42;0.68;0.42	5.55	1.52	0.23074	.	0.693262	0.14816	N	0.296775	T	0.28962	0.0719	N	0.20401	0.57	0.32008	N	0.602414	B;B;B	0.12630	0.006;0.001;0.003	B;B;B	0.08055	0.003;0.002;0.002	T	0.23547	-1.0185	10	0.15499	T	0.54	-17.9665	3.6822	0.08314	0.1726:0.5559:0.0:0.2715	.	92;86;142	Q8TCA0-2;Q8TCA0-3;Q8TCA0	.;.;LRC20_HUMAN	T	142;142;92;86;92;86;142	ENSP00000362321:A142T;ENSP00000348043:A142T;ENSP00000378458:A92T;ENSP00000378457:A86T;ENSP00000350860:A92T;ENSP00000350255:A86T;ENSP00000413745:A142T	ENSP00000348043:A142T	A	-	1	0	LRRC20	71731247	0.001000	0.12720	0.966000	0.40874	0.997000	0.91878	-0.831000	0.04405	0.268000	0.21939	0.655000	0.94253	GCC		0.582	LRRC20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048510.1	NM_018239	
NODAL	4838	broad.mit.edu	37	10	72192776	72192776	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:72192776C>T	ENST00000287139.3	-	3	959	c.960G>A	c.(958-960)ccG>ccA	p.P320P	AC022532.1_ENST00000420338.2_5'Flank	NM_018055.4	NP_060525.3	Q96S42	NODAL_HUMAN	nodal growth differentiation factor	320					axial mesodermal cell fate specification (GO:0048327)|brain development (GO:0007420)|cell migration involved in gastrulation (GO:0042074)|digestive tract morphogenesis (GO:0048546)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic pattern specification (GO:0009880)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|endodermal cell differentiation (GO:0035987)|epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification (GO:0060802)|floor plate morphogenesis (GO:0033505)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|heart looping (GO:0001947)|inhibition of neuroepithelial cell differentiation (GO:0002085)|left lung morphogenesis (GO:0060460)|liver development (GO:0001889)|maternal placenta development (GO:0001893)|maternal process involved in parturition (GO:0060137)|mesendoderm development (GO:0048382)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of chorionic trophoblast cell proliferation (GO:1901383)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of trophoblast cell migration (GO:1901164)|neural fold formation (GO:0001842)|nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900164)|placenta development (GO:0001890)|polarity specification of proximal/distal axis (GO:0010085)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of gastrulation (GO:0010470)|regulation of stem cell maintenance (GO:2000036)|SMAD protein signal transduction (GO:0060395)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway involved in primitive streak formation (GO:0090010)|trophectodermal cellular morphogenesis (GO:0001831)|vasculature development (GO:0001944)	extracellular space (GO:0005615)	morphogen activity (GO:0016015)|type I activin receptor binding (GO:0070698)	p.P320P(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(2)	15						GCATGCTCAGCGGCTTGGTCT	0.512																																					p.P320P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G960A	10						.						232.0	194.0	207.0					10																	72192776		2203	4300	6503	71862782	SO:0001819	synonymous_variant	4838	exon3			BC033585	CCDS7304.1	10q22.1	2012-12-07	2012-12-07		ENSG00000156574	ENSG00000156574			7865	protein-coding gene	gene with protein product		601265	"""nodal, mouse, homolog"", ""nodal homolog (mouse)"""			9354794	Standard	NM_018055		Approved		uc001jrc.2	Q96S42	OTTHUMG00000018408	ENST00000287139.3:c.960G>A	10.37:g.72192776C>T		Somatic		Capture	Illumina HiSeq	Phase_I	71862782	NM_018055	Q2M3A5|Q8N4V3	Silent	SNP	ENST00000287139.3	37	CCDS7304.1																																																																																				0.512	NODAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048511.1	NM_018055	
CDH23	64072	broad.mit.edu	37	10	73567716	73567716	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:73567716C>T	ENST00000224721.6	+	59	8694	c.8689C>T	c.(8689-8691)Cgg>Tgg	p.R2897W	CDH23_ENST00000398788.3_Missense_Mutation_p.R652W|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2892	Cadherin 27. {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.R2897W(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						CCACTACTTCCGGGCCCTTGC	0.577																																					p.R652W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1954T	10						.						33.0	38.0	36.0					10																	73567716		2000	4166	6166	73237722	SO:0001583	missense	64072	exon13			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.8689C>T	10.37:g.73567716C>T	ENSP00000224721:p.Arg2897Trp	Somatic		Capture	Illumina HiSeq	Phase_I	73237722	NM_001171933	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		.	.	.	.	.	.	.	.	.	.	C	18.72	3.683313	0.68157	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	T	0.58506	0.33	5.34	5.34	0.76211	Cadherin (2);Cadherin-like (1);	0.481352	0.21118	N	0.079863	T	0.38612	0.1047	N	0.08118	0	0.33656	D	0.609095	P;D	0.63046	0.92;0.992	B;B	0.42386	0.28;0.386	T	0.57740	-0.7759	10	0.72032	D	0.01	.	12.2199	0.54428	0.2888:0.7112:0.0:0.0	.	2892;2892	E9PEX1;Q9H251	.;CAD23_HUMAN	W	2897;2892;2895;652	ENSP00000381768:R652W	ENSP00000224721:R2897W	R	+	1	2	CDH23	73237722	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.248000	0.58760	2.495000	0.84180	0.455000	0.32223	CGG		0.577	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
SPOCK2	9806	broad.mit.edu	37	10	73828006	73828006	+	Silent	SNP	G	G	A	rs150144417	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:73828006G>A	ENST00000373109.2	-	6	972	c.528C>T	c.(526-528)tgC>tgT	p.C176C	SPOCK2_ENST00000460053.1_5'UTR|SPOCK2_ENST00000317376.4_Silent_p.C176C|SPOCK2_ENST00000536168.1_Silent_p.C176C	NM_001244950.1	NP_001231879.1	Q92563	TICN2_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 2	176	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of cell differentiation (GO:0045595)|signal transduction (GO:0007165)|synapse assembly (GO:0007416)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)	p.C176C(1)		endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						AGGGGCCCTCGCATCGCACCG	0.662													G|||	2	0.000399361	0.0015	0.0	5008	,	,		14657	0.0		0.0	False		,,,				2504	0.0				p.C176C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C528T	10						.	G		17,4383		0,17,2183	26.0	22.0	24.0		528	-2.6	1.0	10	dbSNP_134	24	0,8600		0,0,4300	no	coding-synonymous	SPOCK2	NM_014767.2		0,17,6483	AA,AG,GG		0.0,0.3864,0.1308		176/425	73828006	17,12983	2200	4300	6500	73498012	SO:0001819	synonymous_variant	9806	exon7			AJ001453	CCDS7313.1, CCDS44431.1	10q22.1	2013-09-19			ENSG00000107742	ENSG00000107742			13564	protein-coding gene	gene with protein product		607988				10386950	Standard	NM_014767		Approved	KIAA0275, testican-2	uc001jso.2	Q92563	OTTHUMG00000018430	ENST00000373109.2:c.528C>T	10.37:g.73828006G>A		Somatic		Capture	Illumina HiSeq	Phase_I	73498012	NM_014767	C9J767|Q6UW87	Silent	SNP	ENST00000373109.2	37	CCDS7313.1																																																																																				0.662	SPOCK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048560.2		
OIT3	170392	broad.mit.edu	37	10	74692188	74692188	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:74692188G>A	ENST00000334011.5	+	9	1762	c.1544G>A	c.(1543-1545)cGg>cAg	p.R515Q		NM_152635.1	NP_689848.1	Q8WWZ8	OIT3_HUMAN	oncoprotein induced transcript 3	515	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R515Q(1)		autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)	35	Prostate(51;0.0198)					GGTTGCCACCGGCGAATGCGT	0.602																																					p.R515Q	Colon(7;19 345 13446 17537)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1544A	10						.						92.0	94.0	93.0					10																	74692188		2203	4300	6503	74362194	SO:0001583	missense	170392	exon9				CCDS7318.1	10q22.2-q22.3	2004-04-21			ENSG00000138315	ENSG00000138315			29953	protein-coding gene	gene with protein product		609330				12975309, 12939600	Standard	NM_152635		Approved	LZP, FLJ39116	uc001jte.1	Q8WWZ8	OTTHUMG00000018444	ENST00000334011.5:c.1544G>A	10.37:g.74692188G>A	ENSP00000333900:p.Arg515Gln	Somatic		Capture	Illumina HiSeq	Phase_I	74362194	NM_152635	A0AVP3|Q8N1M8	Missense_Mutation	SNP	ENST00000334011.5	37	CCDS7318.1	.	.	.	.	.	.	.	.	.	.	G	18.50	3.638347	0.67130	.	.	ENSG00000138315	ENST00000334011	D	0.82526	-1.62	6.06	4.22	0.49857	Zona pellucida sperm-binding protein (3);	0.118140	0.36444	N	0.002581	T	0.77164	0.4090	L	0.55481	1.735	0.34782	D	0.734822	B	0.16166	0.016	B	0.12837	0.008	T	0.73500	-0.3963	10	0.13108	T	0.6	-8.8394	12.786	0.57504	0.1316:0.0:0.8684:0.0	.	515	Q8WWZ8	OIT3_HUMAN	Q	515	ENSP00000333900:R515Q	ENSP00000333900:R515Q	R	+	2	0	OIT3	74362194	1.000000	0.71417	0.975000	0.42487	0.961000	0.63080	3.897000	0.56273	0.903000	0.36546	0.655000	0.94253	CGG		0.602	OIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048596.1	NM_152635	
CFAP70	118491	broad.mit.edu	37	10	75091009	75091009	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:75091009G>A	ENST00000310715.3	-	9	1033	c.913C>T	c.(913-915)Cgg>Tgg	p.R305W	TTC18_ENST00000340329.3_Intron|TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000355577.3_5'UTR|TTC18_ENST00000401621.2_Missense_Mutation_p.R305W|TTC18_ENST00000394865.1_Missense_Mutation_p.R305W	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		305						extracellular vesicular exosome (GO:0070062)		p.R305W(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					GGCCAAAGCCGGCAATCGGCA	0.378																																					p.R305W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C913T	10						.						41.0	43.0	43.0					10																	75091009		2203	4300	6503	74761015	SO:0001583	missense	118491	exon9																														ENST00000310715.3:c.913C>T	10.37:g.75091009G>A	ENSP00000310829:p.Arg305Trp	Somatic		Capture	Illumina HiSeq	Phase_I	74761015	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	.	.	.	.	.	.	.	.	.	.	G	18.06	3.538486	0.65085	.	.	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000372928;ENST00000394865	T;T;T	0.43688	1.35;1.35;0.94	5.34	2.43	0.29744	.	0.123920	0.53938	N	0.000054	T	0.37293	0.0998	M	0.66939	2.045	0.42148	D	0.99154	B;B	0.16166	0.005;0.016	B;B	0.04013	0.001;0.001	T	0.22906	-1.0203	10	0.66056	D	0.02	-4.9614	6.6204	0.22800	0.1584:0.0:0.6974:0.1442	.	305;305	Q5T0N1-2;Q5T0N1	.;TTC18_HUMAN	W	305	ENSP00000310829:R305W;ENSP00000384479:R305W;ENSP00000378334:R305W	ENSP00000310829:R305W	R	-	1	2	TTC18	74761015	1.000000	0.71417	0.996000	0.52242	0.981000	0.71138	2.111000	0.41883	0.308000	0.22923	-0.224000	0.12420	CGG		0.378	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
KAT6B	23522	broad.mit.edu	37	10	76784740	76784740	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:76784740A>G	ENST00000287239.4	+	17	3886	c.3397A>G	c.(3397-3399)Agg>Ggg	p.R1133G	KAT6B_ENST00000490365.1_3'UTR|KAT6B_ENST00000372724.1_Missense_Mutation_p.R841G|RP11-77G23.2_ENST00000413431.1_RNA|RP11-77G23.5_ENST00000436608.1_RNA|KAT6B_ENST00000372711.1_Missense_Mutation_p.R950G|KAT6B_ENST00000372725.1_Missense_Mutation_p.R841G|KAT6B_ENST00000372714.1_Missense_Mutation_p.R841G	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1133					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.R1133G(1)									AAAGAAGAAAAGGGGTCGTAA	0.398																																					p.R1133G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3397G	10						.						62.0	61.0	61.0					10																	76784740		2203	4300	6503	76454746	SO:0001583	missense	23522	exon17			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.3397A>G	10.37:g.76784740A>G	ENSP00000287239:p.Arg1133Gly	Somatic		Capture	Illumina HiSeq	Phase_I	76454746	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.850557	0.51270	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	T;T;T;T;D	0.81499	1.2;1.2;0.1;1.2;-1.5	5.8	5.8	0.92144	.	0.000000	0.51477	D	0.000090	D	0.88157	0.6361	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	0.996;1.0;0.987	D;D;D	0.83275	0.99;0.996;0.942	D	0.87838	0.2649	10	0.45353	T	0.12	-13.1838	16.1365	0.81491	1.0:0.0:0.0:0.0	.	950;841;1133	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	G	841;841;1133;841;950	ENSP00000361810:R841G;ENSP00000361809:R841G;ENSP00000287239:R1133G;ENSP00000361799:R841G;ENSP00000361796:R950G	ENSP00000287239:R1133G	R	+	1	2	KAT6B	76454746	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.793000	0.62474	2.212000	0.71576	0.533000	0.62120	AGG		0.398	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330	
ZMIZ1	57178	broad.mit.edu	37	10	81058853	81058853	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:81058853C>T	ENST00000334512.5	+	16	2285	c.1713C>T	c.(1711-1713)ggC>ggT	p.G571G		NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	571					artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.G571G(2)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			TGCGGGATGGCGTGGTGCTGG	0.647																																					p.G571G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1713T	10						.						84.0	63.0	70.0					10																	81058853		2203	4300	6503	80728859	SO:0001819	synonymous_variant	57178	exon16			AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"""Zinc fingers, MIZ-type"""	16493	protein-coding gene	gene with protein product		607159	"""retinoic acid induced 17"""	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.1713C>T	10.37:g.81058853C>T		Somatic		Capture	Illumina HiSeq	Phase_I	80728859	NM_020338	Q5JSH9|Q7Z7E6	Silent	SNP	ENST00000334512.5	37	CCDS7357.1																																																																																				0.647	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338	
MAT1A	4143	broad.mit.edu	37	10	82034845	82034845	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:82034845T>C	ENST00000372213.3	-	7	1139	c.879A>G	c.(877-879)tcA>tcG	p.S293S	MAT1A_ENST00000485270.1_5'UTR	NM_000429.2	NP_000420.1	Q00266	METK1_HUMAN	methionine adenosyltransferase I, alpha	293					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)	p.S293S(1)		endometrium(4)|large_intestine(7)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26			Colorectal(32;0.229)		L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	CATATGCAGCTGAGCGGTCTA	0.612																																					p.S293S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A879G	10						.						34.0	35.0	35.0					10																	82034845		2202	4297	6499	82024825	SO:0001819	synonymous_variant	4143	exon7				CCDS7365.1	10q22	2008-08-01			ENSG00000151224	ENSG00000151224			6903	protein-coding gene	gene with protein product	"""S-adenosylmethionine synthetase"""	610550				8393662	Standard	XM_005269842		Approved	MAT, SAMS, MATA1, SAMS1	uc001kbw.3	Q00266	OTTHUMG00000018613	ENST00000372213.3:c.879A>G	10.37:g.82034845T>C		Somatic		Capture	Illumina HiSeq	Phase_I	82024825	NM_000429	D3DWD5|Q5QP09	Silent	SNP	ENST00000372213.3	37	CCDS7365.1																																																																																				0.612	MAT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049070.1	NM_000429	
LRIT1	26103	broad.mit.edu	37	10	85997031	85997031	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:85997031C>A	ENST00000372105.3	-	2	555	c.534G>T	c.(532-534)tgG>tgT	p.W178C		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	178						integral component of endoplasmic reticulum membrane (GO:0030176)		p.W178C(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						CCAGGTGAGCCCAGGAGACGA	0.637																																					p.W178C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G534T	10						.						13.0	14.0	14.0					10																	85997031		1951	3717	5668	85987011	SO:0001583	missense	26103	exon2			AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	23404	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 9"""		"""leucine rich repeat containing 21"""	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.534G>T	10.37:g.85997031C>A	ENSP00000361177:p.Trp178Cys	Somatic		Capture	Illumina HiSeq	Phase_I	85987011	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	37	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.303787	0.60305	.	.	ENSG00000148602	ENST00000372105	T	0.49139	0.79	4.55	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.46678	0.1405	N	0.03999	-0.3	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60198	-0.7310	10	0.72032	D	0.01	.	14.3264	0.66523	0.0:1.0:0.0:0.0	.	178	Q9P2V4	LRIT1_HUMAN	C	178	ENSP00000361177:W178C	ENSP00000361177:W178C	W	-	3	0	LRIT1	85987011	1.000000	0.71417	0.539000	0.28077	0.580000	0.36256	5.213000	0.65230	2.337000	0.79520	0.655000	0.94253	TGG		0.637	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
PTEN	5728	broad.mit.edu	37	10	89692904	89692904	+	Nonsense_Mutation	SNP	C	C	T	rs121913292|rs121909224		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:89692904C>T	ENST00000371953.3	+	5	1745	c.388C>T	c.(388-390)Cga>Tga	p.R130*		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	130	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.		R -> G (loss of phosphatase activity towards Ins(1,3,4,5)P4 and PtdIns(3,4,5)P3).|R -> L (in CWS1 and endometrial hyperplasia; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes). {ECO:0000269|PubMed:9635567}.|R -> Q (in CWS1; loss of phosphatase activity towards Ins(1,3,4,5)P4; retains ability to bind phospholipid membranes). {ECO:0000269|PubMed:9915974}.		activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R130G(102)|p.R130*(63)|p.0?(37)|p.?(5)|p.R55fs*1(5)|p.K128_R130del(3)|p.Y27fs*1(2)|p.R130R(1)|p.A121_F145del(1)|p.R130fs*4(1)|p.G129fs*51(1)|p.F56fs*2(1)|p.G129fs*50(1)|p.K128fs*47(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TGGAAAGGGACGAACTGGTGT	0.403	R130G(KMBC2_URINARY_TRACT)|R130G(OV56_OVARY)	31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.R130X		yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	PTEN,central_nervous_system,brain,Substitution - Nonsense,0 	.	224	Substitution - Missense(102)|Substitution - Nonsense(63)|Whole gene deletion(37)|Deletion - Frameshift(10)|Unknown(5)|Deletion - In frame(4)|Insertion - Frameshift(2)|Substitution - coding silent(1)	endometrium(125)|central_nervous_system(37)|prostate(21)|ovary(10)|lung(9)|skin(6)|haematopoietic_and_lymphoid_tissue(5)|breast(3)|cervix(2)|large_intestine(2)|soft_tissue(2)|thyroid(1)|urinary_tract(1)	c.C388T	10	GRCh37	CM971273	PTEN	M	rs121909224	.						141.0	131.0	134.0					10																	89692904		2203	4300	6503	89682884	SO:0001587	stop_gained	5728	exon5	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.388C>T	10.37:g.89692904C>T	ENSP00000361021:p.Arg130*	Somatic		Capture	Illumina HiSeq	Phase_I	89682884	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Nonsense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	48	14.299622	0.99789	.	.	ENSG00000171862	ENST00000371953	.	.	.	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.7685	18.7776	0.91918	0.0:1.0:0.0:0.0	.	.	.	.	X	130	.	.	R	+	1	2	PTEN	89682884	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.527000	0.67123	2.411000	0.81874	0.655000	0.94253	CGA		0.403	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
PTEN	5728	broad.mit.edu	37	10	89717672	89717672	+	Nonsense_Mutation	SNP	C	C	T	rs121909219		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:89717672C>T	ENST00000371953.3	+	7	2054	c.697C>T	c.(697-699)Cga>Tga	p.R233*	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	233	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R233*(77)|p.0?(37)|p.R55fs*1(5)|p.R233fs*10(3)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.?(1)|p.R233fs*12(1)|p.R233fs*20(1)|p.R233fs*25(1)|p.R233fs*23(1)|p.R233R(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		AGGACCCACACGACGGGAAGA	0.423	R233*(HEC59_ENDOMETRIUM)|R233*(JHUEM1_ENDOMETRIUM)|R233*(NCIH1155_LUNG)|R233*(SF295_CENTRAL_NERVOUS_SYSTEM)|R233*(SW1783_CENTRAL_NERVOUS_SYSTEM)	31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.R233X		yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	PTEN,central_nervous_system,brain,Substitution - Nonsense,0 	.	133	Substitution - Nonsense(77)|Whole gene deletion(37)|Deletion - Frameshift(11)|Complex - frameshift(3)|Insertion - Frameshift(2)|Deletion - In frame(1)|Unknown(1)|Substitution - coding silent(1)	endometrium(48)|central_nervous_system(21)|prostate(17)|haematopoietic_and_lymphoid_tissue(10)|lung(9)|large_intestine(6)|skin(6)|ovary(5)|cervix(3)|soft_tissue(3)|breast(3)|urinary_tract(2)	c.C697T	10	GRCh37	CM971277	PTEN	M	rs121909219	.						155.0	133.0	141.0					10																	89717672		2203	4300	6503	89707652	SO:0001587	stop_gained	5728	exon7	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.697C>T	10.37:g.89717672C>T	ENSP00000361021:p.Arg233*	Somatic		Capture	Illumina HiSeq	Phase_I	89707652	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Nonsense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	48	14.428311	0.99795	.	.	ENSG00000171862	ENST00000371953	.	.	.	5.15	0.533	0.17121	.	0.063428	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.2458	14.4841	0.67603	0.5413:0.4587:0.0:0.0	.	.	.	.	X	233	.	.	R	+	1	2	PTEN	89707652	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	1.280000	0.33202	0.512000	0.28257	0.585000	0.79938	CGA		0.423	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
ANKRD22	118932	broad.mit.edu	37	10	90591679	90591679	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:90591679C>T	ENST00000371930.4	-	2	336	c.126G>A	c.(124-126)acG>acA	p.T42T		NM_144590.2	NP_653191.2	Q5VYY1	ANR22_HUMAN	ankyrin repeat domain 22	42								p.T42T(1)		NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(3)	10		Colorectal(252;0.0163)		Colorectal(12;6.29e-05)|COAD - Colon adenocarcinoma(12;7.69e-05)		AGATCAGGGGCGTGTCTCCAT	0.483																																					p.T42T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G126A	10						.						271.0	254.0	260.0					10																	90591679		2203	4300	6503	90581659	SO:0001819	synonymous_variant	118932	exon2			BC021671	CCDS7390.1	10q23.31	2013-09-20			ENSG00000152766	ENSG00000152766		"""Ankyrin repeat domain containing"""	28321	protein-coding gene	gene with protein product						12477932	Standard	NM_144590		Approved	MGC22805	uc001kfj.4	Q5VYY1	OTTHUMG00000018699	ENST00000371930.4:c.126G>A	10.37:g.90591679C>T		Somatic		Capture	Illumina HiSeq	Phase_I	90581659	NM_144590	B2R9Y7|Q8WU06	Silent	SNP	ENST00000371930.4	37	CCDS7390.1																																																																																				0.483	ANKRD22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049262.1	NM_144590	
LIPA	3988	broad.mit.edu	37	10	90974675	90974675	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:90974675C>T	ENST00000336233.5	-	10	1432	c.1110G>A	c.(1108-1110)ccG>ccA	p.P370P	LIPA_ENST00000456827.1_Silent_p.P370P|LIPA_ENST00000371837.1_Silent_p.P314P			P38571	LICH_HUMAN	lipase A, lysosomal acid, cholesterol esterase	370					cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cytokine production (GO:0001816)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|lung development (GO:0030324)|tissue remodeling (GO:0048771)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	lipase activity (GO:0016298)|sterol esterase activity (GO:0004771)	p.P370P(1)		endometrium(1)|large_intestine(2)|lung(3)	6		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		GCTCCCATTCCGGAATGCTCT	0.463																																					p.P370P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1110A	10						.						76.0	70.0	72.0					10																	90974675		2203	4300	6503	90964655	SO:0001819	synonymous_variant	3988	exon10			M74775	CCDS7401.1, CCDS73160.1	10q23.2-q23.3	2012-07-13	2008-08-01		ENSG00000107798	ENSG00000107798	3.1.1.13		6617	protein-coding gene	gene with protein product	"""Wolman disease"""	613497				8432549	Standard	NM_000235		Approved	LAL, CESD	uc009xtq.3	P38571	OTTHUMG00000018716	ENST00000336233.5:c.1110G>A	10.37:g.90974675C>T		Somatic		Capture	Illumina HiSeq	Phase_I	90964655	NM_001127605	B2RBH5|D3DR29|Q16529|Q53H21|Q5T074|Q5T771|Q96EJ0	Silent	SNP	ENST00000336233.5	37	CCDS7401.1																																																																																				0.463	LIPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049308.1	NM_000235	
IFIT1	3434	broad.mit.edu	37	10	91152474	91152474	+	Splice_Site	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:91152474G>T	ENST00000371804.3	+	1	172	c.5G>T	c.(4-6)aGt>aTt	p.S2I	LIPA_ENST00000371837.1_Intron	NM_001270927.1|NM_001548.4	NP_001257856.1|NP_001539.3	P09914	IFIT1_HUMAN	interferon-induced protein with tetratricopeptide repeats 1	2					cellular response to exogenous dsRNA (GO:0071360)|cellular response to type I interferon (GO:0071357)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|intracellular transport of viral protein in host cell (GO:0019060)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of helicase activity (GO:0051097)|negative regulation of protein binding (GO:0032091)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	RNA binding (GO:0003723)	p.S2I(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	15						GCAACCATGAGGTAAGGATTT	0.398																																					p.S2I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5T	10						.						114.0	101.0	105.0					10																	91152474		2203	4300	6503	91142454	SO:0001630	splice_region_variant	3434	exon1			M24594	CCDS31243.1, CCDS59220.1	10q23.31	2014-05-22			ENSG00000185745	ENSG00000185745		"""Tetratricopeptide (TTC) repeat domain containing"""	5407	protein-coding gene	gene with protein product		147690		G10P1, IFI56, IFNAI1		1377167, 3360121	Standard	NM_001548		Approved	GARG-16	uc001kgi.4	P09914	OTTHUMG00000018712	ENST00000371804.3:c.5+1G>T	10.37:g.91152474G>T		Somatic		Capture	Illumina HiSeq	Phase_I	91142454	NM_001548	B3KS50|D3DR31|Q5T7J1|Q96QM5	De_novo_Start_OutOfFrame	SNP	ENST00000371804.3	37	CCDS31243.1	.	.	.	.	.	.	.	.	.	.	G	16.61	3.170052	0.57584	.	.	ENSG00000185745	ENST00000371804	T	0.16597	2.33	3.75	3.75	0.43078	.	1.759620	0.03054	U	0.154937	T	0.23249	0.0562	L	0.34521	1.04	0.80722	D	1	D	0.53619	0.961	P	0.47744	0.556	T	0.17501	-1.0367	10	0.87932	D	0	.	11.3662	0.49673	0.0:0.0:1.0:0.0	.	2	P09914	IFIT1_HUMAN	I	2	ENSP00000360869:S2I	ENSP00000360869:S2I	S	+	2	0	IFIT1	91142454	1.000000	0.71417	1.000000	0.80357	0.645000	0.38454	3.577000	0.53885	2.380000	0.81148	0.563000	0.77884	AGT		0.398	IFIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049302.1	NM_001548	Missense_Mutation
HTR7	3363	broad.mit.edu	37	10	92508845	92508845	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:92508845G>A	ENST00000336152.3	-	2	1072	c.1046C>T	c.(1045-1047)gCc>gTc	p.A349V	HTR7_ENST00000371721.3_Missense_Mutation_p.A349V|HTR7_ENST00000371719.2_Missense_Mutation_p.A349V|HTR7_ENST00000277874.6_Missense_Mutation_p.A349V	NM_019859.3	NP_062873.1	P34969	5HT7R_HUMAN	5-hydroxytryptamine (serotonin) receptor 7, adenylate cyclase-coupled	349					blood circulation (GO:0008015)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|smooth muscle contraction (GO:0006939)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)	p.A349V(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30					Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Dopamine(DB00988)|Eletriptan(DB00216)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Iloperidone(DB04946)|Imipramine(DB00458)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Methysergide(DB00247)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	GAAGGGTCTGGCTGTCGAGAG	0.532																																					p.A349V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1046T	10						.						88.0	83.0	85.0					10																	92508845		2203	4300	6503	92498825	SO:0001583	missense	3363	exon2			BC047526	CCDS7408.1, CCDS7409.1, CCDS7410.1	10q21-q24	2012-08-08	2012-02-03		ENSG00000148680	ENSG00000148680		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5302	protein-coding gene	gene with protein product		182137	"""5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-coupled)"""			8226867	Standard	NM_000872		Approved	5-HT7	uc001kha.3	P34969	OTTHUMG00000018732	ENST00000336152.3:c.1046C>T	10.37:g.92508845G>A	ENSP00000337949:p.Ala349Val	Somatic		Capture	Illumina HiSeq	Phase_I	92498825	NM_019859	B5BUP6|P78336|P78372|P78516|Q5VX01|Q5VX02|Q5VX03	Missense_Mutation	SNP	ENST00000336152.3	37	CCDS7408.1	.	.	.	.	.	.	.	.	.	.	G	11.41	1.629455	0.28978	.	.	ENSG00000148680	ENST00000336152;ENST00000277874;ENST00000371719;ENST00000371721	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	5.45	4.54	0.55810	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.35480	0.0933	N	0.11756	0.17	0.48135	D	0.999599	D;P	0.64830	0.994;0.778	D;P	0.65987	0.94;0.526	T	0.10359	-1.0633	10	0.02654	T	1	.	16.2548	0.82510	0.0:0.1329:0.867:0.0	.	349;349	P34969;P34969-2	5HT7R_HUMAN;.	V	349	ENSP00000337949:A349V;ENSP00000277874:A349V;ENSP00000360784:A349V;ENSP00000360786:A349V	ENSP00000277874:A349V	A	-	2	0	HTR7	92498825	1.000000	0.71417	0.275000	0.24674	0.970000	0.65996	9.471000	0.97696	1.274000	0.44362	0.650000	0.86243	GCC		0.532	HTR7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049343.1	NM_000872	
HECTD2	143279	broad.mit.edu	37	10	93260360	93260360	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:93260360G>A	ENST00000298068.5	+	19	2146	c.2052G>A	c.(2050-2052)acG>acA	p.T684T	HECTD2_ENST00000536715.1_Silent_p.T273T|HECTD2_ENST00000446394.1_Silent_p.T688T|HECTD2_ENST00000371667.1_Silent_p.T334T	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	684	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.T684T(1)		breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						ATGCAAAAACGGACTTAACTA	0.423																																					p.T684T	NSCLC(12;376 469 1699 39910 41417)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2052A	10						.						106.0	97.0	100.0					10																	93260360		2203	4300	6503	93250340	SO:0001819	synonymous_variant	143279	exon19			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.2052G>A	10.37:g.93260360G>A		Somatic		Capture	Illumina HiSeq	Phase_I	93250340	NM_182765	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Silent	SNP	ENST00000298068.5	37	CCDS7414.1																																																																																				0.423	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1		
EXOC6	54536	broad.mit.edu	37	10	94659367	94659367	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:94659367T>A	ENST00000260762.6	+	5	438	c.424T>A	c.(424-426)Tac>Aac	p.Y142N	EXOC6_ENST00000371552.4_Missense_Mutation_p.Y137N|EXOC6_ENST00000371547.4_Missense_Mutation_p.Y158N|EXOC6_ENST00000443748.2_Missense_Mutation_p.Y142N|EXOC6_ENST00000371543.1_Missense_Mutation_p.Y142N	NM_019053.4	NP_061926.3	Q8TAG9	EXOC6_HUMAN	exocyst complex component 6	142					cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)|plasma membrane (GO:0005886)		p.Y137N(1)|p.Y142N(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	26		Colorectal(252;0.123)				GCTAGAAATGTACAGTAAGCT	0.269																																					p.Y137N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T409A	10						.						87.0	98.0	94.0					10																	94659367		2202	4300	6502	94649347	SO:0001583	missense	54536	exon5			BC028395	CCDS7424.2, CCDS31247.1	10q23.33	2013-01-22	2006-11-07	2006-11-07	ENSG00000138190	ENSG00000138190			23196	protein-coding gene	gene with protein product		609672	"""SEC15-like 1 (S. cerevisiae)"""	SEC15L1		8889548	Standard	NM_001013848		Approved	SEC15L, FLJ1125, DKFZp761I2124, MGC33397, Sec15p, EXOC6A	uc001kig.3	Q8TAG9	OTTHUMG00000018767	ENST00000260762.6:c.424T>A	10.37:g.94659367T>A	ENSP00000260762:p.Tyr142Asn	Somatic		Capture	Illumina HiSeq	Phase_I	94649347	NM_001013848	E9PHI3|Q5VXH8|Q9NZ24	Missense_Mutation	SNP	ENST00000260762.6	37	CCDS7424.2	.	.	.	.	.	.	.	.	.	.	T	24.0	4.478053	0.84747	.	.	ENSG00000138190	ENST00000371547;ENST00000371552;ENST00000371543;ENST00000443748;ENST00000260762	T;T;T;T;T	0.30448	1.53;1.53;1.58;1.53;1.53	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.60470	0.2271	M	0.84846	2.72	0.45216	D	0.998227	D;D;D;D;D	0.71674	0.993;0.998;0.983;0.97;0.985	D;D;P;P;P	0.78314	0.93;0.991;0.827;0.655;0.769	T	0.67803	-0.5576	10	0.87932	D	0	-7.1484	15.5147	0.75815	0.0:0.0:0.0:1.0	.	158;142;134;142;137	F2Z2Q3;E7EW84;B4DEZ1;Q8TAG9;E9PHI3	.;.;.;EXOC6_HUMAN;.	N	158;137;142;142;142	ENSP00000360602:Y158N;ENSP00000360607:Y137N;ENSP00000360598:Y142N;ENSP00000396206:Y142N;ENSP00000260762:Y142N	ENSP00000260762:Y142N	Y	+	1	0	EXOC6	94649347	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.708000	0.84633	2.069000	0.61940	0.528000	0.53228	TAC		0.269	EXOC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049410.2	NM_019053	
PDLIM1	9124	broad.mit.edu	37	10	97023764	97023764	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:97023764C>T	ENST00000329399.6	-	4	498	c.390G>A	c.(388-390)tcG>tcA	p.S130S	PDLIM1_ENST00000477757.1_5'UTR	NM_020992.2	NP_066272.1	O00151	PDLI1_HUMAN	PDZ and LIM domain 1	130					regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.S130S(1)		endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|skin(2)	10		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		TGGAGGCAGGCGAGGCGGTAA	0.552																																					p.S130S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G390A	10						.						100.0	85.0	90.0					10																	97023764		2203	4300	6503	97013754	SO:0001819	synonymous_variant	9124	exon4			U90878	CCDS7441.1	10q23.1	2008-07-29	2008-07-29		ENSG00000107438	ENSG00000107438			2067	protein-coding gene	gene with protein product	"""carboxyl terminal LIM domain protein 1"", ""elfin"""	605900	"""PDZ and LIM domain 1 (elfin)"""	CLIM1		10861853	Standard	NM_020992		Approved	CLP-36, hCLIM1, CLP36	uc001kkh.4	O00151	OTTHUMG00000018810	ENST00000329399.6:c.390G>A	10.37:g.97023764C>T		Somatic		Capture	Illumina HiSeq	Phase_I	97013754	NM_020992	B2RBS6|Q5VZH5|Q9BPZ9	Silent	SNP	ENST00000329399.6	37	CCDS7441.1																																																																																				0.552	PDLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049508.1		
TLL2	7093	broad.mit.edu	37	10	98180728	98180728	+	Missense_Mutation	SNP	C	C	T	rs535012851		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:98180728C>T	ENST00000357947.3	-	7	1133	c.908G>A	c.(907-909)cGg>cAg	p.R303Q	TLL2_ENST00000469598.1_5'UTR	NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	303	Metalloprotease. {ECO:0000250}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R303Q(1)		NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		GAAGGTGTTCCGGGCGTAGTG	0.507																																					p.R303Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G908A	10						.						280.0	248.0	259.0					10																	98180728		2203	4300	6503	98170718	SO:0001583	missense	7093	exon7			AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.908G>A	10.37:g.98180728C>T	ENSP00000350630:p.Arg303Gln	Somatic		Capture	Illumina HiSeq	Phase_I	98170718	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	37	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	C	35	5.579174	0.96565	.	.	ENSG00000095587	ENST00000357947	T	0.63255	-0.03	5.79	5.79	0.91817	Peptidase M12A, astacin (2);Metallopeptidase, catalytic domain (1);	0.000000	0.41294	D	0.000915	T	0.80460	0.4627	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.80266	-0.1454	10	0.51188	T	0.08	.	19.0281	0.92941	0.0:1.0:0.0:0.0	.	303	Q9Y6L7	TLL2_HUMAN	Q	303	ENSP00000350630:R303Q	ENSP00000350630:R303Q	R	-	2	0	TLL2	98170718	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.736000	0.84948	2.733000	0.93635	0.655000	0.94253	CGG		0.507	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1		
PI4K2A	55361	broad.mit.edu	37	10	99433434	99433434	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:99433434C>T	ENST00000370631.3	+	9	1432	c.1375C>T	c.(1375-1377)Cgg>Tgg	p.R459W	PI4K2A_ENST00000555577.1_Missense_Mutation_p.R429W|PI4K2A_ENST00000370649.3_Missense_Mutation_p.R429W	NM_018425.2	NP_060895.1	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	459					basophil degranulation (GO:0002561)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endosome (GO:0005768)|exocytic vesicle (GO:0070382)|Golgi apparatus (GO:0005794)|growing cell tip (GO:0035838)|host cell presynaptic membrane (GO:0044231)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|AP-3 adaptor complex binding (GO:0035651)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)	p.R429W(1)|p.R459W(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)		TTCCCACCAGCGGTCTTCTAG	0.542																																					p.R459W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1375T	10						.						145.0	140.0	142.0					10																	99433434		2203	4300	6503	99423424	SO:0001583	missense	55361	exon9			AF070611	CCDS7469.1	10q24	2011-02-09			ENSG00000155252	ENSG00000155252			30031	protein-coding gene	gene with protein product		609763				11244087, 11279162	Standard	NM_018425		Approved	PI4KII, DKFZP761G1923, PIK42A	uc001kog.1	Q9BTU6	OTTHUMG00000018863	ENST00000370631.3:c.1375C>T	10.37:g.99433434C>T	ENSP00000359665:p.Arg459Trp	Somatic		Capture	Illumina HiSeq	Phase_I	99423424	NM_018425	D3DR59|Q9NSG8	Missense_Mutation	SNP	ENST00000370631.3	37	CCDS7469.1	.	.	.	.	.	.	.	.	.	.	C	18.44	3.624362	0.66901	.	.	ENSG00000155252;ENSG00000155252;ENSG00000249967	ENST00000555577;ENST00000370631;ENST00000370649	D;D	0.87179	-2.22;-2.22	5.38	5.38	0.77491	.	0.121633	0.52532	D	0.000062	D	0.88085	0.6342	L	0.34521	1.04	0.54753	D	0.999982	D;D;D	0.69078	0.997;0.997;0.997	P;P;P	0.58970	0.849;0.849;0.586	D	0.88896	0.3349	10	0.87932	D	0	-18.1994	14.2013	0.65707	0.1492:0.8508:0.0:0.0	.	429;429;459	E9PAM4;B4DEP8;Q9BTU6	.;.;P4K2A_HUMAN	W	429;459;429	ENSP00000452243:R429W;ENSP00000359683:R429W	ENSP00000359665:R459W	R	+	1	2	PI4K2A;RP11-548K23.11	99423424	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	2.917000	0.48821	2.793000	0.96121	0.655000	0.94253	CGG		0.542	PI4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049735.1	NM_018425	
ZFYVE27	118813	broad.mit.edu	37	10	99510205	99510205	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:99510205C>T	ENST00000393677.4	+	7	986	c.782C>T	c.(781-783)aCg>aTg	p.T261M	ZFYVE27_ENST00000370610.3_Missense_Mutation_p.T163M|ZFYVE27_ENST00000337540.7_Missense_Mutation_p.T229M|ZFYVE27_ENST00000370613.3_Missense_Mutation_p.T143M|ZFYVE27_ENST00000356257.4_Missense_Mutation_p.T261M|ZFYVE27_ENST00000357540.4_Missense_Mutation_p.T175M|ZFYVE27_ENST00000359980.3_Missense_Mutation_p.T261M|ZFYVE27_ENST00000453958.2_Missense_Mutation_p.T261M	NM_144588.6	NP_653189.3	Q5T4F4	ZFY27_HUMAN	zinc finger, FYVE domain containing 27	261					cell death (GO:0008219)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein localization to plasma membrane (GO:0072659)	axon (GO:0030424)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)	metal ion binding (GO:0046872)	p.T261M(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	8		Colorectal(252;0.0846)		Epithelial(162;7.08e-10)|all cancers(201;5.18e-08)		ATGGACAGCACGCCTGCCCTC	0.592																																					p.T261M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C782T	10						.						98.0	78.0	85.0					10																	99510205		2203	4300	6503	99500195	SO:0001583	missense	118813	exon6			BC030621	CCDS31263.1, CCDS31264.1, CCDS53562.1, CCDS53563.1, CCDS53564.1, CCDS53565.1	10q24.2	2013-09-11			ENSG00000155256	ENSG00000155256		"""Zinc fingers, FYVE domain containing"""	26559	protein-coding gene	gene with protein product	"""protrudin"""	610243				14702039	Standard	NM_144588		Approved	FLJ32919, SPG33	uc001kol.2	Q5T4F4	OTTHUMG00000018867	ENST00000393677.4:c.782C>T	10.37:g.99510205C>T	ENSP00000377282:p.Thr261Met	Somatic		Capture	Illumina HiSeq	Phase_I	99500195	NM_001002261	B7Z3S0|B7Z404|B7Z626|G8JLC3|G8JLF0|J3KP98|Q5T4F1|Q5T4F2|Q5T4F3|Q8N1K0|Q8N6D6|Q8NCA0|Q8NDE4|Q96M08	Missense_Mutation	SNP	ENST00000393677.4	37	CCDS31263.1	.	.	.	.	.	.	.	.	.	.	C	18.66	3.671625	0.67928	.	.	ENSG00000155256	ENST00000337540;ENST00000357540;ENST00000370613;ENST00000370610;ENST00000393677;ENST00000453958;ENST00000359980;ENST00000356257;ENST00000423811	T;T;T;T;T;T;T	0.56275	0.47;0.71;1.05;1.02;0.99;1.25;1.25	5.51	4.56	0.56223	.	0.186604	0.56097	D	0.000025	T	0.61640	0.2363	L	0.29908	0.895	0.38157	D	0.938911	D;D;D;D;D;D;D	0.89917	1.0;0.999;0.999;1.0;0.999;1.0;0.999	D;P;D;D;P;D;P	0.71184	0.91;0.863;0.911;0.972;0.87;0.959;0.745	T	0.67998	-0.5525	10	0.66056	D	0.02	-8.6355	17.1029	0.86654	0.0:0.8626:0.1374:0.0	.	229;163;143;175;261;261;261	B7Z404;B7Z3S0;B7Z626;Q5T4F4-5;Q5T4F4-3;Q5T4F4-2;Q5T4F4	.;.;.;.;.;.;ZFY27_HUMAN	M	229;175;143;163;261;261;261;261;239	ENSP00000337993:T229M;ENSP00000359642:T163M;ENSP00000377282:T261M;ENSP00000401580:T261M;ENSP00000353069:T261M;ENSP00000348593:T261M;ENSP00000409594:T239M	ENSP00000337993:T229M	T	+	2	0	ZFYVE27	99500195	0.995000	0.38212	0.944000	0.38274	0.717000	0.41224	3.626000	0.54245	2.590000	0.87494	0.561000	0.74099	ACG		0.592	ZFYVE27-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049745.2	NM_144588	
KNDC1	85442	broad.mit.edu	37	10	135025321	135025321	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr10:135025321G>A	ENST00000304613.3	+	23	4216	c.4195G>A	c.(4195-4197)Gcc>Acc	p.A1399T	KNDC1_ENST00000368572.2_Missense_Mutation_p.A1401T			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1399					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.A1399T(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)		ACCCTTCAACGCCCTCTGTAA	0.672																																					p.A1399T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4195A	10						.						47.0	45.0	46.0					10																	135025321		2202	4299	6501	134875311	SO:0001583	missense	85442	exon23			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.4195G>A	10.37:g.135025321G>A	ENSP00000304437:p.Ala1399Thr	Somatic		Capture	Illumina HiSeq	Phase_I	134875311	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	G	14.53	2.561625	0.45590	.	.	ENSG00000171798	ENST00000304613;ENST00000368572	T;T	0.12879	2.64;2.64	3.34	1.39	0.22231	Ras guanine nucleotide exchange factor, domain (1);	0.570121	0.17003	U	0.190834	T	0.06554	0.0168	L	0.27053	0.805	0.22330	N	0.99919	D	0.53151	0.958	B	0.38880	0.284	T	0.27739	-1.0065	10	0.32370	T	0.25	-5.8994	2.4907	0.04609	0.2688:0.0:0.4945:0.2367	.	1399	Q76NI1	VKIND_HUMAN	T	1399;1401	ENSP00000304437:A1399T;ENSP00000357561:A1401T	ENSP00000304437:A1399T	A	+	1	0	KNDC1	134875311	0.537000	0.26386	0.979000	0.43373	0.668000	0.39293	0.173000	0.16724	0.700000	0.31782	0.282000	0.19409	GCC		0.672	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
MUC6	4588	broad.mit.edu	37	11	1026400	1026401	+	Frame_Shift_Ins	INS	-	-	G	rs200035476		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:1026400_1026401insG	ENST00000421673.2	-	20	2522_2523	c.2472_2473insC	c.(2470-2475)cccgagfs	p.E825fs		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	825					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.E825fs*6(2)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGCACTCCTCGGGGGGCACAC	0.649																																					p.E825fs												.	.	2	Insertion - Frameshift(2)	large_intestine(2)	c.2473_2474insC	11						.																																			1016401	SO:0001589	frameshift_variant	4588	exon20			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.2473dupC	11.37:g.1026406_1026406dupG	ENSP00000406861:p.Glu825fs	Somatic		Capture	Illumina HiSeq	Phase_I	1016400	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Frame_Shift_Ins	INS	ENST00000421673.2	37	CCDS44513.1																																																																																				0.649	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
KIAA1377	57562	broad.mit.edu	37	11	101849120	101849120	+	Missense_Mutation	SNP	G	G	A	rs150274963	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:101849120G>A	ENST00000263468.8	+	7	3158	c.2888G>A	c.(2887-2889)cGg>cAg	p.R963Q	KIAA1377_ENST00000537689.1_Missense_Mutation_p.R764Q	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	963								p.R963Q(1)		breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		GAAACTAAGCGGAGAAATATT	0.333																																					p.R963Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2888A	11						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	149.0	162.0	158.0		2888	-6.2	0.0	11	dbSNP_134	158	2,8596	2.2+/-6.3	0,2,4297	yes	missense	KIAA1377	NM_020802.2	43	0,3,6499	AA,AG,GG		0.0233,0.0227,0.0231	benign	963/1118	101849120	3,13001	2203	4299	6502	101354330	SO:0001583	missense	57562	exon7			AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.2888G>A	11.37:g.101849120G>A	ENSP00000263468:p.Arg963Gln	Somatic		Capture	Illumina HiSeq	Phase_I	101354330	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	37	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	G	1.183	-0.637609	0.03557	2.27E-4	2.33E-4	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.06142	3.34;3.34	5.23	-6.15	0.02105	.	1.588010	0.03474	N	0.214104	T	0.01976	0.0062	N	0.01267	-0.92	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.45556	-0.9253	10	0.20046	T	0.44	6.1992	6.3247	0.21237	0.193:0.1212:0.5764:0.1094	.	963	Q9P2H0	K1377_HUMAN	Q	963;764	ENSP00000263468:R963Q;ENSP00000443184:R764Q	ENSP00000263468:R963Q	R	+	2	0	KIAA1377	101354330	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-0.504000	0.06375	-0.744000	0.04778	-0.259000	0.10710	CGG		0.333	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802	
YAP1	10413	broad.mit.edu	37	11	101984916	101984916	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:101984916G>A	ENST00000282441.5	+	2	751	c.363G>A	c.(361-363)caG>caA	p.Q121Q	YAP1_ENST00000524575.1_5'UTR|YAP1_ENST00000531439.1_Silent_p.Q121Q|YAP1_ENST00000526343.1_Silent_p.Q121Q|YAP1_ENST00000537274.1_Silent_p.Q121Q|YAP1_ENST00000345877.2_Silent_p.Q121Q	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	121					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|contact inhibition (GO:0060242)|embryonic heart tube morphogenesis (GO:0003143)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|keratinocyte differentiation (GO:0030216)|lateral mesoderm development (GO:0048368)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|notochord development (GO:0030903)|paraxial mesoderm development (GO:0048339)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of keratinocyte proliferation (GO:0010837)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of stem cell proliferation (GO:0072091)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.Q121Q(2)		central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		TGACTCCACAGCATGTTCGAG	0.488																																					p.Q121Q	Colon(50;247 1103 7861 28956)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G363A	11						.						54.0	54.0	54.0					11																	101984916		2203	4299	6502	101490126	SO:0001819	synonymous_variant	10413	exon2				CCDS8314.1, CCDS44716.1, CCDS8314.2, CCDS53699.1, CCDS53700.1, CCDS60944.1, CCDS73373.1, CCDS73374.1	11q13	2010-03-19	2010-03-19		ENSG00000137693	ENSG00000137693			16262	protein-coding gene	gene with protein product		606608	"""Yes-associated protein 1, 65kDa"""			7782338	Standard	NM_001130145		Approved	YAP65	uc001pgt.3	P46937	OTTHUMG00000167322	ENST00000282441.5:c.363G>A	11.37:g.101984916G>A		Somatic		Capture	Illumina HiSeq	Phase_I	101490126	NM_006106	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Silent	SNP	ENST00000282441.5	37	CCDS44716.1																																																																																				0.488	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106	
AMPD3	272	broad.mit.edu	37	11	10506536	10506536	+	Silent	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:10506536C>A	ENST00000396554.3	+	5	1127	c.786C>A	c.(784-786)acC>acA	p.T262T	AMPD3_ENST00000444303.2_Silent_p.T94T	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	253					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)	p.T262T(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		ACCTGGAGACCTACACGGTGG	0.577																																					p.T253T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C759A	11						.						76.0	68.0	71.0					11																	10506536		2201	4294	6495	10463112	SO:0001819	synonymous_variant	272	exon5			M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"""erythrocyte-specific AMP deaminase"""	102772	"""adenosine monophosphate deaminase (isoform E)"""			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.786C>A	11.37:g.10506536C>A		Somatic		Capture	Illumina HiSeq	Phase_I	10463112	NM_001025389	A0AUX0|B7Z2S2|B7Z763|B7Z877	Silent	SNP	ENST00000396554.3	37	CCDS7802.1																																																																																				0.577	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480	
DDI1	414301	broad.mit.edu	37	11	103908374	103908374	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:103908374G>A	ENST00000302259.3	+	1	1067	c.824G>A	c.(823-825)cGa>cAa	p.R275Q	PDGFD_ENST00000302251.5_Intron|PDGFD_ENST00000393158.2_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	
CTR9	9646	broad.mit.edu	37	11	10800495	10800495	+	Missense_Mutation	SNP	G	G	A	rs367908001		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:10800495G>A	ENST00000361367.2	+	25	3791	c.3365G>A	c.(3364-3366)cGc>cAc	p.R1122H		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component	1122	Ser-rich.				cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone H3-K4 trimethylation (GO:0080182)|histone monoubiquitination (GO:0010390)|interleukin-6-mediated signaling pathway (GO:0070102)|JAK-STAT cascade (GO:0007259)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K79 methylation (GO:2001162)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|transcriptionally active chromatin (GO:0035327)		p.R1122H(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|pancreas(1)|stomach(1)	40				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		AACGACTCTCGCCCAGCTTCT	0.527																																					p.R1122H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3365A	11						.	G	HIS/ARG	1,4401	2.1+/-5.4	0,1,2200	95.0	104.0	101.0		3365	2.5	0.9	11		101	0,8588		0,0,4294	no	missense	CTR9	NM_014633.3	29	0,1,6494	AA,AG,GG		0.0,0.0227,0.0077	benign	1122/1174	10800495	1,12989	2201	4294	6495	10757071	SO:0001583	missense	9646	exon25			D63875	CCDS7805.1	11p15.3	2013-07-03	2013-07-03	2006-05-22	ENSG00000198730	ENSG00000198730		"""Tetratricopeptide (TTC) repeat domain containing"""	16850	protein-coding gene	gene with protein product		609366	"""SH2 domain binding protein 1 (tetratricopeptide repeat containing)"", ""Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"""	SH2BP1		8590280, 8636124	Standard	NM_014633		Approved	KIAA0155, TSBP, p150TSP	uc001mja.3	Q6PD62	OTTHUMG00000165789	ENST00000361367.2:c.3365G>A	11.37:g.10800495G>A	ENSP00000355013:p.Arg1122His	Somatic		Capture	Illumina HiSeq	Phase_I	10757071	NM_014633	D3DQV8|Q15015	Missense_Mutation	SNP	ENST00000361367.2	37	CCDS7805.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.172755	0.38413	2.27E-4	0.0	ENSG00000198730	ENST00000361367	T	0.48522	0.81	5.5	2.47	0.30058	.	0.165341	0.53938	D	0.000058	T	0.30634	0.0771	N	0.24115	0.695	0.47862	D	0.999538	B	0.27264	0.173	B	0.26202	0.067	T	0.08186	-1.0734	10	0.41790	T	0.15	-7.6789	8.7766	0.34765	0.137:0.1235:0.7394:0.0	.	1122	Q6PD62	CTR9_HUMAN	H	1122	ENSP00000355013:R1122H	ENSP00000355013:R1122H	R	+	2	0	CTR9	10757071	0.943000	0.32029	0.902000	0.35471	0.136000	0.21042	2.371000	0.44248	0.706000	0.31912	-0.137000	0.14449	CGC		0.527	CTR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386215.1	NM_014633	
ELMOD1	55531	broad.mit.edu	37	11	107502339	107502339	+	Missense_Mutation	SNP	G	G	A	rs369345306		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:107502339G>A	ENST00000265840.7	+	5	491	c.226G>A	c.(226-228)Gct>Act	p.A76T	ELMOD1_ENST00000443271.2_Missense_Mutation_p.A76T|ELMOD1_ENST00000531234.1_Missense_Mutation_p.A70T	NM_018712.3	NP_061182.3	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1	76					phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)	cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)	p.A76T(1)		endometrium(2)|large_intestine(5)|liver(2)|lung(7)|pancreas(2)|prostate(1)	19		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)		TCACCCCGACGCTATTGAAAA	0.348																																					p.A76T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G226A	11						.	G	THR/ALA,THR/ALA	1,3675		0,1,1837	49.0	45.0	46.0		226,226	5.7	1.0	11		46	0,8134		0,0,4067	no	missense,missense	ELMOD1	NM_001130037.1,NM_018712.3	58,58	0,1,5904	AA,AG,GG		0.0,0.0272,0.0085	possibly-damaging,possibly-damaging	76/327,76/335	107502339	1,11809	1838	4067	5905	107007549	SO:0001583	missense	55531	exon5			AL359601	CCDS44723.1, CCDS44724.1	11q23.1	2012-10-15	2006-01-20		ENSG00000110675	ENSG00000110675			25334	protein-coding gene	gene with protein product		615456	"""ELMO domain containing 1"""			12477932	Standard	NM_018712		Approved	DKFZp547C176	uc010rvs.2	Q8N336	OTTHUMG00000166361	ENST00000265840.7:c.226G>A	11.37:g.107502339G>A	ENSP00000265840:p.Ala76Thr	Somatic		Capture	Illumina HiSeq	Phase_I	107007549	NM_001130037	B4E167|G5E9S5|Q9NPW3	Missense_Mutation	SNP	ENST00000265840.7	37	CCDS44723.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.316441	0.23908	2.72E-4	0.0	ENSG00000110675	ENST00000531234;ENST00000265840;ENST00000443271	.	.	.	5.66	5.66	0.87406	.	0.271361	0.39544	N	0.001340	T	0.47783	0.1464	L	0.39898	1.24	0.45015	D	0.998037	P;P	0.37824	0.475;0.609	B;B	0.32393	0.069;0.145	T	0.42172	-0.9467	9	0.14656	T	0.56	.	19.736	0.96205	0.0:0.0:1.0:0.0	.	76;76	Q8N336;G5E9S5	ELMD1_HUMAN;.	T	70;76;76	.	ENSP00000265840:A76T	A	+	1	0	ELMOD1	107007549	1.000000	0.71417	0.998000	0.56505	0.422000	0.31414	3.985000	0.56930	2.669000	0.90835	0.591000	0.81541	GCT		0.348	ELMOD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389406.1	NM_018712	
C11orf87	399947	broad.mit.edu	37	11	109294394	109294394	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:109294394C>T	ENST00000327419.6	+	2	438	c.35C>T	c.(34-36)gCg>gTg	p.A12V	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	12						integral component of membrane (GO:0016021)		p.A12V(1)		breast(2)|endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17						CTGAGGCTGGCGTTGCCGCCG	0.711																																					p.A12V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C35T	11						.						28.0	27.0	27.0					11																	109294394		2196	4295	6491	108799604	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.35C>T	11.37:g.109294394C>T	ENSP00000331581:p.Ala12Val	Somatic		Capture	Illumina HiSeq	Phase_I	108799604	NM_207645	B4E169	Missense_Mutation	SNP	ENST00000327419.6	37	CCDS31672.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.008161	0.93287	.	.	ENSG00000185742	ENST00000327419	.	.	.	4.42	4.42	0.53409	.	0.260888	0.19923	U	0.103044	T	0.44477	0.1295	N	0.19112	0.55	0.33172	D	0.548465	D	0.64830	0.994	P	0.50754	0.649	T	0.60515	-0.7248	9	0.66056	D	0.02	.	15.9561	0.79889	0.0:1.0:0.0:0.0	.	12	Q6NUJ2	CK087_HUMAN	V	12	.	ENSP00000331581:A12V	A	+	2	0	C11orf87	108799604	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	6.014000	0.70784	2.188000	0.69820	0.462000	0.41574	GCG		0.711	C11orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390403.1	NM_207645	
ARHGAP20	57569	broad.mit.edu	37	11	110450663	110450663	+	Missense_Mutation	SNP	C	C	T	rs202001398		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:110450663C>T	ENST00000260283.4	-	16	3291	c.3007G>A	c.(3007-3009)Ggt>Agt	p.G1003S	ARHGAP20_ENST00000357139.3_Missense_Mutation_p.G977S|ARHGAP20_ENST00000529591.1_Missense_Mutation_p.G546S|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.G967S|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.G980S|ARHGAP20_ENST00000533353.1_Missense_Mutation_p.G977S|ARHGAP20_ENST00000528829.1_Missense_Mutation_p.G967S	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	1003					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.G1003S(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		GATGAGGGACCGGGCATTCCG	0.507													C|||	1	0.000199681	0.0	0.0	5008	,	,		20149	0.001		0.0	False		,,,				2504	0.0				p.G1003S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3007A	11						.						62.0	61.0	61.0					11																	110450663		2201	4298	6499	109955873	SO:0001583	missense	57569	exon16			AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"""Rho GTPase activating proteins"""	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.3007G>A	11.37:g.110450663C>T	ENSP00000260283:p.Gly1003Ser	Somatic		Capture	Illumina HiSeq	Phase_I	109955873	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	0.893	-0.724850	0.03158	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.07908	3.15;3.15;3.18;3.15;3.15;3.15;3.15	5.9	0.311	0.15831	.	0.363057	0.27181	N	0.020541	T	0.05547	0.0146	L	0.36672	1.1	0.09310	N	1	B;B;B	0.22346	0.004;0.041;0.068	B;B;B	0.17722	0.003;0.009;0.019	T	0.39057	-0.9632	10	0.23302	T	0.38	.	5.9856	0.19432	0.1254:0.4172:0.0:0.4573	.	977;1003;980	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	S	1003;977;546;980;967;977;967	ENSP00000260283:G1003S;ENSP00000349660:G977S;ENSP00000437905:G546S;ENSP00000432076:G980S;ENSP00000436319:G967S;ENSP00000436522:G977S;ENSP00000431399:G967S	ENSP00000260283:G1003S	G	-	1	0	ARHGAP20	109955873	0.000000	0.05858	0.038000	0.18304	0.136000	0.21042	-0.447000	0.06828	0.056000	0.16144	-0.809000	0.03173	GGT		0.507	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809	
ARHGAP20	57569	broad.mit.edu	37	11	110482090	110482090	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:110482090C>T	ENST00000260283.4	-	8	935	c.651G>A	c.(649-651)atG>atA	p.M217I	ARHGAP20_ENST00000357139.3_Missense_Mutation_p.M191I|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.M181I|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.M194I|ARHGAP20_ENST00000533353.1_Missense_Mutation_p.M191I|ARHGAP20_ENST00000528829.1_Missense_Mutation_p.M181I	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	217	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				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.M217I(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		TATCTGAATTCATTACTGTTA	0.249																																					p.M217I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G651A	11						.						40.0	36.0	38.0					11																	110482090		2191	4249	6440	109987300	SO:0001583	missense	57569	exon8			AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"""Rho GTPase activating proteins"""	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.651G>A	11.37:g.110482090C>T	ENSP00000260283:p.Met217Ile	Somatic		Capture	Illumina HiSeq	Phase_I	109987300	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	C	14.70	2.614271	0.46631	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59;1.59	6.16	0.827	0.18835	Ras-association (2);	0.519770	0.25270	N	0.031885	T	0.12305	0.0299	N	0.08118	0	0.23277	N	0.997992	B;B	0.21753	0.03;0.06	B;B	0.24006	0.05;0.03	T	0.13388	-1.0511	10	0.56958	D	0.05	.	1.728	0.02925	0.114:0.407:0.1893:0.2896	.	217;194	Q9P2F6;Q9P2F6-3	RHG20_HUMAN;.	I	217;191;194;181;191;181	ENSP00000260283:M217I;ENSP00000349660:M191I;ENSP00000432076:M194I;ENSP00000436319:M181I;ENSP00000436522:M191I;ENSP00000431399:M181I	ENSP00000260283:M217I	M	-	3	0	ARHGAP20	109987300	0.989000	0.36119	0.885000	0.34714	0.996000	0.88848	0.179000	0.16840	0.489000	0.27749	0.650000	0.86243	ATG		0.249	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809	
TTC12	54970	broad.mit.edu	37	11	113211441	113211441	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:113211441C>T	ENST00000529221.1	+	11	987	c.882C>T	c.(880-882)aaC>aaT	p.N294N	TTC12_ENST00000393020.1_Silent_p.N294N|TTC12_ENST00000314756.3_Silent_p.N294N|TTC12_ENST00000483239.2_Silent_p.N300N	NM_017868.3	NP_060338.3	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	294								p.N294N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		TCAGTGACAACGAGGTCATAA	0.428																																					p.N294N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C882T	11						.						119.0	107.0	111.0					11																	113211441		2201	4296	6497	112716651	SO:0001819	synonymous_variant	54970	exon11			AK000542	CCDS8360.2	11q23.2	2013-01-10			ENSG00000149292	ENSG00000149292		"""Tetratricopeptide (TTC) repeat domain containing"""	23700	protein-coding gene	gene with protein product		610732				12964006	Standard	XM_005271607		Approved	FLJ13859, FLJ20535, TPARM	uc001pnu.3	Q9H892	OTTHUMG00000142832	ENST00000529221.1:c.882C>T	11.37:g.113211441C>T		Somatic		Capture	Illumina HiSeq	Phase_I	112716651	NM_017868	Q8N5H9|Q9NWY3	Silent	SNP	ENST00000529221.1	37	CCDS8360.2																																																																																				0.428	TTC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286455.2	NM_017868	
USP28	57646	broad.mit.edu	37	11	113723244	113723244	+	Missense_Mutation	SNP	C	C	T	rs149069839	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:113723244C>T	ENST00000003302.4	-	3	315	c.247G>A	c.(247-249)Gcc>Acc	p.A83T	USP28_ENST00000545540.1_Intron|USP28_ENST00000542033.1_5'UTR|USP28_ENST00000260188.5_Missense_Mutation_p.A83T|USP28_ENST00000537706.1_Missense_Mutation_p.A83T	NM_020886.2	NP_065937.1	Q96RU2	UBP28_HUMAN	ubiquitin specific peptidase 28	83					cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|protein deubiquitination (GO:0016579)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.A83T(1)		breast(4)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(24)|ovary(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	59		all_cancers(61;3.74e-18)|all_epithelial(67;3.75e-11)|Melanoma(852;1.46e-05)|all_hematologic(158;4.65e-05)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|Prostate(24;0.0153)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|Epithelial(105;0.000122)|all cancers(92;0.00104)		TCCTTGTTGGCAGCACTCCCC	0.448																																					p.A83T	Melanoma(4;162 555 7664)|GBM(79;500 2010 17506)|Esophageal Squamous(9;463 924 15765)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G247A	11						.						201.0	168.0	179.0					11																	113723244		2201	4296	6497	113228454	SO:0001583	missense	57646	exon3			AB040948	CCDS31680.1, CCDS73394.1	11q23	2008-04-11	2005-08-08		ENSG00000048028	ENSG00000048028		"""Ubiquitin-specific peptidases"""	12625	protein-coding gene	gene with protein product		610748	"""ubiquitin specific protease 28"""			12838346, 11597335	Standard	XM_005271630		Approved	KIAA1515	uc001poh.3	Q96RU2	OTTHUMG00000168205	ENST00000003302.4:c.247G>A	11.37:g.113723244C>T	ENSP00000003302:p.Ala83Thr	Somatic		Capture	Illumina HiSeq	Phase_I	113228454	NM_020886	B0YJC0|B0YJC1|Q9P213	Missense_Mutation	SNP	ENST00000003302.4	37	CCDS31680.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.024212	0.35701	.	.	ENSG00000048028	ENST00000003302;ENST00000260188;ENST00000537706	T;T;T	0.30182	1.54;1.54;1.95	5.78	3.9	0.45041	.	0.769976	0.12413	N	0.471139	T	0.17746	0.0426	N	0.19112	0.55	0.21105	N	0.999788	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.002	T	0.31668	-0.9935	10	0.11794	T	0.64	-2.5834	8.284	0.31917	0.0:0.8276:0.0:0.1724	.	83;83;83	B4E2Q2;Q6NZX9;Q96RU2	.;.;UBP28_HUMAN	T	83	ENSP00000003302:A83T;ENSP00000260188:A83T;ENSP00000445743:A83T	ENSP00000003302:A83T	A	-	1	0	USP28	113228454	0.901000	0.30685	0.998000	0.56505	0.759000	0.43091	0.434000	0.21494	0.769000	0.33313	0.563000	0.77884	GCC		0.448	USP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398789.1		
GALNT18	374378	broad.mit.edu	37	11	11454249	11454249	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:11454249G>A	ENST00000227756.4	-	3	925	c.514C>T	c.(514-516)Cgc>Tgc	p.R172C		NM_198516.2	NP_940918.2	Q6P9A2	GLT18_HUMAN	polypeptide N-acetylgalactosaminyltransferase 18	172	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.R172C(1)									TGGATGGAGCGCAGCAGCACT	0.557																																					p.R172C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C514T	11						.						101.0	83.0	89.0					11																	11454249		2201	4293	6494	11410825	SO:0001583	missense	374378	exon3			AK055111	CCDS7807.1	11p15	2014-03-13	2014-03-13	2013-01-25	ENSG00000110328	ENSG00000110328	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	30488	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 18"""	615136	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 4"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18"""	GALNTL4		22186971	Standard	NM_198516		Approved	MGC71806, GALNT15, GalNAc-T18	uc001mjo.2	Q6P9A2	OTTHUMG00000165707	ENST00000227756.4:c.514C>T	11.37:g.11454249G>A	ENSP00000227756:p.Arg172Cys	Somatic		Capture	Illumina HiSeq	Phase_I	11410825	NM_198516	O95903|Q8NDY9	Missense_Mutation	SNP	ENST00000227756.4	37	CCDS7807.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.370965	0.82573	.	.	ENSG00000110328	ENST00000227756	T	0.63913	-0.07	5.78	4.79	0.61399	Glycosyl transferase, family 2 (1);	0.000000	0.64402	D	0.000001	D	0.85500	0.5711	H	0.96398	3.815	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89843	0.4004	10	0.87932	D	0	.	16.3469	0.83138	0.0:0.0:0.8592:0.1408	.	172	Q6P9A2	GLTL4_HUMAN	C	172	ENSP00000227756:R172C	ENSP00000227756:R172C	R	-	1	0	GALNTL4	11410825	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	7.919000	0.87513	2.724000	0.93272	0.655000	0.94253	CGC		0.557	GALNT18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385848.1	NM_198516	
HTR3A	3359	broad.mit.edu	37	11	113856764	113856764	+	Missense_Mutation	SNP	G	G	A	rs199553305		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:113856764G>A	ENST00000504030.2	+	6	1017	c.572G>A	c.(571-573)cGc>cAc	p.R191H	HTR3A_ENST00000375498.2_Missense_Mutation_p.R197H|HTR3A_ENST00000535865.1_Intron|HTR3A_ENST00000299961.5_Missense_Mutation_p.R176H|HTR3A_ENST00000506841.2_Missense_Mutation_p.R191H|HTR3A_ENST00000355556.2_Missense_Mutation_p.R197H			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	191					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.R191H(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)	TCTTTGTGGCGCTTGCCAGAA	0.522													G|||	1	0.000199681	0.0	0.0	5008	,	,		18827	0.0		0.001	False		,,,				2504	0.0				p.R197H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G590A	11						.						196.0	205.0	202.0					11																	113856764		2201	4296	6497	113361974	SO:0001583	missense	3359	exon6			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.572G>A	11.37:g.113856764G>A	ENSP00000424189:p.Arg191His	Somatic		Capture	Illumina HiSeq	Phase_I	113361974	NM_000869	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	37		.	.	.	.	.	.	.	.	.	.	G	31	5.080083	0.94050	.	.	ENSG00000166736	ENST00000504030;ENST00000355556;ENST00000375498;ENST00000506841;ENST00000299961	T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	D	0.87087	0.6090	M	0.65975	2.015	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.998	D	0.86661	0.1904	10	0.44086	T	0.13	-14.1102	18.5998	0.91244	0.0:0.0:1.0:0.0	.	176;197;197	B4DSY6;G5E986;Q7KZM7	.;.;.	H	191;197;197;191;176	ENSP00000424189:R191H;ENSP00000347754:R197H;ENSP00000364648:R197H;ENSP00000424776:R191H;ENSP00000299961:R176H	ENSP00000299961:R176H	R	+	2	0	HTR3A	113361974	1.000000	0.71417	0.947000	0.38551	0.819000	0.46315	9.688000	0.98670	2.457000	0.83068	0.655000	0.94253	CGC		0.522	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869	
BUD13	84811	broad.mit.edu	37	11	116633538	116633538	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:116633538A>G	ENST00000260210.4	-	4	790	c.767T>C	c.(766-768)cTt>cCt	p.L256P	BUD13_ENST00000375445.3_Intron	NM_032725.3	NP_116114.1	Q9BRD0	BUD13_HUMAN	BUD13 homolog (S. cerevisiae)	256	Arg-rich.				mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)	nucleus (GO:0005634)|RES complex (GO:0070274)	poly(A) RNA binding (GO:0044822)	p.L256P(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|pancreas(2)|skin(1)|urinary_tract(1)	22	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.81e-06)|all cancers(92;0.000144)|OV - Ovarian serous cystadenocarcinoma(223;0.154)		TGAAGAGCCAAGAGTCCTCCT	0.527																																					p.L256P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T767C	11						.						141.0	151.0	147.0					11																	116633538		2201	4296	6497	116138748	SO:0001583	missense	84811	exon4			BC006350	CCDS8374.1, CCDS53712.1	11q23.3	2012-06-07	2007-01-12		ENSG00000137656	ENSG00000137656			28199	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 71"""		"""BUD13 homolog (yeast)"""			12477932	Standard	NM_032725		Approved	MGC13125, fSAP71, Cwc26	uc001ppn.3	Q9BRD0	OTTHUMG00000045136	ENST00000260210.4:c.767T>C	11.37:g.116633538A>G	ENSP00000260210:p.Leu256Pro	Somatic		Capture	Illumina HiSeq	Phase_I	116138748	NM_032725	A8K0S0|Q96LS7	Missense_Mutation	SNP	ENST00000260210.4	37	CCDS8374.1	.	.	.	.	.	.	.	.	.	.	A	10.34	1.323101	0.24080	.	.	ENSG00000137656	ENST00000260210	T	0.18338	2.22	4.63	-1.02	0.10135	.	0.658638	0.13426	N	0.388785	T	0.14743	0.0356	M	0.68317	2.08	0.42957	D	0.994397	B;B	0.10296	0.003;0.003	B;B	0.08055	0.003;0.003	T	0.18745	-1.0327	10	0.87932	D	0	-1.2887	1.7018	0.02873	0.3095:0.3654:0.0872:0.238	.	256;256	A8K4Z6;Q9BRD0	.;BUD13_HUMAN	P	256	ENSP00000260210:L256P	ENSP00000260210:L256P	L	-	2	0	BUD13	116138748	0.907000	0.30839	0.584000	0.28653	0.810000	0.45777	0.406000	0.21032	0.015000	0.14971	0.533000	0.62120	CTT		0.527	BUD13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000104864.1	NM_032725	
SIDT2	51092	broad.mit.edu	37	11	117053477	117053477	+	Silent	SNP	C	C	T	rs186971395	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:117053477C>T	ENST00000324225.4	+	6	1188	c.657C>T	c.(655-657)atC>atT	p.I219I	SIDT2_ENST00000431081.2_Silent_p.I219I|SIDT2_ENST00000530948.1_3'UTR	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	219					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)	p.I219I(1)		NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	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;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)		TAGCCTTCATCGGCATGTACC	0.587													C|||	2	0.000399361	0.0	0.0	5008	,	,		21745	0.002		0.0	False		,,,				2504	0.0				p.I219I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C657T	11						.						75.0	51.0	59.0					11																	117053477		2201	4296	6497	116558687	SO:0001819	synonymous_variant	51092	exon6			AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.657C>T	11.37:g.117053477C>T		Somatic		Capture	Illumina HiSeq	Phase_I	116558687	NM_001040455	Q8NBY7|Q9Y357	Silent	SNP	ENST00000324225.4	37	CCDS31682.1																																																																																				0.587	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996	
DSCAML1	57453	broad.mit.edu	37	11	117375678	117375678	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:117375678C>T	ENST00000321322.6	-	10	2324	c.2323G>A	c.(2323-2325)Ggc>Agc	p.G775S	DSCAML1_ENST00000527706.1_Missense_Mutation_p.G505S	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	715	Ig-like C2-type 8.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.G775S(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GGGGGGTAGCCGTCCACCGAG	0.597																																					p.G775S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2323A	11						.						85.0	75.0	78.0					11																	117375678		2201	4296	6497	116880888	SO:0001583	missense	57453	exon10				CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.2323G>A	11.37:g.117375678C>T	ENSP00000315465:p.Gly775Ser	Somatic		Capture	Illumina HiSeq	Phase_I	116880888	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.894924	0.91962	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.79653	-1.29;-1.29	4.31	4.31	0.51392	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.87095	0.6092	M	0.86097	2.795	0.80722	D	1	D	0.54047	0.964	P	0.51385	0.668	D	0.90211	0.4264	9	0.87932	D	0	.	16.5735	0.84631	0.0:1.0:0.0:0.0	.	715	Q8TD84	DSCL1_HUMAN	S	505;775;482	ENSP00000434335:G505S;ENSP00000315465:G775S	ENSP00000315465:G775S	G	-	1	0	DSCAML1	116880888	1.000000	0.71417	0.973000	0.42090	0.825000	0.46686	7.559000	0.82265	2.217000	0.71921	0.305000	0.20034	GGC		0.597	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
TMPRSS13	84000	broad.mit.edu	37	11	117785189	117785189	+	Silent	SNP	C	C	T	rs535811734		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:117785189C>T	ENST00000430170.2	-	4	684	c.597G>A	c.(595-597)gaG>gaA	p.E199E	TMPRSS13_ENST00000445164.2_Silent_p.E199E|TMPRSS13_ENST00000526090.1_Silent_p.E199E|TMPRSS13_ENST00000528626.1_Silent_p.E164E|TMPRSS13_ENST00000524993.1_Silent_p.E199E	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	199	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.E199E(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		TCTCCCTCTGCTCCTTGTACC	0.597													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19454	0.0		0.0	False		,,,				2504	0.0				p.E199E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G597A	11						.						222.0	239.0	233.0					11																	117785189		2158	4258	6416	117290399	SO:0001819	synonymous_variant	84000	exon4			AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.597G>A	11.37:g.117785189C>T		Somatic		Capture	Illumina HiSeq	Phase_I	117290399	NM_001077263	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Silent	SNP	ENST00000430170.2	37	CCDS58185.1																																																																																				0.597	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
KMT2A	4297	broad.mit.edu	37	11	118369217	118369217	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:118369217C>T	ENST00000389506.5	+	22	5926	c.5926C>T	c.(5926-5928)Cga>Tga	p.R1976*	KMT2A_ENST00000534358.1_Nonsense_Mutation_p.R1979*|KMT2A_ENST00000354520.4_Nonsense_Mutation_p.R1938*			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	1976					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.R1976*(1)									ATATTGCCAACGACATCGGGA	0.393																																					p.R1976X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C5926T	11						.						150.0	157.0	155.0					11																	118369217		2200	4296	6496	117874427	SO:0001587	stop_gained	4297	exon22			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.5926C>T	11.37:g.118369217C>T	ENSP00000374157:p.Arg1976*	Somatic		Capture	Illumina HiSeq	Phase_I	117874427	NM_005933	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Nonsense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	C	46	12.359289	0.99660	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	.	.	.	5.91	5.91	0.95273	.	0.065268	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	14.1545	0.65407	0.2489:0.7511:0.0:0.0	.	.	.	.	X	1979;1976;1938;886	.	ENSP00000346516:R1938X	R	+	1	2	MLL	117874427	0.991000	0.36638	0.995000	0.50966	0.994000	0.84299	3.003000	0.49505	2.802000	0.96397	0.655000	0.94253	CGA		0.393	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
KMT2A	4297	broad.mit.edu	37	11	118392075	118392075	+	Silent	SNP	C	C	T	rs200576371		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:118392075C>T	ENST00000389506.5	+	35	11577	c.11577C>T	c.(11575-11577)gcC>gcT	p.A3859A	RP11-770J1.3_ENST00000554407.1_RNA|RP11-770J1.3_ENST00000525992.2_RNA|RP11-770J1.3_ENST00000532597.1_RNA|KMT2A_ENST00000534358.1_Silent_p.A3862A|RP11-770J1.3_ENST00000556583.1_RNA|KMT2A_ENST00000354520.4_Silent_p.A3821A|RP11-770J1.3_ENST00000528578.1_RNA			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	3859	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)	p.A3859A(1)									TTGAGTATGCCGGCAACGTCA	0.483																																					p.A3859A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C11577T	11						.	C	,	1,4399	2.1+/-5.4	0,1,2199	128.0	117.0	121.0		11586,11577	-8.5	0.9	11		121	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous	MLL	NM_001197104.1,NM_005933.3	,	0,1,6494	TT,TC,CC		0.0,0.0227,0.0077	,	3862/3973,3859/3970	118392075	1,12989	2200	4295	6495	117897285	SO:0001819	synonymous_variant	4297	exon35			L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.11577C>T	11.37:g.118392075C>T		Somatic		Capture	Illumina HiSeq	Phase_I	117897285	NM_005933	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Silent	SNP	ENST00000389506.5	37	CCDS31686.1																																																																																				0.483	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
CXCR5	643	broad.mit.edu	37	11	118764550	118764550	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:118764550G>A	ENST00000292174.4	+	2	473	c.297G>A	c.(295-297)ctG>ctA	p.L99L		NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	99					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)	p.L99L(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		CCGACCTCCTGCTGGTCTTCA	0.617																																					p.L54L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G162A	11						.						93.0	85.0	88.0					11																	118764550		2200	4295	6495	118269760	SO:0001819	synonymous_variant	643	exon1			X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	1060	protein-coding gene	gene with protein product		601613	"""Burkitt lymphoma receptor 1, GTP-binding protein"", ""Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"""	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.297G>A	11.37:g.118764550G>A		Somatic		Capture	Illumina HiSeq	Phase_I	118269760	NM_032966	Q14811	Silent	SNP	ENST00000292174.4	37	CCDS8402.1																																																																																				0.617	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716	
CBL	867	broad.mit.edu	37	11	119155973	119155973	+	Silent	SNP	G	G	A	rs375702554		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:119155973G>A	ENST00000264033.4	+	11	2014	c.1638G>A	c.(1636-1638)ccG>ccA	p.P546P		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	546	Pro-rich.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P546P(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		CACCACCACCGCCTCCAGACC	0.557			"""T, Mis S, O"""	MLL	"""AML, JMML, MDS"""				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies		OREG0021401	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0008	0.0	5008	,	,		16738	0.0		0.0	False		,,,				2504	0.0				p.P546P			"""Dom, Rec"""	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1638A	11						.						87.0	85.0	86.0					11																	119155973		2199	4295	6494	118661183	SO:0001819	synonymous_variant	867	exon11	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"""RING-type (C3HC4) zinc fingers"""	1541	protein-coding gene	gene with protein product	"""oncogene CBL2"""	165360	"""Cas-Br-M (murine) ecotropic retroviral transforming sequence"""	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.1638G>A	11.37:g.119155973G>A		Somatic	1494	Capture	Illumina HiSeq	Phase_I	118661183	NM_005188	A3KMP8	Silent	SNP	ENST00000264033.4	37	CCDS8418.1																																																																																				0.557	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188	
PVRL1	5818	broad.mit.edu	37	11	119549447	119549447	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:119549447G>A	ENST00000264025.3	-	2	638	c.108C>T	c.(106-108)aaC>aaT	p.N36N	PVRL1_ENST00000524510.1_5'UTR|PVRL1_ENST00000340882.2_Silent_p.N36N|PVRL1_ENST00000341398.2_Silent_p.N36N	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	36	Ig-like V-type.				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.N36N(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)		ACATGGAGTCGTTCACCTGGA	0.602																																					p.N36N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C108T	11						.						70.0	49.0	56.0					11																	119549447		2199	4295	6494	119054657	SO:0001819	synonymous_variant	5818	exon2			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.108C>T	11.37:g.119549447G>A		Somatic		Capture	Illumina HiSeq	Phase_I	119054657	NM_002855	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Silent	SNP	ENST00000264025.3	37	CCDS8426.1																																																																																				0.602	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1		
GRIK4	2900	broad.mit.edu	37	11	120776054	120776054	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:120776054G>A	ENST00000527524.2	+	13	1615	c.1328G>A	c.(1327-1329)cGc>cAc	p.R443H	GRIK4_ENST00000438375.2_Missense_Mutation_p.R443H	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	443					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.R443H(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)		GGCAATGACCGCTACGAGGGC	0.547																																					p.R443H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1328A	11						.						195.0	191.0	192.0					11																	120776054		2203	4299	6502	120281264	SO:0001583	missense	2900	exon11			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.1328G>A	11.37:g.120776054G>A	ENSP00000435648:p.Arg443His	Somatic		Capture	Illumina HiSeq	Phase_I	120281264	NM_014619	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	37	CCDS8433.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.396411	0.83011	.	.	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.78481	-1.18;-1.18	5.47	5.47	0.80525	Glutamate receptor, L-glutamate/glycine-binding (2);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	D	0.87358	0.6157	M	0.65498	2.005	0.58432	D	0.999999	D;D	0.76494	0.998;0.999	D;D	0.70935	0.971;0.95	D	0.88241	0.2910	10	0.87932	D	0	.	19.323	0.94250	0.0:0.0:1.0:0.0	.	443;443	A6H8K8;Q16099	.;GRIK4_HUMAN	H	443	ENSP00000435648:R443H;ENSP00000404063:R443H	ENSP00000404063:R443H	R	+	2	0	GRIK4	120281264	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.298000	0.65710	2.561000	0.86390	0.655000	0.94253	CGC		0.547	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619	
TECTA	7007	broad.mit.edu	37	11	120980130	120980130	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:120980130G>A	ENST00000392793.1	+	4	680	c.409G>A	c.(409-411)Gca>Aca	p.A137T	TECTA_ENST00000264037.2_Missense_Mutation_p.A137T			O75443	TECTA_HUMAN	tectorin alpha	137	NIDO. {ECO:0000255|PROSITE- ProRule:PRU00570}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.A137T(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		CAAAGACATGGCAACCTTCTC	0.458																																					p.A137T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G409A	11						.						110.0	109.0	109.0					11																	120980130		2203	4299	6502	120485340	SO:0001583	missense	7007	exon3			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.409G>A	11.37:g.120980130G>A	ENSP00000376543:p.Ala137Thr	Somatic		Capture	Illumina HiSeq	Phase_I	120485340	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.639706	0.29157	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.37411	1.2;1.2	5.57	1.31	0.21738	Nidogen, extracellular domain (2);	0.273737	0.36740	N	0.002429	T	0.19005	0.0456	N	0.16656	0.425	0.25431	N	0.988185	B	0.17667	0.023	B	0.20955	0.032	T	0.22417	-1.0217	10	0.18710	T	0.47	.	8.639	0.33966	0.1457:0.447:0.4073:0.0	.	137	O75443	TECTA_HUMAN	T	137	ENSP00000376543:A137T;ENSP00000264037:A137T	ENSP00000264037:A137T	A	+	1	0	TECTA	120485340	0.327000	0.24678	1.000000	0.80357	0.996000	0.88848	-0.089000	0.11180	0.289000	0.22422	-0.126000	0.14955	GCA		0.458	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
TECTA	7007	broad.mit.edu	37	11	120996152	120996152	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:120996152G>A	ENST00000392793.1	+	8	1616	c.1345G>A	c.(1345-1347)Gtc>Atc	p.V449I	TECTA_ENST00000264037.2_Missense_Mutation_p.V449I			O75443	TECTA_HUMAN	tectorin alpha	449	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.V449I(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		CTCCATTTCCGTCCCAGGCTC	0.512																																					p.V449I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1345A	11						.						217.0	236.0	229.0					11																	120996152		2203	4299	6502	120501362	SO:0001583	missense	7007	exon7			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.1345G>A	11.37:g.120996152G>A	ENSP00000376543:p.Val449Ile	Somatic		Capture	Illumina HiSeq	Phase_I	120501362	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.329892	0.24167	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.60548	0.18;0.18	4.72	-5.34	0.02705	von Willebrand factor, type D domain (3);	0.514767	0.20728	N	0.086763	T	0.42040	0.1185	L	0.46885	1.475	0.25809	N	0.984418	B	0.06786	0.001	B	0.11329	0.006	T	0.33904	-0.9850	10	0.24483	T	0.36	.	11.6684	0.51387	0.1781:0.1387:0.6832:0.0	.	449	O75443	TECTA_HUMAN	I	449	ENSP00000376543:V449I;ENSP00000264037:V449I	ENSP00000264037:V449I	V	+	1	0	TECTA	120501362	0.117000	0.22190	0.987000	0.45799	0.966000	0.64601	0.233000	0.17911	-0.561000	0.06094	-1.264000	0.01445	GTC		0.512	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
TECTA	7007	broad.mit.edu	37	11	120998618	120998618	+	Silent	SNP	C	C	T	rs372952940		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:120998618C>T	ENST00000392793.1	+	9	2203	c.1932C>T	c.(1930-1932)tgC>tgT	p.C644C	TECTA_ENST00000264037.2_Silent_p.C644C			O75443	TECTA_HUMAN	tectorin alpha	644	TIL 1.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.C644C(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		CCAGCCAGTGCGTCCCTCTGC	0.652																																					p.C644C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1932T	11						.						74.0	66.0	69.0					11																	120998618		2203	4299	6502	120503828	SO:0001819	synonymous_variant	7007	exon8			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.1932C>T	11.37:g.120998618C>T		Somatic		Capture	Illumina HiSeq	Phase_I	120503828	NM_005422		Silent	SNP	ENST00000392793.1	37	CCDS8434.1																																																																																				0.652	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
TECTA	7007	broad.mit.edu	37	11	121031012	121031012	+	Missense_Mutation	SNP	G	G	A	rs142929996		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:121031012G>A	ENST00000392793.1	+	15	5129	c.4858G>A	c.(4858-4860)Ggt>Agt	p.G1620S	TECTA_ENST00000264037.2_Missense_Mutation_p.G1620S			O75443	TECTA_HUMAN	tectorin alpha	1620	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.G1620S(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		CAAAGTGTGCGGTCTCTGTGG	0.507																																					p.G1620S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4858A	11						.	G	SER/GLY	0,4406		0,0,2203	138.0	132.0	134.0		4858	4.8	1.0	11	dbSNP_134	134	1,8597	1.2+/-3.3	0,1,4298	no	missense	TECTA	NM_005422.2	56	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	1620/2156	121031012	1,13003	2203	4299	6502	120536222	SO:0001583	missense	7007	exon14			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.4858G>A	11.37:g.121031012G>A	ENSP00000376543:p.Gly1620Ser	Somatic		Capture	Illumina HiSeq	Phase_I	120536222	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	G	32	5.155486	0.94686	0.0	1.16E-4	ENSG00000109927	ENST00000392793;ENST00000264037	D;D	0.98732	-5.1;-5.1	4.77	4.77	0.60923	von Willebrand factor, type D domain (3);	0.000000	0.85682	D	0.000000	D	0.99177	0.9715	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99501	1.0953	10	0.87932	D	0	.	17.9956	0.89182	0.0:0.0:1.0:0.0	.	1620	O75443	TECTA_HUMAN	S	1620	ENSP00000376543:G1620S;ENSP00000264037:G1620S	ENSP00000264037:G1620S	G	+	1	0	TECTA	120536222	1.000000	0.71417	0.998000	0.56505	0.896000	0.52359	9.587000	0.98229	2.461000	0.83175	0.655000	0.94253	GGT		0.507	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
SORL1	6653	broad.mit.edu	37	11	121460006	121460006	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:121460006G>A	ENST00000260197.7	+	29	4114	c.3985G>A	c.(3985-3987)Ggt>Agt	p.G1329S	SORL1_ENST00000527934.1_5'Flank|SORL1_ENST00000532694.1_Missense_Mutation_p.G175S|SORL1_ENST00000525532.1_Missense_Mutation_p.G273S|SORL1_ENST00000534286.1_Missense_Mutation_p.G239S	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1329	LDL-receptor class A 7. {ECO:0000255|PROSITE-ProRule:PRU00124}.				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.G1329C(1)|p.G1329S(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)		TGATGAGTTCGGTTTCCAGTG	0.488																																					p.G1329S												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G3985A	11						.						517.0	418.0	451.0					11																	121460006		2203	4299	6502	120965216	SO:0001583	missense	6653	exon29			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.3985G>A	11.37:g.121460006G>A	ENSP00000260197:p.Gly1329Ser	Somatic		Capture	Illumina HiSeq	Phase_I	120965216	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	G	7.508	0.654024	0.14580	.	.	ENSG00000137642	ENST00000260197;ENST00000525532;ENST00000532694;ENST00000534286	D;D;D;D	0.95342	-3.68;-3.68;-3.68;-3.68	5.62	3.52	0.40303	.	0.222050	0.45361	N	0.000361	D	0.83677	0.5306	N	0.12422	0.21	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.71530	-0.4565	10	0.07325	T	0.83	.	5.1397	0.14952	0.691:0.0:0.309:0.0	.	1329	Q92673	SORL_HUMAN	S	1329;273;175;239	ENSP00000260197:G1329S;ENSP00000434634:G273S;ENSP00000432131:G175S;ENSP00000436447:G239S	ENSP00000260197:G1329S	G	+	1	0	SORL1	120965216	1.000000	0.71417	0.884000	0.34674	0.994000	0.84299	5.235000	0.65348	0.581000	0.29539	0.655000	0.94253	GGT		0.488	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105	
MUC5B	727897	broad.mit.edu	37	11	1275426	1275426	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:1275426C>T	ENST00000529681.1	+	34	15380	c.15322C>T	c.(15322-15324)Cgc>Tgc	p.R5108C	MUC5B_ENST00000447027.1_Missense_Mutation_p.R5111C	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5108	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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.R5063C(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)		GATCCATGCACGCTTTGGGAA	0.612																																					p.R5108C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C15322T	11						.						69.0	81.0	77.0					11																	1275426		2159	4275	6434	1232002	SO:0001583	missense	727897	exon34			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.15322C>T	11.37:g.1275426C>T	ENSP00000436812:p.Arg5108Cys	Somatic		Capture	Illumina HiSeq	Phase_I	1232002	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	8.905	0.957362	0.18507	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844	T;T	0.60424	0.19;0.19	4.5	-1.07	0.09968	.	.	.	.	.	T	0.67031	0.2850	M	0.67397	2.05	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.65987	0.94;0.94	T	0.56553	-0.7960	9	0.87932	D	0	.	6.8905	0.24226	0.5006:0.2594:0.24:0.0	.	5443;5111	A7Y9J9;E9PBJ0	.;.	C	5108;5111;5052;7;4820	ENSP00000436812:R5108C;ENSP00000415793:R5111C	ENSP00000343037:R5052C	R	+	1	0	MUC5B	1232002	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.068000	0.11561	0.067000	0.16545	0.400000	0.26472	CGC		0.612	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
HSPA8	3312	broad.mit.edu	37	11	122930692	122930692	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:122930692G>A	ENST00000532636.1	-	5	728	c.609C>T	c.(607-609)ggC>ggT	p.G203G	SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000227378.3_Silent_p.G203G|HSPA8_ENST00000453788.2_Silent_p.G203G|HSPA8_ENST00000533540.1_Intron|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000526110.1_Silent_p.G184G|HSPA8_ENST00000534319.1_5'UTR|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000526862.1_Intron|HSPA8_ENST00000534624.1_Silent_p.G203G			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	203	Interaction with BAG1.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)	p.G203G(1)		breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CATCAAAAGTGCCACCTCCCA	0.408																																					p.G203G	Colon(21;486 594 5900 6733 14272)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C609T	11						.						38.0	40.0	39.0					11																	122930692		2202	4299	6501	122435902	SO:0001819	synonymous_variant	3312	exon5			Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.609C>T	11.37:g.122930692G>A		Somatic		Capture	Illumina HiSeq	Phase_I	122435902	NM_153201	Q9H3R6	Silent	SNP	ENST00000532636.1	37	CCDS8440.1																																																																																				0.408	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1		
OR8B4	283162	broad.mit.edu	37	11	124294278	124294278	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:124294278G>A	ENST00000356130.3	-	1	511	c.490C>T	c.(490-492)Cga>Tga	p.R164*		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	164						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R164*(1)		endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		AAGGTCAGTCGCAGCATGCTT	0.542																																					p.R164X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C490T	11						.						91.0	63.0	73.0					11																	124294278		2201	4299	6500	123799488	SO:0001587	stop_gained	283162	exon1			AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.490C>T	11.37:g.124294278G>A	ENSP00000348449:p.Arg164*	Somatic		Capture	Illumina HiSeq	Phase_I	123799488	NM_001005196	B2RNF8|Q6IFQ7	Nonsense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	.	.	.	.	.	.	.	.	.	.	g	15.83	2.950292	0.53186	.	.	ENSG00000198657	ENST00000356130	.	.	.	4.02	0.253	0.15551	.	0.106321	0.41938	D	0.000795	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.1545	0.20330	0.1504:0.0:0.3179:0.5317	.	.	.	.	X	164	.	ENSP00000348449:R164X	R	-	1	2	OR8B4	123799488	0.000000	0.05858	0.979000	0.43373	0.556000	0.35491	-0.751000	0.04803	0.040000	0.15660	-1.023000	0.02433	CGA		0.542	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
ESAM	90952	broad.mit.edu	37	11	124623827	124623827	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:124623827G>T	ENST00000278927.5	-	7	1017	c.888C>A	c.(886-888)ccC>ccA	p.P296P	VSIG2_ENST00000403470.1_5'Flank|VSIG2_ENST00000326621.5_5'Flank|ESAM_ENST00000442070.2_Intron	NM_138961.2	NP_620411.2	Q96AP7	ESAM_HUMAN	endothelial cell adhesion molecule	296					blood coagulation (GO:0007596)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)|single organismal cell-cell adhesion (GO:0016337)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.P296P(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.022)		TCTTGGGCCAGGGCAGGGTCC	0.592																																					p.P296P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C888A	11						.						54.0	66.0	62.0					11																	124623827		2201	4299	6500	124129037	SO:0001819	synonymous_variant	90952	exon7			AK075396	CCDS8453.1	11q24.2	2013-01-29			ENSG00000149564	ENSG00000149564		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17474	protein-coding gene	gene with protein product		614281				11279107, 11906820	Standard	NM_138961		Approved	W117m	uc001qav.4	Q96AP7	OTTHUMG00000151986	ENST00000278927.5:c.888C>A	11.37:g.124623827G>T		Somatic		Capture	Illumina HiSeq	Phase_I	124129037	NM_138961	B4DVN8|Q96T50	Missense_Mutation	SNP	ENST00000278927.5	37	CCDS8453.1																																																																																				0.592	ESAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324686.1	NM_138961	
ESAM	90952	broad.mit.edu	37	11	124628289	124628289	+	Missense_Mutation	SNP	G	G	A	rs202080091		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:124628289G>A	ENST00000278927.5	-	2	334	c.205C>T	c.(205-207)Ccc>Tcc	p.P69S	RP11-677M14.3_ENST00000504932.2_RNA|ESAM_ENST00000442070.2_Intron	NM_138961.2	NP_620411.2	Q96AP7	ESAM_HUMAN	endothelial cell adhesion molecule	69	Ig-like V-type.				blood coagulation (GO:0007596)|homophilic cell adhesion (GO:0007156)|leukocyte migration (GO:0050900)|single organismal cell-cell adhesion (GO:0016337)	adherens junction (GO:0005912)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.P69S(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.022)		ATCACAAAGGGCACCTCCCAT	0.597											OREG0021463	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P69S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C205T	11						.						97.0	79.0	85.0					11																	124628289		2201	4299	6500	124133499	SO:0001583	missense	90952	exon2			AK075396	CCDS8453.1	11q24.2	2013-01-29			ENSG00000149564	ENSG00000149564		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17474	protein-coding gene	gene with protein product		614281				11279107, 11906820	Standard	NM_138961		Approved	W117m	uc001qav.4	Q96AP7	OTTHUMG00000151986	ENST00000278927.5:c.205C>T	11.37:g.124628289G>A	ENSP00000278927:p.Pro69Ser	Somatic	1535	Capture	Illumina HiSeq	Phase_I	124133499	NM_138961	B4DVN8|Q96T50	Missense_Mutation	SNP	ENST00000278927.5	37	CCDS8453.1	.	.	.	.	.	.	.	.	.	.	G	11.11	1.540988	0.27563	.	.	ENSG00000149564	ENST00000278927	T	0.34275	1.37	4.67	3.77	0.43336	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.552015	0.20403	N	0.093018	T	0.17152	0.0412	N	0.17564	0.495	0.20489	N	0.999898	B;B	0.32467	0.372;0.158	B;B	0.29942	0.109;0.044	T	0.17592	-1.0364	10	0.09338	T	0.73	.	6.5088	0.22210	0.0977:0.183:0.7194:0.0	.	69;69	F8WDW9;Q96AP7	.;ESAM_HUMAN	S	69	ENSP00000278927:P69S	ENSP00000278927:P69S	P	-	1	0	ESAM	124133499	0.258000	0.24033	0.004000	0.12327	0.038000	0.13279	3.233000	0.51311	1.192000	0.43071	0.467000	0.42956	CCC		0.597	ESAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324686.1	NM_138961	
ROBO4	54538	broad.mit.edu	37	11	124763861	124763861	+	Missense_Mutation	SNP	G	G	A	rs201893985		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:124763861G>A	ENST00000306534.3	-	9	1884	c.1399C>T	c.(1399-1401)Cgg>Tgg	p.R467W	ROBO4_ENST00000533054.1_Missense_Mutation_p.R322W|ROBO4_ENST00000526899.1_5'Flank	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	467					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.R467W(1)		NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		ACCTCAGGCCGCTTCAAGGTA	0.647													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19290	0.0		0.0	False		,,,				2504	0.0				p.R467W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1399T	11						.						37.0	35.0	36.0					11																	124763861		2201	4299	6500	124269071	SO:0001583	missense	54538	exon9			AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.1399C>T	11.37:g.124763861G>A	ENSP00000304945:p.Arg467Trp	Somatic		Capture	Illumina HiSeq	Phase_I	124269071	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	37	CCDS8455.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	18.44	3.625347	0.66901	.	.	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.64803	-0.12;0.25	5.31	3.32	0.38043	.	0.000000	0.33401	N	0.004959	T	0.74574	0.3734	M	0.65975	2.015	0.36338	D	0.859267	D;D;D	0.89917	1.0;1.0;1.0	D;P;D	0.91635	0.999;0.897;0.936	T	0.80493	-0.1358	10	0.72032	D	0.01	.	10.7866	0.46409	0.0:0.0:0.6589:0.3411	.	467;357;467	Q8WZ75-2;Q8WZ75-3;Q8WZ75	.;.;ROBO4_HUMAN	W	467;357;322	ENSP00000304945:R467W;ENSP00000437129:R322W	ENSP00000304945:R467W	R	-	1	2	ROBO4	124269071	0.972000	0.33761	0.832000	0.32986	0.675000	0.39556	2.674000	0.46867	1.193000	0.43086	0.655000	0.94253	CGG		0.647	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
CDON	50937	broad.mit.edu	37	11	125888268	125888268	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:125888268A>C	ENST00000392693.3	-	5	724	c.597T>G	c.(595-597)caT>caG	p.H199Q	CDON_ENST00000263577.7_Missense_Mutation_p.H199Q	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	199	Ig-like C2-type 2.				anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.H199Q(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		CTTTTAATTGATGTGTGACAG	0.373																																					p.H199Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T597G	11						.						157.0	139.0	145.0					11																	125888268		2201	4299	6500	125393478	SO:0001583	missense	50937	exon5			AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17104	protein-coding gene	gene with protein product	"""cell adhesion molecule-related/down-regulated by oncogenes"""	608707	"""Cdon homolog (mouse)"""			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.597T>G	11.37:g.125888268A>C	ENSP00000376458:p.His199Gln	Somatic		Capture	Illumina HiSeq	Phase_I	125393478	NM_016952	O14631	Missense_Mutation	SNP	ENST00000392693.3	37	CCDS58192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.07|13.07	2.127916|2.127916	0.37533|0.37533	.|.	.|.	ENSG00000064309|ENSG00000064309	ENST00000392693;ENST00000263577|ENST00000534661	T;T|.	0.75704|.	-0.96;-0.96|.	5.53|5.53	-3.54|-3.54	0.04653|0.04653	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.946947|.	0.08768|.	N|.	0.896671|.	T|T	0.14570|0.14570	0.0352|0.0352	N|N	0.12746|0.12746	0.255|0.255	0.24505|0.24505	N|N	0.994236|0.994236	B;B|.	0.17038|.	0.02;0.009|.	B;B|.	0.17433|.	0.018;0.01|.	T|T	0.26189|0.26189	-1.0110|-1.0110	10|5	0.14252|.	T|.	0.57|.	-0.977|-0.977	2.1373|2.1373	0.03765|0.03765	0.3248:0.2249:0.0678:0.3825|0.3248:0.2249:0.0678:0.3825	.|.	199;199|.	Q4KMG0;Q4KMG0-2|.	CDON_HUMAN;.|.	Q|A	199|175	ENSP00000376458:H199Q;ENSP00000263577:H199Q|.	ENSP00000263577:H199Q|.	H|S	-|-	3|1	2|0	CDON|CDON	125393478|125393478	0.105000|0.105000	0.21958|0.21958	0.865000|0.865000	0.33974|0.33974	0.990000|0.990000	0.78478|0.78478	-0.317000|-0.317000	0.08060|0.08060	-0.350000|-0.350000	0.08262|0.08262	0.402000|0.402000	0.26972|0.26972	CAT|TCA		0.373	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
CDON	50937	broad.mit.edu	37	11	125891225	125891225	+	Silent	SNP	G	G	T	rs143462907		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:125891225G>T	ENST00000392693.3	-	3	394	c.267C>A	c.(265-267)tcC>tcA	p.S89S	CDON_ENST00000263577.7_Silent_p.S89S	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	89	Ig-like C2-type 1.				anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S89S(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		CCAAAAGAGAGGAGTTGAGAG	0.463																																					p.S89S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C267A	11						.						81.0	79.0	80.0					11																	125891225		2201	4299	6500	125396435	SO:0001819	synonymous_variant	50937	exon3			AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17104	protein-coding gene	gene with protein product	"""cell adhesion molecule-related/down-regulated by oncogenes"""	608707	"""Cdon homolog (mouse)"""			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.267C>A	11.37:g.125891225G>T		Somatic		Capture	Illumina HiSeq	Phase_I	125396435	NM_016952	O14631	Silent	SNP	ENST00000392693.3	37	CCDS58192.1	.	.	.	.	.	.	.	.	.	.	G	0.057	-1.232630	0.01505	.	.	ENSG00000064309	ENST00000534661	.	.	.	5.4	-0.209	0.13180	.	.	.	.	.	T	0.20820	0.0501	.	.	.	0.21782	N	0.999543	.	.	.	.	.	.	T	0.23762	-1.0179	4	.	.	.	-5.3616	1.9075	0.03280	0.3946:0.1807:0.3146:0.1101	.	.	.	.	I	65	.	.	L	-	1	0	CDON	125396435	0.035000	0.19736	0.920000	0.36463	0.006000	0.05464	-0.430000	0.06973	0.251000	0.21505	-0.269000	0.10298	CTC		0.463	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
DCPS	28960	broad.mit.edu	37	11	126201357	126201357	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:126201357G>A	ENST00000263579.4	+	3	763	c.434G>A	c.(433-435)cGc>cAc	p.R145H	DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	145					cellular response to menadione (GO:0036245)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA metabolic process (GO:0016071)|negative regulation of programmed cell death (GO:0043069)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	m7G(5')pppN diphosphatase activity (GO:0050072)|RNA 7-methylguanosine cap binding (GO:0000340)	p.R145H(1)		endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		AAGTACCTGCGCCAGGACCTC	0.557																																					p.R145H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G434A	11						.						129.0	122.0	124.0					11																	126201357		2201	4298	6499	125706567	SO:0001583	missense	28960	exon3			AF077201	CCDS8473.1	11q24	2008-02-05			ENSG00000110063	ENSG00000110063			29812	protein-coding gene	gene with protein product		610534				12198172, 14523240	Standard	NM_014026		Approved	HSPC015, HINT-5, HSL1	uc001qdp.3	Q96C86	OTTHUMG00000165829	ENST00000263579.4:c.434G>A	11.37:g.126201357G>A	ENSP00000263579:p.Arg145His	Somatic		Capture	Illumina HiSeq	Phase_I	125706567	NM_014026	Q8NHL8|Q9Y2S5	Missense_Mutation	SNP	ENST00000263579.4	37	CCDS8473.1	.	.	.	.	.	.	.	.	.	.	G	13.19	2.164179	0.38217	.	.	ENSG00000110063	ENST00000263579	T	0.43688	0.94	5.84	3.99	0.46301	Scavenger mRNA decapping enzyme, N-terminal (1);	0.160576	0.64402	N	0.000016	T	0.25938	0.0632	N	0.17901	0.54	0.45403	D	0.998389	B	0.06786	0.001	B	0.04013	0.001	T	0.04870	-1.0921	10	0.44086	T	0.13	-14.2084	7.673	0.28470	0.3127:0.0:0.6873:0.0	.	145	Q96C86	DCPS_HUMAN	H	145	ENSP00000263579:R145H	ENSP00000263579:R145H	R	+	2	0	DCPS	125706567	0.970000	0.33590	1.000000	0.80357	0.987000	0.75469	1.377000	0.34317	0.831000	0.34780	0.655000	0.94253	CGC		0.557	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	
KIRREL3	84623	broad.mit.edu	37	11	126295613	126295613	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:126295613G>A	ENST00000525144.2	-	16	2062	c.1813C>T	c.(1813-1815)Cgg>Tgg	p.R605W	KIRREL3_ENST00000529097.2_Missense_Mutation_p.R593W|KIRREL3_ENST00000416561.2_Missense_Mutation_p.R72W	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	605					hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R564W(1)		central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		AATTCACCCCGGTCCATCTGC	0.493																																					p.R605W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1813T	11						.						42.0	41.0	41.0					11																	126295613		1868	4093	5961	125800823	SO:0001583	missense	84623	exon16			AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.1813C>T	11.37:g.126295613G>A	ENSP00000435466:p.Arg605Trp	Somatic		Capture	Illumina HiSeq	Phase_I	125800823	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Missense_Mutation	SNP	ENST00000525144.2	37	CCDS53723.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.030438	0.75504	.	.	ENSG00000149571	ENST00000525144;ENST00000529097;ENST00000416561	T;T;T	0.77877	-0.65;-0.43;-1.13	5.54	4.6	0.57074	.	0.066514	0.64402	D	0.000010	T	0.79604	0.4474	N	0.22421	0.69	0.46028	D	0.998822	D;D	0.89917	1.0;1.0	D;D	0.74023	0.982;0.982	T	0.81625	-0.0848	10	0.72032	D	0.01	-13.8021	13.3148	0.60401	0.0:0.0:0.6129:0.3871	.	593;605	E9PRX9;Q8IZU9	.;KIRR3_HUMAN	W	605;593;72	ENSP00000435466:R605W;ENSP00000434081:R593W;ENSP00000408692:R72W	ENSP00000408692:R72W	R	-	1	2	KIRREL3	125800823	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.485000	0.53208	2.607000	0.88179	0.650000	0.86243	CGG		0.493	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531	
NFRKB	4798	broad.mit.edu	37	11	129739649	129739649	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:129739649C>T	ENST00000446488.3	-	23	3374	c.3271G>A	c.(3271-3273)Gtg>Atg	p.V1091M	NFRKB_ENST00000524794.1_Missense_Mutation_p.V1116M|NFRKB_ENST00000304521.5_Missense_Mutation_p.V1091M|NFRKB_ENST00000524746.1_Missense_Mutation_p.V1091M	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	1091					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)	p.V1116M(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		AGTCCCTGCACGATGCGGATC	0.587																																					p.V1091M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3271A	11						.						137.0	125.0	129.0					11																	129739649		2201	4297	6498	129244859	SO:0001583	missense	4798	exon24				CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"""INO80 complex subunits"""	7802	protein-coding gene	gene with protein product	"""nuclear factor related to kappa B binding protein"", ""DNA-binding protein R kappa B"", ""INO80 complex subunit G"""	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.3271G>A	11.37:g.129739649C>T	ENSP00000400476:p.Val1091Met	Somatic		Capture	Illumina HiSeq	Phase_I	129244859	NM_001143835	Q12869|Q15312|Q9H048	Missense_Mutation	SNP	ENST00000446488.3	37	CCDS44770.1	.	.	.	.	.	.	.	.	.	.	C	19.16	3.774541	0.70107	.	.	ENSG00000170322	ENST00000304521;ENST00000446488;ENST00000524794;ENST00000524746	.	.	.	5.31	5.31	0.75309	.	0.054811	0.64402	D	0.000001	T	0.46600	0.1401	N	0.19112	0.55	0.52501	D	0.999957	P;D;P	0.55800	0.91;0.973;0.933	B;P;B	0.47075	0.22;0.536;0.439	T	0.41179	-0.9523	9	0.33141	T	0.24	-14.7868	18.9658	0.92695	0.0:1.0:0.0:0.0	.	1091;1090;1116	Q6P4R8;Q6P4R8-3;Q6P4R8-2	NFRKB_HUMAN;.;.	M	1091;1091;1116;1091	.	ENSP00000303800:V1091M	V	-	1	0	NFRKB	129244859	0.996000	0.38824	1.000000	0.80357	0.996000	0.88848	3.242000	0.51384	2.474000	0.83562	0.655000	0.94253	GTG		0.587	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165	
NFRKB	4798	broad.mit.edu	37	11	129747235	129747235	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:129747235C>T	ENST00000446488.3	-	15	1660	c.1557G>A	c.(1555-1557)cgG>cgA	p.R519R	NFRKB_ENST00000524794.1_Silent_p.R544R|NFRKB_ENST00000304521.5_Silent_p.R519R|NFRKB_ENST00000524746.1_Silent_p.R519R	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	519					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)	p.R544R(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		CCTGAAAAACCCGTTTCTCCT	0.512																																					p.R519R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1557A	11						.						223.0	189.0	201.0					11																	129747235		2201	4297	6498	129252445	SO:0001819	synonymous_variant	4798	exon16				CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"""INO80 complex subunits"""	7802	protein-coding gene	gene with protein product	"""nuclear factor related to kappa B binding protein"", ""DNA-binding protein R kappa B"", ""INO80 complex subunit G"""	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.1557G>A	11.37:g.129747235C>T		Somatic		Capture	Illumina HiSeq	Phase_I	129252445	NM_001143835	Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	37	CCDS44770.1																																																																																				0.512	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165	
PRDM10	56980	broad.mit.edu	37	11	129814885	129814885	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:129814885C>T	ENST00000360871.3	-	6	774	c.543G>A	c.(541-543)gcG>gcA	p.A181A	PRDM10_ENST00000304538.6_Silent_p.A95A|PRDM10_ENST00000528746.1_Silent_p.A155A|PRDM10_ENST00000358825.5_Silent_p.A181A|PRDM10_ENST00000423662.2_Silent_p.A95A|PRDM10_ENST00000526082.1_Silent_p.A95A	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	181					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.A181A(1)		breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		CTGAAGCATGCGCGTTATTGC	0.562																																					p.A181A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G543A	11						.						46.0	46.0	46.0					11																	129814885		2201	4297	6498	129320095	SO:0001819	synonymous_variant	56980	exon6			AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"""Zinc fingers, C2H2-type"""	13995	protein-coding gene	gene with protein product	"""PRDM zinc finger transcription factor"", ""PR-domain family member 7"", ""tristanin"""					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.543G>A	11.37:g.129814885C>T		Somatic		Capture	Illumina HiSeq	Phase_I	129320095	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Silent	SNP	ENST00000360871.3	37	CCDS8484.1																																																																																				0.562	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
SNX19	399979	broad.mit.edu	37	11	130748322	130748322	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:130748322A>T	ENST00000265909.4	-	11	3543	c.2974T>A	c.(2974-2976)Tct>Act	p.S992T	SNX19_ENST00000539184.1_Missense_Mutation_p.S435T|SNX19_ENST00000426933.2_Missense_Mutation_p.S160T|SNX19_ENST00000545537.1_Missense_Mutation_p.S232T|SNX19_ENST00000534726.1_Missense_Mutation_p.S232T|SNX19_ENST00000530356.1_Missense_Mutation_p.S372T|SNX19_ENST00000533318.1_5'UTR|SNX19_ENST00000528555.1_Missense_Mutation_p.S372T	NM_014758.2	NP_055573	Q92543	SNX19_HUMAN	sorting nexin 19	992					protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.S992T(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(8)|ovary(3)|prostate(1)|skin(6)|urinary_tract(1)	35	all_hematologic(175;0.0597)	Lung NSC(97;0.000272)|all_lung(97;0.000608)|Breast(109;0.000962)|all_neural(223;0.0298)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;0.0195)|Lung(977;0.233)		ACCAGCTAAGAGGAGACACCC	0.542																																					p.S992T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2974A	11						.						124.0	109.0	114.0					11																	130748322		2201	4297	6498	130253532	SO:0001583	missense	399979	exon11			D87443	CCDS31721.1, CCDS73416.1	11q25	2010-04-20			ENSG00000120451	ENSG00000120451		"""Sorting nexins"""	21532	protein-coding gene	gene with protein product							Standard	NM_014758		Approved	KIAA0254, CHET8	uc001qgk.4	Q92543	OTTHUMG00000165663	ENST00000265909.4:c.2974T>A	11.37:g.130748322A>T	ENSP00000265909:p.Ser992Thr	Somatic		Capture	Illumina HiSeq	Phase_I	130253532	NM_014758	E9PKB9|Q8IV55	Missense_Mutation	SNP	ENST00000265909.4	37	CCDS31721.1	.	.	.	.	.	.	.	.	.	.	A	7.336	0.619891	0.14193	.	.	ENSG00000120451	ENST00000265909;ENST00000534726;ENST00000545537;ENST00000426933;ENST00000528555;ENST00000530356;ENST00000539184	T;T;T;T;T;T;T	0.36699	2.81;1.38;1.38;1.24;1.86;1.86;2.17	5.7	-1.12	0.09808	.	0.836657	0.10415	N	0.677491	T	0.09686	0.0238	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.30268	-0.9984	10	0.08599	T	0.76	.	1.429	0.02329	0.391:0.1963:0.2876:0.1251	.	435;992	F5H5D1;Q92543	.;SNX19_HUMAN	T	992;232;232;160;372;372;435	ENSP00000265909:S992T;ENSP00000433699:S232T;ENSP00000437982:S232T;ENSP00000413345:S160T;ENSP00000435122:S372T;ENSP00000432307:S372T;ENSP00000443480:S435T	ENSP00000265909:S992T	S	-	1	0	SNX19	130253532	0.643000	0.27269	0.003000	0.11579	0.340000	0.28889	-0.026000	0.12392	-0.162000	0.10964	-0.912000	0.02778	TCT		0.542	SNX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385649.1	NM_014758	
NTM	50863	broad.mit.edu	37	11	132016296	132016296	+	Silent	SNP	G	G	A	rs190818488	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:132016296G>A	ENST00000374786.1	+	2	767	c.288G>A	c.(286-288)acG>acA	p.T96T	NTM_ENST00000427481.2_Silent_p.T87T|NTM_ENST00000374784.1_Silent_p.T96T|NTM_ENST00000425719.2_Silent_p.T96T|NTM_ENST00000539799.1_Silent_p.T96T|NTM_ENST00000374791.3_Silent_p.T96T	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	96	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.T96T(2)		breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						ACACCCAAACGCAGTACAGCA	0.577													G|||	7	0.00139776	0.0	0.0072	5008	,	,		19792	0.002		0.0	False		,,,				2504	0.0				p.T96T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G288A	11						.						192.0	133.0	153.0					11																	132016296		2201	4297	6498	131521506	SO:0001819	synonymous_variant	50863	exon2			AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"""Immunoglobulin superfamily / I-set domain containing"""	17941	protein-coding gene	gene with protein product	"""neurotrimin"", ""IgLON family member 2"""	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.288G>A	11.37:g.132016296G>A		Somatic		Capture	Illumina HiSeq	Phase_I	131521506	NM_001144058	A0MTT2|Q6UXJ3|Q86VJ9	Silent	SNP	ENST00000374786.1	37	CCDS8491.1																																																																																				0.577	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522	
IGSF9B	22997	broad.mit.edu	37	11	133801445	133801445	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:133801445A>G	ENST00000321016.8	-	10	1501	c.1271T>C	c.(1270-1272)gTg>gCg	p.V424A	IGSF9B_ENST00000533871.2_Missense_Mutation_p.V424A			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	424	Ig-like 5.				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.V424A(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)		GCCTGGTAGCACCGTGAAATA	0.647																																					p.V424A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1271C	11						.						31.0	37.0	35.0					11																	133801445		1924	4119	6043	133306655	SO:0001583	missense	22997	exon10			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.1271T>C	11.37:g.133801445A>G	ENSP00000317980:p.Val424Ala	Somatic		Capture	Illumina HiSeq	Phase_I	133306655	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	A	27.5	4.840403	0.91117	.	.	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	T;T;T	0.36878	1.23;1.23;1.23	5.21	5.21	0.72293	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.45458	0.1343	L	0.47016	1.485	0.58432	D	0.999998	P	0.36647	0.563	P	0.47786	0.557	T	0.44605	-0.9317	9	0.59425	D	0.04	.	15.0926	0.72207	1.0:0.0:0.0:0.0	.	424	Q9UPX0	TUTLB_HUMAN	A	424;266;424	ENSP00000317980:V424A;ENSP00000436552:V266A;ENSP00000436576:V424A	ENSP00000317980:V424A	V	-	2	0	IGSF9B	133306655	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.328000	0.96403	1.962000	0.57031	0.444000	0.29173	GTG		0.647	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
IGSF9B	22997	broad.mit.edu	37	11	133805549	133805549	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:133805549C>T	ENST00000321016.8	-	7	1160	c.930G>A	c.(928-930)ggG>ggA	p.G310G	IGSF9B_ENST00000533871.2_Silent_p.G310G			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	310	Ig-like 3.				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.G310G(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)		AGGGGGAGCGCCCCAGGCTGT	0.637																																					p.G310G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G930A	11						.						23.0	28.0	27.0					11																	133805549		2009	4163	6172	133310759	SO:0001819	synonymous_variant	22997	exon7			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.930G>A	11.37:g.133805549C>T		Somatic		Capture	Illumina HiSeq	Phase_I	133310759	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																					0.637	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
RIC8A	60626	broad.mit.edu	37	11	205305	205305	+	5'Flank	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:205305C>T	ENST00000526104.1	+	0	0				BET1L_ENST00000529614.2_Silent_p.T92T|BET1L_ENST00000332865.6_3'UTR|RP11-304M2.5_ENST00000526963.1_RNA|BET1L_ENST00000486280.1_Silent_p.T88T|BET1L_ENST00000382762.3_Silent_p.T111T|BET1L_ENST00000410108.1_Intron|BET1L_ENST00000325147.9_3'UTR			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A						adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.T111T(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CACTGGCTCACGTCCTTGCCC	0.557																																					p.T111T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G333A	11						.						40.0	45.0	43.0					11																	205305		2200	4297	6497	195305	SO:0001631	upstream_gene_variant	51272	exon4			AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"""resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"""			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069		11.37:g.205305C>T	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	195305	NM_001098787	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Silent	SNP	ENST00000526104.1	37																																																																																					0.557	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932	
PSMD13	5719	broad.mit.edu	37	11	252542	252542	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:252542C>T	ENST00000532097.1	+	13	1577	c.1073C>T	c.(1072-1074)aCg>aTg	p.T358M	PSMD13_ENST00000431206.2_Missense_Mutation_p.T360M|PSMD13_ENST00000352303.5_Missense_Mutation_p.T331M|PSMD13_ENST00000532025.1_3'UTR	NM_002817.3	NP_002808.3	Q9UNM6	PSD13_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13	358					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)|meiosis I (GO:0007127)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|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.T358M(1)|p.T360M(1)		NS(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	10		all_cancers(49;1.58e-09)|all_epithelial(84;2.71e-06)|Breast(177;0.000162)|Ovarian(85;0.000626)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.79e-27)|Epithelial(43;4e-26)|OV - Ovarian serous cystadenocarcinoma(40;6.02e-21)|BRCA - Breast invasive adenocarcinoma(625;3.93e-05)|Lung(200;0.112)|LUSC - Lung squamous cell carcinoma(625;0.129)		TTCTGGTGCACGGATGTGAAG	0.587																																					p.T358M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1073T	11						.						158.0	142.0	148.0					11																	252542		2203	4300	6503	242542	SO:0001583	missense	5719	exon13			AB009398	CCDS7692.1, CCDS44504.1	11p15.5	2008-05-22			ENSG00000185627	ENSG00000185627		"""Proteasome (prosome, macropain) subunits"""	9558	protein-coding gene	gene with protein product		603481				9714768, 8811196	Standard	NM_002817		Approved	p40.5, Rpn9	uc001loo.2	Q9UNM6	OTTHUMG00000119072	ENST00000532097.1:c.1073C>T	11.37:g.252542C>T	ENSP00000436186:p.Thr358Met	Somatic		Capture	Illumina HiSeq	Phase_I	242542	NM_002817	B3KT15|O75831|Q53XU2|Q9UNV3	Missense_Mutation	SNP	ENST00000532097.1	37	CCDS7692.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.80|16.80	3.223863|3.223863	0.58668|0.58668	.|.	.|.	ENSG00000185627|ENSG00000185627	ENST00000526783|ENST00000532097;ENST00000538343;ENST00000431206;ENST00000352303	.|T;T;T	.|0.18016	.|2.25;2.24;2.25	4.93|4.93	4.02|4.02	0.46733|0.46733	.|.	.|0.210055	.|0.50627	.|D	.|0.000112	T|T	0.17109|0.17109	0.0411|0.0411	N|N	0.19112|0.19112	0.55|0.55	0.38478|0.38478	D|D	0.947644|0.947644	.|D;P;D;D	.|0.63880	.|0.993;0.9;0.965;0.965	.|P;B;P;P	.|0.49708	.|0.62;0.35;0.54;0.54	T|T	0.06570|0.06570	-1.0819|-1.0819	5|10	.|0.49607	.|T	.|0.09	.|.	14.1609|14.1609	0.65446|0.65446	0.0:0.8489:0.1511:0.0|0.0:0.8489:0.1511:0.0	.|.	.|360;293;358;358	.|Q9UNM6-2;B4DJ66;B2RBM7;Q9UNM6	.|.;.;.;PSD13_HUMAN	W|M	203|358;293;360;331	.|ENSP00000436186:T358M;ENSP00000396937:T360M;ENSP00000333811:T331M	.|ENSP00000333811:T331M	R|T	+|+	1|2	2|0	PSMD13|PSMD13	242542|242542	0.971000|0.971000	0.33674|0.33674	0.776000|0.776000	0.31678|0.31678	0.934000|0.934000	0.57294|0.57294	2.070000|2.070000	0.41491|0.41491	1.290000|1.290000	0.44636|0.44636	0.650000|0.650000	0.86243|0.86243	CGG|ACG		0.587	PSMD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239286.2	NM_002817	
CDHR5	53841	broad.mit.edu	37	11	621659	621659	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:621659G>A	ENST00000358353.3	-	6	732	c.410C>T	c.(409-411)aCg>aTg	p.T137M	CDHR5_ENST00000397542.2_Missense_Mutation_p.T137M|CDHR5_ENST00000349570.7_Missense_Mutation_p.T137M|CDHR5_ENST00000529337.1_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	137	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043, ECO:0000305}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)	p.T137M(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						GTTCACTTTCGTGTCCTGGGG	0.627																																					p.T137M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C410T	11						.						114.0	94.0	101.0					11																	621659		2203	4300	6503	611659	SO:0001583	missense	53841	exon5			AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.410C>T	11.37:g.621659G>A	ENSP00000351118:p.Thr137Met	Somatic		Capture	Illumina HiSeq	Phase_I	611659	NM_031264	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Missense_Mutation	SNP	ENST00000358353.3	37	CCDS7707.1	.	.	.	.	.	.	.	.	.	.	g	13.37	2.217232	0.39201	.	.	ENSG00000099834	ENST00000397542;ENST00000358353;ENST00000326366;ENST00000349570;ENST00000526077;ENST00000534311	T;T;T;T;T	0.62498	0.68;0.68;0.66;0.22;0.02	3.91	2.98	0.34508	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.76456	0.3990	M	0.78637	2.42	0.29767	N	0.835105	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.73708	0.981;0.917;0.966;0.917	T	0.70579	-0.4833	9	0.72032	D	0.01	-19.028	9.5994	0.39593	0.0:0.214:0.786:0.0	.	137;137;137;137	Q58EZ6;Q9HBB8-4;Q9HBB8-2;Q9HBB8	.;.;.;CDHR5_HUMAN	M	137;137;137;137;106;114	ENSP00000380676:T137M;ENSP00000351118:T137M;ENSP00000345726:T137M;ENSP00000435082:T106M;ENSP00000436295:T114M	ENSP00000326527:T137M	T	-	2	0	CDHR5	611659	0.995000	0.38212	0.867000	0.34043	0.139000	0.21198	3.210000	0.51129	0.990000	0.38787	0.486000	0.48141	ACG		0.627	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
DEAF1	10522	broad.mit.edu	37	11	678761	678761	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:678761G>A	ENST00000382409.3	-	9	1672	c.1188C>T	c.(1186-1188)ggC>ggT	p.G396G	DEAF1_ENST00000338675.6_Silent_p.G307G|RP11-754B17.1_ENST00000527799.1_RNA|DEAF1_ENST00000525904.1_5'UTR	NM_021008.2	NP_066288.2	O75398	DEAF1_HUMAN	DEAF1 transcription factor	396	Pro-rich.				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.G396G(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)		TGTCCTGATAGCCGGGGTAGT	0.562																																					p.G396G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1188T	11						.						102.0	96.0	98.0					11																	678761		2203	4300	6503	668761	SO:0001819	synonymous_variant	10522	exon9			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.1188C>T	11.37:g.678761G>A		Somatic		Capture	Illumina HiSeq	Phase_I	668761	NM_021008	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Silent	SNP	ENST00000382409.3	37	CCDS31327.1																																																																																				0.562	DEAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383614.3	NM_021008	
CRACR2B	283229	broad.mit.edu	37	11	828870	828870	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:828870C>T	ENST00000525077.1	+	2	285	c.184C>T	c.(184-186)Ccc>Tcc	p.P62S	EFCAB4A_ENST00000450448.1_Missense_Mutation_p.P62S|EFCAB4A_ENST00000528542.2_Missense_Mutation_p.P62S|AP006621.8_ENST00000532946.1_RNA			Q8N4Y2	EFC4A_HUMAN		62					cellular protein localization (GO:0034613)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)	p.P62S(1)		endometrium(1)|large_intestine(1)|lung(1)	3		all_cancers(49;2.31e-08)|all_epithelial(84;3.72e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.179)|all_lung(207;0.227)		all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAGCGACCTGCCCCTCACGCC	0.657																																					p.P62S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C184T	11						.						87.0	98.0	94.0					11																	828870		2096	4211	6307	818870	SO:0001583	missense	283229	exon3																														ENST00000525077.1:c.184C>T	11.37:g.828870C>T	ENSP00000435299:p.Pro62Ser	Somatic		Capture	Illumina HiSeq	Phase_I	818870	NM_173584	D5LPR2|Q8NBW8	Missense_Mutation	SNP	ENST00000525077.1	37		.	.	.	.	.	.	.	.	.	.	C	17.50	3.405259	0.62288	.	.	ENSG00000177685	ENST00000533803;ENST00000527089;ENST00000528542;ENST00000450448;ENST00000321883;ENST00000525077	T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06	4.49	4.49	0.54785	EF-hand-like domain (1);	0.068332	0.64402	U	0.000013	T	0.58250	0.2109	M	0.71871	2.18	0.54753	D	0.999986	P;D;P	0.57899	0.695;0.981;0.9	B;P;P	0.57371	0.133;0.819;0.553	T	0.64850	-0.6310	10	0.87932	D	0	.	14.6988	0.69142	0.0:1.0:0.0:0.0	.	62;62;62	E7EWX3;Q8N4Y2-3;Q8N4Y2	.;.;EFC4A_HUMAN	S	62	ENSP00000433602:P62S;ENSP00000432726:P62S;ENSP00000432334:P62S;ENSP00000409256:P62S;ENSP00000435299:P62S	ENSP00000324024:P62S	P	+	1	0	EFCAB4A	818870	0.996000	0.38824	0.089000	0.20774	0.047000	0.14425	4.671000	0.61590	2.057000	0.61298	0.491000	0.48974	CCC		0.657	EFCAB4A-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000383097.1		
CHID1	66005	broad.mit.edu	37	11	883170	883170	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:883170G>A	ENST00000449825.1	-	10	1293	c.937C>T	c.(937-939)Cgt>Tgt	p.R313C	CHID1_ENST00000323541.7_Missense_Mutation_p.R343C|CHID1_ENST00000323578.8_Missense_Mutation_p.R313C|CHID1_ENST00000528581.1_Missense_Mutation_p.R338C|CHID1_ENST00000436108.2_Missense_Mutation_p.R313C|CHID1_ENST00000336845.5_Missense_Mutation_p.R338C|CHID1_ENST00000429789.2_Missense_Mutation_p.R282C|CHID1_ENST00000526714.1_5'UTR|CHID1_ENST00000454838.2_Missense_Mutation_p.R338C	NM_001142675.1	NP_001136147.1	Q9BWS9	CHID1_HUMAN	chitinase domain containing 1	313					carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|innate immune response (GO:0045087)|negative regulation of cytokine production involved in inflammatory response (GO:1900016)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	chitinase activity (GO:0004568)|oligosaccharide binding (GO:0070492)	p.R313C(1)		endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	13		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.48e-25)|Epithelial(43;3.75e-24)|BRCA - Breast invasive adenocarcinoma(625;4.65e-05)|Lung(200;0.0624)|LUSC - Lung squamous cell carcinoma(625;0.0735)		ACAGGCTCACGGGCATCCTTG	0.612																																					p.R338C	Pancreas(117;992 2327 5172 41921)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1012T	11						.						107.0	100.0	103.0					11																	883170		2203	4299	6502	873170	SO:0001583	missense	66005	exon11			AK124697	CCDS7722.1, CCDS44510.1, CCDS44511.1	11p15.5	2005-10-27			ENSG00000177830	ENSG00000177830			28474	protein-coding gene	gene with protein product		615692					Standard	NM_023947		Approved	MGC3234, FLJ42707	uc001lsm.3	Q9BWS9	OTTHUMG00000133314	ENST00000449825.1:c.937C>T	11.37:g.883170G>A	ENSP00000391255:p.Arg313Cys	Somatic		Capture	Illumina HiSeq	Phase_I	873170	NM_001142676	B3KWB0|Q8NBM9|Q96CZ3|Q96S93|Q96SK0|Q9BY52	Missense_Mutation	SNP	ENST00000449825.1	37	CCDS7722.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.54|10.54	1.378494|1.378494	0.24944|0.24944	.|.	.|.	ENSG00000177830|ENSG00000177830	ENST00000529539|ENST00000323541;ENST00000449825;ENST00000454838;ENST00000323578;ENST00000429789;ENST00000528581;ENST00000336845;ENST00000436108;ENST00000531859	.|T;T;T;T;T;T;T;T	.|0.42900	.|0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96	4.45|4.45	1.24|1.24	0.21308|0.21308	.|Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, superfamily (1);	.|0.193205	.|0.34828	.|N	.|0.003649	T|T	0.40347|0.40347	0.1113|0.1113	L|L	0.29908|0.29908	0.895|0.895	0.42116|0.42116	D|D	0.991409|0.991409	.|D;D;D;D;D	.|0.67145	.|0.994;0.979;0.996;0.985;0.994	.|P;P;P;P;P	.|0.61275	.|0.458;0.84;0.729;0.649;0.886	T|T	0.32955|0.32955	-0.9887|-0.9887	5|10	.|0.66056	.|D	.|0.02	-12.1973|-12.1973	3.7016|3.7016	0.08384|0.08384	0.096:0.4013:0.3448:0.1578|0.096:0.4013:0.3448:0.1578	.|.	.|374;343;282;338;313	.|B4DN31;B7Z705;Q9BWS9-3;Q9BWS9-2;Q9BWS9	.|.;.;.;.;CHID1_HUMAN	L|C	27|343;313;338;313;282;338;338;313;217	.|ENSP00000324821:R343C;ENSP00000391255:R313C;ENSP00000398722:R338C;ENSP00000325055:R313C;ENSP00000416034:R282C;ENSP00000435503:R338C;ENSP00000338838:R338C;ENSP00000388156:R313C	.|ENSP00000324821:R343C	P|R	-|-	2|1	0|0	CHID1|CHID1	873170|873170	0.744000|0.744000	0.28250|0.28250	0.494000|0.494000	0.27515|0.27515	0.001000|0.001000	0.01503|0.01503	2.147000|2.147000	0.42226|0.42226	0.515000|0.515000	0.28320|0.28320	-1.129000|-1.129000	0.01985|0.01985	CCG|CGT		0.612	CHID1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257112.1	NM_023947	
AP2A2	161	broad.mit.edu	37	11	988562	988562	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:988562A>G	ENST00000448903.2	+	10	1283	c.1142A>G	c.(1141-1143)gAc>gGc	p.D381G	AP2A2_ENST00000534328.1_Intron|AP2A2_ENST00000332231.5_Missense_Mutation_p.D382G	NM_001242837.1|NM_012305.3	NP_001229766.1|NP_036437.1	O94973	AP2A2_HUMAN	adaptor-related protein complex 2, alpha 2 subunit	381					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)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|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)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)	p.D382G(1)		breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)	21		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.75e-24)|BRCA - Breast invasive adenocarcinoma(625;5.73e-05)|Lung(200;0.0696)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACTGAGCGGGACGTGAGCGTG	0.642																																					p.D381G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1142G	11						.						113.0	125.0	121.0					11																	988562		2181	4277	6458	978562	SO:0001583	missense	161	exon10			AB020706	CCDS44512.1, CCDS73234.1	11p15.5	2008-07-18			ENSG00000183020	ENSG00000183020			562	protein-coding gene	gene with protein product	"""alpha-adaptin C; Huntingtin interacting protein J"", ""adaptin, alpha B"", ""clathrin-associated/assembly/adaptor protein, large, alpha 2"""	607242		CLAPA2, ADTAB		9700202, 2564002	Standard	NM_012305		Approved	DKFZP564D1864, HYPJ, KIAA0899, HIP9	uc001lst.2	O94973	OTTHUMG00000165627	ENST00000448903.2:c.1142A>G	11.37:g.988562A>G	ENSP00000413234:p.Asp381Gly	Somatic		Capture	Illumina HiSeq	Phase_I	978562	NM_012305	O75403|Q53ET1|Q96SI8	Missense_Mutation	SNP	ENST00000448903.2	37	CCDS44512.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.510014	0.85282	.	.	ENSG00000183020	ENST00000448903;ENST00000332231;ENST00000448757;ENST00000529125;ENST00000452310;ENST00000329626	T;T	0.38722	1.12;1.12	3.81	3.81	0.43845	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.108809	0.64402	D	0.000012	T	0.73016	0.3533	H	0.95645	3.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.82018	-0.0665	10	0.87932	D	0	-6.7936	13.2616	0.60108	1.0:0.0:0.0:0.0	.	382;381	O94973-2;O94973	.;AP2A2_HUMAN	G	381;382;382;118;121;254	ENSP00000413234:D381G;ENSP00000327694:D382G	ENSP00000328024:D254G	D	+	2	0	AP2A2	978562	1.000000	0.71417	0.998000	0.56505	0.943000	0.58893	8.836000	0.92105	1.688000	0.51068	0.454000	0.30748	GAC		0.642	AP2A2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385431.2	NM_012305	
CTSD	1509	broad.mit.edu	37	11	1782667	1782667	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:1782667G>A	ENST00000236671.2	-	2	232	c.100C>T	c.(100-102)Cgg>Tgg	p.R34W	AC068580.1_ENST00000580120.1_RNA|RP11-295K3.1_ENST00000427721.1_5'Flank|AC068580.5_ENST00000446489.1_RNA|AC068580.6_ENST00000449248.1_RNA	NM_001909.4	NP_001900.1	P07339	CATD_HUMAN	cathepsin D	34					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|autophagic vacuole assembly (GO:0000045)|cell death (GO:0008219)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	aspartic-type endopeptidase activity (GO:0004190)	p.R34W(1)		endometrium(1)|large_intestine(4)|lung(8)	13		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	GACATGGTCCGGCGGATGGAC	0.662																																					p.R34W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C100T	11						.						49.0	48.0	48.0					11																	1782667		2202	4299	6501	1739243	SO:0001583	missense	1509	exon2			M11233	CCDS7725.1	11p15.5	2009-06-26	2006-12-05		ENSG00000117984	ENSG00000117984	3.4.23.5	"""Cathepsins"""	2529	protein-coding gene	gene with protein product	"""ceroid-lipofuscinosis, neuronal 10"""	116840	"""cathepsin D (lysosomal aspartyl protease)"""	CPSD		3927292	Standard	NM_001909		Approved	CLN10	uc001luc.2	P07339	OTTHUMG00000044760	ENST00000236671.2:c.100C>T	11.37:g.1782667G>A	ENSP00000236671:p.Arg34Trp	Somatic		Capture	Illumina HiSeq	Phase_I	1739243	NM_001909	Q6IB57	Missense_Mutation	SNP	ENST00000236671.2	37	CCDS7725.1	.	.	.	.	.	.	.	.	.	.	g	16.55	3.154702	0.57259	.	.	ENSG00000117984	ENST00000236671;ENST00000438213	T;T	0.50813	0.73;0.73	3.82	2.89	0.33648	Peptidase aspartic (1);Propeptide, peptidase A1 (1);	0.086407	0.49305	D	0.000151	T	0.64114	0.2569	M	0.65498	2.005	0.43777	D	0.996303	D	0.89917	1.0	D	0.77004	0.989	T	0.67577	-0.5635	10	0.87932	D	0	.	12.3076	0.54910	0.0:0.1724:0.8276:0.0	.	34	P07339	CATD_HUMAN	W	34;19	ENSP00000236671:R34W;ENSP00000415036:R19W	ENSP00000236671:R34W	R	-	1	2	CTSD	1739243	0.801000	0.28930	0.260000	0.24451	0.216000	0.24613	4.016000	0.57159	0.940000	0.37473	0.561000	0.74099	CGG		0.662	CTSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104272.5	NM_001909	
KCNQ1	3784	broad.mit.edu	37	11	2592622	2592622	+	Silent	SNP	G	G	A	rs550887954		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:2592622G>A	ENST00000155840.5	+	4	780	c.672G>A	c.(670-672)acG>acA	p.T224T	KCNQ1_ENST00000335475.5_Silent_p.T97T	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	224					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|cardiovascular system development (GO:0072358)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|gene silencing (GO:0016458)|male gonad development (GO:0008584)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of insulin secretion (GO:0046676)|positive regulation of gastric acid secretion (GO:0060454)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	basolateral plasma membrane (GO:0016323)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)|zymogen granule membrane (GO:0042589)	calmodulin binding (GO:0005516)|delayed rectifier potassium channel activity (GO:0005251)|ion channel binding (GO:0044325)|outward rectifier potassium channel activity (GO:0015271)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|protein phosphatase 1 binding (GO:0008157)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)	p.T224T(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)	21		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	TGTTTGCCACGTCGGCCATCA	0.677													G|||	1	0.000199681	0.0	0.0	5008	,	,		12711	0.0		0.0	False		,,,				2504	0.001				p.T97T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G291A	11						.						125.0	100.0	109.0					11																	2592622		2201	4299	6500	2549198	SO:0001819	synonymous_variant	3784	exon4			AF000571	CCDS7736.1	11p15.5	2014-09-17			ENSG00000053918	ENSG00000053918		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6294	protein-coding gene	gene with protein product	"""Jervell and Lange-Nielsen syndrome 1"""	607542		LQT, KCNA9		8528244, 16382104	Standard	NM_181798		Approved	Kv7.1, KCNA8, KVLQT1, JLNS1, LQT1	uc001lwn.3	P51787	OTTHUMG00000009900	ENST00000155840.5:c.672G>A	11.37:g.2592622G>A		Somatic		Capture	Illumina HiSeq	Phase_I	2549198	NM_181798	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	37	CCDS7736.1																																																																																				0.677	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218	
CARS	833	broad.mit.edu	37	11	3039945	3039945	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:3039945A>C	ENST00000397111.5	-	12	1426	c.1181T>G	c.(1180-1182)tTc>tGc	p.F394C	CARS_ENST00000401769.3_Missense_Mutation_p.F407C|CARS_ENST00000278224.9_Missense_Mutation_p.F394C|CARS_ENST00000380525.4_Missense_Mutation_p.F477C|CARS_ENST00000397114.3_Missense_Mutation_p.F384C			P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase	394					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)	p.F394C(1)	CARS/ALK(5)	central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)	31		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;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	TGTGTGCAGGAAGTACCTGAC	0.483			T	ALK	ALCL																																p.F477C	Ovarian(61;932 1157 5961 20446 52152)		Dom	yes		11	11p15.5	833	cysteinyl-tRNA synthetase		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1430G	11						.						133.0	130.0	131.0					11																	3039945		2202	4298	6500	2996521	SO:0001583	missense	833	exon13			AF288207	CCDS7742.1, CCDS41600.1, CCDS41602.1	11p15.5	2011-07-01			ENSG00000110619	ENSG00000110619	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	1493	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 1, cytoplasmic"""	123859				8468064	Standard	NM_139273		Approved	CARS1	uc001lxf.3	P49589	OTTHUMG00000010927	ENST00000397111.5:c.1181T>G	11.37:g.3039945A>C	ENSP00000380300:p.Phe394Cys	Somatic		Capture	Illumina HiSeq	Phase_I	2996521	NM_001014437	Q53XI8|Q5HYE4|Q9HD24|Q9HD25	Missense_Mutation	SNP	ENST00000397111.5	37	CCDS7742.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.130905	0.77549	.	.	ENSG00000110619	ENST00000380525;ENST00000397111;ENST00000278224;ENST00000397114;ENST00000401769	T;T;T;T;T	0.58358	0.34;0.35;0.35;0.35;0.34	4.95	4.95	0.65309	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.81903	0.4921	H	0.97214	3.96	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;1.0;1.0	D	0.88532	0.3103	10	0.87932	D	0	-35.9574	14.6234	0.68602	1.0:0.0:0.0:0.0	.	407;477;394;394;477;384	B4DKY1;B4DPV7;P49589;P49589-2;Q5HYE4;A8MVQ3	.;.;SYCC_HUMAN;.;.;.	C	477;394;394;384;407	ENSP00000369897:F477C;ENSP00000380300:F394C;ENSP00000278224:F394C;ENSP00000380303:F384C;ENSP00000384069:F407C	ENSP00000278224:F394C	F	-	2	0	CARS	2996521	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	8.757000	0.91657	1.860000	0.53959	0.482000	0.46254	TTC		0.483	CARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030117.4	NM_001751	
ART5	116969	broad.mit.edu	37	11	3661465	3661465	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:3661465C>T	ENST00000397068.3	-	2	586	c.194G>A	c.(193-195)cGg>cAg	p.R65Q	ART5_ENST00000359918.4_Missense_Mutation_p.R65Q|ART5_ENST00000397067.3_Missense_Mutation_p.R65Q|TRPC2_ENST00000526541.1_RNA	NM_053017.3	NP_443750.2	Q96L15	NAR5_HUMAN	ADP-ribosyltransferase 5	65					protein ADP-ribosylation (GO:0006471)	extracellular region (GO:0005576)|membrane (GO:0016020)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ nucleosidase activity (GO:0003953)	p.R65Q(1)		breast(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)	11		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0336)|LUSC - Lung squamous cell carcinoma(625;0.19)		CCAGGATTCCCGCAGCAGGGC	0.587																																					p.R65Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G194A	11						.						46.0	44.0	45.0					11																	3661465		2201	4298	6499	3618041	SO:0001583	missense	116969	exon2			Y16835	CCDS7743.1, CCDS73242.1	11p15.4	2008-02-05			ENSG00000167311	ENSG00000167311			24049	protein-coding gene	gene with protein product		610625				11587854, 10448534	Standard	NM_001079536		Approved		uc001lyb.1	Q96L15	OTTHUMG00000011842	ENST00000397068.3:c.194G>A	11.37:g.3661465C>T	ENSP00000380258:p.Arg65Gln	Somatic		Capture	Illumina HiSeq	Phase_I	3618041	NM_053017	C9IYG7|Q6UX84|Q86W02	Missense_Mutation	SNP	ENST00000397068.3	37	CCDS7743.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.894611	0.52121	.	.	ENSG00000167311	ENST00000397068;ENST00000397067;ENST00000359918;ENST00000425767	T;T;T;T	0.08720	3.06;3.06;3.06;3.06	6.07	3.22	0.36961	.	0.402189	0.25671	N	0.029075	T	0.07863	0.0197	M	0.64170	1.965	0.27245	N	0.959058	P;B	0.38992	0.653;0.426	B;B	0.31751	0.115;0.135	T	0.22243	-1.0222	10	0.17369	T	0.5	-16.4754	9.373	0.38266	0.0:0.7696:0.0:0.2304	.	65;65	Q96L15-2;Q96L15	.;NAR5_HUMAN	Q	65;65;65;44	ENSP00000380258:R65Q;ENSP00000380257:R65Q;ENSP00000352992:R65Q;ENSP00000413852:R44Q	ENSP00000352992:R65Q	R	-	2	0	ART5	3618041	0.000000	0.05858	1.000000	0.80357	0.995000	0.86356	0.079000	0.14782	0.902000	0.36520	0.655000	0.94253	CGG		0.587	ART5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032760.2	NM_053017	
OR52I1	390037	broad.mit.edu	37	11	4615415	4615415	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:4615415C>T	ENST00000530443.2	+	1	147	c.147C>T	c.(145-147)atC>atT	p.I49I	OR52I1_ENST00000450052.2_Silent_p.I73I	NM_001005169.1	NP_001005169.1	Q8NGK6	O52I1_HUMAN	olfactory receptor, family 52, subfamily I, member 1	49						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I74I(1)		central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	15		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;7.98e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACACCCTCATCGTGACTGCAA	0.512																																					p.I49I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C147T	11						.						181.0	142.0	155.0					11																	4615415		2201	4298	6499	4571991	SO:0001819	synonymous_variant	390037	exon1			BK004371	CCDS59223.1	11p15.4	2012-08-09				ENSG00000232268		"""GPCR / Class A : Olfactory receptors"""	15220	protein-coding gene	gene with protein product							Standard	NM_001005169		Approved		uc010qyi.2	Q8NGK6		ENST00000530443.2:c.147C>T	11.37:g.4615415C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4571991	NM_001005169	Q6IF91	Silent	SNP	ENST00000530443.2	37	CCDS59223.1																																																																																				0.512	OR52I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385947.2	NM_001005169	
OR51A4	401666	broad.mit.edu	37	11	4968047	4968047	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:4968047G>A	ENST00000380373.2	-	1	309	c.284C>T	c.(283-285)tCa>tTa	p.S95L	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005329.1	NP_001005329.1	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A, member 4	95						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S95L(1)		large_intestine(3)|lung(15)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGCATTGGATGAAATTTCAGG	0.423																																					p.S95L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C284T	11						.						191.0	178.0	182.0					11																	4968047		2152	4245	6397	4924623	SO:0001583	missense	401666	exon1			AB065798	CCDS31367.1	11p15.4	2012-08-09			ENSG00000205497	ENSG00000205497		"""GPCR / Class A : Olfactory receptors"""	14795	protein-coding gene	gene with protein product							Standard	NM_001005329		Approved		uc010qys.2	Q8NGJ6	OTTHUMG00000066614	ENST00000380373.2:c.284C>T	11.37:g.4968047G>A	ENSP00000369731:p.Ser95Leu	Somatic		Capture	Illumina HiSeq	Phase_I	4924623	NM_001005329		Missense_Mutation	SNP	ENST00000380373.2	37	CCDS31367.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.945588	0.53079	.	.	ENSG00000205497	ENST00000380373	T	0.44881	0.91	3.58	3.58	0.41010	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.71074	0.3297	H	0.96365	3.81	0.19775	N	0.999951	D	0.63046	0.992	P	0.62560	0.904	T	0.64867	-0.6306	9	0.62326	D	0.03	.	11.2818	0.49199	0.0:0.1868:0.8132:0.0	.	95	Q8NGJ6	O51A4_HUMAN	L	95	ENSP00000369731:S95L	ENSP00000369731:S95L	S	-	2	0	OR51A4	4924623	0.000000	0.05858	0.610000	0.28997	0.767000	0.43475	0.047000	0.14056	2.000000	0.58554	0.580000	0.79431	TCA		0.423	OR51A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142821.1	NM_001005329	
HBG2	3048	broad.mit.edu	37	11	5275632	5275632	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:5275632G>A	ENST00000380259.2	-	7	1445	c.205C>T	c.(205-207)Ctg>Ttg	p.L69L	HBG2_ENST00000380252.1_Silent_p.L59L|HBG2_ENST00000336906.4_Silent_p.L69L			P69892	HBG2_HUMAN	hemoglobin, gamma G	69					blood coagulation (GO:0007596)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)	p.L69L(1)		endometrium(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	13		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAGGAAGTCAGCACCTTCTTG	0.537																																					p.L69L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C205T	11						.						288.0	223.0	245.0					11																	5275632		2201	4298	6499	5232208	SO:0001819	synonymous_variant	3048	exon2			BC029387	CCDS7755.1	11p15.5	2014-05-19			ENSG00000196565	ENSG00000196565			4832	protein-coding gene	gene with protein product		142250				2649166	Standard	NM_000184		Approved	HBG-T1		P69892	OTTHUMG00000066673	ENST00000380259.2:c.205C>T	11.37:g.5275632G>A		Somatic		Capture	Illumina HiSeq	Phase_I	5232208	NM_000184	A8MZE0|P02096|P62027|Q14491|Q68NH9|Q96FH6|Q96FH7	Silent	SNP	ENST00000380259.2	37	CCDS7755.1																																																																																				0.537	HBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142967.2	NM_000184	
OR52D1	390066	broad.mit.edu	37	11	5510828	5510828	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:5510828G>C	ENST00000322641.5	+	1	914	c.892G>C	c.(892-894)Gct>Cct	p.A298P	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	298					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.A298P(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCTCTATGGAGCTAGAACCAA	0.458																																					p.A298P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G892C	11						.						82.0	76.0	78.0					11																	5510828		2201	4297	6498	5467404	SO:0001583	missense	390066	exon1			BK004276	CCDS31384.1	11p15.4	2012-08-09			ENSG00000181609	ENSG00000181609		"""GPCR / Class A : Olfactory receptors"""	15212	protein-coding gene	gene with protein product							Standard	NM_001005163		Approved		uc010qzg.2	Q9H346	OTTHUMG00000066895	ENST00000322641.5:c.892G>C	11.37:g.5510828G>C	ENSP00000326232:p.Ala298Pro	Somatic		Capture	Illumina HiSeq	Phase_I	5467404	NM_001005163	B9EGY9|Q6IFI6	Missense_Mutation	SNP	ENST00000322641.5	37	CCDS31384.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.597537	0.46318	.	.	ENSG00000181609	ENST00000322641	T	0.37915	1.17	5.58	4.67	0.58626	.	0.224144	0.33496	N	0.004854	T	0.46073	0.1374	M	0.79123	2.44	0.09310	N	1	D	0.58970	0.984	P	0.50490	0.642	T	0.50406	-0.8832	10	0.87932	D	0	.	7.3343	0.26601	0.2405:0.0:0.7595:0.0	.	298	Q9H346	O52D1_HUMAN	P	298	ENSP00000326232:A298P	ENSP00000326232:A298P	A	+	1	0	OR52D1	5467404	0.001000	0.12720	0.016000	0.15963	0.760000	0.43138	-0.115000	0.10741	1.597000	0.50072	0.655000	0.94253	GCT		0.458	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163	
TRIM6	117854	broad.mit.edu	37	11	5631436	5631436	+	Nonsense_Mutation	SNP	C	C	T	rs138262721		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:5631436C>T	ENST00000278302.5	+	6	975	c.835C>T	c.(835-837)Cga>Tga	p.R279*	TRIM6_ENST00000380107.1_Nonsense_Mutation_p.R253*|TRIM6-TRIM34_ENST00000354852.5_Nonsense_Mutation_p.R307*|AC015691.13_ENST00000394793.2_RNA|TRIM6_ENST00000380097.3_Nonsense_Mutation_p.R307*|TRIM6_ENST00000515022.1_Nonsense_Mutation_p.R104*|TRIM6_ENST00000481603.1_3'UTR|HBG2_ENST00000380259.2_Intron|TRIM6_ENST00000507320.1_Nonsense_Mutation_p.R104*|TRIM6_ENST00000506134.1_Nonsense_Mutation_p.R104*|TRIM6_ENST00000445329.1_Nonsense_Mutation_p.R104*	NM_001198645.1|NM_058166.4	NP_001185574.1|NP_477514.1	Q9C030	TRIM6_HUMAN	tripartite motif containing 6	279					protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)	p.R307*(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(5)|prostate(2)|stomach(1)	22		Lung NSC(207;2.23e-07)|all_lung(207;1.81e-06)|Medulloblastoma(188;0.00225)|Breast(177;0.0101)|all_neural(188;0.0212)		Epithelial(150;1.12e-45)|BRCA - Breast invasive adenocarcinoma(625;0.00101)|LUSC - Lung squamous cell carcinoma(625;0.192)		AAGTATGTTCCGAGCCCCAGA	0.488																																					p.R307X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C919T	11						.	C	stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG	1,4401	2.1+/-5.4	0,1,2200	105.0	107.0	106.0		919,919,310,310,835	4.2	1.0	11	dbSNP_134	106	0,8594		0,0,4297	no	stop-gained,stop-gained,stop-gained,stop-gained,stop-gained	TRIM6,TRIM6-TRIM34	NM_001003818.2,NM_001003819.3,NM_001198644.1,NM_001198645.1,NM_058166.4	,,,,	0,1,6497	TT,TC,CC		0.0,0.0227,0.0077	,,,,	307/517,307/843,104/314,104/314,279/489	5631436	1,12995	2201	4297	6498	5588012	SO:0001587	stop_gained	445372	exon6			AF220030	CCDS31389.1, CCDS31390.1, CCDS55738.1	11p15	2013-01-09	2011-01-25		ENSG00000121236	ENSG00000121236		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16277	protein-coding gene	gene with protein product		607564	"""tripartite motif-containing 6"""			11331580	Standard	NM_058166		Approved	RNF89		Q9C030	OTTHUMG00000150029	ENST00000278302.5:c.835C>T	11.37:g.5631436C>T	ENSP00000278302:p.Arg279*	Somatic		Capture	Illumina HiSeq	Phase_I	5588012	NM_001003818	A8K2A7|B4DDQ5|Q86WZ8|Q9HCR1	Nonsense_Mutation	SNP	ENST00000278302.5	37	CCDS31390.1	.	.	.	.	.	.	.	.	.	.	C	33	5.286384	0.95517	2.27E-4	0.0	ENSG00000121236;ENSG00000121236;ENSG00000121236;ENSG00000121236;ENSG00000121236;ENSG00000121236;ENSG00000121236;ENSG00000121236;ENSG00000258659;ENSG00000258588	ENST00000278302;ENST00000507320;ENST00000380107;ENST00000380097;ENST00000445329;ENST00000396867;ENST00000515022;ENST00000506134;ENST00000337072;ENST00000354852	.	.	.	5.09	4.18	0.49190	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.3245	0.55003	0.0:0.8292:0.1708:0.0	.	.	.	.	X	279;104;253;307;104;186;104;104;307;307	.	ENSP00000278302:R279X	R	+	1	2	TRIM34;TRIM6;TRIM6-TRIM34	5588012	0.953000	0.32496	0.958000	0.39756	0.729000	0.41735	1.689000	0.37700	1.454000	0.47793	-0.257000	0.10917	CGA		0.488	TRIM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143376.2	NM_001003818	
TRIM22	10346	broad.mit.edu	37	11	5717685	5717685	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:5717685G>A	ENST00000379965.3	+	2	500	c.223G>A	c.(223-225)Gcc>Acc	p.A75T	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	75					defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.A75T(1)		kidney(3)|large_intestine(8)|lung(9)|prostate(1)|stomach(2)	23		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		TCGGCATCTGGCCAACATAGT	0.502																																					p.A75T	GBM(104;491 2336 5222)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G223A	11						.						65.0	71.0	69.0					11																	5717685		2186	4296	6482	5674261	SO:0001583	missense	10346	exon2			X82200	CCDS41612.1	11p15	2013-01-09	2011-01-25		ENSG00000132274	ENSG00000132274		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16379	protein-coding gene	gene with protein product		606559	"""tripartite motif-containing 22"""			11331580, 11096452	Standard	NM_006074		Approved	STAF50, GPSTAF50, RNF94	uc001mbr.3	Q8IYM9	OTTHUMG00000066904	ENST00000379965.3:c.223G>A	11.37:g.5717685G>A	ENSP00000369299:p.Ala75Thr	Somatic		Capture	Illumina HiSeq	Phase_I	5674261	NM_001199573	Q05CQ0|Q15521	Missense_Mutation	SNP	ENST00000379965.3	37	CCDS41612.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.305182	0.60305	.	.	ENSG00000132274	ENST00000379965;ENST00000425490;ENST00000454828;ENST00000414641;ENST00000455293	D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87	4.82	2.94	0.34122	Zinc finger, RING/FYVE/PHD-type (1);	.	.	.	.	D	0.86468	0.5940	M	0.91406	3.205	0.27970	N	0.93645	P;P;B	0.42692	0.787;0.635;0.101	B;B;B	0.38020	0.219;0.263;0.036	T	0.80600	-0.1310	9	0.72032	D	0.01	.	9.0127	0.36150	0.1836:0.0:0.8164:0.0	.	75;75;75	C9JWC5;Q8IYM9-2;Q8IYM9	.;.;TRI22_HUMAN	T	75	ENSP00000369299:A75T;ENSP00000400417:A75T;ENSP00000393250:A75T;ENSP00000396849:A75T	ENSP00000369299:A75T	A	+	1	0	TRIM22	5674261	0.026000	0.19158	0.042000	0.18584	0.221000	0.24807	0.582000	0.23834	0.584000	0.29591	0.467000	0.42956	GCC		0.502	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
OR52E6	390078	broad.mit.edu	37	11	5862491	5862491	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:5862491G>T	ENST00000329322.5	-	1	636	c.637C>A	c.(637-639)Ctc>Atc	p.L213I	OR52E6_ENST00000379946.2_Missense_Mutation_p.L217I|TRIM5_ENST00000380027.1_Intron	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	213						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L217I(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATAATAAGGAGCACATCCAAT	0.483																																					p.L213I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C637A	11						.						58.0	58.0	58.0					11																	5862491		2200	4296	6496	5819067	SO:0001583	missense	390078	exon1			AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"""GPCR / Class A : Olfactory receptors"""	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.637C>A	11.37:g.5862491G>T	ENSP00000328878:p.Leu213Ile	Somatic		Capture	Illumina HiSeq	Phase_I	5819067	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	37	CCDS53597.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.677670	0.00102	.	.	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.38401	1.14;1.14	3.45	-6.91	0.01649	GPCR, rhodopsin-like superfamily (1);	1.527580	0.04170	N	0.324706	T	0.13927	0.0337	N	0.16307	0.4	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.36407	-0.9749	10	0.02654	T	1	.	0.0804	0.00031	0.2815:0.2354:0.1868:0.2964	.	213	Q96RD3	O52E6_HUMAN	I	213;217	ENSP00000328878:L213I;ENSP00000369279:L217I	ENSP00000328878:L213I	L	-	1	0	OR52E6	5819067	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-14.654000	0.00000	-3.036000	0.00264	-2.084000	0.00378	CTC		0.483	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
CNGA4	1262	broad.mit.edu	37	11	6261724	6261724	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:6261724G>A	ENST00000379936.2	+	4	815	c.700G>A	c.(700-702)Gat>Aat	p.D234N	CNGA4_ENST00000533426.1_Intron	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	234					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.D234N(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TACAGTGGGCGATACACCGCC	0.597																																					p.D234N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G700A	11						.						64.0	64.0	64.0					11																	6261724		2201	4296	6497	6218300	SO:0001583	missense	1262	exon4			AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2152	protein-coding gene	gene with protein product		609472	"""cyclic nucleotide gated channel beta 2"""	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.700G>A	11.37:g.6261724G>A	ENSP00000369268:p.Asp234Asn	Somatic		Capture	Illumina HiSeq	Phase_I	6218300	NM_001037329		Missense_Mutation	SNP	ENST00000379936.2	37	CCDS31408.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.109926	0.56398	.	.	ENSG00000132259	ENST00000379936	D	0.97352	-4.35	5.3	5.3	0.74995	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97745	0.9260	L	0.57536	1.79	0.50632	D	0.99988	D;P	0.76494	0.999;0.868	D;B	0.65573	0.936;0.355	D	0.97554	1.0094	10	0.42905	T	0.14	.	17.8807	0.88840	0.0:0.0:1.0:0.0	.	234;194	Q8IV77;Q8IV77-2	CNGA4_HUMAN;.	N	234	ENSP00000369268:D234N	ENSP00000369268:D234N	D	+	1	0	CNGA4	6218300	1.000000	0.71417	0.137000	0.22149	0.072000	0.16883	9.420000	0.97426	2.640000	0.89533	0.561000	0.74099	GAT		0.597	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329	
CCKBR	887	broad.mit.edu	37	11	6292299	6292299	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:6292299C>T	ENST00000334619.2	+	5	1063	c.870C>T	c.(868-870)agC>agT	p.S290S	CCKBR_ENST00000532396.1_3'UTR|CCKBR_ENST00000532715.1_Silent_p.S206S|CCKBR_ENST00000525462.1_Silent_p.S359S	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	290					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)	p.S290S(2)|p.S359S(1)		NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	GCGAAGACAGCGATGGCTGCT	0.682																																					p.S290S												.	.	3	Substitution - coding silent(3)	endometrium(2)|large_intestine(1)	c.C870T	11						.						64.0	63.0	64.0					11																	6292299		2201	4296	6497	6248875	SO:0001819	synonymous_variant	887	exon5			D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"""GPCR / Class A : Cholecystokinin receptors"""	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.870C>T	11.37:g.6292299C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6248875	NM_176875	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Silent	SNP	ENST00000334619.2	37	CCDS7761.1																																																																																				0.682	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875	
APBB1	322	broad.mit.edu	37	11	6417405	6417405	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:6417405G>T	ENST00000609360.1	-	13	1812	c.1713C>A	c.(1711-1713)tcC>tcA	p.S571S	APBB1_ENST00000529519.1_Silent_p.S96S|APBB1_ENST00000608704.1_Silent_p.S312S|APBB1_ENST00000608645.1_Silent_p.S312S|APBB1_ENST00000530885.1_Silent_p.S349S|APBB1_ENST00000299402.6_Silent_p.S569S|APBB1_ENST00000311051.3_Silent_p.S569S|APBB1_ENST00000608655.1_Silent_p.S351S|APBB1_ENST00000608394.1_Silent_p.S312S|APBB1_ENST00000609331.1_Silent_p.S336S|APBB1_ENST00000526240.1_5'UTR|APBB1_ENST00000389906.2_Silent_p.S571S	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	571	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)	p.S569S(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		GGCTGCTGGAGGACAGGACTG	0.547																																					p.S571S	GBM(147;1810 2556 5672 39622)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1713A	11						.						115.0	100.0	105.0					11																	6417405		2149	4172	6321	6373981	SO:0001819	synonymous_variant	322	exon12			L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213		ENST00000609360.1:c.1713C>A	11.37:g.6417405G>T		Somatic		Capture	Illumina HiSeq	Phase_I	6373981	NM_001164	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Missense_Mutation	SNP	ENST00000609360.1	37																																																																																					0.547	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164	
OR2AG1	144125	broad.mit.edu	37	11	6806557	6806557	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:6806557T>C	ENST00000307401.4	+	1	310	c.289T>C	c.(289-291)Tgt>Cgt	p.C97R		NM_001004489.2	NP_001004489.1	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG, member 1	97						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C97R(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CTTTGGAGGCTGTGCCCTTCA	0.542																																					p.C97R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T289C	11						.						109.0	96.0	101.0					11																	6806557		2201	4296	6497	6763133	SO:0001583	missense	144125	exon1			AB065823	CCDS31414.1	11p15.4	2012-08-09			ENSG00000170803	ENSG00000170803		"""GPCR / Class A : Olfactory receptors"""	15142	protein-coding gene	gene with protein product				OR2AG3			Standard	NM_001004489		Approved		uc001mer.2	Q9H205	OTTHUMG00000165735	ENST00000307401.4:c.289T>C	11.37:g.6806557T>C	ENSP00000307447:p.Cys97Arg	Somatic		Capture	Illumina HiSeq	Phase_I	6763133	NM_001004489	B9EKV7|Q6IFG7|Q96R26	Missense_Mutation	SNP	ENST00000307401.4	37	CCDS31414.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.430059	0.62844	.	.	ENSG00000170803	ENST00000307401	T	0.00545	6.67	4.03	4.03	0.46877	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000058	T	0.03434	0.0099	H	0.96015	3.755	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00697	-1.1605	10	0.87932	D	0	.	9.5584	0.39353	0.0:0.0:0.0:1.0	.	97	Q9H205	O2AG1_HUMAN	R	97	ENSP00000307447:C97R	ENSP00000307447:C97R	C	+	1	0	OR2AG1	6763133	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.502000	0.81614	1.833000	0.53350	0.482000	0.46254	TGT		0.542	OR2AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385980.1	NM_001004489	
ZNF215	7762	broad.mit.edu	37	11	6964392	6964392	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:6964392C>A	ENST00000278319.5	+	5	1150	c.562C>A	c.(562-564)Ctg>Atg	p.L188M	ZNF215_ENST00000414517.2_Missense_Mutation_p.L188M|ZNF215_ENST00000529903.1_Missense_Mutation_p.L188M|ZNF215_ENST00000527171.1_Intron	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	188	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L188V(1)|p.L188M(1)		NS(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(4)	32				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		TGTAAAGAACCTGTACAGGAA	0.393																																					p.L188M												.	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.C562A	11						.						169.0	160.0	163.0					11																	6964392		2201	4296	6497	6920968	SO:0001583	missense	7762	exon5			AF056618	CCDS7775.1	11p15.4	2013-01-09			ENSG00000149054	ENSG00000149054		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13007	protein-coding gene	gene with protein product		605016					Standard	XM_005253130		Approved	ZKSCAN11, ZSCAN43	uc001mey.3	Q9UL58	OTTHUMG00000165507	ENST00000278319.5:c.562C>A	11.37:g.6964392C>A	ENSP00000278319:p.Leu188Met	Somatic		Capture	Illumina HiSeq	Phase_I	6920968	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	37	CCDS7775.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.685508	0.47991	.	.	ENSG00000149054	ENST00000278319;ENST00000414517;ENST00000529903	T;T;T	0.05258	3.47;3.47;3.47	4.38	1.37	0.22104	Krueppel-associated box (4);	0.270310	0.19863	N	0.104397	T	0.11836	0.0288	M	0.84683	2.71	0.22911	N	0.998576	P;P	0.48230	0.907;0.892	P;P	0.46389	0.515;0.453	T	0.15578	-1.0432	10	0.72032	D	0.01	1.557	3.0264	0.06092	0.1834:0.5397:0.1775:0.0993	.	188;188	Q96C84;Q9UL58	.;ZN215_HUMAN	M	188	ENSP00000278319:L188M;ENSP00000393202:L188M;ENSP00000432306:L188M	ENSP00000278319:L188M	L	+	1	2	ZNF215	6920968	0.038000	0.19896	0.998000	0.56505	0.938000	0.57974	0.068000	0.14531	0.194000	0.20326	-1.045000	0.02358	CTG		0.393	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1		
RBMXL2	27288	broad.mit.edu	37	11	7110368	7110368	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:7110368G>A	ENST00000306904.5	+	1	204	c.17G>A	c.(16-18)cGc>cAc	p.R6H		NM_014469.4	NP_055284.3	O75526	RMXL2_HUMAN	RNA binding motif protein, X-linked-like 2	6						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.R6H(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GAAGCGGATCGCCCGGGGAAG	0.647																																					p.R6H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G17A	11						.						31.0	34.0	33.0					11																	7110368		2201	4296	6497	7066944	SO:0001583	missense	27288	exon1			AF069682	CCDS7777.1	11p15	2013-07-16				ENSG00000170748		"""RNA binding motif (RRM) containing"""	17886	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G T"""	605444				10958650	Standard	NM_014469		Approved	HNRNPG-T, HNRPGT	uc001mfc.2	O75526		ENST00000306904.5:c.17G>A	11.37:g.7110368G>A	ENSP00000304139:p.Arg6His	Somatic		Capture	Illumina HiSeq	Phase_I	7066944	NM_014469	Q6PEZ2|Q9NQU0	Missense_Mutation	SNP	ENST00000306904.5	37	CCDS7777.1	.	.	.	.	.	.	.	.	.	.	G	10.24	1.296385	0.23650	.	.	ENSG00000170748	ENST00000306904	T	0.78481	-1.18	2.78	2.78	0.32641	Nucleotide-binding, alpha-beta plait (1);	0.000000	0.64402	U	0.000001	T	0.66277	0.2773	L	0.43554	1.36	0.51233	D	0.999919	B	0.30741	0.293	B	0.27608	0.081	T	0.62599	-0.6820	10	0.20519	T	0.43	.	11.7503	0.51845	0.0:0.0:1.0:0.0	.	6	O75526	HNRGT_HUMAN	H	6	ENSP00000304139:R6H	ENSP00000304139:R6H	R	+	2	0	RBMXL2	7066944	1.000000	0.71417	0.706000	0.30403	0.329000	0.28539	8.677000	0.91203	1.835000	0.53391	0.455000	0.32223	CGC		0.647	RBMXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384552.1	NM_014469	
OLFML1	283298	broad.mit.edu	37	11	7530737	7530737	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:7530737A>G	ENST00000329293.3	+	3	921	c.527A>G	c.(526-528)tAc>tGc	p.Y176C	OLFML1_ENST00000530135.1_Missense_Mutation_p.Y176C|OLFML1_ENST00000528758.1_3'UTR|CTD-2516F10.2_ENST00000530201.1_RNA	NM_198474.3	NP_940876.2	Q6UWY5	OLFL1_HUMAN	olfactomedin-like 1	176	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.					extracellular region (GO:0005576)		p.Y176C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(3)|prostate(2)	24				Epithelial(150;6.96e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		CCAAAGGTGTACTTATTAATT	0.418																																					p.Y176C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A527G	11						.						108.0	107.0	107.0					11																	7530737		2201	4296	6497	7487313	SO:0001583	missense	283298	exon3			AY358591	CCDS7779.1	11p15	2008-02-05			ENSG00000183801	ENSG00000183801			24473	protein-coding gene	gene with protein product							Standard	NM_198474		Approved	UNQ564	uc001mfi.3	Q6UWY5	OTTHUMG00000165527	ENST00000329293.3:c.527A>G	11.37:g.7530737A>G	ENSP00000332511:p.Tyr176Cys	Somatic		Capture	Illumina HiSeq	Phase_I	7487313	NM_198474	B4DP03|Q569G4	Missense_Mutation	SNP	ENST00000329293.3	37	CCDS7779.1	.	.	.	.	.	.	.	.	.	.	A	18.90	3.721434	0.68959	.	.	ENSG00000183801	ENST00000530135;ENST00000329293	D;D	0.91792	-2.91;-2.91	5.78	5.78	0.91487	Olfactomedin-like (3);	0.000000	0.85682	D	0.000000	D	0.96062	0.8717	M	0.83774	2.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.96533	0.9394	10	0.87932	D	0	.	14.0667	0.64834	1.0:0.0:0.0:0.0	.	40;176	B4DN61;Q6UWY5	.;OLFL1_HUMAN	C	176	ENSP00000433455:Y176C;ENSP00000332511:Y176C	ENSP00000332511:Y176C	Y	+	2	0	OLFML1	7487313	1.000000	0.71417	0.900000	0.35374	0.908000	0.53690	8.926000	0.92839	2.200000	0.70718	0.460000	0.39030	TAC		0.418	OLFML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384656.1	NM_198474	
ST5	6764	broad.mit.edu	37	11	8732400	8732400	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:8732400G>A	ENST00000534127.1	-	14	2729	c.2344C>T	c.(2344-2346)Cgc>Tgc	p.R782C	ST5_ENST00000526757.1_Missense_Mutation_p.R362C|ST5_ENST00000534278.1_5'Flank|ST5_ENST00000530991.1_Missense_Mutation_p.R254C|ST5_ENST00000357665.1_Missense_Mutation_p.R782C|RPL27A_ENST00000531102.1_Intron|ST5_ENST00000526099.1_Missense_Mutation_p.R295C|ST5_ENST00000530438.1_Missense_Mutation_p.R362C|ST5_ENST00000313726.6_Missense_Mutation_p.R782C	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	782	UDENN.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R782C(1)		NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		ACCAGTAAGCGCCTGCAGTAG	0.562																																					p.R782C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2344T	11						.						56.0	52.0	53.0					11																	8732400		2201	4296	6497	8688976	SO:0001583	missense	6764	exon14			U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"""DENN/MADD domain containing"""	11350	protein-coding gene	gene with protein product	"""DENN/MADD domain containing 2B"""	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.2344C>T	11.37:g.8732400G>A	ENSP00000433528:p.Arg782Cys	Somatic		Capture	Illumina HiSeq	Phase_I	8688976	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	37	CCDS7791.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.354473	0.82243	.	.	ENSG00000166444	ENST00000526757;ENST00000534127;ENST00000313726;ENST00000530991;ENST00000357665;ENST00000526099;ENST00000530438;ENST00000533020	T;T;T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77;0.77;0.77	5.61	5.61	0.85477	uDENN (3);	0.000000	0.85682	D	0.000000	T	0.67748	0.2926	M	0.73430	2.235	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.988;0.979;0.993	T	0.70757	-0.4785	10	0.87932	D	0	-13.7794	13.6176	0.62118	0.0:0.0:0.741:0.259	.	295;362;782	B4DDL8;P78524-2;P78524	.;.;ST5_HUMAN	C	362;782;782;254;782;295;362;254	ENSP00000435097:R362C;ENSP00000433528:R782C;ENSP00000319678:R782C;ENSP00000432887:R254C;ENSP00000350294:R782C;ENSP00000436808:R295C;ENSP00000436802:R362C;ENSP00000433588:R254C	ENSP00000319678:R782C	R	-	1	0	ST5	8688976	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.034000	0.57289	2.652000	0.90054	0.655000	0.94253	CGC		0.562	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418	
ST5	6764	broad.mit.edu	37	11	8737173	8737173	+	Missense_Mutation	SNP	G	G	A	rs537720382		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:8737173G>A	ENST00000534127.1	-	9	2207	c.1822C>T	c.(1822-1824)Cgc>Tgc	p.R608C	ST5_ENST00000526757.1_Missense_Mutation_p.R188C|ST5_ENST00000530991.1_Missense_Mutation_p.R80C|ST5_ENST00000357665.1_Missense_Mutation_p.R608C|ST5_ENST00000526099.1_Missense_Mutation_p.R121C|ST5_ENST00000530438.1_Missense_Mutation_p.R188C|ST5_ENST00000313726.6_Missense_Mutation_p.R608C	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	608					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R608C(1)		NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		CGGGCCCGGCGGCTGGACAGC	0.667													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13229	0.0		0.0	False		,,,				2504	0.0				p.R608C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1822T	11						.						32.0	36.0	34.0					11																	8737173		2192	4256	6448	8693749	SO:0001583	missense	6764	exon9			U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"""DENN/MADD domain containing"""	11350	protein-coding gene	gene with protein product	"""DENN/MADD domain containing 2B"""	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.1822C>T	11.37:g.8737173G>A	ENSP00000433528:p.Arg608Cys	Somatic		Capture	Illumina HiSeq	Phase_I	8693749	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	37	CCDS7791.1	.	.	.	.	.	.	.	.	.	.	G	34	5.358481	0.95854	.	.	ENSG00000166444	ENST00000526757;ENST00000534127;ENST00000313726;ENST00000530991;ENST00000357665;ENST00000526099;ENST00000530438;ENST00000533020;ENST00000447053;ENST00000530593;ENST00000528527;ENST00000531060	T;T;T;T;T;T;T;T;T;T	0.10192	2.9;2.9;2.9;2.9;2.9;2.9;2.9;2.9;2.9;2.9	5.54	5.54	0.83059	.	0.051947	0.85682	D	0.000000	T	0.29620	0.0739	L	0.49126	1.545	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.68943	0.932;0.961;0.95	T	0.00565	-1.1668	10	0.87932	D	0	-14.5202	19.4701	0.94959	0.0:0.0:1.0:0.0	.	121;188;608	B4DDL8;P78524-2;P78524	.;.;ST5_HUMAN	C	188;608;608;80;608;121;188;80;218;80;80;97	ENSP00000435097:R188C;ENSP00000433528:R608C;ENSP00000319678:R608C;ENSP00000432887:R80C;ENSP00000350294:R608C;ENSP00000436808:R121C;ENSP00000436802:R188C;ENSP00000433588:R80C;ENSP00000437096:R80C;ENSP00000431580:R80C	ENSP00000319678:R608C	R	-	1	0	ST5	8693749	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.828000	0.92047	2.604000	0.88044	0.655000	0.94253	CGC		0.667	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418	
ST5	6764	broad.mit.edu	37	11	8751513	8751513	+	Missense_Mutation	SNP	G	G	A	rs577617101		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:8751513G>A	ENST00000534127.1	-	6	1709	c.1324C>T	c.(1324-1326)Cgc>Tgc	p.R442C	ST5_ENST00000526757.1_Intron|ST5_ENST00000357665.1_Missense_Mutation_p.R442C|ST5_ENST00000530438.1_Intron|ST5_ENST00000313726.6_Missense_Mutation_p.R442C	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	442	Interaction with ABL1.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R442C(1)		NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		TGGGACTTGCGGTGACCACGC	0.572																																					p.R442C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1324T	11						.						294.0	287.0	289.0					11																	8751513		2201	4296	6497	8708089	SO:0001583	missense	6764	exon6			U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"""DENN/MADD domain containing"""	11350	protein-coding gene	gene with protein product	"""DENN/MADD domain containing 2B"""	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.1324C>T	11.37:g.8751513G>A	ENSP00000433528:p.Arg442Cys	Somatic		Capture	Illumina HiSeq	Phase_I	8708089	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	37	CCDS7791.1	.	.	.	.	.	.	.	.	.	.	G	17.68	3.450165	0.63290	.	.	ENSG00000166444	ENST00000534127;ENST00000313726;ENST00000357665	T;T;T	0.06142	3.34;3.34;3.34	6.11	6.11	0.99139	.	0.318346	0.37053	N	0.002271	T	0.14056	0.0340	L	0.40543	1.245	0.45962	D	0.998784	D	0.71674	0.998	P	0.55871	0.786	T	0.00036	-1.2253	10	0.72032	D	0.01	-9.1709	15.3208	0.74120	0.0:0.0:0.8282:0.1718	.	442	P78524	ST5_HUMAN	C	442	ENSP00000433528:R442C;ENSP00000319678:R442C;ENSP00000350294:R442C	ENSP00000319678:R442C	R	-	1	0	ST5	8708089	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.425000	0.44723	2.906000	0.99361	0.655000	0.94253	CGC		0.572	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418	
DENND5A	23258	broad.mit.edu	37	11	9163529	9163529	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:9163529C>T	ENST00000328194.3	-	22	3958	c.3638G>A	c.(3637-3639)gGc>gAc	p.G1213D	DENND5A_ENST00000530044.1_Missense_Mutation_p.G1213D|DENND5A_ENST00000527700.1_Missense_Mutation_p.G556D	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	1213	RUN 2. {ECO:0000255|PROSITE- ProRule:PRU00178}.				positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.G1213D(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						GCCATCCTTGCCGATGTTCCG	0.532																																					p.G1213D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3638A	11						.						143.0	127.0	132.0					11																	9163529		2201	4296	6497	9120105	SO:0001583	missense	23258	exon22			AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"""DENN/MADD domain containing"""	19344	protein-coding gene	gene with protein product			"""RAB6 interacting protein 1"""	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.3638G>A	11.37:g.9163529C>T	ENSP00000328524:p.Gly1213Asp	Somatic		Capture	Illumina HiSeq	Phase_I	9120105	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	37	CCDS31423.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.316368|5.316368	0.95655|0.95655	.|.	.|.	ENSG00000184014|ENSG00000184014	ENST00000528725;ENST00000533737;ENST00000525784|ENST00000328194;ENST00000530044;ENST00000527700	.|T;T;T	.|0.18502	.|2.66;2.21;2.66	5.56|5.56	5.56|5.56	0.83823|0.83823	.|RUN (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.48768|0.48768	0.1518|0.1518	M|M	0.83603|0.83603	2.65|2.65	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|0.999;1.0	T|T	0.52102|0.52102	-0.8620|-0.8620	5|10	.|0.72032	.|D	.|0.01	.|.	19.5479|19.5479	0.95307|0.95307	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1213;1213	.|E9PS91;Q6IQ26	.|.;DEN5A_HUMAN	T|D	112;101;192|1213;1213;556	.|ENSP00000328524:G1213D;ENSP00000435866:G1213D;ENSP00000432549:G556D	.|ENSP00000328524:G1213D	A|G	-|-	1|2	0|0	DENND5A|DENND5A	9120105|9120105	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.956000|0.956000	0.61745|0.61745	7.772000|7.772000	0.85439|0.85439	2.633000|2.633000	0.89246|0.89246	0.655000|0.655000	0.94253|0.94253	GCA|GGC		0.532	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213	
DENND5A	23258	broad.mit.edu	37	11	9192306	9192306	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:9192306C>T	ENST00000328194.3	-	9	2245	c.1925G>A	c.(1924-1926)cGt>cAt	p.R642H	DENND5A_ENST00000530044.1_Missense_Mutation_p.R642H|DENND5A_ENST00000527700.1_5'UTR	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	642					positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R642H(1)		breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TTTTGCCAGACGCAGCTCAAT	0.408																																					p.R642H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1925A	11						.						156.0	151.0	153.0					11																	9192306		2201	4296	6497	9148882	SO:0001583	missense	23258	exon9			AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"""DENN/MADD domain containing"""	19344	protein-coding gene	gene with protein product			"""RAB6 interacting protein 1"""	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.1925G>A	11.37:g.9192306C>T	ENSP00000328524:p.Arg642His	Somatic		Capture	Illumina HiSeq	Phase_I	9148882	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	37	CCDS31423.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.719750	0.89205	.	.	ENSG00000184014	ENST00000328194;ENST00000530044	T;T	0.11930	2.75;2.73	5.84	5.84	0.93424	.	0.045062	0.85682	D	0.000000	T	0.43986	0.1272	M	0.79926	2.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	T	0.34229	-0.9837	10	0.87932	D	0	.	20.1432	0.98067	0.0:1.0:0.0:0.0	.	642;642	E9PS91;Q6IQ26	.;DEN5A_HUMAN	H	642	ENSP00000328524:R642H;ENSP00000435866:R642H	ENSP00000328524:R642H	R	-	2	0	DENND5A	9148882	1.000000	0.71417	0.998000	0.56505	0.569000	0.35902	7.743000	0.85020	2.769000	0.95229	0.561000	0.74099	CGT		0.408	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213	
ZNF143	7702	broad.mit.edu	37	11	9534059	9534059	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:9534059C>T	ENST00000396602.2	+	13	1559	c.1440C>T	c.(1438-1440)gaC>gaT	p.D480D	ZNF143_ENST00000530463.1_Silent_p.D479D|ZNF143_ENST00000396604.1_Silent_p.D479D|ZNF143_ENST00000396597.3_Silent_p.D449D|ZNF143_ENST00000299606.2_Silent_p.D452D	NM_001282656.1|NM_001282657.1|NM_003442.5	NP_001269585.1|NP_001269586.1|NP_003433.3	P52747	ZN143_HUMAN	zinc finger protein 143	480					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D480D(1)		endometrium(1)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	13				all cancers(16;4.12e-09)|Epithelial(150;2.29e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0212)		AAGGGGACGACGTTGTTTCTA	0.418																																					p.D480D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1440T	11						.						170.0	147.0	155.0					11																	9534059		2201	4294	6495	9490635	SO:0001819	synonymous_variant	7702	exon13			U09850	CCDS7799.2, CCDS60720.1, CCDS60721.1	11p15.4	2013-01-08	2006-06-13		ENSG00000166478	ENSG00000166478		"""Zinc fingers, C2H2-type"""	12928	protein-coding gene	gene with protein product		603433	"""zinc finger protein 143 (clone pHZ-1)"""				Standard	NM_003442		Approved	SBF, pHZ-1, STAF	uc001mhr.3	P52747	OTTHUMG00000149922	ENST00000396602.2:c.1440C>T	11.37:g.9534059C>T		Somatic		Capture	Illumina HiSeq	Phase_I	9490635	NM_003442	A8K518|B4DLY5|E7ER34|O75559|Q8WUK9	Silent	SNP	ENST00000396602.2	37	CCDS7799.2	.	.	.	.	.	.	.	.	.	.	C	5.736	0.320271	0.10845	.	.	ENSG00000166478	ENST00000447186	.	.	.	5.49	-0.831	0.10789	.	.	.	.	.	T	0.57651	0.2068	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52449	-0.8574	4	.	.	.	.	10.9429	0.47283	0.0:0.4422:0.0:0.5578	.	.	.	.	C	6	.	.	R	+	1	0	ZNF143	9490635	0.984000	0.35163	0.983000	0.44433	0.636000	0.38137	0.024000	0.13555	-0.318000	0.08665	-0.367000	0.07326	CGT		0.418	ZNF143-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313921.2	NM_003442	
ARNTL	406	broad.mit.edu	37	11	13397168	13397168	+	Missense_Mutation	SNP	C	C	T	rs370345058		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:13397168C>T	ENST00000403290.1	+	15	1539	c.1184C>T	c.(1183-1185)aCg>aTg	p.T395M	ARNTL_ENST00000361003.4_Missense_Mutation_p.T277M|ARNTL_ENST00000389708.3_Missense_Mutation_p.T395M|ARNTL_ENST00000403482.3_Missense_Mutation_p.T393M|ARNTL_ENST00000403510.3_Missense_Mutation_p.T351M|ARNTL_ENST00000396441.3_Missense_Mutation_p.T394M|ARNTL_ENST00000401424.1_Missense_Mutation_p.T352M|ARNTL_ENST00000389707.4_Missense_Mutation_p.T394M			O00327	BMAL1_HUMAN	aryl hydrocarbon receptor nuclear translocator-like	395	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|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)|protein import into nucleus, translocation (GO:0000060)|regulation of cell cycle (GO:0051726)|regulation of cellular senescence (GO:2000772)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|nuclear body (GO:0016604)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|Hsp90 protein binding (GO:0051879)|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)|signal transducer activity (GO:0004871)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.T394M(2)		breast(1)|endometrium(2)|large_intestine(11)|lung(5)|upper_aerodigestive_tract(1)	20				Epithelial(150;0.0243)		GTTTTACAGACGAGAGAAAAA	0.323																																					p.T351M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1052T	11						.	C	MET/THR,MET/THR,MET/THR	2,4398	4.2+/-10.8	0,2,2198	40.0	41.0	41.0		1181,1052,1181	5.4	0.9	11		41	0,8584		0,0,4292	no	missense,missense,missense	ARNTL	NM_001178.4,NM_001030273.1,NM_001030272.1	81,81,81	0,2,6490	TT,TC,CC		0.0,0.0455,0.0154	benign,benign,benign	394/626,351/583,394/626	13397168	2,12982	2200	4292	6492	13353744	SO:0001583	missense	406	exon15			D89722	CCDS31430.1, CCDS44543.1, CCDS73259.1	11p15	2013-05-21			ENSG00000133794	ENSG00000133794		"""Basic helix-loop-helix proteins"""	701	protein-coding gene	gene with protein product		602550				9144434, 9079689	Standard	XM_005252930		Approved	MOP3, JAP3, BMAL1, PASD3, bHLHe5	uc001mkp.3	O00327	OTTHUMG00000150623	ENST00000403290.1:c.1184C>T	11.37:g.13397168C>T	ENSP00000384517:p.Thr395Met	Somatic		Capture	Illumina HiSeq	Phase_I	13353744	NM_001030273	A2I2N6|A8K645|B5ME11|B7WPG7|D3DQW6|O00313|O00314|O00315|O00316|O00317|Q4G136|Q8IUT4|Q99631|Q99649	De_novo_Start_OutOfFrame	SNP	ENST00000403290.1	37		.	.	.	.	.	.	.	.	.	.	C	13.79	2.342650	0.41498	4.55E-4	0.0	ENSG00000133794	ENST00000396441;ENST00000389707;ENST00000401424;ENST00000403290;ENST00000361003;ENST00000389708;ENST00000403510;ENST00000339640;ENST00000403482	T;T;T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25	5.4	5.4	0.78164	PAS fold-3 (1);PAS (2);	0.092020	0.85682	D	0.000000	T	0.14399	0.0348	N	0.22421	0.69	0.43874	D	0.996489	B;B;B;B;B;B	0.27192	0.002;0.171;0.008;0.004;0.004;0.081	B;B;B;B;B;B	0.20184	0.004;0.027;0.01;0.006;0.003;0.028	T	0.04467	-1.0949	10	0.46703	T	0.11	.	18.7646	0.91866	0.0:1.0:0.0:0.0	.	277;393;352;395;394;351	O00327-4;O00327-7;O00327-1;O00327;O00327-8;A2I2N6	.;.;.;BMAL1_HUMAN;.;.	M	394;394;352;395;277;395;351;351;393	ENSP00000379718:T394M;ENSP00000374357:T394M;ENSP00000385915:T352M;ENSP00000384517:T395M;ENSP00000354278:T277M;ENSP00000374358:T395M;ENSP00000385581:T351M;ENSP00000385897:T393M	ENSP00000340289:T351M	T	+	2	0	ARNTL	13353744	1.000000	0.71417	0.947000	0.38551	0.884000	0.51177	5.587000	0.67510	2.510000	0.84645	0.555000	0.69702	ACG		0.323	ARNTL-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000319173.1	NM_001178	
KCNC1	3746	broad.mit.edu	37	11	17793865	17793865	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:17793865G>A	ENST00000379472.3	+	2	1254	c.1224G>A	c.(1222-1224)ccG>ccA	p.P408P	KCNC1_ENST00000265969.6_Silent_p.P408P	NM_004976.4	NP_004967.1	P48547	KCNC1_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 1	408					potassium ion transport (GO:0006813)|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)|voltage-gated potassium channel activity (GO:0005249)	p.P408P(1)		breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(7)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33					Dalfampridine(DB06637)	ACATGTACCCGCAGACGTGGT	0.627																																					p.P408P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1224A	11						.						87.0	85.0	86.0					11																	17793865		2200	4293	6493	17750441	SO:0001819	synonymous_variant	3746	exon2			M96747	CCDS7827.1, CCDS44547.1	11p15	2012-07-05			ENSG00000129159	ENSG00000129159		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6233	protein-coding gene	gene with protein product		176258				8449507, 16382104	Standard	NM_004976		Approved	Kv3.1	uc009yhc.1	P48547	OTTHUMG00000166359	ENST00000379472.3:c.1224G>A	11.37:g.17793865G>A		Somatic		Capture	Illumina HiSeq	Phase_I	17750441	NM_004976	K4DI87	Silent	SNP	ENST00000379472.3	37	CCDS7827.1																																																																																				0.627	KCNC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389389.1	NM_004976	
MRGPRX3	117195	broad.mit.edu	37	11	18159394	18159394	+	Silent	SNP	C	C	T	rs201290239		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:18159394C>T	ENST00000396275.2	+	3	1006	c.645C>T	c.(643-645)taC>taT	p.Y215Y		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	215						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.Y215Y(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						CCAGGCTGTACGTGACCATCC	0.562																																					p.Y215Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C645T	11						.						114.0	107.0	110.0					11																	18159394		2200	4293	6493	18115970	SO:0001819	synonymous_variant	117195	exon3				CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"""GPCR / Class A : Orphans"""	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.645C>T	11.37:g.18159394C>T		Somatic		Capture	Illumina HiSeq	Phase_I	18115970	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Silent	SNP	ENST00000396275.2	37	CCDS7830.1																																																																																				0.562	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031	
TMEM86A	144110	broad.mit.edu	37	11	18723296	18723296	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:18723296G>A	ENST00000280734.2	+	3	559	c.463G>A	c.(463-465)Ggc>Agc	p.G155S		NM_153347.1	NP_699178.1	Q8N2M4	TM86A_HUMAN	transmembrane protein 86A	155						integral component of membrane (GO:0016021)		p.G155S(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	11						GGCCCTTATCGGCTTCATGGG	0.627																																					p.G155S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G463A	11						.						61.0	57.0	58.0					11																	18723296		2199	4293	6492	18679872	SO:0001583	missense	144110	exon3			BC035692	CCDS7844.1	11p15.1	2005-10-28				ENSG00000151117			26890	protein-coding gene	gene with protein product							Standard	NM_153347		Approved	FLJ90119	uc001moz.1	Q8N2M4		ENST00000280734.2:c.463G>A	11.37:g.18723296G>A	ENSP00000280734:p.Gly155Ser	Somatic		Capture	Illumina HiSeq	Phase_I	18679872	NM_153347	Q96AJ0	Missense_Mutation	SNP	ENST00000280734.2	37	CCDS7844.1	.	.	.	.	.	.	.	.	.	.	G	9.365	1.069102	0.20147	.	.	ENSG00000151117	ENST00000535380;ENST00000280734	T	0.20332	2.08	5.43	-4.07	0.03975	.	0.534882	0.23526	N	0.047240	T	0.09774	0.0240	N	0.12569	0.235	0.38559	D	0.949659	B	0.12013	0.005	B	0.11329	0.006	T	0.24693	-1.0153	9	.	.	.	-0.3856	15.0775	0.72087	0.2603:0.0:0.7397:0.0	.	155	Q8N2M4	TM86A_HUMAN	S	155	ENSP00000280734:G155S	.	G	+	1	0	TMEM86A	18679872	0.932000	0.31603	0.092000	0.20876	0.860000	0.49131	1.511000	0.35801	-0.607000	0.05738	-0.880000	0.02959	GGC		0.627	TMEM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387812.1	NM_153347	
PTPN5	84867	broad.mit.edu	37	11	18754871	18754871	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:18754871C>T	ENST00000358540.2	-	11	1559	c.1129G>A	c.(1129-1131)Gtc>Atc	p.V377I	PTPN5_ENST00000396168.1_Missense_Mutation_p.V353I|PTPN5_ENST00000477854.1_Missense_Mutation_p.V181I|PTPN5_ENST00000396171.4_Missense_Mutation_p.V377I|PTPN5_ENST00000396166.3_5'Flank|PTPN5_ENST00000396170.1_Missense_Mutation_p.V345I|PTPN5_ENST00000396167.2_Missense_Mutation_p.V345I|RP11-1081L13.4_ENST00000527285.1_RNA	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	377	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)	p.V377I(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						ACCGTGCTGACGATGGGTCCC	0.617																																					p.V377I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1129A	11						.						189.0	150.0	163.0					11																	18754871		2199	4293	6492	18711447	SO:0001583	missense	84867	exon11			BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.1129G>A	11.37:g.18754871C>T	ENSP00000351342:p.Val377Ile	Somatic		Capture	Illumina HiSeq	Phase_I	18711447	NM_032781	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Missense_Mutation	SNP	ENST00000358540.2	37	CCDS7845.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.261476	0.39995	.	.	ENSG00000110786	ENST00000477854;ENST00000358540;ENST00000396170;ENST00000396171;ENST00000396167;ENST00000396168	T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58	5.42	5.42	0.78866	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.000000	0.64402	D	0.000001	T	0.17789	0.0427	N	0.16233	0.39	0.53005	D	0.999965	B;P	0.42941	0.004;0.794	B;B	0.37550	0.003;0.253	T	0.05146	-1.0903	10	0.20046	T	0.44	-3.6946	12.5429	0.56182	0.0:0.924:0.0:0.076	.	377;345	P54829;B3KXG7	PTN5_HUMAN;.	I	181;377;345;377;345;353	ENSP00000435056:V181I;ENSP00000351342:V377I;ENSP00000379473:V345I;ENSP00000379474:V377I;ENSP00000379470:V345I;ENSP00000379471:V353I	ENSP00000351342:V377I	V	-	1	0	PTPN5	18711447	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	3.947000	0.56652	2.553000	0.86117	0.655000	0.94253	GTC		0.617	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970	
CSRP3	8048	broad.mit.edu	37	11	19207814	19207814	+	Silent	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:19207814A>C	ENST00000533783.1	-	5	603	c.363T>G	c.(361-363)ccT>ccG	p.P121P	CSRP3_ENST00000265968.3_Silent_p.P121P	NM_003476.4	NP_003467.1	P50461	CSRP3_HUMAN	cysteine and glycine-rich protein 3 (cardiac LIM protein)	121	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue development (GO:0048738)|cardiac myofibril assembly (GO:0055003)|cellular calcium ion homeostasis (GO:0006874)|detection of muscle stretch (GO:0035995)|protein localization to organelle (GO:0033365)|regulation of the force of heart contraction (GO:0002026)|skeletal muscle tissue development (GO:0007519)	cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)	actinin binding (GO:0042805)|structural constituent of muscle (GO:0008307)|telethonin binding (GO:0031433)|zinc ion binding (GO:0008270)	p.P121P(1)		kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(2)	10						TGCCACATCGAGGGCACTTCT	0.517																																					p.P121P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T363G	11						.						152.0	128.0	136.0					11																	19207814		2199	4293	6492	19164390	SO:0001819	synonymous_variant	8048	exon4			U20324	CCDS7848.1	11p15.1	2014-09-17				ENSG00000129170			2472	protein-coding gene	gene with protein product		600824				7490106	Standard	NM_003476		Approved	CLP, MLP, CMD1M	uc001mpk.3	P50461		ENST00000533783.1:c.363T>G	11.37:g.19207814A>C		Somatic		Capture	Illumina HiSeq	Phase_I	19164390	NM_003476	Q9P131	Silent	SNP	ENST00000533783.1	37	CCDS7848.1																																																																																				0.517	CSRP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394484.1	NM_003476	
NAV2	89797	broad.mit.edu	37	11	19955610	19955610	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:19955610G>A	ENST00000396087.3	+	8	1988	c.1889G>A	c.(1888-1890)gGc>gAc	p.G630D	NAV2_ENST00000527559.2_Missense_Mutation_p.G559D|NAV2_ENST00000349880.4_Missense_Mutation_p.G607D|NAV2_ENST00000396085.1_Missense_Mutation_p.G607D|NAV2_ENST00000360655.4_Missense_Mutation_p.G543D|NAV2_ENST00000540292.1_Missense_Mutation_p.G561D	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	630					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)	p.G630D(1)		NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CAGCTGGACGGCAGACACTCC	0.637																																					p.G543D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1628A	11						.						45.0	48.0	47.0					11																	19955610		2199	4293	6492	19912186	SO:0001583	missense	89797	exon7			AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.1889G>A	11.37:g.19955610G>A	ENSP00000379396:p.Gly630Asp	Somatic		Capture	Illumina HiSeq	Phase_I	19912186	NM_001111018	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.125098	0.37533	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292	T;T;T;T;T;T	0.28069	1.63;1.73;1.74;1.75;1.64;1.64	5.52	5.52	0.82312	.	0.339314	0.28354	N	0.015658	T	0.23171	0.0560	N	0.14661	0.345	0.80722	D	1	B;B	0.27971	0.032;0.196	B;B	0.32211	0.038;0.142	T	0.06734	-1.0810	9	.	.	.	.	19.4398	0.94813	0.0:0.0:1.0:0.0	.	607;543	Q8IVL1-3;Q8IVL1-4	.;.	D	543;607;607;630;559;561	ENSP00000353871:G543D;ENSP00000379394:G607D;ENSP00000309577:G607D;ENSP00000379396:G630D;ENSP00000435395:G559D;ENSP00000443489:G561D	.	G	+	2	0	NAV2	19912186	1.000000	0.71417	0.983000	0.44433	0.931000	0.56810	6.565000	0.73974	2.590000	0.87494	0.563000	0.77884	GGC		0.637	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
NAV2	89797	broad.mit.edu	37	11	19970370	19970370	+	Missense_Mutation	SNP	G	G	A	rs140354139		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:19970370G>A	ENST00000396087.3	+	11	2557	c.2458G>A	c.(2458-2460)Gcc>Acc	p.A820T	NAV2_ENST00000527559.2_Missense_Mutation_p.A749T|NAV2_ENST00000349880.4_Missense_Mutation_p.A797T|NAV2_ENST00000396085.1_Missense_Mutation_p.A797T|NAV2_ENST00000360655.4_Missense_Mutation_p.A733T|NAV2_ENST00000540292.1_Missense_Mutation_p.A751T	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	820					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)	p.A820T(2)		NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						AGCAGGAGACGCCCCCTCAAT	0.612																																					p.A733T												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G2197A	11						.	G	THR/ALA,THR/ALA,THR/ALA	0,4398		0,0,2199	64.0	56.0	59.0		2197,2389,2389	5.1	1.0	11	dbSNP_134	59	1,8585	1.2+/-3.3	0,1,4292	no	missense,missense,missense	NAV2	NM_001111018.1,NM_145117.4,NM_182964.5	58,58,58	0,1,6491	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	733/2366,797/2430,797/2433	19970370	1,12983	2199	4293	6492	19926946	SO:0001583	missense	89797	exon10			AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.2458G>A	11.37:g.19970370G>A	ENSP00000379396:p.Ala820Thr	Somatic		Capture	Illumina HiSeq	Phase_I	19926946	NM_001111018	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	.	.	.	.	.	.	.	.	.	.	G	35	5.480863	0.96307	0.0	1.16E-4	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292	T;T;T;T;T;T	0.15603	2.41;2.41;2.41;2.41;2.41;2.41	5.1	5.1	0.69264	.	0.000000	0.64402	D	0.000010	T	0.39009	0.1062	L	0.56199	1.76	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.03493	-1.1031	9	.	.	.	.	18.8846	0.92370	0.0:0.0:1.0:0.0	.	797;733	Q8IVL1-3;Q8IVL1-4	.;.	T	733;797;797;820;749;751	ENSP00000353871:A733T;ENSP00000379394:A797T;ENSP00000309577:A797T;ENSP00000379396:A820T;ENSP00000435395:A749T;ENSP00000443489:A751T	.	A	+	1	0	NAV2	19926946	1.000000	0.71417	0.978000	0.43139	0.952000	0.60782	9.765000	0.98953	2.530000	0.85305	0.563000	0.77884	GCC		0.612	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
DBX1	120237	broad.mit.edu	37	11	20177985	20177985	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:20177985G>A	ENST00000524983.2	-	4	1095	c.807C>T	c.(805-807)ggC>ggT	p.G269G	DBX1_ENST00000227256.3_Silent_p.G308G			A6NMT0	DBX1_HUMAN	developing brain homeobox 1	269					regulation of transcription from RNA polymerase II promoter (GO:0006357)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.G308G(1)		endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)	21						GGCCCTTCTGGCCCACGTCGC	0.711																																					p.G269G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C807T	11						.						11.0	13.0	12.0					11																	20177985		2197	4291	6488	20134561	SO:0001819	synonymous_variant	120237	exon4					11p15.1	2011-06-20				ENSG00000109851		"""Homeoboxes / ANTP class : NKL subclass"""	33185	protein-coding gene	gene with protein product						11239429	Standard	NM_001029865		Approved		uc021qey.1	A6NMT0		ENST00000524983.2:c.807C>T	11.37:g.20177985G>A		Somatic		Capture	Illumina HiSeq	Phase_I	20134561	NM_001029865		Silent	SNP	ENST00000524983.2	37																																																																																					0.711	DBX1-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387585.2	NM_001029865	
MUC15	143662	broad.mit.edu	37	11	26586916	26586916	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:26586916T>C	ENST00000455601.2	-	2	608	c.490A>G	c.(490-492)Agt>Ggt	p.S164G	MUC15_ENST00000436318.2_Missense_Mutation_p.S191G|ANO3_ENST00000531568.1_Intron|MUC15_ENST00000281268.8_Missense_Mutation_p.S191G|ANO3_ENST00000525139.1_Intron|ANO3_ENST00000537978.1_Intron|ANO3_ENST00000256737.3_Intron|MUC15_ENST00000529533.1_Missense_Mutation_p.S191G|MUC15_ENST00000527569.1_Missense_Mutation_p.S191G	NM_145650.3	NP_663625.2	Q8N387	MUC15_HUMAN	mucin 15, cell surface associated	164					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S164G(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25						GTAATGGAACTGTTATCAGGA	0.453																																					p.S191G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A571G	11						.						148.0	139.0	142.0					11																	26586916		2203	4300	6503	26543492	SO:0001583	missense	143662	exon3			AJ417818	CCDS7859.1, CCDS44556.1, CCDS44557.1	11p14.3	2007-01-17	2006-03-14					"""Mucins"""	14956	protein-coding gene	gene with protein product		608566				12047385	Standard	NM_145650		Approved		uc001mqw.3	Q8N387		ENST00000455601.2:c.490A>G	11.37:g.26586916T>C	ENSP00000397339:p.Ser164Gly	Somatic		Capture	Illumina HiSeq	Phase_I	26543492	NM_001135092	B3KY00|E9PII6|F8W945|Q6UWS3|Q8IXI8|Q8WW41	Missense_Mutation	SNP	ENST00000455601.2	37	CCDS7859.1	.	.	.	.	.	.	.	.	.	.	T	11.42	1.633799	0.29068	.	.	ENSG00000169550	ENST00000455601;ENST00000436318;ENST00000281268;ENST00000529533;ENST00000527569	T;T;T;T;T	0.27104	1.76;1.75;1.69;1.75;1.69	4.66	3.53	0.40419	.	0.484857	0.20589	N	0.089392	T	0.19208	0.0461	L	0.42245	1.32	0.09310	N	0.999992	B;P;P	0.40731	0.02;0.728;0.728	B;B;B	0.36666	0.05;0.23;0.23	T	0.10800	-1.0614	10	0.49607	T	0.09	-8.2619	7.4039	0.26979	0.0:0.1018:0.0:0.8982	.	191;164;191	F8W945;Q8N387;E9PII6	.;MUC15_HUMAN;.	G	164;191;191;191;191	ENSP00000397339:S164G;ENSP00000416753:S191G;ENSP00000281268:S191G;ENSP00000431983:S191G;ENSP00000431945:S191G	ENSP00000281268:S191G	S	-	1	0	MUC15	26543492	0.958000	0.32768	0.005000	0.12908	0.002000	0.02628	2.140000	0.42159	0.895000	0.36342	0.528000	0.53228	AGT		0.453	MUC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387866.1	NM_145650	
ANO3	63982	broad.mit.edu	37	11	26621224	26621224	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:26621224T>A	ENST00000256737.3	+	17	2651	c.1799T>A	c.(1798-1800)gTc>gAc	p.V600D	ANO3_ENST00000531568.1_Missense_Mutation_p.V454D|ANO3_ENST00000525139.1_Missense_Mutation_p.V584D|ANO3_ENST00000537978.1_Missense_Mutation_p.V584D	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	600					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)	p.V600D(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						GCTGCTGCTGTCTGTATCAAT	0.403																																					p.V600D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1799A	11						.						200.0	172.0	182.0					11																	26621224		2203	4299	6502	26577800	SO:0001583	missense	63982	exon17			AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	14004	protein-coding gene	gene with protein product	"""transmembrane protein 16C (eight membrane-spanning domains)"""	610110	"""chromosome 11 open reading frame 25"", ""transmembrane protein 16C"""	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.1799T>A	11.37:g.26621224T>A	ENSP00000256737:p.Val600Asp	Somatic		Capture	Illumina HiSeq	Phase_I	26577800	NM_031418	B7Z3F5	Missense_Mutation	SNP	ENST00000256737.3	37	CCDS31447.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.337035	0.81801	.	.	ENSG00000134343	ENST00000537978;ENST00000525139;ENST00000256737;ENST00000538001;ENST00000531568	T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.79896	0.4525	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.82464	-0.0444	10	0.87932	D	0	.	16.2792	0.82664	0.0:0.0:0.0:1.0	.	502;600	B7Z7Y6;Q9BYT9	.;ANO3_HUMAN	D	584;584;600;502;454	ENSP00000440737:V584D;ENSP00000432576:V584D;ENSP00000256737:V600D;ENSP00000432394:V454D	ENSP00000256737:V600D	V	+	2	0	ANO3	26577800	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.988000	0.88194	2.243000	0.73865	0.533000	0.62120	GTC		0.403	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418	
ANO3	63982	broad.mit.edu	37	11	26664825	26664825	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:26664825C>T	ENST00000256737.3	+	23	3224	c.2372C>T	c.(2371-2373)gCa>gTa	p.A791V	ANO3_ENST00000531568.1_Missense_Mutation_p.A645V|ANO3_ENST00000525139.1_Missense_Mutation_p.A775V|ANO3_ENST00000537978.1_Missense_Mutation_p.A775V	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	791					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)	p.A791V(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						AGGCTGGATGCATACAAATTT	0.418																																					p.A791V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2372T	11						.						104.0	97.0	100.0					11																	26664825		2203	4299	6502	26621401	SO:0001583	missense	63982	exon23			AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	14004	protein-coding gene	gene with protein product	"""transmembrane protein 16C (eight membrane-spanning domains)"""	610110	"""chromosome 11 open reading frame 25"", ""transmembrane protein 16C"""	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.2372C>T	11.37:g.26664825C>T	ENSP00000256737:p.Ala791Val	Somatic		Capture	Illumina HiSeq	Phase_I	26621401	NM_031418	B7Z3F5	Missense_Mutation	SNP	ENST00000256737.3	37	CCDS31447.1	.	.	.	.	.	.	.	.	.	.	C	35	5.567936	0.96540	.	.	ENSG00000134343	ENST00000537978;ENST00000525139;ENST00000256737;ENST00000538001;ENST00000531568	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.86986	0.6065	M	0.92649	3.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.89286	0.3615	10	0.87932	D	0	.	19.9738	0.97296	0.0:1.0:0.0:0.0	.	693;791	B7Z7Y6;Q9BYT9	.;ANO3_HUMAN	V	775;775;791;693;645	ENSP00000440737:A775V;ENSP00000432576:A775V;ENSP00000256737:A791V;ENSP00000432394:A645V	ENSP00000256737:A791V	A	+	2	0	ANO3	26621401	1.000000	0.71417	0.999000	0.59377	0.974000	0.67602	7.764000	0.85297	2.732000	0.93576	0.655000	0.94253	GCA		0.418	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418	
QSER1	79832	broad.mit.edu	37	11	32953929	32953929	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:32953929C>T	ENST00000399302.2	+	4	1073	c.738C>T	c.(736-738)aaC>aaT	p.N246N	QSER1_ENST00000527788.1_Intron	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	246	Ser-rich.							p.N246N(1)		breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					AGGTGAGCAACGGAGGATTAC	0.423																																					p.N246N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C738T	11						.						78.0	73.0	74.0					11																	32953929		1888	4110	5998	32910505	SO:0001819	synonymous_variant	79832	exon4			AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.738C>T	11.37:g.32953929C>T		Somatic		Capture	Illumina HiSeq	Phase_I	32910505	NM_001076786	Q6ZU30|Q6ZUR5	Silent	SNP	ENST00000399302.2	37	CCDS41631.1																																																																																				0.423	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774	
CSTF3	1479	broad.mit.edu	37	11	33163172	33163172	+	Intron	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:33163172C>T	ENST00000323959.4	-	3	365				CSTF3_ENST00000431742.2_3'UTR|CSTF3_ENST00000524827.1_Intron|CSTF3_ENST00000526480.1_Intron|CSTF3_ENST00000438862.2_Missense_Mutation_p.S89N	NM_001326.2	NP_001317.1	Q12996	CSTF3_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kDa						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|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)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.S89N(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|stomach(1)	19						ACAGTGAATGCTGCAATACTG	0.353																																					p.S89N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G266A	11						.						30.0	30.0	30.0					11																	33163172		2196	4297	6493	33119748	SO:0001627	intron_variant	1479	exon3			U15782	CCDS7883.1, CCDS44563.1, CCDS44564.1	11p13	2007-01-05	2002-08-29		ENSG00000176102	ENSG00000176102			2485	protein-coding gene	gene with protein product		600367	"""cleavage stimulation factor, 3' pre-RNA, subunit 3, 77kD"""			7984242	Standard	XM_006718154		Approved	CstF-77	uc001muh.3	Q12996	OTTHUMG00000166268	ENST00000323959.4:c.225+40G>A	11.37:g.33163172C>T		Somatic		Capture	Illumina HiSeq	Phase_I	33119748	NM_001033505	A8K471|D3DR04|E9PB40|Q32P22|Q96FQ8|Q96QD6|Q96QK4	Missense_Mutation	SNP	ENST00000323959.4	37	CCDS7883.1	.	.	.	.	.	.	.	.	.	.	C	12.10	1.837969	0.32513	.	.	ENSG00000176102	ENST00000438862	.	.	.	5.34	-1.4	0.08968	.	.	.	.	.	T	0.44138	0.1279	.	.	.	0.49483	D	0.999796	B	0.02656	0.0	B	0.01281	0.0	T	0.27706	-1.0066	7	0.87932	D	0	.	7.155	0.25632	0.0:0.3715:0.1184:0.5101	.	89	Q96QK4	.	N	89	.	ENSP00000388711:S89N	S	-	2	0	CSTF3	33119748	0.568000	0.26635	0.959000	0.39883	0.971000	0.66376	-0.234000	0.09028	-0.201000	0.10284	0.650000	0.86243	AGC		0.353	CSTF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388801.1	NM_001326	
HIPK3	10114	broad.mit.edu	37	11	33370815	33370815	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:33370815C>T	ENST00000303296.4	+	14	3094	c.2789C>T	c.(2788-2790)cCc>cTc	p.P930L	HIPK3_ENST00000525975.1_Missense_Mutation_p.P909L|HIPK3_ENST00000379016.3_Missense_Mutation_p.P909L|HIPK3_ENST00000456517.1_Missense_Mutation_p.P909L	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	930	Interaction with AR. {ECO:0000250}.|Required for localization to nuclear speckles. {ECO:0000250}.|Ser-rich.				apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.P930L(1)		endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						AGCCCATCCCCCTGCAAGAGA	0.403																																					p.P909L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2726T	11						.						85.0	83.0	83.0					11																	33370815		2202	4298	6500	33327391	SO:0001583	missense	10114	exon13			AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"""homeodomain-interacting protein kinase 3"""			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.2789C>T	11.37:g.33370815C>T	ENSP00000304226:p.Pro930Leu	Somatic		Capture	Illumina HiSeq	Phase_I	33327391	NM_001048200	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	37	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.174832	0.78564	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.57436	0.4;0.45;0.4;0.4	5.81	5.81	0.92471	.	0.100459	0.44483	D	0.000448	T	0.63307	0.2500	L	0.38175	1.15	0.80722	D	1	D;D	0.89917	0.968;1.0	P;D	0.87578	0.66;0.998	T	0.52495	-0.8568	10	0.10902	T	0.67	.	20.0763	0.97746	0.0:1.0:0.0:0.0	.	909;930	Q9H422-2;Q9H422	.;HIPK3_HUMAN	L	909;930;909;909	ENSP00000431710:P909L;ENSP00000304226:P930L;ENSP00000368301:P909L;ENSP00000398241:P909L	ENSP00000304226:P930L	P	+	2	0	HIPK3	33327391	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	5.425000	0.66470	2.756000	0.94617	0.655000	0.94253	CCC		0.403	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734	
CAT	847	broad.mit.edu	37	11	34489839	34489839	+	Missense_Mutation	SNP	G	G	A	rs138694186		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:34489839G>A	ENST00000241052.4	+	11	1420	c.1331G>A	c.(1330-1332)cGg>cAg	p.R444Q		NM_001752.3	NP_001743.1	P04040	CATA_HUMAN	catalase	444					aerobic respiration (GO:0009060)|cellular response to growth factor stimulus (GO:0071363)|cholesterol metabolic process (GO:0008203)|hemoglobin metabolic process (GO:0020027)|hydrogen peroxide catabolic process (GO:0042744)|menopause (GO:0042697)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleobase-containing small molecule metabolic process (GO:0055086)|osteoblast differentiation (GO:0001649)|positive regulation of cell division (GO:0051781)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to reactive oxygen species (GO:0000302)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|ureteric bud development (GO:0001657)|UV protection (GO:0009650)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	aminoacylase activity (GO:0004046)|antioxidant activity (GO:0016209)|catalase activity (GO:0004096)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|oxidoreductase activity, acting on peroxide as acceptor (GO:0016684)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R444Q(1)		breast(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(3)	26		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)	GAGCAGGTGCGGGCATTCTAT	0.418																																					p.R444Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1331A	11						.	G	GLN/ARG	1,4403	2.1+/-5.4	0,1,2201	113.0	114.0	114.0		1331	4.7	1.0	11	dbSNP_134	114	1,8595	1.2+/-3.3	0,1,4297	yes	missense	CAT	NM_001752.3	43	0,2,6498	AA,AG,GG		0.0116,0.0227,0.0154	possibly-damaging	444/528	34489839	2,12998	2202	4298	6500	34446415	SO:0001583	missense	847	exon11			AY028632	CCDS7891.1	11p13	2012-10-02			ENSG00000121691	ENSG00000121691	1.11.1.6		1516	protein-coding gene	gene with protein product		115500					Standard	NM_001752		Approved		uc001mvm.3	P04040	OTTHUMG00000044353	ENST00000241052.4:c.1331G>A	11.37:g.34489839G>A	ENSP00000241052:p.Arg444Gln	Somatic		Capture	Illumina HiSeq	Phase_I	34446415	NM_001752	A8K6C0|B2RCZ9|D3DR07|Q2M1U4|Q4VXX5|Q9BWT9|Q9UC85	Missense_Mutation	SNP	ENST00000241052.4	37	CCDS7891.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.172950	0.38413	2.27E-4	1.16E-4	ENSG00000121691	ENST00000241052	D	0.92199	-2.99	5.59	4.67	0.58626	Catalase domain (1);Catalase-related immune responsive (1);	0.057031	0.64402	D	0.000001	D	0.88716	0.6512	M	0.73319	2.225	0.50171	D	0.999858	P	0.43412	0.806	B	0.33042	0.157	D	0.88849	0.3318	10	0.49607	T	0.09	-20.7757	11.1854	0.48653	0.1443:0.0:0.8557:0.0	.	444	P04040	CATA_HUMAN	Q	444	ENSP00000241052:R444Q	ENSP00000241052:R444Q	R	+	2	0	CAT	34446415	0.998000	0.40836	0.954000	0.39281	0.476000	0.33039	3.689000	0.54706	2.635000	0.89317	0.555000	0.69702	CGG		0.418	CAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103197.2	NM_001752	
ELF5	2001	broad.mit.edu	37	11	34515034	34515034	+	Missense_Mutation	SNP	C	C	T	rs371514980		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:34515034C>T	ENST00000312319.2	-	3	606	c.377G>A	c.(376-378)cGc>cAc	p.R126H	ELF5_ENST00000528709.1_Intron|ELF5_ENST00000532417.1_Missense_Mutation_p.R116H|ELF5_ENST00000257832.2_Missense_Mutation_p.R116H|ELF5_ENST00000429939.2_Intron	NM_001243081.1|NM_198381.1	NP_001230010.1|NP_938195.1	Q9UKW6	ELF5_HUMAN	E74-like factor 5 (ets domain transcription factor)	126	PNT. {ECO:0000255|PROSITE- ProRule:PRU00762}.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|ectoderm development (GO:0007398)|mammary gland epithelial cell differentiation (GO:0060644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	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 positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R126H(1)		large_intestine(4)|skin(1)	5		Acute lymphoblastic leukemia(5;0.0087)|all_hematologic(20;0.0384)				ACCTTGTGTGCGGATGTTCTG	0.552											OREG0020879	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R116H	Melanoma(61;202 1660 4348 21594)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G347A	11						.						50.0	37.0	41.0					11																	34515034		2202	4298	6500	34471610	SO:0001583	missense	2001	exon3			AF049703	CCDS7892.1, CCDS7893.1, CCDS58129.1, CCDS73273.1	11p13-p12	2008-05-14			ENSG00000135374	ENSG00000135374			3320	protein-coding gene	gene with protein product		605169				9840936	Standard	NM_001422		Approved		uc001mvp.2	Q9UKW6	OTTHUMG00000166451	ENST00000312319.2:c.377G>A	11.37:g.34515034C>T	ENSP00000311010:p.Arg126His	Somatic	848	Capture	Illumina HiSeq	Phase_I	34471610	NM_001422	A6XAE6|A8K452|O95175|Q8N2K9|Q96QY3|Q9UKW5	Missense_Mutation	SNP	ENST00000312319.2	37	CCDS7892.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.759146	0.69763	.	.	ENSG00000135374	ENST00000257832;ENST00000312319;ENST00000532417	T;T;T	0.35236	1.32;1.32;1.32	4.66	4.66	0.58398	Sterile alpha motif/pointed domain (2);Pointed domain (3);	0.000000	0.64402	D	0.000009	T	0.52141	0.1716	L	0.55990	1.75	0.37883	D	0.930457	D;D	0.89917	1.0;0.999	D;D	0.71414	0.973;0.922	T	0.57980	-0.7717	10	0.54805	T	0.06	.	12.0785	0.53657	0.0:0.9169:0.0:0.0831	.	116;126	Q9UKW6-3;Q9UKW6	.;ELF5_HUMAN	H	116;126;116	ENSP00000257832:R116H;ENSP00000311010:R126H;ENSP00000436386:R116H	ENSP00000257832:R116H	R	-	2	0	ELF5	34471610	1.000000	0.71417	0.997000	0.53966	0.799000	0.45148	2.009000	0.40903	2.146000	0.66826	0.561000	0.74099	CGC		0.552	ELF5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389845.1	NM_198381	
TRIM44	54765	broad.mit.edu	37	11	35685076	35685076	+	Silent	SNP	C	C	T	rs369333767		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:35685076C>T	ENST00000299413.5	+	1	724	c.417C>T	c.(415-417)agC>agT	p.S139S	RP1-276E15.1_ENST00000525573.2_lincRNA	NM_017583.4	NP_060053.2	Q96DX7	TRI44_HUMAN	tripartite motif containing 44	139	Glu-rich.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.S139S(1)		endometrium(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18	all_lung(20;0.0317)|Lung NSC(22;0.0661)|all_epithelial(35;0.115)	all_hematologic(20;0.107)				agcaagaaagcgaggccgaag	0.498																																					p.S139S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C417T	11						.						193.0	176.0	182.0					11																	35685076		2202	4298	6500	35641652	SO:0001819	synonymous_variant	54765	exon1			BC024031	CCDS31461.1	11p13	2011-04-20	2011-01-25		ENSG00000166326	ENSG00000166326		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19016	protein-coding gene	gene with protein product		612298	"""tripartite motif-containing 44"""				Standard	NM_017583		Approved	DIPB, MC7	uc001mwi.2	Q96DX7	OTTHUMG00000166312	ENST00000299413.5:c.417C>T	11.37:g.35685076C>T		Somatic		Capture	Illumina HiSeq	Phase_I	35641652	NM_017583	D3DR14|Q96QY2|Q9UGK0	Silent	SNP	ENST00000299413.5	37	CCDS31461.1																																																																																				0.498	TRIM44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389081.1	NM_017583	
LDLRAD3	143458	broad.mit.edu	37	11	36103278	36103278	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:36103278G>A	ENST00000315571.5	+	3	290	c.269G>A	c.(268-270)cGg>cAg	p.R90Q	LDLRAD3_ENST00000524419.1_Missense_Mutation_p.R41Q|LDLRAD3_ENST00000528989.1_Missense_Mutation_p.R41Q	NM_174902.2	NP_777562.1	Q86YD5	LRAD3_HUMAN	low density lipoprotein receptor class A domain containing 3	90	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				receptor-mediated endocytosis (GO:0006898)|regulation of protein processing (GO:0070613)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)	p.R90Q(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(7)|skin(1)	28	all_lung(20;0.089)|Lung NSC(22;0.175)|all_epithelial(35;0.177)	all_hematologic(20;0.124)				GGTCGCTTCCGGTGCAATGGG	0.532																																					p.R90Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G269A	11						.						158.0	130.0	139.0					11																	36103278		2202	4298	6500	36059854	SO:0001583	missense	143458	exon3			AK075546	CCDS31462.1	11p13	2014-06-05			ENSG00000179241	ENSG00000179241			27046	protein-coding gene	gene with protein product						21795536	Standard	NM_174902		Approved	LRAD3	uc001mwk.1	Q86YD5	OTTHUMG00000166313	ENST00000315571.5:c.269G>A	11.37:g.36103278G>A	ENSP00000318607:p.Arg90Gln	Somatic		Capture	Illumina HiSeq	Phase_I	36059854	NM_174902	B7Z1U3|B9EG81|Q8NBJ0	Missense_Mutation	SNP	ENST00000315571.5	37	CCDS31462.1	.	.	.	.	.	.	.	.	.	.	G	15.95	2.984328	0.53934	.	.	ENSG00000179241	ENST00000528989;ENST00000524419;ENST00000545142;ENST00000315571	D;D;D	0.95724	-3.79;-3.79;-3.79	5.95	4.02	0.46733	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.119843	0.56097	N	0.000033	D	0.90109	0.6910	L	0.38649	1.16	0.35335	D	0.785982	B;B	0.25521	0.128;0.008	B;B	0.19946	0.027;0.01	D	0.87278	0.2290	10	0.15499	T	0.54	.	9.2104	0.37316	0.2298:0.0:0.7702:0.0	.	41;90	B7Z1U3;Q86YD5	.;LRAD3_HUMAN	Q	41;41;90;90	ENSP00000433954:R41Q;ENSP00000434313:R41Q;ENSP00000318607:R90Q	ENSP00000318607:R90Q	R	+	2	0	LDLRAD3	36059854	1.000000	0.71417	0.932000	0.37286	0.910000	0.53928	2.776000	0.47709	1.463000	0.47967	0.650000	0.86243	CGG		0.532	LDLRAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389085.1	NM_174902	
TRAF6	7189	broad.mit.edu	37	11	36522810	36522810	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:36522810C>T	ENST00000526995.1	-	2	502	c.256G>A	c.(256-258)Ggc>Agc	p.G86S	TRAF6_ENST00000348124.5_Missense_Mutation_p.G86S	NM_004620.3	NP_004611.1	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6, E3 ubiquitin protein ligase	86	Interaction with TAX1BP1.				activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of protein kinase activity (GO:0032147)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|apoptotic signaling pathway (GO:0097190)|bone resorption (GO:0045453)|cell development (GO:0048468)|cellular response to lipopolysaccharide (GO:0071222)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|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)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein autoubiquitination (GO:0051865)|protein complex assembly (GO:0006461)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|regulation of immunoglobulin secretion (GO:0051023)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|T-helper 1 type immune response (GO:0042088)|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)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	histone deacetylase binding (GO:0042826)|ligase activity (GO:0016874)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G86S(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)	27	all_lung(20;0.211)	all_hematologic(20;0.107)				AACCTATGGCCGCATGGCGTT	0.448																																					p.G86S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G256A	11						.						52.0	41.0	45.0					11																	36522810		2202	4298	6500	36479386	SO:0001583	missense	7189	exon3				CCDS7901.1	11p12	2013-01-09	2012-02-23		ENSG00000175104	ENSG00000175104		"""RING-type (C3HC4) zinc fingers"""	12036	protein-coding gene	gene with protein product		602355	"""TNF receptor-associated factor 6"""			8837778	Standard	NM_004620		Approved	RNF85	uc001mws.2	Q9Y4K3	OTTHUMG00000166391	ENST00000526995.1:c.256G>A	11.37:g.36522810C>T	ENSP00000433623:p.Gly86Ser	Somatic		Capture	Illumina HiSeq	Phase_I	36479386	NM_145803	A6NKI7|A8KAB3|D3DR16|Q8NEH5	Missense_Mutation	SNP	ENST00000526995.1	37	CCDS7901.1	.	.	.	.	.	.	.	.	.	.	C	35	5.548982	0.96488	.	.	ENSG00000175104	ENST00000526995;ENST00000348124	D;D	0.89746	-2.56;-2.56	5.62	5.62	0.85841	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type, conserved site (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.85682	D	0.000000	D	0.94748	0.8305	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94879	0.8037	10	0.87932	D	0	-17.0203	19.6539	0.95828	0.0:1.0:0.0:0.0	.	86	Q9Y4K3	TRAF6_HUMAN	S	86	ENSP00000433623:G86S;ENSP00000337853:G86S	ENSP00000337853:G86S	G	-	1	0	TRAF6	36479386	1.000000	0.71417	0.976000	0.42696	0.853000	0.48598	7.818000	0.86416	2.653000	0.90120	0.467000	0.42956	GGC		0.448	TRAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389530.1	NM_145803	
LRRC4C	57689	broad.mit.edu	37	11	40136639	40136639	+	Missense_Mutation	SNP	G	G	A	rs375987229		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:40136639G>A	ENST00000278198.2	-	2	3167	c.1204C>T	c.(1204-1206)Cgg>Tgg	p.R402W	LRRC4C_ENST00000527150.1_Missense_Mutation_p.R402W|LRRC4C_ENST00000528697.1_Missense_Mutation_p.R402W|LRRC4C_ENST00000530763.1_Missense_Mutation_p.R402W			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	402	Ig-like C2-type.				regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)		p.R402W(2)		NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				ACAGCTATCCGCACTTTGTAC	0.458																																					p.R402W												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.C1204T	11						.	G	TRP/ARG	0,4406		0,0,2203	202.0	175.0	184.0		1204	1.7	1.0	11		184	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRRC4C	NM_020929.1	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	402/641	40136639	1,13005	2203	4300	6503	40093215	SO:0001583	missense	57689	exon2			AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.1204C>T	11.37:g.40136639G>A	ENSP00000278198:p.Arg402Trp	Somatic		Capture	Illumina HiSeq	Phase_I	40093215	NM_020929	A8K0T1|Q7L0N3	Missense_Mutation	SNP	ENST00000278198.2	37	CCDS31464.1	.	.	.	.	.	.	.	.	.	.	G	13.02	2.113502	0.37339	0.0	1.16E-4	ENSG00000148948	ENST00000278198;ENST00000527150;ENST00000528697;ENST00000530763	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	5.87	1.71	0.24356	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.73210	0.3558	H	0.95539	3.685	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.81163	-0.1058	10	0.87932	D	0	.	15.2704	0.73696	0.0:0.0:0.4837:0.5163	.	402	Q9HCJ2	LRC4C_HUMAN	W	402	ENSP00000278198:R402W;ENSP00000436976:R402W;ENSP00000437132:R402W;ENSP00000434761:R402W	ENSP00000278198:R402W	R	-	1	2	LRRC4C	40093215	1.000000	0.71417	0.993000	0.49108	0.964000	0.63967	3.023000	0.49666	0.053000	0.16036	-0.158000	0.13435	CGG		0.458	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929	
CHST1	8534	broad.mit.edu	37	11	45671402	45671402	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:45671402C>T	ENST00000308064.2	-	4	1742	c.1072G>A	c.(1072-1074)Gag>Aag	p.E358K	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	358					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.E358K(2)		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)		CGCCACTTCTCGGCCGTGGCC	0.672																																					p.E358K												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G1072A	11						.						49.0	53.0	51.0					11																	45671402		2203	4299	6502	45627978	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.1072G>A	11.37:g.45671402C>T	ENSP00000309270:p.Glu358Lys	Somatic		Capture	Illumina HiSeq	Phase_I	45627978	NM_003654	D3DQP2	Missense_Mutation	SNP	ENST00000308064.2	37	CCDS7913.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.657712	0.47467	.	.	ENSG00000175264	ENST00000308064	T	0.80909	-1.43	4.62	4.62	0.57501	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.78817	0.4343	M	0.71296	2.17	0.58432	D	0.999999	D	0.55800	0.973	B	0.42188	0.379	T	0.78046	-0.2357	10	0.12430	T	0.62	-25.2434	17.4573	0.87610	0.0:1.0:0.0:0.0	.	358	O43916	CHST1_HUMAN	K	358	ENSP00000309270:E358K	ENSP00000309270:E358K	E	-	1	0	CHST1	45627978	1.000000	0.71417	0.985000	0.45067	0.419000	0.31324	5.995000	0.70631	2.099000	0.63709	0.313000	0.20887	GAG		0.672	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390127.1	NM_003654	
CHST1	8534	broad.mit.edu	37	11	45671602	45671602	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:45671602G>A	ENST00000308064.2	-	4	1542	c.872C>T	c.(871-873)cCg>cTg	p.P291L	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	291					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.P291L(1)|p.P291Q(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)		CTTGAGCCACGGGGGCCGCAT	0.622																																					p.P291L												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C872T	11						.						84.0	76.0	79.0					11																	45671602		2203	4299	6502	45628178	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.872C>T	11.37:g.45671602G>A	ENSP00000309270:p.Pro291Leu	Somatic		Capture	Illumina HiSeq	Phase_I	45628178	NM_003654	D3DQP2	Missense_Mutation	SNP	ENST00000308064.2	37	CCDS7913.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.489058	0.26686	.	.	ENSG00000175264	ENST00000308064	T	0.80909	-1.43	4.89	3.02	0.34903	Sulfotransferase domain (1);	0.411085	0.26812	N	0.022364	T	0.76271	0.3964	M	0.73598	2.24	0.09310	N	0.999994	B	0.32829	0.386	B	0.25987	0.065	T	0.65216	-0.6222	10	0.41790	T	0.15	-22.9397	10.726	0.46068	0.1549:0.0:0.8451:0.0	.	291	O43916	CHST1_HUMAN	L	291	ENSP00000309270:P291L	ENSP00000309270:P291L	P	-	2	0	CHST1	45628178	0.935000	0.31712	0.026000	0.17262	0.987000	0.75469	5.223000	0.65283	0.483000	0.27608	0.462000	0.41574	CCG		0.622	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390127.1	NM_003654	
CHST1	8534	broad.mit.edu	37	11	45672314	45672314	+	Missense_Mutation	SNP	C	C	T	rs140694718		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:45672314C>T	ENST00000308064.2	-	4	830	c.160G>A	c.(160-162)Gcc>Acc	p.A54T	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	54					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.A54T(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)		AGGTTGTAGGCGAAGGTGGGG	0.662													C|||	1	0.000199681	0.0	0.0	5008	,	,		16163	0.0		0.0	False		,,,				2504	0.001				p.A54T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G160A	11						.	C	THR/ALA	0,4406		0,0,2203	84.0	81.0	82.0		160	-6.2	0.8	11	dbSNP_134	82	1,8597	1.2+/-3.3	0,1,4298	no	missense	CHST1	NM_003654.5	58	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	54/412	45672314	1,13003	2203	4299	6502	45628890	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.160G>A	11.37:g.45672314C>T	ENSP00000309270:p.Ala54Thr	Somatic		Capture	Illumina HiSeq	Phase_I	45628890	NM_003654	D3DQP2	Missense_Mutation	SNP	ENST00000308064.2	37	CCDS7913.1	.	.	.	.	.	.	.	.	.	.	C	9.849	1.193247	0.22037	0.0	1.16E-4	ENSG00000175264	ENST00000308064	D	0.96073	-3.9	4.86	-6.15	0.02105	.	1.049230	0.07435	N	0.896390	D	0.83207	0.5204	N	0.08118	0	0.22354	N	0.99918	B	0.02656	0.0	B	0.01281	0.0	T	0.75309	-0.3363	10	0.15066	T	0.55	-14.1323	1.1685	0.01820	0.2377:0.2684:0.2969:0.1971	.	54	O43916	CHST1_HUMAN	T	54	ENSP00000309270:A54T	ENSP00000309270:A54T	A	-	1	0	CHST1	45628890	0.000000	0.05858	0.827000	0.32855	0.896000	0.52359	-0.454000	0.06770	-1.183000	0.02723	-0.448000	0.05591	GCC		0.662	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390127.1	NM_003654	
MAPK8IP1	9479	broad.mit.edu	37	11	45926729	45926729	+	Silent	SNP	C	C	T	rs544815653		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:45926729C>T	ENST00000241014.2	+	11	2162	c.1992C>T	c.(1990-1992)ccC>ccT	p.P664P	RP11-618K13.2_ENST00000533218.1_RNA|MAPK8IP1_ENST00000395629.2_Silent_p.P654P	NM_005456.3	NP_005447.1	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting protein 1	664	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				JUN phosphorylation (GO:0007258)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|positive regulation of signal transduction (GO:0009967)|regulation of JNK cascade (GO:0046328)|regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic growth cone (GO:0044294)|dentate gyrus mossy fiber (GO:0044302)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)|protein kinase inhibitor activity (GO:0004860)	p.P664P(2)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)	24				GBM - Glioblastoma multiforme(35;0.231)		CCAAGCACCCCGCCGACCACC	0.632													c|||	1	0.000199681	0.0	0.0	5008	,	,		15782	0.0		0.001	False		,,,				2504	0.0				p.P664P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1992T	11						.						59.0	57.0	58.0					11																	45926729		2203	4299	6502	45883305	SO:0001819	synonymous_variant	9479	exon11				CCDS7916.1	11p11.2	2009-07-24			ENSG00000121653	ENSG00000121653			6882	protein-coding gene	gene with protein product		604641		PRKM8IP		9235893, 9442013	Standard	NM_005456		Approved	IB1, JIP-1, JIP1	uc001nbr.3	Q9UQF2	OTTHUMG00000134324	ENST00000241014.2:c.1992C>T	11.37:g.45926729C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45883305	NM_005456	D3DQP4|O43407	Silent	SNP	ENST00000241014.2	37	CCDS7916.1																																																																																				0.632	MAPK8IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259405.1	NM_005456	
PHF21A	51317	broad.mit.edu	37	11	45955597	45955597	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:45955597G>A	ENST00000418153.2	-	18	2164	c.1965C>T	c.(1963-1965)gcC>gcT	p.A655A	PHF21A_ENST00000323180.6_Silent_p.A609A|PHF21A_ENST00000257821.4_Silent_p.A656A			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	655	Required for transcriptional repression.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.A609A(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						TGGAGGTGGCGGCATTGGCAG	0.627																																					p.A655A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1965T	11						.						31.0	37.0	35.0					11																	45955597		2202	4299	6501	45912173	SO:0001819	synonymous_variant	51317	exon18			AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"""Zinc fingers, PHD-type"""	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.1965C>T	11.37:g.45955597G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45912173	NM_001101802	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Silent	SNP	ENST00000418153.2	37	CCDS44578.1																																																																																				0.627	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621	
CREB3L1	90993	broad.mit.edu	37	11	46333924	46333924	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:46333924C>T	ENST00000529193.1	+	6	1253	c.802C>T	c.(802-804)Cgg>Tgg	p.R268W	CREB3L1_ENST00000288400.3_Missense_Mutation_p.R268W			Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like 1	268					regulation of bone mineralization (GO:0030500)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|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)	p.R268W(1)	FUS/CREB3L1(6)	NS(2)|breast(1)|large_intestine(4)|lung(2)|ovary(3)	12				GBM - Glioblastoma multiforme(35;0.0285)		GGAGGAGAAGCGGACCCTGAT	0.537			T	FUS	myxofibrosarcoma																																p.R268W	Pancreas(3;159 194 19597 26278 47995)		Dom	yes		11	11p11.2	90993	cAMP responsive element binding protein 3-like 1		M	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C802T	11						.						33.0	37.0	35.0					11																	46333924		2154	4285	6439	46290500	SO:0001583	missense	90993	exon6				CCDS53620.1	11q11	2013-01-10				ENSG00000157613		"""basic leucine zipper proteins"""	18856	protein-coding gene	gene with protein product	"""BBF-2 homolog (drosophila)"""						Standard	NM_052854		Approved	OASIS	uc021qil.1	Q96BA8		ENST00000529193.1:c.802C>T	11.37:g.46333924C>T	ENSP00000434939:p.Arg268Trp	Somatic		Capture	Illumina HiSeq	Phase_I	46290500	NM_052854	Q8N2D5|Q96CP0	Missense_Mutation	SNP	ENST00000529193.1	37	CCDS53620.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.316590	0.81469	.	.	ENSG00000157613	ENST00000529193;ENST00000288400;ENST00000446415;ENST00000530518	T;T;T	0.77750	-1.12;-1.12;-1.12	4.72	4.72	0.59763	Eukaryotic transcription factor, Skn-1-like, DNA-binding (1);	0.107190	0.64402	D	0.000012	D	0.89660	0.6779	M	0.87682	2.9	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.91618	0.5308	10	0.87932	D	0	-3.7758	17.873	0.88816	0.0:1.0:0.0:0.0	.	268	Q96BA8	CR3L1_HUMAN	W	268;268;180;28	ENSP00000434939:R268W;ENSP00000288400:R268W;ENSP00000436574:R28W	ENSP00000288400:R268W	R	+	1	2	CREB3L1	46290500	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	2.277000	0.43417	2.461000	0.83175	0.655000	0.94253	CGG		0.537	CREB3L1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389702.1	NM_052854	
CREB3L1	90993	broad.mit.edu	37	11	46339005	46339005	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:46339005C>A	ENST00000529193.1	+	10	1676	c.1225C>A	c.(1225-1227)Ctg>Atg	p.L409M	CREB3L1_ENST00000288400.3_Missense_Mutation_p.L409M|CREB3L1_ENST00000534616.1_3'UTR			Q96BA8	CR3L1_HUMAN	cAMP responsive element binding protein 3-like 1	409					regulation of bone mineralization (GO:0030500)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|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)	p.L409M(1)	FUS/CREB3L1(6)	NS(2)|breast(1)|large_intestine(4)|lung(2)|ovary(3)	12				GBM - Glioblastoma multiforme(35;0.0285)		GGAAGACCCCCTGGCCGCAGA	0.672			T	FUS	myxofibrosarcoma																																p.L409M	Pancreas(3;159 194 19597 26278 47995)		Dom	yes		11	11p11.2	90993	cAMP responsive element binding protein 3-like 1		M	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1225A	11						.						43.0	47.0	46.0					11																	46339005		1987	4168	6155	46295581	SO:0001583	missense	90993	exon10				CCDS53620.1	11q11	2013-01-10				ENSG00000157613		"""basic leucine zipper proteins"""	18856	protein-coding gene	gene with protein product	"""BBF-2 homolog (drosophila)"""						Standard	NM_052854		Approved	OASIS	uc021qil.1	Q96BA8		ENST00000529193.1:c.1225C>A	11.37:g.46339005C>A	ENSP00000434939:p.Leu409Met	Somatic		Capture	Illumina HiSeq	Phase_I	46295581	NM_052854	Q8N2D5|Q96CP0	Missense_Mutation	SNP	ENST00000529193.1	37	CCDS53620.1	.	.	.	.	.	.	.	.	.	.	C	9.876	1.200273	0.22121	.	.	ENSG00000157613	ENST00000529193;ENST00000288400;ENST00000446415	T;T	0.66460	-0.21;-0.21	5.17	-3.74	0.04385	.	1.353330	0.04472	N	0.376276	T	0.45236	0.1332	N	0.12746	0.255	0.09310	N	0.999992	B;B	0.23128	0.08;0.001	B;B	0.23275	0.045;0.001	T	0.30679	-0.9970	10	0.37606	T	0.19	-1.6643	6.907	0.24315	0.3126:0.3652:0.3222:0.0	.	321;409	Q96BA8-2;Q96BA8	.;CR3L1_HUMAN	M	409;409;321	ENSP00000434939:L409M;ENSP00000288400:L409M	ENSP00000288400:L409M	L	+	1	2	CREB3L1	46295581	0.000000	0.05858	0.428000	0.26697	0.766000	0.43426	-0.404000	0.07205	-0.580000	0.05944	-0.264000	0.10439	CTG		0.672	CREB3L1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389702.1	NM_052854	
DGKZ	8525	broad.mit.edu	37	11	46395757	46395757	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:46395757C>T	ENST00000454345.1	+	16	2066	c.1941C>T	c.(1939-1941)caC>caT	p.H647H	DGKZ_ENST00000395574.3_Silent_p.H425H|DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000456247.2_Silent_p.H458H|DGKZ_ENST00000343674.6_Silent_p.H475H|DGKZ_ENST00000528615.1_Silent_p.H237H|DGKZ_ENST00000527911.1_Silent_p.H459H|DGKZ_ENST00000318201.8_Silent_p.H436H|DGKZ_ENST00000532868.2_Silent_p.H463H|DGKZ_ENST00000421244.2_Silent_p.H459H|MIR4688_ENST00000577966.1_RNA	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	647					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.H475H(1)|p.H647H(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)		TTGACGCCCACGTCACCCTGG	0.607																																					p.H459H												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1377T	11						.						92.0	83.0	86.0					11																	46395757		2202	4299	6501	46352333	SO:0001819	synonymous_variant	8525	exon15			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.1941C>T	11.37:g.46395757C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46352333	NM_003646	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Silent	SNP	ENST00000454345.1	37	CCDS41640.1																																																																																				0.607	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540	
AMBRA1	55626	broad.mit.edu	37	11	46419316	46419316	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:46419316G>A	ENST00000458649.2	-	18	3999	c.3581C>T	c.(3580-3582)aCg>aTg	p.T1194M	AMBRA1_ENST00000534300.1_Missense_Mutation_p.T1134M|AMBRA1_ENST00000533727.1_Missense_Mutation_p.T1075M|AMBRA1_ENST00000426438.1_Missense_Mutation_p.T1165M|AMBRA1_ENST00000528950.1_Missense_Mutation_p.T1165M|AMBRA1_ENST00000314845.3_Missense_Mutation_p.T1104M|AMBRA1_ENST00000298834.3_Missense_Mutation_p.T1134M			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	1194					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.T1194M(1)|p.T1104M(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)		TTCAGTGCCCGTCTGAGAGCT	0.667																																					p.T1104M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3311T	11						.						99.0	77.0	84.0					11																	46419316		2202	4299	6501	46375892	SO:0001583	missense	55626	exon19			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.3581C>T	11.37:g.46419316G>A	ENSP00000415327:p.Thr1194Met	Somatic		Capture	Illumina HiSeq	Phase_I	46375892	NM_017749	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	37		.	.	.	.	.	.	.	.	.	.	G	22.9	4.355791	0.82243	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000458649;ENST00000526545;ENST00000528950	T;T;T;T;T;T;T	0.79554	-1.19;-1.28;-0.94;-1.07;-0.94;-1.06;-1.07	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	D	0.84665	0.5522	L	0.27053	0.805	0.58432	D	0.999999	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	0.87578	0.994;0.997;0.997;0.997;0.998;0.997	D	0.86638	0.1890	10	0.87932	D	0	.	18.8444	0.92198	0.0:0.0:1.0:0.0	.	1194;1165;1134;1075;1197;1104	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	M	1104;1075;1134;1165;1134;1194;152;1165	ENSP00000318313:T1104M;ENSP00000433372:T1075M;ENSP00000431926:T1134M;ENSP00000410899:T1165M;ENSP00000298834:T1134M;ENSP00000415327:T1194M;ENSP00000433945:T1165M	ENSP00000298834:T1134M	T	-	2	0	AMBRA1	46375892	1.000000	0.71417	0.997000	0.53966	0.840000	0.47671	9.183000	0.94887	2.679000	0.91253	0.655000	0.94253	ACG		0.667	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749	
F2	2147	broad.mit.edu	37	11	46747647	46747647	+	Silent	SNP	C	C	T	rs138260543	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:46747647C>T	ENST00000311907.5	+	7	854	c.798C>T	c.(796-798)gaC>gaT	p.D266D	F2_ENST00000530231.1_Silent_p.D266D	NM_000506.3	NP_000497.1	P00734	THRB_HUMAN	coagulation factor II (thrombin)	266	Kringle 2. {ECO:0000255|PROSITE- ProRule:PRU00121}.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell surface receptor signaling pathway (GO:0007166)|cellular protein metabolic process (GO:0044267)|cytosolic calcium ion homeostasis (GO:0051480)|fibrinolysis (GO:0042730)|leukocyte migration (GO:0050900)|multicellular organismal development (GO:0007275)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|negative regulation of proteolysis (GO:0045861)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900738)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of blood coagulation (GO:0030193)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|thrombospondin receptor activity (GO:0070053)	p.D266D(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	27		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|ART-123(DB05777)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Dabigatran etexilate(DB06695)|Drotrecogin alfa(DB00055)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Suramin(DB04786)|Ximelagatran(DB04898)	GCAACCCAGACGGGGATGAGG	0.637													C|||	6	0.00119808	0.0	0.0014	5008	,	,		18478	0.0		0.0	False		,,,				2504	0.0051				p.D266D	Esophageal Squamous(147;1147 1808 2148 38609 51144)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C798T	11						.	C		0,4402		0,0,2201	77.0	89.0	85.0		798	-2.3	0.3	11	dbSNP_134	85	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	F2	NM_000506.3		0,1,6499	TT,TC,CC		0.0116,0.0,0.0077		266/623	46747647	1,12999	2201	4299	6500	46704223	SO:0001819	synonymous_variant	2147	exon7			M33031	CCDS31476.1	11p11.2	2013-02-28			ENSG00000180210	ENSG00000180210	3.4.21.5	"""Endogenous ligands"""	3535	protein-coding gene	gene with protein product	"""prepro-coagulation factor II"""	176930					Standard	NM_000506		Approved		uc001ndf.4	P00734	OTTHUMG00000150344	ENST00000311907.5:c.798C>T	11.37:g.46747647C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46704223	NM_000506	B2R7F7|B4E1A7|Q4QZ40|Q53H04|Q53H06|Q69EZ7|Q7Z7P3|Q9UCA1	Silent	SNP	ENST00000311907.5	37	CCDS31476.1																																																																																				0.637	F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317706.1		
NR1H3	10062	broad.mit.edu	37	11	47283147	47283147	+	Missense_Mutation	SNP	G	G	A	rs565653980		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:47283147G>A	ENST00000467728.1	+	5	1996	c.758G>A	c.(757-759)cGc>cAc	p.R253H	NR1H3_ENST00000529540.1_3'UTR|NR1H3_ENST00000405853.3_Intron|NR1H3_ENST00000481889.2_Missense_Mutation_p.R208H|NR1H3_ENST00000441012.2_Missense_Mutation_p.R253H|NR1H3_ENST00000405576.1_Intron|NR1H3_ENST00000395397.3_Missense_Mutation_p.R208H|NR1H3_ENST00000407404.1_Intron|NR1H3_ENST00000527949.1_Intron			Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	253	Ligand-binding. {ECO:0000255}.				apoptotic cell clearance (GO:0043277)|cellular lipid metabolic process (GO:0044255)|cellular response to lipopolysaccharide (GO:0071222)|cholesterol homeostasis (GO:0042632)|gene expression (GO:0010467)|lipid homeostasis (GO:0055088)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage activation (GO:0043031)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of pinocytosis (GO:0048550)|negative regulation of proteolysis (GO:0045861)|negative regulation of secretion of lysosomal enzymes (GO:0090341)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|response to progesterone (GO:0032570)|sterol homeostasis (GO:0055092)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|DNA binding (GO:0003677)|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 positive regulation of transcription (GO:0001077)|steroid hormone receptor activity (GO:0003707)|sterol response element binding (GO:0032810)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.R253H(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(5)	20						CGTCAGCAGCGCTTTGCCCAC	0.597																																					p.R208H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G623A	11						.						69.0	68.0	69.0					11																	47283147		2201	4298	6499	47239723	SO:0001583	missense	10062	exon5			U22662	CCDS7929.1, CCDS44584.1, CCDS44585.1, CCDS73285.1	11p11.2	2013-01-16			ENSG00000025434	ENSG00000025434		"""Nuclear hormone receptors"""	7966	protein-coding gene	gene with protein product	"""liver X receptor-alpha"""	602423				8621574, 7744246	Standard	NM_005693		Approved	LXR-a, RLD-1	uc009ylm.3	Q13133	OTTHUMG00000150628	ENST00000467728.1:c.758G>A	11.37:g.47283147G>A	ENSP00000420656:p.Arg253His	Somatic		Capture	Illumina HiSeq	Phase_I	47239723	NM_001130102	A8K3J9|D3DQR1|Q8IW13|Q96H87	Missense_Mutation	SNP	ENST00000467728.1	37	CCDS7929.1	.	.	.	.	.	.	.	.	.	.	G	34	5.328775	0.95733	.	.	ENSG00000025434	ENST00000395397;ENST00000481889;ENST00000441012;ENST00000467728	D;D;D;D	0.96716	-4.1;-4.1;-4.1;-4.1	5.77	5.77	0.91146	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (1);	0.000000	0.85682	D	0.000000	D	0.97791	0.9275	M	0.64170	1.965	0.80722	D	1	D;D;D	0.89917	0.974;1.0;1.0	P;D;D	0.91635	0.477;0.999;0.999	D	0.97507	1.0064	10	0.51188	T	0.08	.	20.3626	0.98863	0.0:0.0:1.0:0.0	.	259;253;208	B4DXU5;Q13133;E9PLL4	.;NR1H3_HUMAN;.	H	208;208;253;253	ENSP00000378793:R208H;ENSP00000433271:R208H;ENSP00000387946:R253H;ENSP00000420656:R253H	ENSP00000378793:R208H	R	+	2	0	NR1H3	47239723	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.885000	0.99019	0.655000	0.94253	CGC		0.597	NR1H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319214.3		
MADD	8567	broad.mit.edu	37	11	47304002	47304002	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:47304002C>T	ENST00000311027.5	+	9	1705	c.1540C>T	c.(1540-1542)Cgc>Tgc	p.R514C	MADD_ENST00000407859.3_Missense_Mutation_p.R514C|MADD_ENST00000342922.4_Missense_Mutation_p.R514C|MADD_ENST00000395336.3_Missense_Mutation_p.R514C|MADD_ENST00000406482.1_Missense_Mutation_p.R514C|MADD_ENST00000395344.3_Missense_Mutation_p.R514C|MADD_ENST00000402799.1_Missense_Mutation_p.R514C|MADD_ENST00000402192.2_Missense_Mutation_p.R514C|MADD_ENST00000489415.1_3'UTR|MADD_ENST00000349238.3_Missense_Mutation_p.R514C	NM_003682.3	NP_003673.3			MAP-kinase activating death domain									p.R514C(1)		breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		GCGTACCCTGCGCCTCTTTCC	0.557																																					p.R514C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1540T	11						.						114.0	110.0	111.0					11																	47304002		2201	4298	6499	47260578	SO:0001583	missense	8567	exon9			AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.1540C>T	11.37:g.47304002C>T	ENSP00000310933:p.Arg514Cys	Somatic		Capture	Illumina HiSeq	Phase_I	47260578	NM_003682		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.034181	0.93575	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8	5.7	4.78	0.61160	dDENN (3);	0.000000	0.85682	D	0.000000	T	0.67581	0.2908	M	0.69358	2.11	0.80722	D	1	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	D;D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;0.999;0.998;0.998;0.999;0.998;0.999;1.0;1.0	T	0.72297	-0.4335	10	0.87932	D	0	-9.3776	16.3338	0.83052	0.1334:0.8666:0.0:0.0	.	514;514;514;514;514;514;514;514;514;514	B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;MADD_HUMAN;.	C	514	ENSP00000343902:R514C;ENSP00000385585:R514C;ENSP00000384435:R514C;ENSP00000304505:R514C;ENSP00000310933:R514C;ENSP00000384204:R514C;ENSP00000378753:R514C;ENSP00000378745:R514C;ENSP00000384287:R514C	ENSP00000310933:R514C	R	+	1	0	MADD	47260578	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.690000	0.68241	1.521000	0.48983	0.655000	0.94253	CGC		0.557	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
MADD	8567	broad.mit.edu	37	11	47331084	47331084	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:47331084G>A	ENST00000311027.5	+	28	4244	c.4079G>A	c.(4078-4080)cGg>cAg	p.R1360Q	MADD_ENST00000407859.3_Missense_Mutation_p.R1278Q|MADD_ENST00000342922.4_Missense_Mutation_p.R1301Q|MADD_ENST00000395336.3_Missense_Mutation_p.R1360Q|MADD_ENST00000405573.2_Missense_Mutation_p.R170Q|MADD_ENST00000406482.1_Missense_Mutation_p.R1258Q|MADD_ENST00000395344.3_Missense_Mutation_p.R1254Q|MADD_ENST00000402799.1_Missense_Mutation_p.R1258Q|MADD_ENST00000402192.2_Missense_Mutation_p.R1300Q|MADD_ENST00000349238.3_Missense_Mutation_p.R1321Q	NM_003682.3	NP_003673.3			MAP-kinase activating death domain									p.R1360Q(1)		breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		GAACATGACCGGAAGCGCCTG	0.502																																					p.R1360Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4079A	11						.						152.0	134.0	140.0					11																	47331084		2201	4298	6499	47287660	SO:0001583	missense	8567	exon28			AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.4079G>A	11.37:g.47331084G>A	ENSP00000310933:p.Arg1360Gln	Somatic		Capture	Illumina HiSeq	Phase_I	47287660	NM_003682		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.962697	0.92791	.	.	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192;ENST00000405573	T;T;T;T;T;T;T;T;T;T	0.58506	2.91;2.75;2.75;2.89;2.83;2.76;2.79;2.82;2.91;0.33	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.71273	0.3320	L	0.48642	1.525	0.80722	D	1	D;P;P;D;P;D;D;D;D;D;D	0.89917	0.997;0.933;0.888;1.0;0.932;0.96;0.96;0.999;1.0;0.999;0.999	P;B;B;D;B;B;B;D;D;D;D	0.85130	0.894;0.187;0.187;0.997;0.346;0.346;0.346;0.996;0.996;0.992;0.996	T	0.72064	-0.4403	10	0.49607	T	0.09	-15.5906	18.4016	0.90518	0.0:0.0:1.0:0.0	.	170;1254;1254;1360;1258;1258;1258;1321;1278;1360;1301	F8W8U2;B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;.;MADD_HUMAN;.	Q	1301;1258;1258;1258;1321;1360;1278;1254;1360;1300;170	ENSP00000343902:R1301Q;ENSP00000385585:R1258Q;ENSP00000384435:R1258Q;ENSP00000304505:R1321Q;ENSP00000310933:R1360Q;ENSP00000384204:R1278Q;ENSP00000378753:R1254Q;ENSP00000378745:R1360Q;ENSP00000384287:R1300Q;ENSP00000384483:R170Q	ENSP00000310933:R1360Q	R	+	2	0	MADD	47287660	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.655000	0.83696	2.327000	0.79052	0.563000	0.77884	CGG		0.502	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
NDUFS3	4722	broad.mit.edu	37	11	47603682	47603682	+	Missense_Mutation	SNP	C	C	T	rs146407178		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:47603682C>T	ENST00000263774.4	+	5	506	c.424C>T	c.(424-426)Cgt>Tgt	p.R142C	NDUFS3_ENST00000533507.1_3'UTR	NM_004551.2	NP_004542.1	O75489	NDUS3_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)	142					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)	p.R142C(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)	9					Doxorubicin(DB00997)	CTCACGGATCCGTGTGAAGAC	0.517																																					p.R142C	Pancreas(15;551 601 22438 23457 52512)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C424T	11						.	C	CYS/ARG	0,4402		0,0,2201	175.0	161.0	166.0		424	5.2	1.0	11	dbSNP_134	166	1,8595	1.2+/-3.3	0,1,4297	no	missense	NDUFS3	NM_004551.2	180	0,1,6498	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	142/265	47603682	1,12997	2201	4298	6499	47560258	SO:0001583	missense	4722	exon5			AF067139	CCDS7941.1	11p11.11	2011-08-03	2002-08-29		ENSG00000213619	ENSG00000213619	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7710	protein-coding gene	gene with protein product	"""complex I 30kDa subunit"", ""NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial"""	603846	"""NADH dehydrogenase (ubiquinone) Fe-S protein 3 (30kD) (NADH-coenzyme Q reductase)"""			9763677	Standard	NM_004551		Approved	CI-30	uc001nga.2	O75489	OTTHUMG00000166893	ENST00000263774.4:c.424C>T	11.37:g.47603682C>T	ENSP00000263774:p.Arg142Cys	Somatic		Capture	Illumina HiSeq	Phase_I	47560258	NM_004551	B2R9J1|B4DFM8|Q9UNQ8	Missense_Mutation	SNP	ENST00000263774.4	37	CCDS7941.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.912382	0.92178	0.0	1.16E-4	ENSG00000213619	ENST00000263774	D	0.87256	-2.23	6.08	5.17	0.71159	NADH:ubiquinone oxidoreductase, 30kDa subunit (2);	0.044975	0.85682	D	0.000000	D	0.92808	0.7713	M	0.93062	3.375	0.80722	D	1	P;D	0.56968	0.947;0.978	P;P	0.51453	0.529;0.67	D	0.94308	0.7543	10	0.87932	D	0	-17.7513	15.3227	0.74135	0.0:0.9332:0.0:0.0668	.	142;68	O75489;Q9UF24	NDUS3_HUMAN;.	C	142	ENSP00000263774:R142C	ENSP00000263774:R142C	R	+	1	0	NDUFS3	47560258	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.265000	0.78442	1.580000	0.49851	0.655000	0.94253	CGT		0.517	NDUFS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391749.1	NM_004551	
FNBP4	23360	broad.mit.edu	37	11	47754094	47754094	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:47754094C>A	ENST00000263773.5	-	11	1827	c.1815G>T	c.(1813-1815)tgG>tgT	p.W605C	FNBP4_ENST00000534003.1_5'UTR	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	605	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.					nucleus (GO:0005634)		p.W605C(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						CGTACCTGTCCCAGTGGCAGG	0.458																																					p.W605C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1815T	11						.						209.0	227.0	221.0					11																	47754094		2056	4206	6262	47710670	SO:0001583	missense	23360	exon11			BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.1815G>T	11.37:g.47754094C>A	ENSP00000263773:p.Trp605Cys	Somatic		Capture	Illumina HiSeq	Phase_I	47710670	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Missense_Mutation	SNP	ENST00000263773.5	37	CCDS41644.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490336	0.64074	.	.	ENSG00000109920	ENST00000263773	D	0.83335	-1.71	5.66	5.66	0.87406	WW/Rsp5/WWP (6);	0.000000	0.85682	D	0.000000	D	0.93177	0.7827	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93954	0.7234	10	0.87932	D	0	-5.377	19.7604	0.96314	0.0:1.0:0.0:0.0	.	605	Q8N3X1	FNBP4_HUMAN	C	605	ENSP00000263773:W605C	ENSP00000263773:W605C	W	-	3	0	FNBP4	47710670	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.675000	0.91044	0.655000	0.94253	TGG		0.458	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3		
FNBP4	23360	broad.mit.edu	37	11	47774584	47774584	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:47774584G>T	ENST00000263773.5	-	4	533	c.521C>A	c.(520-522)cCt>cAt	p.P174H	FNBP4_ENST00000534003.1_5'UTR	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	174						nucleus (GO:0005634)		p.P174H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						CTCTGGTCGAGGTGGAGTTGG	0.478																																					p.P174H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C521A	11						.						112.0	112.0	112.0					11																	47774584		1966	4147	6113	47731160	SO:0001583	missense	23360	exon4			BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.521C>A	11.37:g.47774584G>T	ENSP00000263773:p.Pro174His	Somatic		Capture	Illumina HiSeq	Phase_I	47731160	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Missense_Mutation	SNP	ENST00000263773.5	37	CCDS41644.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650023	0.87958	.	.	ENSG00000109920	ENST00000263773	T	0.33865	1.39	5.85	5.85	0.93711	.	0.052085	0.85682	D	0.000000	T	0.61337	0.2339	M	0.66939	2.045	0.58432	D	0.999995	D	0.89917	1.0	D	0.78314	0.991	T	0.60255	-0.7299	10	0.59425	D	0.04	-15.9603	19.76	0.96311	0.0:0.0:1.0:0.0	.	174	Q8N3X1	FNBP4_HUMAN	H	174	ENSP00000263773:P174H	ENSP00000263773:P174H	P	-	2	0	FNBP4	47731160	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.081000	0.71309	2.753000	0.94483	0.655000	0.94253	CCT		0.478	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3		
OR4X1	390113	broad.mit.edu	37	11	48285855	48285855	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:48285855G>A	ENST00000320048.1	+	1	443	c.443G>A	c.(442-444)gGc>gAc	p.G148D		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	148						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G148D(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	28						ATAGCATGGGGCGGGGGCCTG	0.557																																					p.G148D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G443A	11						.						90.0	81.0	84.0					11																	48285855		2201	4298	6499	48242431	SO:0001583	missense	390113	exon1			AB065544	CCDS31487.1	11p11.2	2013-10-10	2013-10-10		ENSG00000176567	ENSG00000176567		"""GPCR / Class A : Olfactory receptors"""	14854	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily X, member 1"""				Standard	NM_001004726		Approved		uc010rht.2	Q8NH49	OTTHUMG00000165301	ENST00000320048.1:c.443G>A	11.37:g.48285855G>A	ENSP00000321506:p.Gly148Asp	Somatic		Capture	Illumina HiSeq	Phase_I	48242431	NM_001004726	Q6IF74	Missense_Mutation	SNP	ENST00000320048.1	37	CCDS31487.1	.	.	.	.	.	.	.	.	.	.	G	9.480	1.097906	0.20552	.	.	ENSG00000176567	ENST00000320048	T	0.38240	1.15	4.28	-0.442	0.12253	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.36853	0.0982	M	0.72479	2.2	0.09310	N	1	P	0.34864	0.473	B	0.37144	0.242	T	0.38045	-0.9679	9	0.87932	D	0	.	7.9304	0.29899	0.0:0.1419:0.2917:0.5664	.	148	Q8NH49	OR4X1_HUMAN	D	148	ENSP00000321506:G148D	ENSP00000321506:G148D	G	+	2	0	OR4X1	48242431	0.000000	0.05858	0.010000	0.14722	0.490000	0.33462	-1.005000	0.03674	0.144000	0.18951	0.539000	0.68188	GGC		0.557	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726	
OR5I1	10798	broad.mit.edu	37	11	55703444	55703444	+	Missense_Mutation	SNP	G	G	A	rs565054095		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:55703444G>A	ENST00000301532.3	-	1	432	c.433C>T	c.(433-435)Cgg>Tgg	p.R145W		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	145					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R145W(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						ACAATCAACCGCATACAGATG	0.428													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19540	0.0		0.0	False		,,,				2504	0.0				p.R145W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C433T	11						.						81.0	85.0	83.0					11																	55703444		2201	4296	6497	55460020	SO:0001583	missense	10798	exon1			BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"""GPCR / Class A : Olfactory receptors"""	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.433C>T	11.37:g.55703444G>A	ENSP00000301532:p.Arg145Trp	Somatic		Capture	Illumina HiSeq	Phase_I	55460020	NM_006637	Q6IEU4	Missense_Mutation	SNP	ENST00000301532.3	37	CCDS7949.1	.	.	.	.	.	.	.	.	.	.	G	4.275	0.050126	0.08243	.	.	ENSG00000167825	ENST00000301532	T	0.00130	8.69	4.94	-5.59	0.02505	GPCR, rhodopsin-like superfamily (1);	0.678027	0.13048	N	0.417906	T	0.00073	0.0002	N	0.13352	0.335	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.11792	-1.0573	10	0.36615	T	0.2	.	8.6427	0.33987	0.3803:0.1249:0.4947:0.0	.	145	Q13606	OR5I1_HUMAN	W	145	ENSP00000301532:R145W	ENSP00000301532:R145W	R	-	1	2	OR5I1	55460020	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-6.454000	0.00065	-1.036000	0.03287	-1.239000	0.01543	CGG		0.428	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637	
OR5T2	219464	broad.mit.edu	37	11	55999585	55999585	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:55999585delT	ENST00000313264.4	-	1	1152	c.1077delA	c.(1075-1077)aaafs	p.K359fs		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	359						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	?(1)		endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TTATAATTTATTTTTTAGTAT	0.338																																					p.K359fs												.	.	1	Unknown(1)	large_intestine(1)	c.1077delA	11						.						11.0	12.0	12.0					11																	55999585		2101	4162	6263	55756161	SO:0001589	frameshift_variant	219464	exon1			AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.1077delA	11.37:g.55999585delT	ENSP00000323688:p.Lys359fs	Somatic		Capture	Illumina HiSeq	Phase_I	55756161	NM_001004746	B9EGX5|Q6IFC8	Frame_Shift_Del	DEL	ENST00000313264.4	37	CCDS31523.1																																																																																				0.338	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
LRRC55	219527	broad.mit.edu	37	11	56950146	56950146	+	Missense_Mutation	SNP	G	G	A	rs201169874		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:56950146G>A	ENST00000497933.1	+	1	926	c.779G>A	c.(778-780)cGc>cAc	p.R260H		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	230	LRRCT.				ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R260H(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						CGGATCCAGCGCTGTACAGCA	0.607																																					p.R260H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G779A	11						.	G	HIS/ARG	0,4402		0,0,2201	64.0	60.0	61.0		779	5.5	1.0	11		61	1,8589	1.2+/-3.3	0,1,4294	yes	missense	LRRC55	NM_001005210.2	29	0,1,6495	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	260/342	56950146	1,12991	2201	4295	6496	56706722	SO:0001583	missense	219527	exon1				CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	ENST00000497933.1:c.779G>A	11.37:g.56950146G>A	ENSP00000419542:p.Arg260His	Somatic		Capture	Illumina HiSeq	Phase_I	56706722	NM_001005210	A7E2U7|B2RN81	Missense_Mutation	SNP	ENST00000497933.1	37	CCDS31539.1	.	.	.	.	.	.	.	.	.	.	G	18.22	3.575277	0.65878	0.0	1.16E-4	ENSG00000183908	ENST00000497933	T	0.22336	1.96	5.53	5.53	0.82687	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.64402	D	0.000016	T	0.18718	0.0449	L	0.55481	1.735	0.53688	D	0.99997	P	0.36789	0.57	B	0.17433	0.018	T	0.03017	-1.1082	10	0.32370	T	0.25	.	16.3896	0.83531	0.0:0.0:1.0:0.0	.	230	Q6ZSA7	LRC55_HUMAN	H	260	ENSP00000419542:R260H	ENSP00000419542:R260H	R	+	2	0	LRRC55	56706722	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	4.630000	0.61297	2.608000	0.88229	0.561000	0.74099	CGC		0.607	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210	
SLC43A3	29015	broad.mit.edu	37	11	57193027	57193027	+	Missense_Mutation	SNP	G	G	A	rs140882001		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:57193027G>A	ENST00000395123.2	-	4	605	c.301C>T	c.(301-303)Cgc>Tgc	p.R101C	SLC43A3_ENST00000529554.1_Missense_Mutation_p.R101C|SLC43A3_ENST00000533524.1_Missense_Mutation_p.R114C|SLC43A3_ENST00000352187.1_Missense_Mutation_p.R101C|SLC43A3_ENST00000528098.1_5'UTR|SLC43A3_ENST00000395124.1_Missense_Mutation_p.R101C	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	101					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.R101C(1)		central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						GCTATGAGGCGTGCCACGGTG	0.527																																					p.R101C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C301T	11						.	G	CYS/ARG,CYS/ARG,CYS/ARG	0,4402		0,0,2201	117.0	103.0	108.0		301,301,301	3.5	1.0	11	dbSNP_134	108	1,8591	1.2+/-3.3	0,1,4295	no	missense,missense,missense	SLC43A3	NM_014096.2,NM_017611.2,NM_199329.1	180,180,180	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	101/492,101/492,101/492	57193027	1,12993	2201	4296	6497	56949603	SO:0001583	missense	29015	exon4			AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"""Solute carriers"""	17466	protein-coding gene	gene with protein product	"""likely ortholog of mouse embryonic epithelial gene 1"""					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.301C>T	11.37:g.57193027G>A	ENSP00000378555:p.Arg101Cys	Somatic		Capture	Illumina HiSeq	Phase_I	56949603	NM_199329	B4DNR8|E7EQD2|Q9NSS4	Missense_Mutation	SNP	ENST00000395123.2	37	CCDS7956.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.011325	0.75046	0.0	1.16E-4	ENSG00000134802	ENST00000395123;ENST00000395124;ENST00000352187;ENST00000529554;ENST00000533524;ENST00000530005;ENST00000529113;ENST00000525474;ENST00000529112;ENST00000528187;ENST00000529494;ENST00000533245;ENST00000533235;ENST00000524863	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.17;0.25	5.4	3.51	0.40186	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.74854	0.3771	M	0.87900	2.915	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	0.72953	-0.4135	10	0.38643	T	0.18	-23.4735	8.3563	0.32331	0.079:0.0:0.7667:0.1542	.	101;114;101	B4DV87;E7EQD2;Q8NBI5	.;.;S43A3_HUMAN	C	101;101;101;101;114;101;48;101;101;114;101;101;101;101	ENSP00000378555:R101C;ENSP00000378556:R101C;ENSP00000337561:R101C;ENSP00000436254:R101C;ENSP00000434515:R114C;ENSP00000435893:R101C;ENSP00000434293:R48C;ENSP00000436055:R101C;ENSP00000434913:R101C;ENSP00000435273:R114C;ENSP00000433974:R101C;ENSP00000431762:R101C;ENSP00000435156:R101C;ENSP00000434569:R101C	ENSP00000337561:R101C	R	-	1	0	SLC43A3	56949603	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	2.284000	0.43478	0.633000	0.30452	0.561000	0.74099	CGC		0.527	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611	
SERPING1	710	broad.mit.edu	37	11	57373678	57373678	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:57373678A>G	ENST00000278407.4	+	5	1108	c.881A>G	c.(880-882)tAc>tGc	p.Y294C	SERPING1_ENST00000378324.2_Missense_Mutation_p.Y242C|SERPING1_ENST00000403558.1_Missense_Mutation_p.Y328C|SERPING1_ENST00000378323.4_Missense_Mutation_p.Y299C|SERPING1_ENST00000340687.6_Missense_Mutation_p.Y294C	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	294					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.Y294C(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(1)	27						AATGCTATCTACCTGAGTGGT	0.537																																					p.Y294C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A881G	11						.						158.0	148.0	151.0					11																	57373678		2201	4296	6497	57130254	SO:0001583	missense	710	exon5			X54486	CCDS7962.1	11q12.1	2014-09-17	2008-07-31		ENSG00000149131	ENSG00000149131		"""Serine (or cysteine) peptidase inhibitors"""	1228	protein-coding gene	gene with protein product	"""plasma protease C1 inhibitor"", ""angioedema, hereditary"""	606860	"""serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)"""	C1NH		2026152, 24172014	Standard	NM_000062		Approved	C1IN, C1-INH, HAE1, HAE2	uc001nkp.1	P05155	OTTHUMG00000150304	ENST00000278407.4:c.881A>G	11.37:g.57373678A>G	ENSP00000278407:p.Tyr294Cys	Somatic		Capture	Illumina HiSeq	Phase_I	57130254	NM_000062	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Missense_Mutation	SNP	ENST00000278407.4	37	CCDS7962.1	.	.	.	.	.	.	.	.	.	.	A	14.88	2.668253	0.47677	.	.	ENSG00000149131	ENST00000278407;ENST00000340687;ENST00000378323;ENST00000378324;ENST00000403558	D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37	5.14	2.74	0.32292	Serpin domain (3);	0.299670	0.33161	N	0.005206	D	0.94647	0.8274	M	0.91300	3.195	0.40334	D	0.978956	D;D;D;D	0.89917	0.998;1.0;0.998;0.998	D;D;D;D	0.76071	0.962;0.987;0.962;0.962	D	0.93887	0.7176	10	0.87932	D	0	.	10.1614	0.42853	0.6765:0.3235:0.0:0.0	.	299;328;294;294	B4E1F0;E9PGN7;E9KL26;P05155	.;.;.;IC1_HUMAN	C	294;294;299;242;328	ENSP00000278407:Y294C;ENSP00000341861:Y294C;ENSP00000367574:Y299C;ENSP00000367575:Y242C;ENSP00000384420:Y328C	ENSP00000278407:Y294C	Y	+	2	0	SERPING1	57130254	1.000000	0.71417	0.986000	0.45419	0.812000	0.45895	2.316000	0.43761	0.272000	0.22027	0.459000	0.35465	TAC		0.537	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062	
CNTF	1270	broad.mit.edu	37	11	58390315	58390315	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:58390315C>T	ENST00000361987.4	+	1	170	c.90C>T	c.(88-90)gaC>gaT	p.D30D	ZFP91-CNTF_ENST00000389919.4_3'UTR	NM_000614.3	NP_000605.1	P26441	CNTF_HUMAN	ciliary neurotrophic factor	30					ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|growth (GO:0040007)|muscle organ morphogenesis (GO:0048644)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of photoreceptor cell differentiation (GO:0046533)|neuron development (GO:0048666)|positive regulation of cell proliferation (GO:0008284)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of retinal cell programmed cell death (GO:0046668)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor activity (GO:0008083)|interleukin-6 receptor binding (GO:0005138)	p.D30D(1)		NS(1)|breast(1)|kidney(2)|large_intestine(4)|lung(1)|ovary(1)	10		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				TTCGTTCAGACCTGACTGCTC	0.478																																					p.D30D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C90T	11						.						130.0	119.0	123.0					11																	58390315		2201	4295	6496	58146891	SO:0001819	synonymous_variant	1270	exon1			BC068030	CCDS31554.1	11q12	2011-07-21			ENSG00000242689	ENSG00000242689			2169	protein-coding gene	gene with protein product		118945				1840538, 1714745	Standard	NM_000614		Approved	HCNTF	uc001nna.4	P26441	OTTHUMG00000137476	ENST00000361987.4:c.90C>T	11.37:g.58390315C>T		Somatic		Capture	Illumina HiSeq	Phase_I	58146891	NM_000614	B2RAB2	Silent	SNP	ENST00000361987.4	37	CCDS31554.1																																																																																				0.478	CNTF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268673.1	NM_000614	
GLYAT	10249	broad.mit.edu	37	11	58478160	58478160	+	Missense_Mutation	SNP	G	G	A	rs200442404	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:58478160G>A	ENST00000344743.3	-	5	532	c.391C>T	c.(391-393)Cgc>Tgc	p.R131C	GLYAT_ENST00000278400.3_Missense_Mutation_p.R131C|GLYAT_ENST00000529732.1_Missense_Mutation_p.R131C	NM_201648.2	NP_964011.2	Q6IB77	GLYAT_HUMAN	glycine-N-acyltransferase	131					acyl-CoA metabolic process (GO:0006637)|glycine metabolic process (GO:0006544)|monocarboxylic acid metabolic process (GO:0032787)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)|glycine N-benzoyltransferase activity (GO:0047962)|transferase activity, transferring acyl groups (GO:0016746)	p.R131C(1)		NS(1)|autonomic_ganglia(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16		Breast(21;0.0044)|all_epithelial(135;0.0157)			Glycine(DB00145)	TAGAGAATGCGTTGTGTTTGT	0.428													G|||	11	0.00219649	0.0	0.0	5008	,	,		20019	0.0		0.0	False		,,,				2504	0.0112				p.R131C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C391T	11						.						172.0	155.0	161.0					11																	58478160		2201	4295	6496	58234736	SO:0001583	missense	10249	exon5			AF023466	CCDS7970.1, CCDS7971.1	11q12.1	2008-03-11					2.3.1.13		13734	protein-coding gene	gene with protein product		607424					Standard	NM_201648		Approved	GAT, ACGNAT	uc001nnb.3	Q6IB77		ENST00000344743.3:c.391C>T	11.37:g.58478160G>A	ENSP00000340200:p.Arg131Cys	Somatic		Capture	Illumina HiSeq	Phase_I	58234736	NM_201648	O14833|Q96QK7	Missense_Mutation	SNP	ENST00000344743.3	37	CCDS7970.1	.	.	.	.	.	.	.	.	.	.	G	10.69	1.419945	0.25552	.	.	ENSG00000149124	ENST00000344743;ENST00000529732;ENST00000278400	T;T;T	0.16743	2.32;2.32;2.32	5.88	-11.8	0.00035	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	1.761000	0.02153	N	0.058160	T	0.03739	0.0106	N	0.01122	-1.005	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.33394	-0.9870	10	0.22706	T	0.39	-0.0383	4.6346	0.12518	0.1113:0.0801:0.2257:0.5829	.	131;131	Q6IB77-2;Q6IB77	.;GLYAT_HUMAN	C	131	ENSP00000340200:R131C;ENSP00000431688:R131C;ENSP00000278400:R131C	ENSP00000278400:R131C	R	-	1	0	GLYAT	58234736	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.479000	0.02327	-1.461000	0.01909	-1.147000	0.01851	CGC		0.428	GLYAT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394593.1		
GLYATL2	219970	broad.mit.edu	37	11	58604852	58604852	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:58604852C>T	ENST00000287275.1	-	4	595	c.205G>A	c.(205-207)Gat>Aat	p.D69N	GLYATL2_ENST00000533636.1_5'UTR|GLYATL2_ENST00000532258.1_Missense_Mutation_p.D69N	NM_145016.3	NP_659453.3	Q8WU03	GLYL2_HUMAN	glycine-N-acyltransferase-like 2	69						endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)	p.D69N(1)		breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	23		Breast(21;0.0044)|all_epithelial(135;0.0216)			Glycine(DB00145)	GTATAATGATCCTGGTCATCT	0.368																																					p.D69N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G205A	11						.						189.0	177.0	181.0					11																	58604852		1853	4104	5957	58361428	SO:0001583	missense	219970	exon4			AF426250	CCDS41649.1	11q12.1	2008-02-05				ENSG00000156689			24178	protein-coding gene	gene with protein product		614762				12477932	Standard	NM_145016		Approved	BXMAS2-10, MGC24009	uc001nnd.4	Q8WU03		ENST00000287275.1:c.205G>A	11.37:g.58604852C>T	ENSP00000287275:p.Asp69Asn	Somatic		Capture	Illumina HiSeq	Phase_I	58361428	NM_145016	A5LGC7|Q86WC3|Q96AT2	Missense_Mutation	SNP	ENST00000287275.1	37	CCDS41649.1	.	.	.	.	.	.	.	.	.	.	C	16.89	3.248203	0.59103	.	.	ENSG00000156689	ENST00000287275;ENST00000532258	T;T	0.28255	1.62;1.62	4.24	3.3	0.37823	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	0.413669	0.22322	U	0.061590	T	0.53706	0.1813	M	0.83012	2.62	0.19945	N	0.99994	D	0.89917	1.0	D	0.91635	0.999	T	0.39121	-0.9629	10	0.59425	D	0.04	.	8.6115	0.33806	0.0:0.8858:0.0:0.1142	.	69	Q8WU03	GLYL2_HUMAN	N	69	ENSP00000287275:D69N;ENSP00000434277:D69N	ENSP00000287275:D69N	D	-	1	0	GLYATL2	58361428	0.935000	0.31712	0.332000	0.25469	0.818000	0.46254	1.972000	0.40540	1.947000	0.56498	0.644000	0.83932	GAT		0.368	GLYATL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394599.1	NM_145016	
OR4D10	390197	broad.mit.edu	37	11	59245201	59245201	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:59245201A>G	ENST00000530162.1	+	1	356	c.299A>G	c.(298-300)cAg>cGg	p.Q100R		NM_001004705.1	NP_001004705.1	Q8NGI6	OR4DA_HUMAN	olfactory receptor, family 4, subfamily D, member 10	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q98R(1)		NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TGCTTCACTCAGATGTTTCTA	0.468																																					p.Q100R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A299G	11						.						98.0	98.0	98.0					11																	59245201		2097	4237	6334	59001777	SO:0001583	missense	390197	exon1			AB065808	CCDS53636.1	11q12.1	2012-10-03		2004-03-10	ENSG00000254466	ENSG00000254466		"""GPCR / Class A : Olfactory receptors"""	15173	protein-coding gene	gene with protein product				OR4D10P			Standard	NM_001004705		Approved	OST711	uc001nnz.1	Q8NGI6	OTTHUMG00000167341	ENST00000530162.1:c.299A>G	11.37:g.59245201A>G	ENSP00000436424:p.Gln100Arg	Somatic		Capture	Illumina HiSeq	Phase_I	59001777	NM_001004705	B2RNH6	Missense_Mutation	SNP	ENST00000530162.1	37	CCDS53636.1	.	.	.	.	.	.	.	.	.	.	A	15.92	2.975639	0.53720	.	.	ENSG00000254466	ENST00000530162	T	0.01981	4.52	4.22	4.22	0.49857	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.23532	0.0569	H	0.98901	4.365	0.35613	D	0.808771	D	0.89917	1.0	D	0.91635	0.999	T	0.57359	-0.7825	9	0.87932	D	0	.	12.4202	0.55516	1.0:0.0:0.0:0.0	.	100	Q8NGI6	OR4DA_HUMAN	R	100	ENSP00000436424:Q100R	ENSP00000436424:Q100R	Q	+	2	0	OR4D10	59001777	1.000000	0.71417	0.982000	0.44146	0.233000	0.25261	8.239000	0.89811	1.650000	0.50662	0.533000	0.62120	CAG		0.468	OR4D10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394235.1	NM_001004705	
STX3	6809	broad.mit.edu	37	11	59562908	59562908	+	Nonsense_Mutation	SNP	C	C	T	rs575668968		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:59562908C>T	ENST00000337979.4	+	9	1286	c.739C>T	c.(739-741)Cga>Tga	p.R247*	STX3_ENST00000535361.1_Intron|STX3_ENST00000300150.7_Nonsense_Mutation_p.R216*|STX3_ENST00000529177.1_Nonsense_Mutation_p.R247*|STX3_ENST00000437946.2_Intron	NM_001178040.1|NM_004177.4	NP_001171511.1|NP_004168.1	Q13277	STX3_HUMAN	syntaxin 3	247	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|long-term synaptic potentiation (GO:0060291)|membrane fusion (GO:0061025)|neuron projection development (GO:0031175)|neurotransmitter transport (GO:0006836)	apical plasma membrane (GO:0016324)|azurophil granule (GO:0042582)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|SNARE complex (GO:0031201)|specific granule (GO:0042581)|vacuole (GO:0005773)	arachidonic acid binding (GO:0050544)	p.R247*(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|skin(1)	13						GGAGAAGGCACGAGATGAAAC	0.468																																					p.R247X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C739T	11						.						124.0	100.0	108.0					11																	59562908		2201	4295	6496	59319484	SO:0001587	stop_gained	6809	exon9			AJ002076	CCDS7975.1, CCDS53637.1	11q12.1	2008-02-05	2006-04-25	2006-04-25	ENSG00000166900	ENSG00000166900			11438	protein-coding gene	gene with protein product		600876	"""syntaxin 3A"""	STX3A		16598260, 16339081	Standard	NM_004177		Approved		uc001nog.3	Q13277	OTTHUMG00000167353	ENST00000337979.4:c.739C>T	11.37:g.59562908C>T	ENSP00000338562:p.Arg247*	Somatic		Capture	Illumina HiSeq	Phase_I	59319484	NM_001178040	B4DME0|O43750|O43751|Q15360	Nonsense_Mutation	SNP	ENST00000337979.4	37	CCDS7975.1	.	.	.	.	.	.	.	.	.	.	C	35	5.476777	0.96291	.	.	ENSG00000166900	ENST00000300150;ENST00000337979;ENST00000529177;ENST00000530221	.	.	.	5.72	2.61	0.31194	.	1.072320	0.07170	N	0.852191	.	.	.	.	.	.	0.19575	N	0.999964	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	-16.249	7.4091	0.27007	0.2963:0.6232:0.0:0.0805	.	.	.	.	X	216;247;247;34	.	ENSP00000300150:R216X	R	+	1	2	STX3	59319484	0.070000	0.21116	0.171000	0.22900	0.995000	0.86356	3.593000	0.54001	0.736000	0.32559	0.585000	0.79938	CGA		0.468	STX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394264.1	NM_004177	
MS4A1	931	broad.mit.edu	37	11	60233497	60233497	+	Nonsense_Mutation	SNP	T	T	A	rs538978795		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:60233497T>A	ENST00000534668.1	+	5	729	c.440T>A	c.(439-441)tTa>tAa	p.L147*	MS4A1_ENST00000389939.2_Nonsense_Mutation_p.L147*|MS4A1_ENST00000532073.1_Nonsense_Mutation_p.L147*|MS4A1_ENST00000345732.4_Nonsense_Mutation_p.L147*|MS4A1_ENST00000528313.1_Intron	NM_152866.2	NP_690605.1	P11836	CD20_HUMAN	membrane-spanning 4-domains, subfamily A, member 1	147	Epitope 2.				B cell proliferation (GO:0042100)|humoral immune response (GO:0006959)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	MHC class II protein complex binding (GO:0023026)	p.L147*(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24					Ibritumomab(DB00078)|Obinutuzumab(DB08935)|Rituximab(DB00073)|Tositumomab(DB00081)	TCCCATTTTTTAAAAATGGAG	0.328													T|||	1	0.000199681	0.0	0.0	5008	,	,		18878	0.0		0.0	False		,,,				2504	0.001				p.L147X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.T440A	11						.						47.0	49.0	49.0					11																	60233497		2202	4299	6501	59990073	SO:0001587	stop_gained	931	exon5			M27394	CCDS31570.1	11q12-q13.1	2014-09-17				ENSG00000156738		"""CD molecules"""	7315	protein-coding gene	gene with protein product		112210		CD20		2448768	Standard	NM_152866		Approved	B1, Bp35, MS4A2	uc001npq.3	P11836		ENST00000534668.1:c.440T>A	11.37:g.60233497T>A	ENSP00000433277:p.Leu147*	Somatic		Capture	Illumina HiSeq	Phase_I	59990073	NM_021950	A6NMS4|B4DT24|P08984|Q13963	Nonsense_Mutation	SNP	ENST00000534668.1	37	CCDS31570.1	.	.	.	.	.	.	.	.	.	.	T	37	6.033554	0.97221	.	.	ENSG00000156738	ENST00000345732;ENST00000532073;ENST00000534668;ENST00000389939	.	.	.	5.29	5.29	0.74685	.	0.309591	0.23178	N	0.051048	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-26.3929	11.8987	0.52671	0.0:0.0:0.0:1.0	.	.	.	.	X	147	.	ENSP00000314620:L147X	L	+	2	0	MS4A1	59990073	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.595000	0.54016	2.132000	0.65825	0.533000	0.62120	TTA		0.328	MS4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395402.1		
PRPF19	27339	broad.mit.edu	37	11	60668388	60668388	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:60668388G>A	ENST00000227524.4	-	9	861	c.656C>T	c.(655-657)gCc>gTc	p.A219V		NM_014502.4	NP_055317.1			pre-mRNA processing factor 19									p.A219V(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	22						AGGAATGCTGGCACTGTGCAA	0.607																																					p.A219V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C656T	11						.						62.0	58.0	59.0					11																	60668388		2203	4299	6502	60424964	SO:0001583	missense	27339	exon9			BC018698	CCDS7995.1	11q12.2	2014-05-20	2013-06-10	2005-04-01	ENSG00000110107	ENSG00000110107		"""WD repeat domain containing"", ""U-box domain containing"""	17896	protein-coding gene	gene with protein product	"""nuclear matrix protein NMP200 related to splicing factor PRP19"", ""psoralen 4"""	608330	"""PRP19/PSO4 homolog (S. cerevisiae)"", ""PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)"""	PRP19		12960389	Standard	NM_014502		Approved	UBOX4, NMP200, PSO4, hPSO4	uc001nqf.3	Q9UMS4	OTTHUMG00000167798	ENST00000227524.4:c.656C>T	11.37:g.60668388G>A	ENSP00000227524:p.Ala219Val	Somatic		Capture	Illumina HiSeq	Phase_I	60424964	NM_014502		Missense_Mutation	SNP	ENST00000227524.4	37	CCDS7995.1	.	.	.	.	.	.	.	.	.	.	G	33	5.217250	0.95104	.	.	ENSG00000110107	ENST00000227524;ENST00000541371	T	0.62498	0.02	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.68220	0.2977	M	0.78223	2.4	0.80722	D	1	B	0.29481	0.245	B	0.32677	0.15	T	0.67142	-0.5745	10	0.45353	T	0.12	-28.1755	19.3834	0.94546	0.0:0.0:1.0:0.0	.	219	Q9UMS4	PRP19_HUMAN	V	219	ENSP00000227524:A219V	ENSP00000227524:A219V	A	-	2	0	PRPF19	60424964	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.461000	0.97646	2.677000	0.91161	0.655000	0.94253	GCC		0.607	PRPF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396334.1	NM_014502	
CD5	921	broad.mit.edu	37	11	60885695	60885695	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:60885695T>C	ENST00000347785.3	+	3	309	c.143T>C	c.(142-144)cTg>cCg	p.L48P		NM_014207.3	NP_055022.2	P06127	CD5_HUMAN	CD5 molecule	48	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic signaling pathway (GO:0097190)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)	p.L48P(1)		central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_lung(304;5.94e-05)|Lung NSC(402;7.26e-05)		BRCA - Breast invasive adenocarcinoma(625;0.000946)|Lung(977;0.0086)|LUSC - Lung squamous cell carcinoma(625;0.0528)		CAGGGCCAGCTGGAGGTCTAC	0.622																																					p.L48P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T143C	11						.						111.0	115.0	113.0					11																	60885695		2203	4299	6502	60642271	SO:0001583	missense	921	exon3			X04391	CCDS8000.1	11q13	2008-07-18	2006-03-28		ENSG00000110448	ENSG00000110448		"""CD molecules"""	1685	protein-coding gene	gene with protein product		153340	"""CD5 antigen (p56-62)"""	LEU1		1711157	Standard	NM_014207		Approved	T1	uc009ynk.3	P06127	OTTHUMG00000167825	ENST00000347785.3:c.143T>C	11.37:g.60885695T>C	ENSP00000342681:p.Leu48Pro	Somatic		Capture	Illumina HiSeq	Phase_I	60642271	NM_014207	A0N0P4|A8K9I3	Missense_Mutation	SNP	ENST00000347785.3	37	CCDS8000.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.968375	0.53614	.	.	ENSG00000110448	ENST00000347785;ENST00000544014	T;T	0.42131	0.98;0.98	3.86	3.86	0.44501	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.554041	0.13930	N	0.352960	T	0.58793	0.2147	M	0.64997	1.995	0.53005	D	0.999969	D	0.89917	1.0	D	0.80764	0.994	T	0.59490	-0.7445	10	0.87932	D	0	-9.4516	9.3637	0.38212	0.0:0.0:0.0:1.0	.	48	P06127	CD5_HUMAN	P	48	ENSP00000342681:L48P;ENSP00000440899:L48P	ENSP00000342681:L48P	L	+	2	0	CD5	60642271	0.993000	0.37304	0.947000	0.38551	0.608000	0.37181	3.466000	0.53071	1.992000	0.58205	0.459000	0.35465	CTG		0.622	CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396465.2	NM_014207	
VWCE	220001	broad.mit.edu	37	11	61050363	61050363	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:61050363G>T	ENST00000335613.5	-	6	942	c.556C>A	c.(556-558)Cta>Ata	p.L186I		NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	186	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.L186I(1)		biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GGAGTCCCTAGGCATTCGTCA	0.512																																					p.L186I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C556A	11						.						307.0	272.0	284.0					11																	61050363		2203	4299	6502	60806939	SO:0001583	missense	220001	exon6			AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.556C>A	11.37:g.61050363G>T	ENSP00000334186:p.Leu186Ile	Somatic		Capture	Illumina HiSeq	Phase_I	60806939	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Missense_Mutation	SNP	ENST00000335613.5	37	CCDS8002.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.578442	0.65878	.	.	ENSG00000167992	ENST00000335613	D	0.91894	-2.93	5.5	1.81	0.25067	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.43416	D	0.000571	D	0.88108	0.6348	L	0.41961	1.31	0.80722	D	1	P	0.52577	0.954	P	0.49799	0.622	D	0.83825	0.0249	10	0.35671	T	0.21	.	3.7395	0.08524	0.3646:0.0:0.4644:0.171	.	186	Q96DN2	VWCE_HUMAN	I	186	ENSP00000334186:L186I	ENSP00000301770:L186I	L	-	1	2	VWCE	60806939	1.000000	0.71417	0.996000	0.52242	0.963000	0.63663	2.052000	0.41316	1.231000	0.43661	0.655000	0.94253	CTA		0.512	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718	
TMEM138	51524	broad.mit.edu	37	11	61135401	61135401	+	Missense_Mutation	SNP	C	C	T	rs202210746		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:61135401C>T	ENST00000278826.6	+	4	866	c.307C>T	c.(307-309)Cgc>Tgc	p.R103C	TMEM138_ENST00000542946.1_3'UTR|TMEM138_ENST00000381787.2_Missense_Mutation_p.R45C	NM_016464.4	NP_057548.1	Q9NPI0	TM138_HUMAN	transmembrane protein 138	103					cilium assembly (GO:0042384)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|vacuole (GO:0005773)		p.R103C(2)		central_nervous_system(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	5						TCAGAACTTACGCTGGAAAAA	0.443													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20554	0.0		0.0	False		,,,				2504	0.0				p.R103C												.	.	2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	c.C307T	11						.						224.0	228.0	227.0					11																	61135401		2203	4299	6502	60891977	SO:0001583	missense	51524	exon4			AF151030	CCDS8005.1	11q12.2	2014-01-28			ENSG00000149483	ENSG00000149483			26944	protein-coding gene	gene with protein product		614459					Standard	NM_016464		Approved	HSPC196, JBTS16	uc001nrl.2	Q9NPI0	OTTHUMG00000168145	ENST00000278826.6:c.307C>T	11.37:g.61135401C>T	ENSP00000278826:p.Arg103Cys	Somatic		Capture	Illumina HiSeq	Phase_I	60891977	NM_016464	A6NGA7|B4E044|Q5JPE1	Missense_Mutation	SNP	ENST00000278826.6	37	CCDS8005.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	26.9	4.785055	0.90282	.	.	ENSG00000149483	ENST00000278826;ENST00000381787	D;D	0.89875	-2.58;-2.58	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.95004	0.8383	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.982	D	0.94888	0.8045	10	0.87932	D	0	-1.7267	19.9089	0.97019	0.0:1.0:0.0:0.0	.	103;103	B4E044;Q9NPI0	.;TM138_HUMAN	C	103;45	ENSP00000278826:R103C;ENSP00000371206:R45C	ENSP00000278826:R103C	R	+	1	0	TMEM138	60891977	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	3.336000	0.52113	2.793000	0.96121	0.655000	0.94253	CGC		0.443	TMEM138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398399.2	NM_016464	
BEST1	7439	broad.mit.edu	37	11	61724470	61724470	+	Splice_Site	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:61724470C>T	ENST00000378043.4	+	5	1279	c.636C>T	c.(634-636)aaC>aaT	p.N212N	BEST1_ENST00000435278.2_Splice_Site_p.N212N|BEST1_ENST00000301774.9_Intron|BEST1_ENST00000526988.1_Splice_Site_p.N106N|BEST1_ENST00000378042.3_Splice_Site_p.N152N|BEST1_ENST00000534553.1_Intron|BEST1_ENST00000449131.2_Splice_Site_p.N152N	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	212					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.N212N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						GCCTGCTGAACGTGAGCCCAC	0.587																																					p.N212N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C636T	11						.						76.0	67.0	70.0					11																	61724470		2202	4299	6501	61481046	SO:0001630	splice_region_variant	7439	exon5			AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.636+1C>T	11.37:g.61724470C>T		Somatic		Capture	Illumina HiSeq	Phase_I	61481046	NM_004183	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																				0.587	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	Silent
GANAB	23193	broad.mit.edu	37	11	62406565	62406565	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:62406565C>T	ENST00000356638.3	-	4	286	c.270G>A	c.(268-270)gaG>gaA	p.E90E	GANAB_ENST00000346178.4_Silent_p.E90E|GANAB_ENST00000540933.1_5'UTR|GANAB_ENST00000534779.1_Intron|GANAB_ENST00000534422.1_5'UTR	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	90					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|glucosidase II complex (GO:0017177)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|glucan 1,3-alpha-glucosidase activity (GO:0033919)|poly(A) RNA binding (GO:0044822)	p.E90E(1)		central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|skin(2)|urinary_tract(3)	35					Miglitol(DB00491)	GCCCCTGAAGCTCTAGCACCA	0.527																																					p.E90E	Melanoma(23;1005 1074 15747 18937)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G270A	11						.						69.0	67.0	68.0					11																	62406565		2202	4299	6501	62163141	SO:0001819	synonymous_variant	23193	exon4			AF144074	CCDS8026.1, CCDS41656.1, CCDS60817.1, CCDS60818.1	11q12.3	2012-10-02			ENSG00000089597	ENSG00000089597	3.2.1.20		4138	protein-coding gene	gene with protein product		104160				10764838, 6342981	Standard	NM_198335		Approved	GluII, G2AN, KIAA0088	uc001nua.4	Q14697	OTTHUMG00000167696	ENST00000356638.3:c.270G>A	11.37:g.62406565C>T		Somatic		Capture	Illumina HiSeq	Phase_I	62163141	NM_198335	A6NC20|Q8WTS9|Q9P0X0	Silent	SNP	ENST00000356638.3	37	CCDS8026.1																																																																																				0.527	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334	
INTS5	80789	broad.mit.edu	37	11	62416860	62416860	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:62416860C>T	ENST00000330574.2	-	2	744	c.692G>A	c.(691-693)gGc>gAc	p.G231D	GANAB_ENST00000356638.3_5'Flank|GANAB_ENST00000346178.4_5'Flank|GANAB_ENST00000540933.1_5'Flank|GANAB_ENST00000534779.1_5'Flank	NM_030628.1	NP_085131.1	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	231					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)		p.G231D(1)		breast(1)|endometrium(4)|large_intestine(6)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	36						AAAAGAGGAGCCAATATGTGC	0.542																																					p.G231D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G692A	11						.						149.0	122.0	131.0					11																	62416860		2202	4299	6501	62173436	SO:0001583	missense	80789	exon2			AK123587	CCDS8027.1	11q12.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000185085	ENSG00000185085			29352	protein-coding gene	gene with protein product		611349	"""KIAA1698"""	KIAA1698		16239144	Standard	NM_030628		Approved	INT5	uc001nud.3	Q6P9B9	OTTHUMG00000167605	ENST00000330574.2:c.692G>A	11.37:g.62416860C>T	ENSP00000327889:p.Gly231Asp	Somatic		Capture	Illumina HiSeq	Phase_I	62173436	NM_030628	Q8N6W5|Q9C0G5	Missense_Mutation	SNP	ENST00000330574.2	37	CCDS8027.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.286944	0.80803	.	.	ENSG00000185085	ENST00000330574	.	.	.	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.77565	0.4149	M	0.71581	2.175	0.52099	D	0.999949	D	0.89917	1.0	D	0.97110	1.0	T	0.80549	-0.1333	9	0.87932	D	0	.	14.8911	0.70609	0.0:1.0:0.0:0.0	.	231	Q6P9B9	INT5_HUMAN	D	231	.	ENSP00000327889:G231D	G	-	2	0	INTS5	62173436	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.208000	0.77907	2.378000	0.81104	0.650000	0.86243	GGC		0.542	INTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395327.1	NM_030628	
INTS5	80789	broad.mit.edu	37	11	62416995	62416995	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:62416995G>A	ENST00000330574.2	-	2	609	c.557C>T	c.(556-558)aCg>aTg	p.T186M	GANAB_ENST00000356638.3_5'Flank|GANAB_ENST00000346178.4_5'Flank|GANAB_ENST00000540933.1_5'Flank|GANAB_ENST00000534779.1_5'Flank	NM_030628.1	NP_085131.1	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	186					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)		p.T186M(1)		breast(1)|endometrium(4)|large_intestine(6)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	36						TAATGTACGCGTGGCCCTACA	0.557																																					p.T186M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C557T	11						.						112.0	104.0	107.0					11																	62416995		2202	4299	6501	62173571	SO:0001583	missense	80789	exon2			AK123587	CCDS8027.1	11q12.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000185085	ENSG00000185085			29352	protein-coding gene	gene with protein product		611349	"""KIAA1698"""	KIAA1698		16239144	Standard	NM_030628		Approved	INT5	uc001nud.3	Q6P9B9	OTTHUMG00000167605	ENST00000330574.2:c.557C>T	11.37:g.62416995G>A	ENSP00000327889:p.Thr186Met	Somatic		Capture	Illumina HiSeq	Phase_I	62173571	NM_030628	Q8N6W5|Q9C0G5	Missense_Mutation	SNP	ENST00000330574.2	37	CCDS8027.1	.	.	.	.	.	.	.	.	.	.	G	19.84	3.902420	0.72754	.	.	ENSG00000185085	ENST00000330574	.	.	.	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.69450	0.3112	L	0.54323	1.7	0.47949	D	0.999558	D	0.69078	0.997	D	0.63703	0.917	T	0.72972	-0.4129	9	0.87932	D	0	.	15.1127	0.72372	0.0:0.0:1.0:0.0	.	186	Q6P9B9	INT5_HUMAN	M	186	.	ENSP00000327889:T186M	T	-	2	0	INTS5	62173571	1.000000	0.71417	0.998000	0.56505	0.808000	0.45660	9.194000	0.94962	2.437000	0.82529	0.650000	0.86243	ACG		0.557	INTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395327.1	NM_030628	
STX5	6811	broad.mit.edu	37	11	62594869	62594869	+	Splice_Site	SNP	G	G	A	rs143457390		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:62594869G>A	ENST00000294179.3	-	4	451	c.298C>T	c.(298-300)Cgc>Tgc	p.R100C	STX5_ENST00000377897.4_Splice_Site_p.R100C|STX5_ENST00000541317.1_Splice_Site_p.R4C|STX5_ENST00000394690.1_Splice_Site_p.R46C	NM_001244666.1|NM_003164.4	NP_001231595.1|NP_003155.2	Q13190	STX5_HUMAN	syntaxin 5	100					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion with Golgi apparatus (GO:0048280)|vesicle targeting (GO:0006903)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|SNARE complex (GO:0031201)	protein N-terminus binding (GO:0047485)|SNAP receptor activity (GO:0005484)	p.R100C(1)		breast(2)|endometrium(2)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	18						TTCCCAATGCGCCTGCAAATG	0.498																																					p.R100C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C298T	11						.	G	CYS/ARG	2,4400	4.2+/-10.8	0,2,2199	120.0	107.0	112.0		298	5.5	1.0	11	dbSNP_134	112	0,8598		0,0,4299	yes	missense-near-splice	STX5	NM_003164.4	180	0,2,6498	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	100/356	62594869	2,12998	2201	4299	6500	62351445	SO:0001630	splice_region_variant	6811	exon4			U26648	CCDS8038.2, CCDS58140.1	11q12.3	2008-02-05	2006-04-25	2006-04-25	ENSG00000162236	ENSG00000162236			11440	protein-coding gene	gene with protein product		603189	"""syntaxin 5A"""	STX5A		9188044, 11959998	Standard	NM_003164		Approved	SED5	uc001nvh.3	Q13190	OTTHUMG00000143864	ENST00000294179.3:c.297-1C>T	11.37:g.62594869G>A		Somatic		Capture	Illumina HiSeq	Phase_I	62351445	NM_003164	B2R8T2|F8W8Q9|Q5U0D4|Q7Z3T6|Q9BUG1	Missense_Mutation	SNP	ENST00000294179.3	37	CCDS8038.2	.	.	.	.	.	.	.	.	.	.	G	15.42	2.829203	0.50845	4.54E-4	0.0	ENSG00000162236	ENST00000377897;ENST00000294179;ENST00000394690;ENST00000541317	T;T;T;T	0.17528	2.27;2.27;2.27;2.27	5.47	5.47	0.80525	t-SNARE (1);Syntaxin, N-terminal (1);	0.149349	0.64402	D	0.000017	T	0.23806	0.0576	M	0.69358	2.11	0.80722	D	1	B;B	0.18013	0.02;0.025	B;B	0.17098	0.016;0.017	T	0.02115	-1.1211	10	0.59425	D	0.04	-2.7166	16.8262	0.85931	0.0:0.0:1.0:0.0	.	100;100	F8W8Q9;Q13190	.;STX5_HUMAN	C	100;100;46;4	ENSP00000367129:R100C;ENSP00000294179:R100C;ENSP00000378182:R46C;ENSP00000441428:R4C	ENSP00000294179:R100C	R	-	1	0	STX5	62351445	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	5.351000	0.66022	2.571000	0.86741	0.655000	0.94253	CGC		0.498	STX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290113.1	NM_003164	Missense_Mutation
RCOR2	283248	broad.mit.edu	37	11	63683827	63683827	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:63683827G>A	ENST00000301459.4	-	1	489	c.102C>T	c.(100-102)gaC>gaT	p.D34D		NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	34					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.D34D(1)		kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						CCTCGCTGCTGTCATCCTCCG	0.701											OREG0021039	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D34D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C102T	11						.						31.0	29.0	30.0					11																	63683827		2199	4296	6495	63440403	SO:0001819	synonymous_variant	283248	exon1			BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.102C>T	11.37:g.63683827G>A		Somatic	1070	Capture	Illumina HiSeq	Phase_I	63440403	NM_173587	Q96FP3	Silent	SNP	ENST00000301459.4	37	CCDS8052.1																																																																																				0.701	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1	NM_173587	
MACROD1	28992	broad.mit.edu	37	11	63885031	63885031	+	Intron	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:63885031C>T	ENST00000255681.6	-	3	584				FLRT1_ENST00000246841.3_Missense_Mutation_p.A431V|RP11-21A7A.3_ENST00000543817.1_RNA	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)	p.A431V(1)		breast(1)|large_intestine(3)|lung(6)|skin(1)	11						TACCCCATGGCCACGGGTGAT	0.647																																					p.A431V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1292T	11						.						35.0	34.0	34.0					11																	63885031		2200	4296	6496	63641607	SO:0001627	intron_variant	23769	exon2			AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+33679G>A	11.37:g.63885031C>T		Somatic		Capture	Illumina HiSeq	Phase_I	63641607	NM_013280	Q9UH96	Missense_Mutation	SNP	ENST00000255681.6	37	CCDS8056.1	.	.	.	.	.	.	.	.	.	.	C	1.651	-0.513999	0.04200	.	.	ENSG00000126500	ENST00000246841	T	0.50001	0.76	5.07	4.16	0.48862	.	0.352448	0.28130	N	0.016496	T	0.15955	0.0384	N	0.01874	-0.695	0.33475	D	0.58669	B	0.28820	0.224	B	0.24701	0.055	T	0.32348	-0.9910	10	0.02654	T	1	-36.1494	7.7313	0.28789	0.1618:0.7539:0.0:0.0844	.	403	Q9NZU1	FLRT1_HUMAN	V	431	ENSP00000246841:A431V	ENSP00000246841:A431V	A	+	2	0	FLRT1	63641607	0.904000	0.30761	0.990000	0.47175	0.022000	0.10575	0.442000	0.21628	1.266000	0.44231	0.650000	0.86243	GCC		0.647	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
PLCB3	5331	broad.mit.edu	37	11	64026391	64026391	+	Missense_Mutation	SNP	C	C	T	rs141811797		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:64026391C>T	ENST00000540288.1	+	12	1391	c.1288C>T	c.(1288-1290)Cgc>Tgc	p.R430C	PLCB3_ENST00000325234.5_Missense_Mutation_p.R363C|PLCB3_ENST00000279230.6_Missense_Mutation_p.R430C	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	430	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.R430C(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						TGAGTACTGCCGCTCCATCTT	0.627													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14801	0.0		0.0	False		,,,				2504	0.0				p.R363C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1087T	11						.	C	CYS/ARG,CYS/ARG	1,4401	2.1+/-5.4	0,1,2200	63.0	65.0	65.0		1288,1087	3.8	1.0	11	dbSNP_134	65	0,8594		0,0,4297	no	missense,missense	PLCB3	NM_000932.2,NM_001184883.1	180,180	0,1,6497	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	430/1235,363/1168	64026391	1,12995	2201	4297	6498	63782967	SO:0001583	missense	5331	exon10			Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.1288C>T	11.37:g.64026391C>T	ENSP00000443631:p.Arg430Cys	Somatic		Capture	Illumina HiSeq	Phase_I	63782967	NM_001184883	A5PKZ6|G5E960|Q8N1A4	Missense_Mutation	SNP	ENST00000540288.1	37	CCDS8064.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	13.22	2.171635	0.38315	2.27E-4	0.0	ENSG00000149782	ENST00000279230;ENST00000540288;ENST00000325234	T;T;T	0.65364	-0.15;-0.15;-0.15	4.73	3.78	0.43462	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.053456	0.64402	D	0.000003	T	0.77671	0.4165	M	0.83118	2.625	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.78540	-0.2165	10	0.87932	D	0	.	8.7869	0.34825	0.1707:0.6641:0.1652:0.0	.	363;430	G5E960;Q01970	.;PLCB3_HUMAN	C	430;430;363	ENSP00000279230:R430C;ENSP00000443631:R430C;ENSP00000324660:R363C	ENSP00000279230:R430C	R	+	1	0	PLCB3	63782967	1.000000	0.71417	1.000000	0.80357	0.050000	0.14768	1.306000	0.33505	0.934000	0.37316	0.313000	0.20887	CGC		0.627	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
CCDC88B	283234	broad.mit.edu	37	11	64118705	64118705	+	Missense_Mutation	SNP	G	G	A	rs566542432		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:64118705G>A	ENST00000356786.5	+	17	2980	c.2936G>A	c.(2935-2937)cGg>cAg	p.R979Q	CCDC88B_ENST00000359902.2_Missense_Mutation_p.R131Q|CCDC88B_ENST00000463837.1_3'UTR|CCDC88B_ENST00000301897.4_5'UTR	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	979						membrane (GO:0016020)		p.R979Q(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CAGAATGTGCGGCTTATTGAG	0.677													G|||	1	0.000199681	0.0	0.0	5008	,	,		15827	0.001		0.0	False		,,,				2504	0.0				p.R979Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2936A	11						.						33.0	35.0	35.0					11																	64118705		1884	3551	5435	63875281	SO:0001583	missense	283234	exon17			AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.2936G>A	11.37:g.64118705G>A	ENSP00000349238:p.Arg979Gln	Somatic		Capture	Illumina HiSeq	Phase_I	63875281	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Missense_Mutation	SNP	ENST00000356786.5	37	CCDS8072.2	.	.	.	.	.	.	.	.	.	.	g	19.09	3.760786	0.69763	.	.	ENSG00000168071	ENST00000377638;ENST00000356786;ENST00000359902	T;T	0.57436	1.14;0.4	5.0	5.0	0.66597	.	.	.	.	.	T	0.71384	0.3333	M	0.79011	2.435	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.934;0.992	T	0.71869	-0.4462	9	0.41790	T	0.15	.	14.1771	0.65549	0.0:0.0:1.0:0.0	.	979;115;979	B2RTU8;A6NC98-5;A6NC98	.;.;CC88B_HUMAN	Q	979;979;131	ENSP00000349238:R979Q;ENSP00000352974:R131Q	ENSP00000349238:R979Q	R	+	2	0	CCDC88B	63875281	1.000000	0.71417	0.993000	0.49108	0.084000	0.17831	3.395000	0.52558	2.496000	0.84212	0.549000	0.68633	CGG		0.677	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
RASGRP2	10235	broad.mit.edu	37	11	64508421	64508421	+	Splice_Site	SNP	C	C	T	rs375059620		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:64508421C>T	ENST00000354024.3	-	5	622	c.370G>A	c.(370-372)Gtc>Atc	p.V124I	RASGRP2_ENST00000394429.1_3'UTR|RASGRP2_ENST00000394430.1_Missense_Mutation_p.V124M|RASGRP2_ENST00000377487.1_Missense_Mutation_p.V124M|RASGRP2_ENST00000377489.1_Missense_Mutation_p.V124M|RASGRP2_ENST00000394428.1_3'UTR|RASGRP2_ENST00000394432.3_Splice_Site_p.V124I|RASGRP2_ENST00000377497.3_Splice_Site_p.V124I|RASGRP2_ENST00000377486.3_Missense_Mutation_p.V124M|RASGRP2_ENST00000377494.1_Splice_Site_p.V124I	NM_153819.1	NP_722541.1	Q7LDG7	GRP2_HUMAN	RAS guanyl releasing protein 2 (calcium and DAG-regulated)	124	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				blood coagulation (GO:0007596)|cellular response to calcium ion (GO:0071277)|platelet activation (GO:0030168)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)	p.V186I(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CCCACGCACACGCTGTCTATG	0.532											OREG0004006	type=REGULATORY REGION|Gene=RASGRP2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.V124I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G370A	11						.	C	ILE/VAL,ILE/VAL,ILE/VAL	0,4402		0,0,2201	69.0	55.0	60.0		370,370,370	4.3	1.0	11		60	1,8593	1.2+/-3.3	0,1,4296	no	missense-near-splice,missense-near-splice,missense-near-splice	RASGRP2	NM_001098670.1,NM_001098671.1,NM_153819.1	29,29,29	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	124/610,124/610,124/610	64508421	1,12995	2201	4297	6498	64264997	SO:0001630	splice_region_variant	10235	exon5			U78170	CCDS31598.1	11q13	2014-09-17			ENSG00000068831	ENSG00000068831		"""EF-hand domain containing"""	9879	protein-coding gene	gene with protein product		605577				9789079	Standard	NM_001098670		Approved	CALDAG-GEFI	uc009ypv.3	Q7LDG7	OTTHUMG00000045420	ENST00000354024.3:c.371+1G>A	11.37:g.64508421C>T		Somatic	1077	Capture	Illumina HiSeq	Phase_I	64264997	NM_001098670	A6NDC7|O00538|Q9UL65	Missense_Mutation	SNP	ENST00000354024.3	37	CCDS31598.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.449|5.449	0.267863|0.267863	0.10349|0.10349	0.0|0.0	1.16E-4|1.16E-4	ENSG00000068831|ENSG00000068831	ENST00000377494;ENST00000394432;ENST00000377497;ENST00000354024;ENST00000431822|ENST00000377486;ENST00000377487;ENST00000377489;ENST00000394430;ENST00000439594	T;T;T;T;T|T;T;T;T	0.29917|0.42513	1.55;1.55;1.55;1.55;1.55|0.97;0.97;0.97;0.97	4.3|4.3	4.3|4.3	0.51218|0.51218	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (2);|.	0.000000|0.000000	0.85682|0.85682	U|U	0.000000|0.000000	T|T	0.35998|0.35998	0.0951|0.0951	N|N	0.12746|0.12746	0.255|0.255	0.41635|0.41635	D|D	0.989041|0.989041	B|.	0.31351|.	0.32|.	B|.	0.17433|.	0.018|.	T|T	0.45116|0.45116	-0.9283|-0.9283	10|8	0.11485|0.72032	T|D	0.65|0.01	-15.4956|-15.4956	14.692|14.692	0.69093|0.69093	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	124|.	Q7LDG7|.	GRP2_HUMAN|.	I|M	124|124	ENSP00000366714:V124I;ENSP00000377953:V124I;ENSP00000366717:V124I;ENSP00000338864:V124I;ENSP00000399114:V124I|ENSP00000366706:V124M;ENSP00000366707:V124M;ENSP00000366709:V124M;ENSP00000377951:V124M	ENSP00000338864:V124I|ENSP00000366706:V124M	V|V	-|-	1|1	0|0	RASGRP2|RASGRP2	64264997|64264997	0.843000|0.843000	0.29541|0.29541	0.992000|0.992000	0.48379|0.48379	0.779000|0.779000	0.44077|0.44077	1.327000|1.327000	0.33746|0.33746	2.118000|2.118000	0.64928|0.64928	0.485000|0.485000	0.47835|0.47835	GTC|GTG		0.532	RASGRP2-002	NOVEL	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142062.1	NM_153819	Missense_Mutation
ATG2A	23130	broad.mit.edu	37	11	64681314	64681314	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:64681314G>A	ENST00000377264.3	-	4	681	c.569C>T	c.(568-570)gCc>gTc	p.A190V	ATG2A_ENST00000421419.2_Missense_Mutation_p.A190V	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	190					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.A190V(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						GACCTCGACGGCCACACCACG	0.637																																					p.A190V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C569T	11						.						125.0	103.0	110.0					11																	64681314		2201	4297	6498	64437890	SO:0001583	missense	23130	exon4				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.569C>T	11.37:g.64681314G>A	ENSP00000366475:p.Ala190Val	Somatic		Capture	Illumina HiSeq	Phase_I	64437890	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	.	.	.	.	.	.	.	.	.	.	g	29.4	5.000651	0.93227	.	.	ENSG00000110046	ENST00000421419;ENST00000377264;ENST00000227459	T;T	0.56444	0.46;0.46	3.89	3.89	0.44902	.	0.000000	0.64402	D	0.000001	T	0.69708	0.3141	M	0.72118	2.19	0.58432	D	0.999998	D	0.76494	0.999	D	0.78314	0.991	T	0.74359	-0.3691	10	0.87932	D	0	.	13.7924	0.63150	0.0:0.0:1.0:0.0	.	190	Q2TAZ0	ATG2A_HUMAN	V	190	ENSP00000410522:A190V;ENSP00000366475:A190V	ENSP00000227459:A190V	A	-	2	0	ATG2A	64437890	1.000000	0.71417	0.878000	0.34440	0.223000	0.24884	6.614000	0.74197	2.205000	0.71048	0.457000	0.33378	GCC		0.637	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
SNX15	29907	broad.mit.edu	37	11	64802605	64802605	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:64802605G>A	ENST00000377244.3	+	5	577	c.447G>A	c.(445-447)ccG>ccA	p.P149P	RP11-399J13.3_ENST00000301886.3_3'UTR|SNX15_ENST00000352068.5_Silent_p.P149P	NM_013306.4|NM_147777.3	NP_037438.2|NP_680086.2	Q9NRS6	SNX15_HUMAN	sorting nexin 15	149					intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	phosphatidylinositol binding (GO:0035091)	p.P149P(1)		endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14						TCCCCACCCCGCCCCCTGATG	0.637																																					p.P149P	Esophageal Squamous(56;269 1304 3324 8253)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G447A	11						.						8.0	9.0	8.0					11																	64802605		2158	4235	6393	64559181	SO:0001819	synonymous_variant	29907	exon5			AF175267	CCDS8089.1, CCDS8090.1	11q12	2008-05-22			ENSG00000110025	ENSG00000110025		"""Sorting nexins"""	14978	protein-coding gene	gene with protein product		605964				11208079	Standard	NM_013306		Approved			Q9NRS6	OTTHUMG00000037387	ENST00000377244.3:c.447G>A	11.37:g.64802605G>A		Somatic		Capture	Illumina HiSeq	Phase_I	64559181	NM_013306	E5KQS6|Q9NRS5	Silent	SNP	ENST00000377244.3	37	CCDS8089.1																																																																																				0.637	SNX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091004.3		
CAPN1	823	broad.mit.edu	37	11	64972199	64972199	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:64972199C>T	ENST00000527323.1	+	10	1451	c.1211C>T	c.(1210-1212)aCg>aTg	p.T404M	CAPN1_ENST00000524773.1_Missense_Mutation_p.T404M|CAPN1_ENST00000533129.1_Missense_Mutation_p.T404M|CAPN1_ENST00000279247.6_Missense_Mutation_p.T404M|CAPN1_ENST00000533820.1_Missense_Mutation_p.T404M			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit	404	Domain III.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)	p.T404M(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		CTGGATGAGACGGATGACCCG	0.672											OREG0021073	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T404M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1211T	11						.						43.0	52.0	49.0					11																	64972199		2078	4201	6279	64728775	SO:0001583	missense	823	exon11			X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"""EF-hand domain containing"""	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614	ENST00000527323.1:c.1211C>T	11.37:g.64972199C>T	ENSP00000431984:p.Thr404Met	Somatic	1080	Capture	Illumina HiSeq	Phase_I	64728775	NM_001198868	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	37	CCDS44644.1	.	.	.	.	.	.	.	.	.	.	C	6.725	0.502592	0.12822	.	.	ENSG00000014216	ENST00000533820;ENST00000533129;ENST00000524773;ENST00000279247;ENST00000259755;ENST00000527323	D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37	4.51	-1.48	0.08745	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.769192	0.11900	N	0.518712	T	0.78824	0.4344	L	0.34521	1.04	0.23107	N	0.998281	B	0.18863	0.031	B	0.14578	0.011	T	0.65643	-0.6118	10	0.52906	T	0.07	.	3.332	0.07088	0.2903:0.3697:0.0:0.34	.	404	P07384	CAN1_HUMAN	M	404;404;404;404;350;404	ENSP00000435272:T404M;ENSP00000431686:T404M;ENSP00000434176:T404M;ENSP00000279247:T404M;ENSP00000431984:T404M	ENSP00000259755:T350M	T	+	2	0	CAPN1	64728775	0.000000	0.05858	0.126000	0.21872	0.005000	0.04900	-0.418000	0.07080	-0.040000	0.13580	-1.012000	0.02466	ACG		0.672	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
SCYL1	57410	broad.mit.edu	37	11	65303776	65303776	+	Missense_Mutation	SNP	C	C	T	rs377549319		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:65303776C>T	ENST00000270176.5	+	12	1699	c.1622C>T	c.(1621-1623)tCg>tTg	p.S541L	SCYL1_ENST00000279270.6_Missense_Mutation_p.S541L|SCYL1_ENST00000524944.1_Missense_Mutation_p.S541L|SCYL1_ENST00000420247.2_Missense_Mutation_p.S541L|SCYL1_ENST00000525364.1_Missense_Mutation_p.S541L|SCYL1_ENST00000533862.1_Missense_Mutation_p.S541L|SCYL1_ENST00000527009.1_Missense_Mutation_p.S398L	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	541					peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)	p.S541L(1)		ovary(1)|skin(1)	2						GAGTCTGTGTCGGAGGACCCG	0.582																																					p.S541L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1622T	11						.	C	LEU/SER,LEU/SER	1,4057		0,1,2028	66.0	73.0	71.0		1622,1622	5.5	1.0	11		71	1,8327		0,1,4163	no	missense,missense	SCYL1	NM_001048218.1,NM_020680.3	145,145	0,2,6191	TT,TC,CC		0.012,0.0246,0.0161	probably-damaging,probably-damaging	541/792,541/809	65303776	2,12384	2029	4164	6193	65060352	SO:0001583	missense	57410	exon12			AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"""teratoma-associated tyrosine kinase"", ""telomerase transcriptional elements-interacting factor"", ""telomerase regulation-associated protein"""	607982	"""N-terminal kinase-like"""	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.1622C>T	11.37:g.65303776C>T	ENSP00000270176:p.Ser541Leu	Somatic		Capture	Illumina HiSeq	Phase_I	65060352	NM_001048218	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Missense_Mutation	SNP	ENST00000270176.5	37	CCDS41672.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.993808	0.93167	2.46E-4	1.2E-4	ENSG00000142186	ENST00000270176;ENST00000525364;ENST00000420247;ENST00000533862;ENST00000527630;ENST00000349495;ENST00000279270;ENST00000524944;ENST00000527009;ENST00000528545	T;T;T;T;T;T;T;T;T	0.61859	1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48;0.07	5.46	5.46	0.80206	Armadillo-type fold (1);	0.319538	0.30093	N	0.010422	T	0.78464	0.4287	M	0.82823	2.61	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	0.83275	0.97;0.996;0.987;0.992;0.991	T	0.81274	-0.1007	10	0.72032	D	0.01	-4.2363	16.7806	0.85562	0.0:1.0:0.0:0.0	.	541;541;541;541;541	E9PS17;Q96KG9-4;Q96KG9-6;Q96KG9-2;Q96KG9	.;.;.;.;NTKL_HUMAN	L	541;541;541;541;541;541;541;541;398;14	ENSP00000270176:S541L;ENSP00000431635:S541L;ENSP00000408192:S541L;ENSP00000437254:S541L;ENSP00000433450:S541L;ENSP00000279270:S541L;ENSP00000432175:S541L;ENSP00000436993:S398L;ENSP00000433604:S14L	ENSP00000270176:S541L	S	+	2	0	SCYL1	65060352	0.998000	0.40836	0.998000	0.56505	0.887000	0.51463	3.943000	0.56621	2.577000	0.86979	0.462000	0.41574	TCG		0.582	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680	
LTBP3	4054	broad.mit.edu	37	11	65319791	65319791	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:65319791G>C	ENST00000301873.5	-	7	1541	c.1273C>G	c.(1273-1275)Cgc>Ggc	p.R425G	LTBP3_ENST00000322147.4_Missense_Mutation_p.R425G|LTBP3_ENST00000536982.1_Missense_Mutation_p.R51G	NM_001130144.2	NP_001123616.1	Q9NS15	LTBP3_HUMAN	latent transforming growth factor beta binding protein 3	425	TB 2.				bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|extracellular matrix organization (GO:0030198)|lung saccule development (GO:0060430)|negative regulation of bone mineralization (GO:0030502)|negative regulation of chondrocyte differentiation (GO:0032331)|positive regulation of bone resorption (GO:0045780)|positive regulation of mesenchymal stem cell differentiation (GO:2000741)|positive regulation of mesenchymal stem cell proliferation (GO:1902462)|transforming growth factor beta activation (GO:0036363)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)	p.R425G(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(3)	23						CAGAGCTGGCGGGTCAGGCGG	0.672											OREG0021081	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R425G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1273G	11						.						57.0	65.0	62.0					11																	65319791		2201	4297	6498	65076367	SO:0001583	missense	4054	exon7			AF135960	CCDS8103.1, CCDS44647.1	11q12	2011-10-20			ENSG00000168056	ENSG00000168056		"""Latent transforming growth factor, beta binding proteins"""	6716	protein-coding gene	gene with protein product		602090		LTBP2		7719025	Standard	NM_001164266		Approved		uc001oej.3	Q9NS15	OTTHUMG00000166575	ENST00000301873.5:c.1273C>G	11.37:g.65319791G>C	ENSP00000301873:p.Arg425Gly	Somatic	1083	Capture	Illumina HiSeq	Phase_I	65076367	NM_021070	O15107|Q96HB9|Q9H7K2|Q9UFN4	Missense_Mutation	SNP	ENST00000301873.5	37	CCDS44647.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.3|24.3	4.519635|4.519635	0.85495|0.85495	.|.	.|.	ENSG00000168056|ENSG00000168056	ENST00000526927|ENST00000322147;ENST00000301873;ENST00000536982;ENST00000530866;ENST00000530426	.|D;D;D;D;D	.|0.92965	.|-3.14;-3.14;-3.14;-3.14;-3.14	3.99|3.99	3.99|3.99	0.46301|0.46301	.|Matrix fibril-associated (3);TGF-beta binding (1);	.|0.068244	.|0.64402	.|D	.|0.000009	D|D	0.93625|0.93625	0.7964|0.7964	L|L	0.56199|0.56199	1.76|1.76	0.47407|0.47407	D|D	0.99941|0.99941	.|D;D;D;D;D	.|0.89917	.|1.0;0.995;0.994;1.0;0.996	.|D;D;D;D;D	.|0.91635	.|0.999;0.909;0.932;0.999;0.918	D|D	0.91020|0.91020	0.4856|0.4856	5|10	.|0.13853	.|T	.|0.58	.|.	13.6128|13.6128	0.62091|0.62091	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|336;51;308;425;425	.|E9PKW1;F5GWC4;B9EG76;Q9NS15;Q9NS15-2	.|.;.;.;LTBP3_HUMAN;.	R|G	75|425;425;51;336;105	.|ENSP00000326647:R425G;ENSP00000301873:R425G;ENSP00000441912:R51G;ENSP00000435276:R336G;ENSP00000432476:R105G	.|ENSP00000301873:R425G	P|R	-|-	2|1	0|0	LTBP3|LTBP3	65076367|65076367	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	4.197000|4.197000	0.58413|0.58413	2.064000|2.064000	0.61679|0.61679	0.407000|0.407000	0.27541|0.27541	CCG|CGC		0.672	LTBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390538.1	NM_021070	
EHBP1L1	254102	broad.mit.edu	37	11	65346593	65346593	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:65346593G>A	ENST00000309295.4	+	2	414	c.149G>A	c.(148-150)cGc>cAc	p.R50H		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	50						membrane (GO:0016020)		p.R50H(2)		central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						CGGAACCGACGCATCTGCTCC	0.647																																					p.R50H												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G149A	11						.						22.0	23.0	22.0					11																	65346593		1932	4129	6061	65103169	SO:0001583	missense	254102	exon2			AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.149G>A	11.37:g.65346593G>A	ENSP00000312671:p.Arg50His	Somatic		Capture	Illumina HiSeq	Phase_I	65103169	NM_001099409	Q8TB89|Q9H7M7	Missense_Mutation	SNP	ENST00000309295.4	37	CCDS44649.1	.	.	.	.	.	.	.	.	.	.	G	35	5.455714	0.96223	.	.	ENSG00000173442	ENST00000309295;ENST00000533237	T;T	0.44083	0.93;0.93	5.05	5.05	0.67936	.	0.080155	0.43416	D	0.000570	T	0.66694	0.2815	M	0.83483	2.645	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72144	-0.4379	10	0.87932	D	0	.	13.9053	0.63831	0.0:0.0:1.0:0.0	.	50	Q8N3D4	EH1L1_HUMAN	H	50	ENSP00000312671:R50H;ENSP00000431996:R50H	ENSP00000312671:R50H	R	+	2	0	EHBP1L1	65103169	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	6.835000	0.75344	2.345000	0.79718	0.561000	0.74099	CGC		0.647	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
EHBP1L1	254102	broad.mit.edu	37	11	65347811	65347811	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:65347811C>T	ENST00000309295.4	+	6	760	c.495C>T	c.(493-495)gaC>gaT	p.D165D		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	165						membrane (GO:0016020)		p.D165D(1)		central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						CTCCCAGGGACGATGACATGC	0.577																																					p.D165D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C495T	11						.						79.0	85.0	83.0					11																	65347811		2191	4281	6472	65104387	SO:0001819	synonymous_variant	254102	exon6			AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.495C>T	11.37:g.65347811C>T		Somatic		Capture	Illumina HiSeq	Phase_I	65104387	NM_001099409	Q8TB89|Q9H7M7	Silent	SNP	ENST00000309295.4	37	CCDS44649.1																																																																																				0.577	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
MAP3K11	4296	broad.mit.edu	37	11	65375494	65375494	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:65375494C>T	ENST00000530153.1	-	3	718	c.197G>A	c.(196-198)cGt>cAt	p.R66H	MAP3K11_ENST00000309100.3_Missense_Mutation_p.R323H|MAP3K11_ENST00000532507.1_5'Flank|MAP3K11_ENST00000534432.1_5'Flank					mitogen-activated protein kinase kinase kinase 11									p.R323H(1)		breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(14)|skin(1)	24						GTCAATGCCACGGTATGGCAC	0.602																																					p.R323H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G968A	11						.						107.0	81.0	90.0					11																	65375494		2201	4297	6498	65132070	SO:0001583	missense	4296	exon3				CCDS8107.1	11q13.1-q13.3	2011-06-09			ENSG00000173327	ENSG00000173327	2.7.10.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6850	protein-coding gene	gene with protein product		600050		MLK3, PTK1		9267807, 8183572	Standard	NM_002419		Approved	SPRK, MEKK11	uc001oew.3	Q16584	OTTHUMG00000166529	ENST00000530153.1:c.197G>A	11.37:g.65375494C>T	ENSP00000433886:p.Arg66His	Somatic		Capture	Illumina HiSeq	Phase_I	65132070	NM_002419		Missense_Mutation	SNP	ENST00000530153.1	37		.	.	.	.	.	.	.	.	.	.	C	19.73	3.881843	0.72294	.	.	ENSG00000173327	ENST00000309100;ENST00000530153;ENST00000526293;ENST00000529839	D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65	4.66	4.66	0.58398	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.146210	0.46145	D	0.000301	T	0.79246	0.4413	N	0.26092	0.79	0.49798	D	0.99982	P	0.52577	0.954	P	0.48552	0.581	T	0.82057	-0.0646	10	0.59425	D	0.04	.	15.083	0.72130	0.0:1.0:0.0:0.0	.	323	Q16584	M3K11_HUMAN	H	323;66;73;66	ENSP00000309597:R323H;ENSP00000433886:R66H;ENSP00000435970:R73H;ENSP00000435237:R66H	ENSP00000309597:R323H	R	-	2	0	MAP3K11	65132070	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.870000	0.69620	2.431000	0.82371	0.491000	0.48974	CGT		0.602	MAP3K11-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000390233.2		
PCNXL3	399909	broad.mit.edu	37	11	65394448	65394448	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:65394448C>T	ENST00000355703.3	+	21	3992	c.3453C>T	c.(3451-3453)ccC>ccT	p.P1151P		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	1151						integral component of membrane (GO:0016021)		p.P1151P(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						TCATCTACCCCGCCGTGGTGC	0.612																																					p.P1151P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3453T	11						.						52.0	61.0	58.0					11																	65394448		2138	4222	6360	65151024	SO:0001819	synonymous_variant	399909	exon21			BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.3453C>T	11.37:g.65394448C>T		Somatic		Capture	Illumina HiSeq	Phase_I	65151024	NM_032223	Q6MZN8	Silent	SNP	ENST00000355703.3	37	CCDS44650.1																																																																																				0.612	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
RELA	5970	broad.mit.edu	37	11	65422200	65422200	+	Silent	SNP	C	C	T	rs370929917		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:65422200C>T	ENST00000406246.3	-	11	1566	c.1305G>A	c.(1303-1305)acG>acA	p.T435T	RELA_ENST00000525693.1_3'UTR|RELA_ENST00000308639.9_Silent_p.T432T	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	435	Activation domain.				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.T435T(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						cctctGACAGCGTTCCTTCCC	0.662																																					p.T435T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1305A	11						.	C	,	2,4390		0,2,2194	20.0	21.0	21.0		1296,1305	-5.4	0.5	11		21	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous	RELA	NM_001145138.1,NM_021975.3	,	0,2,6490	TT,TC,CC		0.0,0.0455,0.0154	,	432/549,435/552	65422200	2,12982	2196	4296	6492	65178776	SO:0001819	synonymous_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.1305G>A	11.37:g.65422200C>T		Somatic		Capture	Illumina HiSeq	Phase_I	65178776	NM_021975	Q6GTV1|Q6SLK1	Silent	SNP	ENST00000406246.3	37	CCDS31609.1																																																																																				0.662	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975	
BANF1	8815	broad.mit.edu	37	11	65771231	65771231	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:65771231C>T	ENST00000312175.2	+	3	766	c.258C>T	c.(256-258)gaC>gaT	p.D86D	EIF1AD_ENST00000525767.1_5'Flank|BANF1_ENST00000524628.1_3'UTR|EIF1AD_ENST00000526451.1_5'Flank|EIF1AD_ENST00000529964.1_5'Flank|EIF1AD_ENST00000312234.2_5'Flank|BANF1_ENST00000527348.1_Silent_p.D86D|EIF1AD_ENST00000533544.1_5'Flank|BANF1_ENST00000445560.2_Silent_p.D86D|BANF1_ENST00000533166.1_Silent_p.D86D|EIF1AD_ENST00000527249.1_5'Flank	NM_001143985.1|NM_003860.3	NP_001137457.1|NP_003851.1	O75531	BAF_HUMAN	barrier to autointegration factor 1	86					DNA integration (GO:0015074)|establishment of integrated proviral latency (GO:0075713)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|response to virus (GO:0009615)|viral process (GO:0016032)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D86D(1)		large_intestine(2)|prostate(1)	3						AGTGGTGCGACGCCTTCTTGT	0.567																																					p.D86D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C258T	11						.						64.0	61.0	62.0					11																	65771231		2201	4296	6497	65527807	SO:0001819	synonymous_variant	8815	exon3			AF068235	CCDS8125.1	11q13.1	2012-04-19			ENSG00000175334	ENSG00000175334			17397	protein-coding gene	gene with protein product		603811				9465049	Standard	NM_003860		Approved	BAF	uc001ogp.3	O75531	OTTHUMG00000166749	ENST00000312175.2:c.258C>T	11.37:g.65771231C>T		Somatic		Capture	Illumina HiSeq	Phase_I	65527807	NM_001143985	O60558|Q6FGG7	Silent	SNP	ENST00000312175.2	37	CCDS8125.1																																																																																				0.567	BANF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391340.1	NM_003860	
CATSPER1	117144	broad.mit.edu	37	11	65793395	65793395	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:65793395G>T	ENST00000312106.5	-	1	593	c.456C>A	c.(454-456)ccC>ccA	p.P152P		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	152	His-rich.				calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.P152P(1)		breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						CGAGATATTGGGGTCTGCCAT	0.567																																					p.P152P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C456A	11						.						61.0	53.0	56.0					11																	65793395		2201	4296	6497	65549971	SO:0001819	synonymous_variant	117144	exon1			AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"""Voltage-gated ion channels / Cation channels, sperm associated"""	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.456C>A	11.37:g.65793395G>T		Somatic		Capture	Illumina HiSeq	Phase_I	65549971	NM_053054	Q96P76	Silent	SNP	ENST00000312106.5	37	CCDS8127.1																																																																																				0.567	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	
SF3B2	10992	broad.mit.edu	37	11	65824822	65824822	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:65824822G>A	ENST00000322535.6	+	7	802	c.753G>A	c.(751-753)ccG>ccA	p.P251P	SF3B2_ENST00000528302.1_Silent_p.P234P	NM_006842.2	NP_006833.2	Q13435	SF3B2_HUMAN	splicing factor 3b, subunit 2, 145kDa	251	Poly-Pro.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	poly(A) RNA binding (GO:0044822)	p.P251P(1)		breast(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(2)|lung(14)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	41						GTCCCCCACCGCCCCCTGGAG	0.532																																					p.P251P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G753A	11						.						50.0	62.0	58.0					11																	65824822		2198	4293	6491	65581398	SO:0001819	synonymous_variant	10992	exon7			U41371	CCDS31612.1	11q13	2010-07-21	2002-08-29		ENSG00000087365	ENSG00000087365			10769	protein-coding gene	gene with protein product		605591	"""splicing factor 3b, subunit 2, 145kD"""			8566756	Standard	XM_005273726		Approved	SAP145, SF3b1, Cus1, SF3b145	uc001ogy.1	Q13435	OTTHUMG00000166751	ENST00000322535.6:c.753G>A	11.37:g.65824822G>A		Somatic		Capture	Illumina HiSeq	Phase_I	65581398	NM_006842	A8K485|B4DT19|Q7L4T5|Q7Z627|Q969K1|Q96CM6|Q9BWD2	Silent	SNP	ENST00000322535.6	37	CCDS31612.1																																																																																				0.532	SF3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391352.2		
PACS1	55690	broad.mit.edu	37	11	66001370	66001370	+	Silent	SNP	C	C	T	rs115328615		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:66001370C>T	ENST00000320580.4	+	16	1986	c.1953C>T	c.(1951-1953)tcC>tcT	p.S651S	PACS1_ENST00000529757.1_Silent_p.S187S	NM_018026.3	NP_060496.2	Q6VY07	PACS1_HUMAN	phosphofurin acidic cluster sorting protein 1	651					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.S651S(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						ACAAGACCTCCGACTGGCTTG	0.597																																					p.S651S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1953T	11						.	C		0,4400		0,0,2200	90.0	70.0	77.0		1953	-4.3	0.9	11	dbSNP_132	77	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	PACS1	NM_018026.2		0,1,6494	TT,TC,CC		0.0116,0.0,0.0077		651/964	66001370	1,12989	2200	4295	6495	65757946	SO:0001819	synonymous_variant	55690	exon16			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.1953C>T	11.37:g.66001370C>T		Somatic		Capture	Illumina HiSeq	Phase_I	65757946	NM_018026	Q6PJY6|Q6PKB6|Q7Z590|Q7Z5W4|Q8N8K6|Q96MW0|Q9NW92|Q9ULP5	Silent	SNP	ENST00000320580.4	37	CCDS8129.1																																																																																				0.597	PACS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391690.2	NM_018026	
KLC2	64837	broad.mit.edu	37	11	66031853	66031853	+	Missense_Mutation	SNP	C	C	T	rs532282605		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:66031853C>T	ENST00000417856.1	+	9	1397	c.1154C>T	c.(1153-1155)gCg>gTg	p.A385V	KLC2_ENST00000421552.1_Missense_Mutation_p.A308V|RP11-755F10.3_ENST00000533576.1_RNA|KLC2_ENST00000394066.2_Missense_Mutation_p.A308V|KLC2_ENST00000394078.1_Intron|KLC2_ENST00000316924.5_Missense_Mutation_p.A385V|KLC2_ENST00000394065.2_Missense_Mutation_p.A246V|KLC2_ENST00000394067.2_Missense_Mutation_p.A385V|RP11-867G23.1_ENST00000530805.1_RNA	NM_001134775.1	NP_001128247.1	Q9H0B6	KLC2_HUMAN	kinesin light chain 2	385					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.A385V(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						TACCAGGATGCGGAGACCTTG	0.562													C|||	1	0.000199681	0.0008	0.0	5008	,	,		21210	0.0		0.0	False		,,,				2504	0.0				p.A385V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1154T	11						.						108.0	85.0	93.0					11																	66031853		2200	4295	6495	65788429	SO:0001583	missense	64837	exon9			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.1154C>T	11.37:g.66031853C>T	ENSP00000399403:p.Ala385Val	Somatic		Capture	Illumina HiSeq	Phase_I	65788429	NM_001134775	A8MXL7|B2RDY4|Q9H9C8|Q9HA20	Missense_Mutation	SNP	ENST00000417856.1	37	CCDS8130.1	.	.	.	.	.	.	.	.	.	.	C	31	5.060508	0.93846	.	.	ENSG00000174996	ENST00000417856;ENST00000394067;ENST00000316924;ENST00000421552;ENST00000394066;ENST00000394065	D;D;D;D;D;D	0.88896	-2.44;-2.44;-2.44;-2.44;-2.44;-2.44	3.81	3.81	0.43845	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.64402	D	0.000003	D	0.95245	0.8458	M	0.91663	3.23	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.984;0.975;0.998	D	0.96221	0.9160	10	0.72032	D	0.01	-9.7998	14.6519	0.68803	0.0:1.0:0.0:0.0	.	246;308;385	A8MZ87;A8MXL7;Q9H0B6	.;.;KLC2_HUMAN	V	385;385;385;308;308;246	ENSP00000399403:A385V;ENSP00000377631:A385V;ENSP00000314837:A385V;ENSP00000408484:A308V;ENSP00000377630:A308V;ENSP00000377629:A246V	ENSP00000314837:A385V	A	+	2	0	KLC2	65788429	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	7.495000	0.81514	1.988000	0.58038	0.462000	0.41574	GCG		0.562	KLC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258200.1	NM_022822	
RAB1B	81876	broad.mit.edu	37	11	66039307	66039307	+	Silent	SNP	C	C	T	rs140622155	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:66039307C>T	ENST00000311481.6	+	2	201	c.54C>T	c.(52-54)ggC>ggT	p.G18G	RP11-867G23.3_ENST00000501708.1_lincRNA|RAB1B_ENST00000527397.1_Silent_p.G18G	NM_030981.2	NP_112243.1	Q9H0U4	RAB1B_HUMAN	RAB1B, member RAS oncogene family	18					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.G18G(1)		large_intestine(2)|lung(1)|ovary(1)|prostate(1)	5						GCGACTCAGGCGTGGGCAAGT	0.577																																					p.G18G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C54T	11						.	C		3,4397	6.2+/-15.9	0,3,2197	133.0	107.0	115.0		54	2.3	1.0	11	dbSNP_134	115	0,8590		0,0,4295	no	coding-synonymous	RAB1B	NM_030981.2		0,3,6492	TT,TC,CC		0.0,0.0682,0.0231		18/202	66039307	3,12987	2200	4295	6495	65795883	SO:0001819	synonymous_variant	81876	exon2			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.54C>T	11.37:g.66039307C>T		Somatic		Capture	Illumina HiSeq	Phase_I	65795883	NM_030981	A8K7S1	Silent	SNP	ENST00000311481.6	37	CCDS31613.1																																																																																				0.577	RAB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391886.2	NM_030981	
CTSF	8722	broad.mit.edu	37	11	66331416	66331416	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:66331416C>T	ENST00000310325.5	-	13	1552	c.1443G>A	c.(1441-1443)gcG>gcA	p.A481A	ACTN3_ENST00000502692.1_RNA|CTSF_ENST00000533168.1_5'Flank|ACTN3_ENST00000513398.1_RNA	NM_003793.3	NP_003784.2	Q9UBX1	CATF_HUMAN	cathepsin F	481				SDVPFWAIKNSWGTDWGEKGYYYLHRGSGACGVNTMASSAV VD -> EFRCLSCIQPGHRQGWDHSISGPLEGK (in Ref. 9). {ECO:0000305}.	antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|vesicle (GO:0031982)	cysteine-type endopeptidase activity (GO:0004197)	p.A481A(1)		endometrium(1)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	19						AGTCCACCACCGCCGAGCTGG	0.672																																					p.A481A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1443A	11						.						25.0	28.0	27.0					11																	66331416		2199	4294	6493	66087992	SO:0001819	synonymous_variant	8722	exon13			AF071749	CCDS8144.1	11q13.2	2012-02-29			ENSG00000174080	ENSG00000174080		"""Cathepsins"""	2531	protein-coding gene	gene with protein product		603539				9822672, 10318784	Standard	NM_003793		Approved	CATSF, CLN13	uc001oip.3	Q9UBX1	OTTHUMG00000167090	ENST00000310325.5:c.1443G>A	11.37:g.66331416C>T		Somatic		Capture	Illumina HiSeq	Phase_I	66087992	NM_003793	B2R964|O95240|Q9NSU4|Q9UKQ5	Silent	SNP	ENST00000310325.5	37	CCDS8144.1																																																																																				0.672	CTSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393047.1	NM_003793	
RBM4B	83759	broad.mit.edu	37	11	66444440	66444440	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:66444440G>A	ENST00000525754.1	-	1	779	c.111C>T	c.(109-111)taC>taT	p.Y37Y	RBM4B_ENST00000531969.1_Silent_p.Y37Y|RBM4B_ENST00000531036.2_Silent_p.Y37Y|RBM4B_ENST00000310046.4_Silent_p.Y37Y|RBM4B_ENST00000524637.1_Silent_p.Y37Y			Q9BQ04	RBM4B_HUMAN	RNA binding motif protein 4B	37	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|entrainment of circadian clock by photoperiod (GO:0043153)|mRNA processing (GO:0006397)|positive regulation of gene expression (GO:0010628)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.Y37Y(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(1)|urinary_tract(2)	10						GCACAAAGCCGTAATTCTTAA	0.507																																					p.Y37Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C111T	11						.						99.0	97.0	98.0					11																	66444440		2199	4276	6475	66201016	SO:0001819	synonymous_variant	83759	exon2			AK095158	CCDS8149.1, CCDS66144.1	11q13	2013-02-12	2006-01-25	2006-01-25				"""Zinc fingers, CCHC domain containing"", ""RNA binding motif (RRM) containing"""	28842	protein-coding gene	gene with protein product			"""RNA binding motif protein 30"""	RBM30		12477932	Standard	XR_247213		Approved	MGC10871, ZCCHC15, RBM4L, ZCRB3B, ZCCHC21B	uc001ojb.3	Q9BQ04		ENST00000525754.1:c.111C>T	11.37:g.66444440G>A		Somatic		Capture	Illumina HiSeq	Phase_I	66201016	NM_031492	B3KT83	Silent	SNP	ENST00000525754.1	37	CCDS8149.1																																																																																				0.507	RBM4B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393851.1	NM_031492	
SPTBN2	6712	broad.mit.edu	37	11	66483393	66483393	+	Missense_Mutation	SNP	G	G	A	rs536375005		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:66483393G>A	ENST00000533211.1	-	4	548	c.217C>T	c.(217-219)Cgg>Tgg	p.R73W	RN7SL12P_ENST00000473849.2_RNA|SPTBN2_ENST00000529997.1_Missense_Mutation_p.R73W|SPTBN2_ENST00000309996.2_Missense_Mutation_p.R73W			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	73	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)	p.R73W(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						CACGTGACCCGGGCCAGGTGC	0.587																																					p.R73W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C217T	11						.						99.0	74.0	83.0					11																	66483393		2200	4295	6495	66239969	SO:0001583	missense	6712	exon3			AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.217C>T	11.37:g.66483393G>A	ENSP00000432568:p.Arg73Trp	Somatic		Capture	Illumina HiSeq	Phase_I	66239969	NM_006946	O14872|O14873	Missense_Mutation	SNP	ENST00000533211.1	37	CCDS8150.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.203502	0.79127	.	.	ENSG00000173898	ENST00000533211;ENST00000309996;ENST00000529997;ENST00000443262;ENST00000527010	T;T;T;T	0.60672	0.17;0.17;0.17;0.17	5.04	4.07	0.47477	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	T	0.77253	0.4103	M	0.87900	2.915	0.58432	D	0.999996	D	0.89917	1.0	D	0.87578	0.998	T	0.80921	-0.1166	10	0.87932	D	0	.	12.4625	0.55738	0.0:0.0:0.7599:0.2401	.	73	O15020	SPTN2_HUMAN	W	73	ENSP00000432568:R73W;ENSP00000311489:R73W;ENSP00000433593:R73W;ENSP00000433631:R73W	ENSP00000311489:R73W	R	-	1	2	SPTBN2	66239969	0.986000	0.35501	1.000000	0.80357	0.989000	0.77384	1.571000	0.36450	2.611000	0.88343	0.561000	0.74099	CGG		0.587	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
CABP4	57010	broad.mit.edu	37	11	67225053	67225053	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:67225053G>A	ENST00000325656.5	+	4	628	c.551G>A	c.(550-552)cGt>cAt	p.R184H	CABP4_ENST00000438189.2_Missense_Mutation_p.R79H|CTC-1337H24.1_ENST00000602912.1_lincRNA	NM_145200.3	NP_660201.1	P57796	CABP4_HUMAN	calcium binding protein 4	184	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				photoreceptor cell morphogenesis (GO:0008594)|phototransduction (GO:0007602)|retinal bipolar neuron differentiation (GO:0060040)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytosol (GO:0005829)|extracellular region (GO:0005576)|synapse (GO:0045202)|terminal bouton (GO:0043195)	calcium ion binding (GO:0005509)	p.R184H(1)		central_nervous_system(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)	11			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			GTGGGCGGCCGTGTGGACTTT	0.617																																					p.R184H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G551A	11						.						55.0	48.0	51.0					11																	67225053		2199	4289	6488	66981629	SO:0001583	missense	57010	exon4			AC005849	CCDS8166.1, CCDS73333.1	11q13.2	2013-09-20			ENSG00000175544	ENSG00000175544		"""EF-hand domain containing"""	1386	protein-coding gene	gene with protein product		608965				10625670, 16960802	Standard	NM_145200		Approved	CSNB2B	uc001olo.3	P57796	OTTHUMG00000168033	ENST00000325656.5:c.551G>A	11.37:g.67225053G>A	ENSP00000324960:p.Arg184His	Somatic		Capture	Illumina HiSeq	Phase_I	66981629	NM_145200	Q8N4Z2|Q8WWY5	Missense_Mutation	SNP	ENST00000325656.5	37	CCDS8166.1	.	.	.	.	.	.	.	.	.	.	G	12.00	1.807263	0.31961	.	.	ENSG00000175544	ENST00000438189;ENST00000325656	T;T	0.31769	1.48;1.48	4.58	2.54	0.30619	EF-hand-like domain (1);	0.364662	0.28847	N	0.013957	T	0.18841	0.0452	L	0.31207	0.915	0.34657	D	0.722278	B;B	0.21688	0.059;0.006	B;B	0.14023	0.01;0.001	T	0.11867	-1.0570	10	0.72032	D	0.01	-3.0792	4.6346	0.12518	0.1895:0.0:0.5855:0.2249	.	184;79	P57796;P57796-2	CABP4_HUMAN;.	H	79;184	ENSP00000401555:R79H;ENSP00000324960:R184H	ENSP00000324960:R184H	R	+	2	0	CABP4	66981629	0.000000	0.05858	0.998000	0.56505	0.998000	0.95712	-0.086000	0.11233	0.518000	0.28383	0.655000	0.94253	CGT		0.617	CABP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397624.2		
NDUFV1	4723	broad.mit.edu	37	11	67378571	67378571	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:67378571G>A	ENST00000322776.6	+	6	959	c.806G>A	c.(805-807)cGc>cAc	p.R269H	NDUFV1_ENST00000526169.1_3'UTR|NDUFV1_ENST00000415352.2_Missense_Mutation_p.R262H|NDUFV1_ENST00000529927.1_Missense_Mutation_p.R260H|NDUFV1_ENST00000532303.1_Missense_Mutation_p.R168H|DOC2GP_ENST00000495263.1_RNA	NM_001166102.1|NM_007103.3	NP_001159574.1|NP_009034.2	P49821	NDUV1_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 1, 51kDa	269					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.R269H(1)		breast(1)|endometrium(3)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	16						GGCAGAGAACGCAACTCAGGC	0.547																																					p.R260H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G779A	11						.						128.0	106.0	114.0					11																	67378571		2200	4294	6494	67135147	SO:0001583	missense	4723	exon6			AF092131	CCDS8173.1, CCDS53669.1	11q13	2011-07-04	2002-08-29		ENSG00000167792	ENSG00000167792	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7716	protein-coding gene	gene with protein product	"""complex I 51kDa subunit"", ""NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial"""	161015	"""NADH dehydrogenase (ubiquinone) flavoprotein 1 (51kD)"""			1478657	Standard	NM_007103		Approved	CI-51K	uc001omj.2	P49821	OTTHUMG00000166215	ENST00000322776.6:c.806G>A	11.37:g.67378571G>A	ENSP00000322450:p.Arg269His	Somatic		Capture	Illumina HiSeq	Phase_I	67135147	NM_001166102	O60924|O60940|Q16104|Q6IBR3|Q96BF8|Q96HS7	Missense_Mutation	SNP	ENST00000322776.6	37	CCDS8173.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.305496	0.81247	.	.	ENSG00000167792	ENST00000322776;ENST00000532303;ENST00000529927;ENST00000415352;ENST00000453836	D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23	4.84	3.89	0.44902	.	0.050918	0.85682	D	0.000000	D	0.93805	0.8019	M	0.88377	2.95	0.80722	D	1	D;D;D;D	0.89917	0.962;0.989;0.989;1.0	P;P;P;D	0.91635	0.551;0.81;0.81;0.999	D	0.94347	0.7576	10	0.66056	D	0.02	-21.3924	12.951	0.58401	0.0:0.0:0.8365:0.1635	.	168;262;260;269	B4DE93;G3V0I5;P49821-2;P49821	.;.;.;NDUV1_HUMAN	H	269;168;260;262;140	ENSP00000322450:R269H;ENSP00000432015:R168H;ENSP00000436766:R260H;ENSP00000395368:R262H	ENSP00000322450:R269H	R	+	2	0	NDUFV1	67135147	1.000000	0.71417	0.998000	0.56505	0.813000	0.45954	9.534000	0.98061	1.200000	0.43188	0.491000	0.48974	CGC		0.547	NDUFV1-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388406.1	NM_007103	
PPP6R3	55291	broad.mit.edu	37	11	68369412	68369412	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:68369412G>A	ENST00000393800.2	+	21	2528	c.2274G>A	c.(2272-2274)gcG>gcA	p.A758A	PPP6R3_ENST00000265636.5_Silent_p.A678A|PPP6R3_ENST00000265637.4_Silent_p.A712A|PPP6R3_ENST00000393799.2_Silent_p.A758A|PPP6R3_ENST00000524904.1_Silent_p.A752A|PPP6R3_ENST00000393801.3_Silent_p.A758A|PPP6R3_ENST00000529710.1_Silent_p.A678A|PPP6R3_ENST00000527403.2_Silent_p.A723A|PPP6R3_ENST00000524845.1_Silent_p.A729A|PPP6R3_ENST00000534534.1_Silent_p.A526A	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	758					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)	p.A758A(1)|p.A678A(1)		breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						CTCCCAGTGCGGCTGCCCTGG	0.522																																					p.A678A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G2034A	11						.						74.0	83.0	80.0					11																	68369412		2200	4294	6494	68125988	SO:0001819	synonymous_variant	55291	exon20			AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	1173	protein-coding gene	gene with protein product	"""sporulation-induced transcript 4-associated protein"""	610879	"""chromosome 11 open reading frame 23"", ""SAPS domain family, member 3"""	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.2274G>A	11.37:g.68369412G>A		Somatic		Capture	Illumina HiSeq	Phase_I	68125988	NM_001164164	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Silent	SNP	ENST00000393800.2	37	CCDS53672.1																																																																																				0.522	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312	
TPCN2	219931	broad.mit.edu	37	11	68840442	68840442	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:68840442C>T	ENST00000294309.3	+	13	1304	c.1203C>T	c.(1201-1203)aaC>aaT	p.N401N	TPCN2_ENST00000442692.2_Intron|TPCN2_ENST00000542467.1_Silent_p.N401N	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	401					calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)	p.N401N(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			AGCTCTTCAACGAGCTTGACA	0.582																																					p.N401N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1203T	11						.						106.0	103.0	104.0					11																	68840442		2200	4294	6494	68597018	SO:0001819	synonymous_variant	219931	exon13			AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.1203C>T	11.37:g.68840442C>T		Somatic		Capture	Illumina HiSeq	Phase_I	68597018	NM_139075	Q9NT82	Silent	SNP	ENST00000294309.3	37	CCDS8189.1																																																																																				0.582	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
KRTAP5-9	3846	broad.mit.edu	37	11	71259818	71259818	+	Missense_Mutation	SNP	G	G	A	rs146869772	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:71259818G>A	ENST00000528743.2	+	1	353	c.115G>A	c.(115-117)Gtc>Atc	p.V39I		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	39	8 X 4 AA repeats of C-C-X-P.				epidermis development (GO:0008544)	keratin filament (GO:0045095)		p.V39I(1)		kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						CTGTGCACCCGTCTACTGCTG	0.667													g|||	10	0.00199681	0.0068	0.0014	5008	,	,		17781	0.0		0.0	False		,,,				2504	0.0				p.V39I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G115A	11						.	G	ILE/VAL	37,4363		0,37,2163	80.0	91.0	87.0		115	1.6	0.0	11	dbSNP_134	87	0,8588		0,0,4294	no	missense	KRTAP5-9	NM_005553.3	29	0,37,6457	AA,AG,GG		0.0,0.8409,0.2849	possibly-damaging	39/170	71259818	37,12951	2200	4294	6494	70937466	SO:0001583	missense	3846	exon1			AB126078	CCDS53677.1	11q13.4	2008-02-05				ENSG00000254997		"""Keratin associated proteins"""	23604	protein-coding gene	gene with protein product		148021		KRN1		15144888	Standard	NM_005553		Approved	KRTAP5.9, KRTAP5-1	uc001oqs.1	P26371		ENST00000528743.2:c.115G>A	11.37:g.71259818G>A	ENSP00000431443:p.Val39Ile	Somatic		Capture	Illumina HiSeq	Phase_I	70937466	NM_005553	Q14564|Q3MIP8	Missense_Mutation	SNP	ENST00000528743.2	37	CCDS53677.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	N	4.044	0.005754	0.07866	0.008409	0.0	ENSG00000254997	ENST00000528743	T	0.03745	3.82	1.57	1.57	0.23409	.	.	.	.	.	T	0.04003	0.0112	L	0.42487	1.325	0.09310	N	1	P	0.51537	0.946	P	0.50270	0.636	T	0.38067	-0.9678	9	0.49607	T	0.09	.	6.6099	0.22745	0.0:0.0:1.0:0.0	.	39	P26371	KRA59_HUMAN	I	39	ENSP00000431443:V39I	ENSP00000431443:V39I	V	+	1	0	KRTAP5-9	70937466	0.000000	0.05858	0.015000	0.15790	0.167000	0.22549	-0.373000	0.07494	1.189000	0.43028	0.442000	0.29010	GTC		0.667	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2		
NUMA1	4926	broad.mit.edu	37	11	71726898	71726898	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:71726898G>A	ENST00000393695.3	-	15	1982	c.1651C>T	c.(1651-1653)Cac>Tac	p.H551Y	NUMA1_ENST00000358965.6_Missense_Mutation_p.H551Y|RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000351960.6_Intron	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1									p.H551Y(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						TCCACCTGGTGGCGGAGGCCC	0.602			T	RARA	APL						OREG0021187	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.H551Y			Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1651T	11						.						160.0	157.0	158.0					11																	71726898		2200	4293	6493	71404546	SO:0001583	missense	4926	exon15			Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.1651C>T	11.37:g.71726898G>A	ENSP00000377298:p.His551Tyr	Somatic	1132	Capture	Illumina HiSeq	Phase_I	71404546	NM_006185		Missense_Mutation	SNP	ENST00000393695.3	37	CCDS31633.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.447810	0.43429	.	.	ENSG00000137497	ENST00000358965;ENST00000393695;ENST00000359652;ENST00000542977;ENST00000537217	T;T;T;T	0.44482	2.72;2.72;1.5;0.92	5.82	5.82	0.92795	.	0.956066	0.08784	N	0.894213	T	0.31136	0.0787	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.29766	0.256;0.168;0.073;0.256	B;B;B;B	0.31547	0.132;0.058;0.04;0.132	T	0.17228	-1.0376	10	0.51188	T	0.08	.	11.3435	0.49546	0.0:0.1352:0.7249:0.1399	.	557;35;551;551	Q4LE64;Q59HB8;Q14980-2;Q14980	.;.;.;NUMA1_HUMAN	Y	551;551;114;551;551	ENSP00000351851:H551Y;ENSP00000377298:H551Y;ENSP00000444880:H551Y;ENSP00000442936:H551Y	ENSP00000351851:H551Y	H	-	1	0	NUMA1	71404546	0.007000	0.16637	0.941000	0.38009	0.976000	0.68499	1.683000	0.37638	2.756000	0.94617	0.561000	0.74099	CAC		0.602	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
NUMA1	4926	broad.mit.edu	37	11	71730542	71730542	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:71730542G>A	ENST00000393695.3	-	9	913	c.582C>T	c.(580-582)aaC>aaT	p.N194N	NUMA1_ENST00000358965.6_Silent_p.N194N|RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000351960.6_Silent_p.N194N	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1									p.N194N(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						GAACATACTTGTTCCCACTGG	0.527			T	RARA	APL																																p.N194N			Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C582T	11						.						132.0	111.0	118.0					11																	71730542		2200	4293	6493	71408190	SO:0001819	synonymous_variant	4926	exon9			Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.582C>T	11.37:g.71730542G>A		Somatic		Capture	Illumina HiSeq	Phase_I	71408190	NM_006185		Silent	SNP	ENST00000393695.3	37	CCDS31633.1																																																																																				0.527	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
FOLR1	2348	broad.mit.edu	37	11	71906995	71906995	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:71906995C>A	ENST00000393679.1	+	5	984	c.548C>A	c.(547-549)cCc>cAc	p.P183H	FOLR1_ENST00000393681.2_Missense_Mutation_p.P183H|RP11-807H22.7_ENST00000378140.3_RNA|FOLR1_ENST00000312293.4_Missense_Mutation_p.P183H|FOLR1_ENST00000393676.3_Missense_Mutation_p.P183H			P15328	FOLR1_HUMAN	folate receptor 1 (adult)	183					cell death (GO:0008219)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|receptor-mediated endocytosis (GO:0006898)	anchored component of external side of plasma membrane (GO:0031362)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|receptor activity (GO:0004872)	p.P183H(1)		cervix(2)|endometrium(1)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	14					Methotrexate(DB00563)	TTCTACTTCCCCACACCCACT	0.547																																					p.P183H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C548A	11						.						101.0	96.0	98.0					11																	71906995		2200	4293	6493	71584643	SO:0001583	missense	2348	exon6			J05013	CCDS8211.1	11q13.3-q14.1	2010-04-09			ENSG00000110195	ENSG00000110195			3791	protein-coding gene	gene with protein product		136430		FOLR		1717147	Standard	NM_000802		Approved		uc001osa.2	P15328		ENST00000393679.1:c.548C>A	11.37:g.71906995C>A	ENSP00000377284:p.Pro183His	Somatic		Capture	Illumina HiSeq	Phase_I	71584643	NM_016724	Q53EW2|Q6FGT8|Q6LC90|Q9UCT2	Missense_Mutation	SNP	ENST00000393679.1	37	CCDS8211.1	.	.	.	.	.	.	.	.	.	.	c	14.86	2.660145	0.47572	.	.	ENSG00000110195	ENST00000312293;ENST00000393681;ENST00000393679;ENST00000393676	T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09	4.11	4.11	0.48088	Folate receptor-like (1);	0.000000	0.85682	D	0.000000	D	0.88269	0.6391	M	0.85373	2.75	0.58432	D	0.999997	D	0.89917	1.0	D	0.83275	0.996	D	0.89404	0.3698	10	0.52906	T	0.07	-12.0567	14.2199	0.65820	0.0:1.0:0.0:0.0	.	183	P15328	FOLR1_HUMAN	H	183	ENSP00000308137:P183H;ENSP00000377286:P183H;ENSP00000377284:P183H;ENSP00000377281:P183H	ENSP00000308137:P183H	P	+	2	0	FOLR1	71584643	1.000000	0.71417	0.961000	0.40146	0.069000	0.16628	6.494000	0.73661	2.266000	0.75297	0.563000	0.77884	CCC		0.547	FOLR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396773.1	NM_016725	
UCP3	7352	broad.mit.edu	37	11	73714978	73714978	+	Missense_Mutation	SNP	C	C	T	rs138705669		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:73714978C>T	ENST00000314032.4	-	6	1270	c.718G>A	c.(718-720)Gtg>Atg	p.V240M	UCP3_ENST00000348534.4_Missense_Mutation_p.V138M|UCP3_ENST00000426995.2_Missense_Mutation_p.V240M|UCP3_ENST00000545271.1_5'Flank	NM_003356.3	NP_003347.1	P55916	UCP3_HUMAN	uncoupling protein 3 (mitochondrial, proton carrier)	240					aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to hormone stimulus (GO:0032870)|fatty acid metabolic process (GO:0006631)|lipid metabolic process (GO:0006629)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|response to activity (GO:0014823)|response to cold (GO:0009409)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to superoxide (GO:0000303)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)|transporter activity (GO:0005215)	p.V240M(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12	Breast(11;2.08e-05)					GTCTTCACCACGTCCACCGGG	0.572													C|||	1	0.000199681	0.0	0.0	5008	,	,		18084	0.0		0.001	False		,,,				2504	0.0				p.V240M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G718A	11						.						54.0	56.0	55.0					11																	73714978		2200	4293	6493	73392626	SO:0001583	missense	7352	exon6			AF001787	CCDS8229.1, CCDS44677.1	11q13.4	2013-05-22				ENSG00000175564		"""Solute carriers"""	12519	protein-coding gene	gene with protein product		602044				9480760, 9196039	Standard	NM_003356		Approved	SLC25A9	uc001our.3	P55916		ENST00000314032.4:c.718G>A	11.37:g.73714978C>T	ENSP00000323740:p.Val240Met	Somatic		Capture	Illumina HiSeq	Phase_I	73392626	NM_022803	O60475|Q96HL3	Missense_Mutation	SNP	ENST00000314032.4	37	CCDS8229.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	31	5.062620	0.93898	.	.	ENSG00000175564	ENST00000314032;ENST00000348534;ENST00000426995	D;D;D	0.83250	-1.7;-1.61;-1.7	5.07	5.07	0.68467	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.91845	0.7419	M	0.82630	2.6	0.58432	D	0.999991	D	0.89917	1.0	D	0.87578	0.998	D	0.92706	0.6179	10	0.66056	D	0.02	1.0447	18.4155	0.90568	0.0:1.0:0.0:0.0	.	240	P55916	UCP3_HUMAN	M	240;138;240	ENSP00000323740:V240M;ENSP00000343615:V138M;ENSP00000392143:V240M	ENSP00000323740:V240M	V	-	1	0	UCP3	73392626	1.000000	0.71417	0.979000	0.43373	0.935000	0.57460	7.722000	0.84778	2.528000	0.85240	0.655000	0.94253	GTG		0.572	UCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398200.1	NM_003356	
C2CD3	26005	broad.mit.edu	37	11	73843994	73843994	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:73843994C>T	ENST00000334126.7	-	7	1338	c.1112G>A	c.(1111-1113)cGg>cAg	p.R371Q	C2CD3_ENST00000313663.7_Missense_Mutation_p.R371Q|C2CD3_ENST00000539061.1_Missense_Mutation_p.R371Q			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	371					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)		p.R371P(1)|p.R371Q(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					GTCTTTAAACCGATTCCTAGA	0.388																																					p.R371Q												.	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.G1112A	11						.						171.0	155.0	160.0					11																	73843994		2200	4293	6493	73521642	SO:0001583	missense	26005	exon7			BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.1112G>A	11.37:g.73843994C>T	ENSP00000334379:p.Arg371Gln	Somatic		Capture	Illumina HiSeq	Phase_I	73521642	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.724|9.724	1.160566|1.160566	0.21454|0.21454	.|.	.|.	ENSG00000168014|ENSG00000168014	ENST00000289350|ENST00000334126;ENST00000313663;ENST00000313681;ENST00000539061	.|T;T	.|0.09630	.|2.96;2.96	5.2|5.2	-0.211|-0.211	0.13172|0.13172	.|.	.|1.109980	.|0.06889	.|N	.|0.803948	T|T	0.03348|0.03348	0.0097|0.0097	N|N	0.00926|0.00926	-1.1|-1.1	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.43845|0.43845	-0.9366|-0.9366	6|10	0.22109|0.26408	T|T	0.4|0.33	6.7573|6.7573	5.9902|5.9902	0.19456|0.19456	0.0:0.3639:0.2564:0.3797|0.0:0.3639:0.2564:0.3797	.|.	.|371;371	.|Q4AC94;Q4AC94-1	.|C2CD3_HUMAN;.	S|Q	371|371	.|ENSP00000334379:R371Q;ENSP00000323339:R371Q	ENSP00000289350:G371S|ENSP00000323339:R371Q	G|R	-|-	1|2	0|0	C2CD3|C2CD3	73521642|73521642	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.144000|0.144000	0.21451|0.21451	0.034000|0.034000	0.13776|0.13776	-0.270000|-0.270000	0.09285|0.09285	-0.254000|-0.254000	0.11334|0.11334	GGT|CGG		0.388	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
MAP6	4135	broad.mit.edu	37	11	75319277	75319277	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:75319277A>G	ENST00000304771.3	-	2	1746	c.996T>C	c.(994-996)caT>caC	p.H332H	MAP6_ENST00000434603.2_Silent_p.H332H|MAP6_ENST00000526740.1_Silent_p.H3H	NM_033063.1	NP_149052.1	Q96JE9	MAP6_HUMAN	microtubule-associated protein 6	332					dendrite morphogenesis (GO:0048813)|lysosome localization (GO:0032418)|microtubule cytoskeleton organization (GO:0000226)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)		p.H332H(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	19	Ovarian(111;0.11)					AGCTGGTCTCATGAACCATCT	0.493																																					p.H332H	Esophageal Squamous(181;1115 2007 8647 17065 22697)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T996C	11						.						177.0	153.0	161.0					11																	75319277		2200	4293	6493	74996925	SO:0001819	synonymous_variant	4135	exon2			AK123340	CCDS31641.1, CCDS44686.1	11q13.5	2005-10-11			ENSG00000171533	ENSG00000171533			6868	protein-coding gene	gene with protein product		601783				10516426, 12231625	Standard	NM_207577		Approved	KIAA1878, STOP, FLJ41346	uc001owu.3	Q96JE9	OTTHUMG00000165343	ENST00000304771.3:c.996T>C	11.37:g.75319277A>G		Somatic		Capture	Illumina HiSeq	Phase_I	74996925	NM_033063	A7E2A1|Q6P3T0|Q6ZWB8	Silent	SNP	ENST00000304771.3	37	CCDS31641.1																																																																																				0.493	MAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383527.1	NM_033063	
WNT11	7481	broad.mit.edu	37	11	75905765	75905765	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:75905765G>T	ENST00000322563.3	-	3	567	c.443C>A	c.(442-444)cCc>cAc	p.P148H	RP11-619A14.2_ENST00000527314.1_RNA	NM_004626.2	NP_004617.2	O96014	WNT11_HUMAN	wingless-type MMTV integration site family, member 11	148					adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|bone mineralization (GO:0030282)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|cloacal septation (GO:0060197)|embryonic skeletal system development (GO:0048706)|lung-associated mesenchyme development (GO:0060484)|mesonephric duct development (GO:0072177)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of fibroblast growth factor production (GO:0090272)|negative regulation of mesenchymal cell proliferation (GO:0072201)|negative regulation of transcription, DNA-templated (GO:0045892)|neuroendocrine cell differentiation (GO:0061101)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway (GO:0035567)|osteoblast differentiation (GO:0001649)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta2 production (GO:0032915)|protein localization to cell surface (GO:0034394)|protein phosphorylation (GO:0006468)|response to nutrient levels (GO:0031667)|tight junction assembly (GO:0070830)|ureteric bud morphogenesis (GO:0060675)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|protein kinase activator activity (GO:0030295)|Ras GTPase activator activity (GO:0005099)|transcription regulatory region DNA binding (GO:0044212)	p.P148H(1)		breast(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	20						CCCGGGCCCGGGTGGCTCACC	0.677																																					p.P148H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C443A	11						.						18.0	16.0	17.0					11																	75905765		1914	3804	5718	75583413	SO:0001583	missense	7481	exon3			Y12692	CCDS8242.1	11q13.5	2008-02-05			ENSG00000085741	ENSG00000085741		"""Wingless-type MMTV integration sites"""	12776	protein-coding gene	gene with protein product		603699				9757009	Standard	NM_004626		Approved		uc001oxe.3	O96014	OTTHUMG00000165264	ENST00000322563.3:c.443C>A	11.37:g.75905765G>T	ENSP00000325526:p.Pro148His	Somatic		Capture	Illumina HiSeq	Phase_I	75583413	NM_004626	B2R8Z6|Q14DE8|Q8WZ98	Missense_Mutation	SNP	ENST00000322563.3	37	CCDS8242.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.051759	0.75960	.	.	ENSG00000085741	ENST00000322563;ENST00000531317;ENST00000447195	T	0.75589	-0.95	4.95	4.95	0.65309	.	0.052385	0.85682	D	0.000000	D	0.82351	0.5018	L	0.49455	1.56	0.58432	D	0.999999	D	0.76494	0.999	D	0.66716	0.946	D	0.83697	0.0180	10	0.56958	D	0.05	.	17.1651	0.86814	0.0:0.0:1.0:0.0	.	148	O96014	WNT11_HUMAN	H	148	ENSP00000325526:P148H	ENSP00000325526:P148H	P	-	2	0	WNT11	75583413	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.762000	0.68809	2.287000	0.76781	0.555000	0.69702	CCC		0.677	WNT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383083.1	NM_004626	
C11orf30	56946	broad.mit.edu	37	11	76174989	76174989	+	Silent	SNP	T	T	C	rs145349152	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:76174989T>C	ENST00000529032.1	+	6	696	c.696T>C	c.(694-696)acT>acC	p.T232T	C11orf30_ENST00000525038.1_Silent_p.T247T|C11orf30_ENST00000525919.1_Silent_p.T233T|C11orf30_ENST00000343878.3_Silent_p.T232T|C11orf30_ENST00000334736.3_Silent_p.T232T|C11orf30_ENST00000533248.1_Silent_p.T246T|C11orf30_ENST00000524767.1_Silent_p.T247T|C11orf30_ENST00000524490.1_Silent_p.T233T			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	232	Interaction with BRCA2.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.T232T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						AGACGATCACTGTGCCTGTGA	0.463													T|||	3	0.000599042	0.0023	0.0	5008	,	,		18906	0.0		0.0	False		,,,				2504	0.0				p.T232T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T696C	11						.	T		1,4399	2.1+/-5.4	0,1,2199	194.0	182.0	186.0		696	1.9	1.0	11	dbSNP_134	186	0,8584		0,0,4292	no	coding-synonymous	C11orf30	NM_020193.3		0,1,6491	CC,CT,TT		0.0,0.0227,0.0077		232/1323	76174989	1,12983	2200	4292	6492	75852637	SO:0001819	synonymous_variant	56946	exon7			AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.696T>C	11.37:g.76174989T>C		Somatic		Capture	Illumina HiSeq	Phase_I	75852637	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Silent	SNP	ENST00000529032.1	37	CCDS8244.1																																																																																				0.463	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193	
TSKU	25987	broad.mit.edu	37	11	76507119	76507119	+	Silent	SNP	G	G	A	rs374281937		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:76507119G>A	ENST00000527881.1	+	2	1485	c.459G>A	c.(457-459)acG>acA	p.T153T	TSKU_ENST00000333090.4_Silent_p.T153T			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	153					anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)		p.T153T(1)		NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					CCTTCACGACGCACAGTCAGG	0.657																																					p.T153T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G459A	11						.						77.0	75.0	76.0					11																	76507119		2200	4292	6492	76184767	SO:0001819	synonymous_variant	25987	exon2			AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"""leucine rich repeat containing 54"", ""tsukushin"", ""tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"""	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.459G>A	11.37:g.76507119G>A		Somatic		Capture	Illumina HiSeq	Phase_I	76184767	NM_015516	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	Silent	SNP	ENST00000527881.1	37	CCDS8246.1																																																																																				0.657	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516	
TSKU	25987	broad.mit.edu	37	11	76507583	76507583	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:76507583T>C	ENST00000527881.1	+	2	1949	c.923T>C	c.(922-924)gTc>gCc	p.V308A	TSKU_ENST00000333090.4_Missense_Mutation_p.V308A			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	308			V -> I (in dbSNP:rs3740771).		anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)		p.V308A(1)		NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					CTGCAGAGCGTCAGCGTGGGC	0.701																																					p.V308A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T923C	11						.						21.0	23.0	22.0					11																	76507583		2198	4290	6488	76185231	SO:0001583	missense	25987	exon2			AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"""leucine rich repeat containing 54"", ""tsukushin"", ""tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"""	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.923T>C	11.37:g.76507583T>C	ENSP00000434847:p.Val308Ala	Somatic		Capture	Illumina HiSeq	Phase_I	76185231	NM_015516	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	Missense_Mutation	SNP	ENST00000527881.1	37	CCDS8246.1	.	.	.	.	.	.	.	.	.	.	T	10.44	1.351252	0.24512	.	.	ENSG00000182704	ENST00000333090;ENST00000439807;ENST00000527881	T;T	0.04758	3.56;3.56	4.64	4.64	0.57946	.	0.276343	0.38837	N	0.001552	T	0.08582	0.0213	L	0.60455	1.87	0.24075	N	0.995964	B	0.22146	0.065	B	0.30029	0.11	T	0.12785	-1.0534	10	0.87932	D	0	-11.956	13.1856	0.59680	0.0:0.0:0.0:1.0	.	308	Q8WUA8	TSK_HUMAN	A	308;276;308	ENSP00000332668:V308A;ENSP00000434847:V308A	ENSP00000332668:V308A	V	+	2	0	TSKU	76185231	1.000000	0.71417	0.642000	0.29436	0.014000	0.08584	6.040000	0.70980	1.857000	0.53885	0.459000	0.35465	GTC		0.701	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516	
RSF1	51773	broad.mit.edu	37	11	77388003	77388003	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:77388003G>A	ENST00000308488.6	-	13	3477	c.3175C>T	c.(3175-3177)Cgt>Tgt	p.R1059C	RSF1_ENST00000360355.2_Missense_Mutation_p.R1028C|RSF1_ENST00000480887.1_Missense_Mutation_p.R807C			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1059					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)	p.R1059C(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			TCTTTCCCACGATGACCTGTG	0.453																																					p.R1059C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3175T	11						.						83.0	88.0	86.0					11																	77388003		2200	4292	6492	77065651	SO:0001583	missense	51773	exon13			AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"""Zinc fingers, PHD-type"""	18118	protein-coding gene	gene with protein product		608522	"""hepatitis B virus x associated protein"""	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.3175C>T	11.37:g.77388003G>A	ENSP00000311513:p.Arg1059Cys	Somatic		Capture	Illumina HiSeq	Phase_I	77065651	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Missense_Mutation	SNP	ENST00000308488.6	37	CCDS8253.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.278091	0.80692	.	.	ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355;ENST00000531026	T;D;T;T	0.87103	0.3;-2.21;0.3;0.3	4.65	4.65	0.58169	.	0.000000	0.48767	D	0.000177	D	0.90477	0.7017	L	0.38175	1.15	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.91654	0.5337	10	0.87932	D	0	-8.1414	17.6998	0.88291	0.0:0.0:1.0:0.0	.	1059	Q96T23	RSF1_HUMAN	C	1059;807;1028;168	ENSP00000311513:R1059C;ENSP00000434509:R807C;ENSP00000353511:R1028C;ENSP00000433603:R168C	ENSP00000311513:R1059C	R	-	1	0	RSF1	77065651	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.196000	0.58407	2.589000	0.87451	0.655000	0.94253	CGT		0.453	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
ALG8	79053	broad.mit.edu	37	11	77815466	77815466	+	Silent	SNP	C	C	T	rs200575151		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:77815466C>T	ENST00000299626.5	-	11	1283	c.1212G>A	c.(1210-1212)tcG>tcA	p.S404S	ALG8_ENST00000376156.3_Silent_p.S404S|ALG8_ENST00000532552.2_5'UTR	NM_024079.4	NP_076984.2	Q9BVK2	ALG8_HUMAN	ALG8, alpha-1,3-glucosyltransferase	404					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)	p.S404S(2)		NS(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	30	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			TCAGAAAAATCGAAGCGTCTC	0.353																																					p.S404S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1212A	11						.						65.0	66.0	65.0					11																	77815466		2200	4292	6492	77493114	SO:0001819	synonymous_variant	79053	exon11			AJ224875	CCDS8258.1, CCDS41692.1	11q14.1	2013-03-01	2013-03-01		ENSG00000159063	ENSG00000159063	2.4.1.265		23161	protein-coding gene	gene with protein product	"""dolichyl-P-Glc:Glc(1)Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"""	608103	"""asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase)"", ""asparagine-linked glycosylation 8, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"""				Standard	XM_005274247		Approved	MGC2840	uc001oza.1	Q9BVK2	OTTHUMG00000166594	ENST00000299626.5:c.1212G>A	11.37:g.77815466C>T		Somatic		Capture	Illumina HiSeq	Phase_I	77493114	NM_001007027	A6NDW6|O60860	Silent	SNP	ENST00000299626.5	37	CCDS8258.1	.	.	.	.	.	.	.	.	.	.	C	0.139	-1.104892	0.01828	.	.	ENSG00000159063	ENST00000530608;ENST00000532306	.	.	.	4.94	-9.88	0.00467	.	.	.	.	.	T	0.43523	0.1251	.	.	.	0.53688	D	0.999979	.	.	.	.	.	.	T	0.55140	-0.8187	4	.	.	.	-5.1213	5.9378	0.19175	0.0678:0.5041:0.2167:0.2114	.	.	.	.	Q	106;191	.	.	R	-	2	0	ALG8	77493114	0.001000	0.12720	0.010000	0.14722	0.206000	0.24218	-1.893000	0.01609	-3.612000	0.00132	-2.926000	0.00089	CGA		0.353	ALG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390637.1	NM_024079	
ALG8	79053	broad.mit.edu	37	11	77838457	77838457	+	Nonsense_Mutation	SNP	G	G	A	rs200888240		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:77838457G>A	ENST00000299626.5	-	2	192	c.121C>T	c.(121-123)Cga>Tga	p.R41*	ALG8_ENST00000376156.3_Nonsense_Mutation_p.R41*|ALG8_ENST00000532552.2_Intron	NM_024079.4	NP_076984.2	Q9BVK2	ALG8_HUMAN	ALG8, alpha-1,3-glucosyltransferase	41					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)	p.R41*(1)|p.R41G(1)		NS(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	30	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			AGCCAGTTTCGGTGTACTTCA	0.294													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18060	0.0		0.0	False		,,,				2504	0.0				p.R41X												.	.	2	Substitution - Missense(1)|Substitution - Nonsense(1)	ovary(1)|large_intestine(1)	c.C121T	11						.						87.0	84.0	85.0					11																	77838457		2200	4292	6492	77516105	SO:0001587	stop_gained	79053	exon2			AJ224875	CCDS8258.1, CCDS41692.1	11q14.1	2013-03-01	2013-03-01		ENSG00000159063	ENSG00000159063	2.4.1.265		23161	protein-coding gene	gene with protein product	"""dolichyl-P-Glc:Glc(1)Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"""	608103	"""asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase)"", ""asparagine-linked glycosylation 8, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"""				Standard	XM_005274247		Approved	MGC2840	uc001oza.1	Q9BVK2	OTTHUMG00000166594	ENST00000299626.5:c.121C>T	11.37:g.77838457G>A	ENSP00000299626:p.Arg41*	Somatic		Capture	Illumina HiSeq	Phase_I	77516105	NM_001007027	A6NDW6|O60860	Nonsense_Mutation	SNP	ENST00000299626.5	37	CCDS8258.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	24.2	4.499659	0.85176	.	.	ENSG00000159063	ENST00000299626;ENST00000376156;ENST00000530454;ENST00000530910;ENST00000525761	.	.	.	5.26	4.27	0.50696	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.172	12.7775	0.57457	0.0:0.0:0.6858:0.3142	.	.	.	.	X	41;41;42;32;15	.	ENSP00000299626:R41X	R	-	1	2	ALG8	77516105	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	2.713000	0.47194	2.458000	0.83093	0.460000	0.39030	CGA		0.294	ALG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390637.1	NM_024079	
TENM4	26011	broad.mit.edu	37	11	78387253	78387253	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:78387253G>A	ENST00000278550.7	-	30	5902	c.5440C>T	c.(5440-5442)Cgc>Tgc	p.R1814C		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1814					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.R1814S(2)|p.R1814C(1)									TTGCGCTGGCGCCACTCCACC	0.667																																					p.R1814C												.	.	3	Substitution - Missense(3)	lung(2)|large_intestine(1)	c.C5440T	11						.						16.0	20.0	18.0					11																	78387253		2085	4188	6273	78064901	SO:0001583	missense	26011	exon30			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.5440C>T	11.37:g.78387253G>A	ENSP00000278550:p.Arg1814Cys	Somatic		Capture	Illumina HiSeq	Phase_I	78064901	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	G	19.64	3.865242	0.71949	.	.	ENSG00000149256	ENST00000278550;ENST00000530738	D;T	0.90955	-2.76;0.59	4.47	-0.11	0.13580	.	0.000000	0.85682	D	0.000000	D	0.94515	0.8234	M	0.82517	2.595	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.93649	0.6971	9	.	.	.	.	14.3181	0.66465	0.0:0.0:0.2336:0.7663	.	1814	Q6N022	TEN4_HUMAN	C	1814;278	ENSP00000278550:R1814C;ENSP00000431711:R278C	.	R	-	1	0	ODZ4	78064901	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.041000	0.41213	0.179000	0.19938	-0.158000	0.13435	CGC		0.667	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
DDIAS	220042	broad.mit.edu	37	11	82645026	82645026	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:82645026C>T	ENST00000533655.1	+	6	2858	c.2646C>T	c.(2644-2646)ggC>ggT	p.G882G	C11orf82_ENST00000525361.1_Intron|C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000329143.3_Silent_p.G581G|C11orf82_ENST00000430323.2_Silent_p.G882G	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		882					apoptotic process (GO:0006915)|cellular response to cytokine stimulus (GO:0071345)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to hydroperoxide (GO:0071447)|cellular response to UV (GO:0034644)|hemopoiesis (GO:0030097)|mitotic cell cycle arrest (GO:0071850)|negative regulation of fibroblast apoptotic process (GO:2000270)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.G882G(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	33						GATTCCAAGGCATAGGTCTAG	0.403																																					p.G882G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2646T	11						.						69.0	68.0	68.0					11																	82645026		2203	4300	6503	82322674	SO:0001819	synonymous_variant	220042	exon6																														ENST00000533655.1:c.2646C>T	11.37:g.82645026C>T		Somatic		Capture	Illumina HiSeq	Phase_I	82322674	NM_145018	Q96LK6|Q9H856	Silent	SNP	ENST00000533655.1	37	CCDS8263.1																																																																																				0.403	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1		
PCF11	51585	broad.mit.edu	37	11	82877503	82877503	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:82877503C>T	ENST00000298281.4	+	5	2016	c.1564C>T	c.(1564-1566)Cgc>Tgc	p.R522C		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	522					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.R522C(1)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						TGGAAAGATTCGCCAATCTGG	0.443																																					p.R522C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1564T	11						.						129.0	124.0	126.0					11																	82877503		1964	4149	6113	82555151	SO:0001583	missense	51585	exon5			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.1564C>T	11.37:g.82877503C>T	ENSP00000298281:p.Arg522Cys	Somatic		Capture	Illumina HiSeq	Phase_I	82555151	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	C	17.48	3.399824	0.62177	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.60299	1.13;0.2;0.31	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000012	T	0.68970	0.3059	L	0.34521	1.04	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.63532	-0.6616	9	.	.	.	-5.286	20.6593	0.99626	0.0:1.0:0.0:0.0	.	522;522	E9PQ01;O94913	.;PCF11_HUMAN	C	522	ENSP00000298281:R522C;ENSP00000434540:R522C;ENSP00000431567:R522C	.	R	+	1	0	PCF11	82555151	0.993000	0.37304	1.000000	0.80357	0.971000	0.66376	3.039000	0.49791	2.885000	0.99019	0.655000	0.94253	CGC		0.443	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
PCF11	51585	broad.mit.edu	37	11	82892935	82892935	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:82892935C>T	ENST00000298281.4	+	13	4659	c.4207C>T	c.(4207-4209)Cgg>Tgg	p.R1403W	RP11-727A23.4_ENST00000528133.1_RNA	NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	1403					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.R1403W(1)		cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						TCTGGAAGAACGGGCAAAGAG	0.368																																					p.R1403W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4207T	11						.						61.0	64.0	63.0					11																	82892935		1823	4086	5909	82570583	SO:0001583	missense	51585	exon13			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.4207C>T	11.37:g.82892935C>T	ENSP00000298281:p.Arg1403Trp	Somatic		Capture	Illumina HiSeq	Phase_I	82570583	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.525195	0.85600	.	.	ENSG00000165494	ENST00000298281;ENST00000530906	T;T	0.52057	1.62;0.68	5.63	5.63	0.86233	.	0.000000	0.50627	D	0.000109	T	0.69513	0.3119	M	0.75085	2.285	0.58432	D	0.999999	D	0.89917	1.0	D	0.69654	0.965	T	0.68644	-0.5354	9	.	.	.	-4.9657	19.6933	0.96010	0.0:1.0:0.0:0.0	.	1403	O94913	PCF11_HUMAN	W	1403;188	ENSP00000298281:R1403W;ENSP00000437076:R188W	.	R	+	1	2	PCF11	82570583	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.451000	0.66632	2.651000	0.90000	0.467000	0.42956	CGG		0.368	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
SYTL2	54843	broad.mit.edu	37	11	85431935	85431935	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:85431935G>T	ENST00000528231.1	-	8	1804	c.1527C>A	c.(1525-1527)tcC>tcA	p.S509S	SYTL2_ENST00000354566.3_Silent_p.S831S|SYTL2_ENST00000528566.1_5'Flank|SYTL2_ENST00000524452.1_Silent_p.S509S|SYTL2_ENST00000527523.1_Silent_p.S461S|SYTL2_ENST00000389958.3_5'Flank|SYTL2_ENST00000316356.4_Silent_p.S510S|SYTL2_ENST00000389960.4_Silent_p.S509S|SYTL2_ENST00000525423.1_Silent_p.S831S|SYTL2_ENST00000533892.1_5'Flank|SYTL2_ENST00000529581.1_5'Flank|SYTL2_ENST00000359152.5_Silent_p.S1355S	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	509					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.S831S(1)|p.S510S(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		CTAGACTTTTGGAAGGCATTT	0.403																																					p.S509S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1527A	11						.						107.0	105.0	106.0					11																	85431935		2203	4299	6502	85109583	SO:0001819	synonymous_variant	54843	exon9			AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1527C>A	11.37:g.85431935G>T		Somatic		Capture	Illumina HiSeq	Phase_I	85109583	NM_032943	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																				0.403	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
GRM5	2915	broad.mit.edu	37	11	88338013	88338013	+	Missense_Mutation	SNP	C	C	T	rs112643728		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:88338013C>T	ENST00000305447.4	-	4	1416	c.1267G>A	c.(1267-1269)Gca>Aca	p.A423T	GRM5_ENST00000455756.2_Missense_Mutation_p.A423T|GRM5_ENST00000305432.5_Missense_Mutation_p.A423T|GRM5_ENST00000418177.2_Missense_Mutation_p.A423T|GRM5_ENST00000393297.1_Missense_Mutation_p.A423T	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	423					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.A423T(1)		NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	CAGAGTCCTGCATAGCCTGGG	0.463																																					p.A423T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1267A	11						.						88.0	78.0	81.0					11																	88338013		2201	4299	6500	87977661	SO:0001583	missense	2915	exon5			D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4597	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 86"""	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1267G>A	11.37:g.88338013C>T	ENSP00000306138:p.Ala423Thr	Somatic		Capture	Illumina HiSeq	Phase_I	87977661	NM_000842	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	37	CCDS44694.1	.	.	.	.	.	.	.	.	.	.	C	2.025	-0.423825	0.04734	.	.	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447;ENST00000393297	D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04	5.89	4.99	0.66335	Extracellular ligand-binding receptor (1);	0.206543	0.49916	D	0.000132	T	0.70185	0.3195	N	0.05280	-0.08	0.09310	N	1	B;B	0.26547	0.152;0.008	B;B	0.24394	0.053;0.023	T	0.55386	-0.8149	9	.	.	.	.	15.1569	0.72749	0.0:0.9323:0.0:0.0677	.	423;423	P41594-2;P41594	.;GRM5_HUMAN	T	423	ENSP00000402912:A423T;ENSP00000405690:A423T;ENSP00000305905:A423T;ENSP00000306138:A423T;ENSP00000376975:A423T	.	A	-	1	0	GRM5	87977661	0.879000	0.30193	0.068000	0.19968	0.425000	0.31504	2.178000	0.42519	1.502000	0.48669	0.544000	0.68410	GCA		0.463	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842	
FAT3	120114	broad.mit.edu	37	11	92533005	92533005	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:92533005C>T	ENST00000298047.6	+	9	6843	c.6826C>T	c.(6826-6828)Cta>Tta	p.L2276L	FAT3_ENST00000409404.2_Silent_p.L2276L|FAT3_ENST00000525166.1_Silent_p.L2126L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2276	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L2276L(2)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TGTTGACTTGCTAGTTAATGA	0.423										TCGA Ovarian(4;0.039)																											p.L2276L												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C6826T	11						.						97.0	86.0	90.0					11																	92533005		1911	4129	6040	92172653	SO:0001819	synonymous_variant	120114	exon9			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.6826C>T	11.37:g.92533005C>T		Somatic		Capture	Illumina HiSeq	Phase_I	92172653	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																					0.423	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
HEPHL1	341208	broad.mit.edu	37	11	93796822	93796822	+	Silent	SNP	G	G	A	rs375814141		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:93796822G>A	ENST00000315765.9	+	3	572	c.564G>A	c.(562-564)tcG>tcA	p.S188S		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	188	Plastocyanin-like 1.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)	p.S189S(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				TGTACCATTCGCACATCGACG	0.542																																					p.S188S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G564A	11						.	G		0,3958		0,0,1979	110.0	109.0	109.0		564	-10.8	0.7	11		109	1,8325		0,1,4162	no	coding-synonymous	HEPHL1	NM_001098672.1		0,1,6141	AA,AG,GG		0.012,0.0,0.0081		188/1160	93796822	1,12283	1979	4163	6142	93436470	SO:0001819	synonymous_variant	341208	exon3			BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.564G>A	11.37:g.93796822G>A		Somatic		Capture	Illumina HiSeq	Phase_I	93436470	NM_001098672	Q3C1W7	Silent	SNP	ENST00000315765.9	37	CCDS44710.1																																																																																				0.542	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947	
HEPHL1	341208	broad.mit.edu	37	11	93803617	93803617	+	Missense_Mutation	SNP	C	C	T	rs12291622	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:93803617C>T	ENST00000315765.9	+	6	1149	c.1141C>T	c.(1141-1143)Cgc>Tgc	p.R381C		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	381	Plastocyanin-like 3.		R -> C (in dbSNP:rs12291622).		copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)	p.R382C(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				TCAACAGAGGCGCTACTTTAT	0.443													c|||	11	0.00219649	0.0076	0.0014	5008	,	,		19632	0.0		0.0	False		,,,				2504	0.0				p.R381C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1141T	11						.	T	CYS/ARG	29,3671		0,29,1821	51.0	48.0	49.0		1141	3.7	0.7	11	dbSNP_120	49	0,8176		0,0,4088	yes	missense	HEPHL1	NM_001098672.1	180	0,29,5909	TT,TC,CC		0.0,0.7838,0.2442	possibly-damaging	381/1160	93803617	29,11847	1850	4088	5938	93443265	SO:0001583	missense	341208	exon6			BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.1141C>T	11.37:g.93803617C>T	ENSP00000313699:p.Arg381Cys	Somatic		Capture	Illumina HiSeq	Phase_I	93443265	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	37	CCDS44710.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	c	14.67	2.604621	0.46423	0.007838	0.0	ENSG00000181333	ENST00000315765	D	0.98947	-5.26	5.7	3.7	0.42460	Cupredoxin (2);	0.680056	0.16003	N	0.234209	D	0.96253	0.8778	M	0.62723	1.935	0.09310	N	1	D	0.56746	0.977	P	0.44860	0.462	D	0.92086	0.5676	10	0.52906	T	0.07	.	8.9244	0.35632	0.2173:0.6983:0.0:0.0844	rs12291622;rs52805514;rs12291622	381	Q6MZM0	HPHL1_HUMAN	C	381	ENSP00000313699:R381C	ENSP00000313699:R381C	R	+	1	0	HEPHL1	93443265	0.054000	0.20591	0.739000	0.30968	0.764000	0.43329	0.970000	0.29383	1.416000	0.47057	-0.127000	0.14921	CGC		0.443	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947	
PIWIL4	143689	broad.mit.edu	37	11	94316701	94316701	+	Missense_Mutation	SNP	G	G	A	rs554791169		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:94316701G>A	ENST00000299001.6	+	5	812	c.601G>A	c.(601-603)Gtg>Atg	p.V201M	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	201					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)	p.V201M(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				AAGTTCTCCCGTGTGCATCCA	0.428																																					p.V201M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G601A	11						.						160.0	161.0	161.0					11																	94316701		2201	4298	6499	93956349	SO:0001583	missense	143689	exon5			AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.601G>A	11.37:g.94316701G>A	ENSP00000299001:p.Val201Met	Somatic		Capture	Illumina HiSeq	Phase_I	93956349	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	37	CCDS31656.1	.	.	.	.	.	.	.	.	.	.	G	7.553	0.663087	0.14710	.	.	ENSG00000134627	ENST00000299001	T	0.09538	2.97	5.54	-0.611	0.11601	Argonaute/Dicer protein, PAZ (1);	0.436962	0.21027	N	0.081403	T	0.07728	0.0194	L	0.28400	0.85	0.26662	N	0.971897	B	0.19073	0.033	B	0.15052	0.012	T	0.25745	-1.0123	10	0.48119	T	0.1	-5.971	10.9541	0.47347	0.376:0.0:0.624:0.0	.	201	Q7Z3Z4	PIWL4_HUMAN	M	201	ENSP00000299001:V201M	ENSP00000299001:V201M	V	+	1	0	PIWIL4	93956349	0.042000	0.20092	0.144000	0.22314	0.401000	0.30781	0.326000	0.19646	-0.017000	0.14103	-0.143000	0.13931	GTG		0.428	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
PIWIL4	143689	broad.mit.edu	37	11	94340781	94340781	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:94340781C>T	ENST00000299001.6	+	14	2026	c.1815C>T	c.(1813-1815)ggC>ggT	p.G605G	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	605	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)	p.G605G(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				AGCTCGGAGGCGAGCTGTGGG	0.418																																					p.G605G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1815T	11						.						69.0	67.0	68.0					11																	94340781		2201	4298	6499	93980429	SO:0001819	synonymous_variant	143689	exon14			AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.1815C>T	11.37:g.94340781C>T		Somatic		Capture	Illumina HiSeq	Phase_I	93980429	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	37	CCDS31656.1																																																																																				0.418	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
AMOTL1	154810	broad.mit.edu	37	11	94592757	94592757	+	Missense_Mutation	SNP	G	G	A	rs35278871|rs376912369		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:94592757G>A	ENST00000433060.2	+	9	2153	c.2012G>A	c.(2011-2013)cGg>cAg	p.R671Q	AMOTL1_ENST00000317837.9_Intron|AMOTL1_ENST00000317829.8_Missense_Mutation_p.R621Q	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	671					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)	p.R672Q(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				GAACTTGTGCGGGAGAAGGAG	0.537													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19247	0.0		0.0	False		,,,				2504	0.0				p.R671Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2012A	11						.	G	GLN/ARG	0,4398		0,0,2199	44.0	48.0	47.0		2012	6.1	1.0	11		47	1,8595	1.2+/-3.3	0,1,4297	no	missense	AMOTL1	NM_130847.2	43	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	671/957	94592757	1,12993	2199	4298	6497	94232405	SO:0001583	missense	154810	exon9			AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"""junction-enriched and associated protein"""	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2012G>A	11.37:g.94592757G>A	ENSP00000387739:p.Arg671Gln	Somatic		Capture	Illumina HiSeq	Phase_I	94232405	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	G	37	6.073325	0.97256	0.0	1.16E-4	ENSG00000166025	ENST00000317829;ENST00000433060	T;T	0.27402	1.69;1.67	6.08	6.08	0.98989	Angiomotin, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.59838	0.2223	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;0.994	D;P	0.70487	0.969;0.906	T	0.57335	-0.7829	10	0.52906	T	0.07	-34.9699	20.6634	0.99662	0.0:0.0:1.0:0.0	.	621;671	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	Q	621;671	ENSP00000320968:R621Q;ENSP00000387739:R671Q	ENSP00000320968:R621Q	R	+	2	0	AMOTL1	94232405	1.000000	0.71417	0.999000	0.59377	0.951000	0.60555	9.611000	0.98342	2.894000	0.99253	0.655000	0.94253	CGG		0.537	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
AMOTL1	154810	broad.mit.edu	37	11	94597926	94597926	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:94597926G>A	ENST00000433060.2	+	10	2303	c.2162G>A	c.(2161-2163)cGg>cAg	p.R721Q	AMOTL1_ENST00000317837.9_Intron|AMOTL1_ENST00000317829.8_Missense_Mutation_p.R671Q	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	721					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)	p.R722Q(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				AACCACTCACGGAATGGCAGC	0.522																																					p.R721Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2162A	11						.						112.0	116.0	114.0					11																	94597926		2069	4210	6279	94237574	SO:0001583	missense	154810	exon10			AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"""junction-enriched and associated protein"""	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2162G>A	11.37:g.94597926G>A	ENSP00000387739:p.Arg721Gln	Somatic		Capture	Illumina HiSeq	Phase_I	94237574	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.742625	0.69418	.	.	ENSG00000166025	ENST00000317829;ENST00000433060	T;T	0.17054	2.3;2.3	5.45	4.53	0.55603	Angiomotin, C-terminal (1);	0.169168	0.37669	N	0.001995	T	0.16342	0.0393	L	0.36672	1.1	0.58432	D	0.999997	P;B	0.46142	0.873;0.202	P;B	0.46917	0.531;0.122	T	0.02391	-1.1166	10	0.15952	T	0.53	-33.5478	10.9092	0.47099	0.1429:0.0:0.8571:0.0	.	671;721	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	Q	671;721	ENSP00000320968:R671Q;ENSP00000387739:R721Q	ENSP00000320968:R671Q	R	+	2	0	AMOTL1	94237574	0.773000	0.28580	0.930000	0.37139	0.986000	0.74619	1.632000	0.37102	2.550000	0.86006	0.561000	0.74099	CGG		0.522	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
JAM3	83700	broad.mit.edu	37	11	134015866	134015866	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr11:134015866A>T	ENST00000299106.4	+	6	797	c.638A>T	c.(637-639)gAc>gTc	p.D213V	JAM3_ENST00000441717.3_Missense_Mutation_p.D162V|JAM3_ENST00000529443.2_Missense_Mutation_p.D258V			Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3	213	Ig-like C2-type.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|establishment of cell polarity (GO:0030010)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|myelination (GO:0042552)|myeloid progenitor cell differentiation (GO:0002318)|neutrophil homeostasis (GO:0001780)|regulation of actin cytoskeleton organization by cell-cell adhesion (GO:0090138)|regulation of neutrophil chemotaxis (GO:0090022)|spermatid development (GO:0007286)|transmission of nerve impulse (GO:0019226)	cell-cell contact zone (GO:0044291)|desmosome (GO:0030057)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	integrin binding (GO:0005178)	p.D258V(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)	10	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)		CACAAGGACGACTCTGGGCAG	0.507																																					p.D258V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A773T	11						.						132.0	121.0	125.0					11																	134015866		2201	4297	6498	133521076	SO:0001583	missense	83700	exon6			AF356518	CCDS8494.1, CCDS55799.1, CCDS8494.2	11q25	2013-01-29			ENSG00000166086	ENSG00000166086		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15532	protein-coding gene	gene with protein product		606871					Standard	NM_032801		Approved	JAM-C, JAMC	uc001qhb.3	Q9BX67	OTTHUMG00000167130	ENST00000299106.4:c.638A>T	11.37:g.134015866A>T	ENSP00000299106:p.Asp213Val	Somatic		Capture	Illumina HiSeq	Phase_I	133521076	NM_032801	B3KWG9|Q8WWL8|Q96FL1	Missense_Mutation	SNP	ENST00000299106.4	37	CCDS8494.2	.	.	.	.	.	.	.	.	.	.	A	18.93	3.727901	0.69074	.	.	ENSG00000166086	ENST00000299106;ENST00000441717	T	0.76186	-1.0	5.07	3.95	0.45737	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.90055	0.6894	H	0.97806	4.08	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90702	0.4621	10	0.72032	D	0.01	.	9.5172	0.39113	0.9205:0.0:0.0795:0.0	.	162;213	B3KWG9;Q9BX67	.;JAM3_HUMAN	V	258;162	ENSP00000395742:D162V	ENSP00000299106:D258V	D	+	2	0	JAM3	133521076	1.000000	0.71417	0.919000	0.36401	0.665000	0.39181	8.230000	0.89793	0.959000	0.37980	0.528000	0.53228	GAC		0.507	JAM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393303.4	NM_032801	
TMEM52B	120939	broad.mit.edu	37	12	10339140	10339140	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:10339140A>G	ENST00000381923.2	+	5	663	c.259A>G	c.(259-261)Acc>Gcc	p.T87A	TMEM52B_ENST00000298530.3_Missense_Mutation_p.T67A|TMEM52B_ENST00000536952.1_Missense_Mutation_p.T87A			Q4KMG9	TM52B_HUMAN	transmembrane protein 52B	87						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.T67A(1)									CTGTGAAGTGACCGTCATTGC	0.542																																					p.T67A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A199G	12						.						106.0	93.0	97.0					12																	10339140		2203	4300	6503	10230407	SO:0001583	missense	120939	exon3			AY358845	CCDS8619.1, CCDS66314.1	12p13.2	2012-08-15	2012-08-15	2012-08-15	ENSG00000165685	ENSG00000165685			26438	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 59"""	C12orf59		12975309	Standard	XM_005253299		Approved	FLJ31166	uc001qxq.3	Q4KMG9	OTTHUMG00000168410	ENST00000381923.2:c.259A>G	12.37:g.10339140A>G	ENSP00000371348:p.Thr87Ala	Somatic		Capture	Illumina HiSeq	Phase_I	10230407	NM_153022	Q96NA7	Missense_Mutation	SNP	ENST00000381923.2	37		.	.	.	.	.	.	.	.	.	.	A	16.68	3.190862	0.58017	.	.	ENSG00000165685	ENST00000381923;ENST00000298530;ENST00000543484;ENST00000536952	T;T;T;T	0.34859	1.34;1.34;1.34;1.34	5.21	5.21	0.72293	.	0.000000	0.64402	D	0.000001	T	0.49779	0.1577	L	0.41415	1.275	0.42852	D	0.99408	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.49504	-0.8933	10	0.52906	T	0.07	-18.9767	13.0872	0.59149	1.0:0.0:0.0:0.0	.	87;67	Q4KMG9;Q4KMG9-2	CL059_HUMAN;.	A	87;67;87;87	ENSP00000371348:T87A;ENSP00000298530:T67A;ENSP00000445582:T87A;ENSP00000446102:T87A	ENSP00000298530:T67A	T	+	1	0	C12orf59	10230407	1.000000	0.71417	0.980000	0.43619	0.325000	0.28411	5.647000	0.67923	2.187000	0.69744	0.528000	0.53228	ACC		0.542	TMEM52B-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000399645.1	NM_153022	
MYBPC1	4604	broad.mit.edu	37	12	102036334	102036334	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:102036334G>A	ENST00000550270.1	+	9	728	c.728G>A	c.(727-729)cGc>cAc	p.R243H	MYBPC1_ENST00000452455.2_Missense_Mutation_p.R243H|MYBPC1_ENST00000441232.1_Missense_Mutation_p.R243H|MYBPC1_ENST00000545503.2_Missense_Mutation_p.R243H|MYBPC1_ENST00000361685.2_Missense_Mutation_p.R268H|MYBPC1_ENST00000536007.1_Missense_Mutation_p.R224H|MYBPC1_ENST00000547405.1_Missense_Mutation_p.R217H|MYBPC1_ENST00000549145.1_Missense_Mutation_p.R256H|MYBPC1_ENST00000361466.2_Missense_Mutation_p.R268H|MYBPC1_ENST00000553190.1_Missense_Mutation_p.R243H|MYBPC1_ENST00000547509.1_Missense_Mutation_p.R229H|MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000551300.1_Missense_Mutation_p.R144H|MYBPC1_ENST00000541119.1_Missense_Mutation_p.R231H|MYBPC1_ENST00000360610.2_Missense_Mutation_p.R243H|MYBPC1_ENST00000392934.3_Missense_Mutation_p.R230H			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	243					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.R268H(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						CGACTCAAGCGCATGCGCAGA	0.622																																					p.R268H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G803A	12						.						57.0	48.0	51.0					12																	102036334		2203	4300	6503	100560465	SO:0001583	missense	4604	exon11				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.728G>A	12.37:g.102036334G>A	ENSP00000449702:p.Arg243His	Somatic		Capture	Illumina HiSeq	Phase_I	100560465	NM_002465	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	37	CCDS9085.1	.	.	.	.	.	.	.	.	.	.	G	34	5.295539	0.95574	.	.	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000540770;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.58797	0.33;0.33;0.32;0.33;0.33;0.31;0.34;0.32;0.34;0.31;0.36;0.32;0.32;0.36;0.33	5.53	5.53	0.82687	.	0.000000	0.47852	D	0.000207	T	0.69468	0.3114	L	0.44542	1.39	0.48571	D	0.999677	D;D;D;D;D;D;D;D;D;D;D	0.76494	0.996;0.997;0.996;0.998;0.995;0.995;0.997;0.998;0.997;0.999;0.999	P;P;P;P;P;P;P;P;D;P;D	0.67900	0.815;0.794;0.815;0.794;0.836;0.791;0.899;0.836;0.91;0.899;0.954	T	0.66143	-0.5997	9	.	.	.	.	19.4713	0.94963	0.0:0.0:1.0:0.0	.	224;231;243;243;230;217;243;243;268;268;256	B7ZL02;B7ZL10;E7EWS6;B7ZL09;E7ESM5;Q17RR7;Q00872-3;Q00872;G3XAE8;Q00872-2;F8VZY0	.;.;.;.;.;.;.;MYPC1_HUMAN;.;.;.	H	217;243;243;243;230;229;268;256;243;268;243;224;231;268;144;243	ENSP00000448175:R217H;ENSP00000400908:R243H;ENSP00000388989:R243H;ENSP00000353822:R243H;ENSP00000376665:R230H;ENSP00000447362:R229H;ENSP00000354845:R268H;ENSP00000447660:R256H;ENSP00000447900:R243H;ENSP00000440034:R243H;ENSP00000446128:R224H;ENSP00000442847:R231H;ENSP00000354849:R268H;ENSP00000447116:R144H;ENSP00000449702:R243H	.	R	+	2	0	MYBPC1	100560465	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	6.017000	0.70805	2.587000	0.87381	0.563000	0.77884	CGC		0.622	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1		
STAB2	55576	broad.mit.edu	37	12	104134523	104134523	+	Missense_Mutation	SNP	G	G	A	rs538346576		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:104134523G>A	ENST00000388887.2	+	55	6074	c.5870G>A	c.(5869-5871)cGa>cAa	p.R1957Q		NM_017564.9	NP_060034.9			stabilin 2									p.R1957Q(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TACTTCGGGCGAGACTGTCAG	0.547																																					p.R1957Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5870A	12						.						104.0	92.0	96.0					12																	104134523		2203	4300	6503	102658653	SO:0001583	missense	55576	exon55			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.5870G>A	12.37:g.104134523G>A	ENSP00000373539:p.Arg1957Gln	Somatic		Capture	Illumina HiSeq	Phase_I	102658653	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.467995	0.43839	.	.	ENSG00000136011	ENST00000388887;ENST00000258495	D	0.89617	-2.54	5.46	0.237	0.15475	.	0.669394	0.13322	N	0.396591	D	0.89901	0.6849	M	0.83118	2.625	0.09310	N	1	D	0.63880	0.993	P	0.50754	0.649	T	0.80502	-0.1354	10	0.13853	T	0.58	.	10.4664	0.44611	0.0682:0.6269:0.2158:0.0891	.	1957	Q8WWQ8	STAB2_HUMAN	Q	1957;644	ENSP00000373539:R1957Q	ENSP00000258495:R644Q	R	+	2	0	STAB2	102658653	0.022000	0.18835	0.012000	0.15200	0.722000	0.41435	0.455000	0.21843	-0.262000	0.09392	-0.176000	0.13171	CGA		0.547	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
STAB2	55576	broad.mit.edu	37	12	104151978	104151978	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:104151978C>T	ENST00000388887.2	+	64	7222	c.7018C>T	c.(7018-7020)Cga>Tga	p.R2340*	RP11-341G23.4_ENST00000551299.1_RNA	NM_017564.9	NP_060034.9			stabilin 2									p.R2340*(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CAGCTCAGCTCGAGGCCGTGC	0.582																																					p.R2340X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C7018T	12						.						117.0	86.0	96.0					12																	104151978		2203	4300	6503	102676108	SO:0001587	stop_gained	55576	exon64			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.7018C>T	12.37:g.104151978C>T	ENSP00000373539:p.Arg2340*	Somatic		Capture	Illumina HiSeq	Phase_I	102676108	NM_017564		Nonsense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	47|47	13.633190|13.633190	0.99754|0.99754	.|.	.|.	ENSG00000136011|ENSG00000136011	ENST00000388887|ENST00000258495	.|.	.|.	.|.	4.55|4.55	0.799|0.799	0.18667|0.18667	.|.	0.808461|.	0.10863|.	N|.	0.625844|.	.|T	.|0.57184	.|0.2036	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.65829	.|-0.6073	.|4	0.02654|0.52906	T|T	1|0.07	.|.	11.4886|11.4886	0.50369|0.50369	0.3981:0.6019:0.0:0.0|0.3981:0.6019:0.0:0.0	.|.	.|.	.|.	.|.	X|L	2340|991	.|.	ENSP00000373539:R2340X|ENSP00000258495:S991L	R|S	+|+	1|2	2|0	STAB2|STAB2	102676108|102676108	0.384000|0.384000	0.25164|0.25164	0.750000|0.750000	0.31169|0.31169	0.623000|0.623000	0.37688|0.37688	1.228000|1.228000	0.32588|0.32588	-0.114000|-0.114000	0.11936|0.11936	-0.397000|-0.397000	0.06425|0.06425	CGA|TCG		0.582	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
EID3	493861	broad.mit.edu	37	12	104697833	104697833	+	Missense_Mutation	SNP	C	C	T	rs377416878		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:104697833C>T	ENST00000527879.1	+	1	317	c.121C>T	c.(121-123)Cgc>Tgc	p.R41C	TXNRD1_ENST00000354940.6_Intron|TXNRD1_ENST00000526390.1_Intron|TXNRD1_ENST00000524698.1_Intron|TXNRD1_ENST00000378070.4_Intron|TXNRD1_ENST00000388854.3_Intron|TXNRD1_ENST00000542918.1_Intron|TXNRD1_ENST00000540716.1_Intron|TXNRD1_ENST00000503506.2_Intron|TXNRD1_ENST00000429002.2_Intron|TXNRD1_ENST00000526691.1_Intron|TXNRD1_ENST00000397736.2_Intron|TXNRD1_ENST00000529546.1_Intron|TXNRD1_ENST00000525566.1_Intron	NM_001008394.2	NP_001008395.1			EP300 interacting inhibitor of differentiation 3									p.R41C(1)		large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						CCGCAGCATCCGCAGGCAGTA	0.647																																					p.R41C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C121T	12						.						32.0	37.0	36.0					12																	104697833		2102	4220	6322	103221963	SO:0001583	missense	493861	exon1			BC027612	CCDS53822.1	12q23.3	2006-11-24				ENSG00000255150			32961	protein-coding gene	gene with protein product		612986				15987788, 15752197	Standard	NM_001008394		Approved	FLJ25832, NSMCE4B, NSE4B	uc001tkw.3	Q8N140		ENST00000527879.1:c.121C>T	12.37:g.104697833C>T	ENSP00000435619:p.Arg41Cys	Somatic		Capture	Illumina HiSeq	Phase_I	103221963	NM_001008394		Missense_Mutation	SNP	ENST00000527879.1	37	CCDS53822.1	.	.	.	.	.	.	.	.	.	.	C	19.87	3.907179	0.72868	.	.	ENSG00000255150	ENST00000527879	T	0.61980	0.06	4.7	4.7	0.59300	.	.	.	.	.	T	0.77418	0.4127	M	0.73962	2.25	0.50632	D	0.999881	D	0.89917	1.0	D	0.91635	0.999	T	0.78760	-0.2078	9	0.56958	D	0.05	.	13.4057	0.60911	0.0:1.0:0.0:0.0	.	41	Q8N140	EID3_HUMAN	C	41	ENSP00000435619:R41C	ENSP00000435619:R41C	R	+	1	0	EID3	103221963	1.000000	0.71417	1.000000	0.80357	0.455000	0.32408	3.556000	0.53734	2.621000	0.88768	0.555000	0.69702	CGC		0.647	EID3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387034.1	NM_001008394	
CHST11	50515	broad.mit.edu	37	12	105150920	105150920	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:105150920G>A	ENST00000303694.5	+	3	837	c.398G>A	c.(397-399)cGg>cAg	p.R133Q	CHST11_ENST00000549260.1_Missense_Mutation_p.R128Q	NM_018413.5	NP_060883.1	Q9NPF2	CHSTB_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 11	133					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondrocyte development (GO:0002063)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|developmental growth (GO:0048589)|embryonic digit morphogenesis (GO:0042733)|embryonic viscerocranium morphogenesis (GO:0048703)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|polysaccharide localization (GO:0033037)|post-anal tail morphogenesis (GO:0036342)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)|N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity (GO:0050659)	p.R133Q(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(1)	18						AACTGGAAGCGGCTCATGATG	0.622																																					p.R128Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G383A	12						.						66.0	64.0	64.0					12																	105150920		2203	4300	6503	103675050	SO:0001583	missense	50515	exon3			AB042326	CCDS9099.1, CCDS55878.1	12q23.3	2008-02-05				ENSG00000171310	2.8.2.5	"""Sulfotransferases, membrane-bound"""	17422	protein-coding gene	gene with protein product		610128				10781601	Standard	NM_018413		Approved	C4ST1, C4St-1, C4ST, HSA269537	uc001tkz.3	Q9NPF2	OTTHUMG00000169803	ENST00000303694.5:c.398G>A	12.37:g.105150920G>A	ENSP00000305725:p.Arg133Gln	Somatic		Capture	Illumina HiSeq	Phase_I	103675050	NM_001173982	A8K4F8|Q9NXY6|Q9NY36	Missense_Mutation	SNP	ENST00000303694.5	37	CCDS9099.1	.	.	.	.	.	.	.	.	.	.	G	34	5.325582	0.95708	.	.	ENSG00000171310	ENST00000549260;ENST00000303694;ENST00000549016	T;T;T	0.76186	-1.0;-1.0;-1.0	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	D	0.89643	0.6774	M	0.91300	3.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.988;0.997	D	0.91278	0.5049	10	0.66056	D	0.02	-6.7567	19.4315	0.94772	0.0:0.0:1.0:0.0	.	128;133	Q9NPF2-2;Q9NPF2	.;CHSTB_HUMAN	Q	128;133;93	ENSP00000450004:R128Q;ENSP00000305725:R133Q;ENSP00000449095:R93Q	ENSP00000305725:R133Q	R	+	2	0	CHST11	103675050	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.600000	0.87896	0.655000	0.94253	CGG		0.622	CHST11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405960.2	NM_018413	
APPL2	55198	broad.mit.edu	37	12	105583831	105583831	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:105583831C>T	ENST00000258530.3	-	15	1569	c.1344G>A	c.(1342-1344)acG>acA	p.T448T	APPL2_ENST00000539978.2_Silent_p.T405T|APPL2_ENST00000551662.1_Silent_p.T454T	NM_001251904.1|NM_018171.3	NP_001238833.1|NP_060641.2	Q06481	APLP2_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	0					cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)	p.T448T(1)		breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						ATTGAATCGGCGTTCCAGGCG	0.458																																					p.T448T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1344A	12						.						124.0	117.0	119.0					12																	105583831		2203	4300	6503	104107961	SO:0001819	synonymous_variant	55198	exon15			AY113704	CCDS9101.1, CCDS58275.1, CCDS58276.1	12q23.3	2014-08-12			ENSG00000136044	ENSG00000136044		"""Pleckstrin homology (PH) domain containing"""	18242	protein-coding gene	gene with protein product		606231				11431708, 17030088	Standard	NM_001251904		Approved	FLJ10659, DIP13B	uc010swu.1	Q8NEU8	OTTHUMG00000169853	ENST00000258530.3:c.1344G>A	12.37:g.105583831C>T		Somatic		Capture	Illumina HiSeq	Phase_I	104107961	NM_018171	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Silent	SNP	ENST00000258530.3	37	CCDS9101.1																																																																																				0.458	APPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406238.3	NM_018171	
RFX4	5992	broad.mit.edu	37	12	107090150	107090150	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:107090150C>T	ENST00000392842.1	+	8	1173	c.759C>T	c.(757-759)ggC>ggT	p.G253G	RFX4_ENST00000229387.5_Silent_p.G159G|RFX4_ENST00000357881.4_Silent_p.G262G|RP11-144F15.1_ENST00000551505.1_Intron	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	253					cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.G262G(1)|p.G253G(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						ACATTGTCGGCGTGTGTGACT	0.542																																					p.G159G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C477T	12						.						158.0	128.0	138.0					12																	107090150		2203	4300	6503	105614280	SO:0001819	synonymous_variant	5992	exon4			AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.759C>T	12.37:g.107090150C>T		Somatic		Capture	Illumina HiSeq	Phase_I	105614280	NM_032491	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	37	CCDS9106.1																																																																																				0.542	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491	
BTBD11	121551	broad.mit.edu	37	12	108013938	108013938	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:108013938C>T	ENST00000280758.5	+	11	3156	c.2628C>T	c.(2626-2628)agC>agT	p.S876S	RP11-128P10.1_ENST00000548473.1_RNA|BTBD11_ENST00000357167.4_Silent_p.S413S|BTBD11_ENST00000490090.2_Silent_p.S876S|BTBD11_ENST00000420571.2_Silent_p.S757S	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	876						integral component of membrane (GO:0016021)		p.S876S(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						TGAAAGCGAGCAAGGTATGTG	0.502																																					p.S413S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1239T	12						.						112.0	110.0	110.0					12																	108013938		2203	4300	6503	106538068	SO:0001819	synonymous_variant	121551	exon9			AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.2628C>T	12.37:g.108013938C>T		Somatic		Capture	Illumina HiSeq	Phase_I	106538068	NM_001017523	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	37	CCDS31893.1																																																																																				0.502	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
ASCL4	121549	broad.mit.edu	37	12	108169004	108169004	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:108169004G>A	ENST00000342331.4	+	1	843	c.12G>A	c.(10-12)acG>acA	p.T4T		NM_203436.2	NP_982260.2	Q6XD76	ASCL4_HUMAN	achaete-scute family bHLH transcription factor 4	3					regulation of transcription from RNA polymerase II promoter (GO:0006357)|skin development (GO:0043588)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T3T(1)		breast(2)|central_nervous_system(1)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	13						TGATGGAGACGCGTAAACCGG	0.597																																					p.T4T	GBM(170;776 3695 11650)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G12A	12						.						72.0	81.0	78.0					12																	108169004		2203	4300	6503	106693134	SO:0001819	synonymous_variant	121549	exon1			AY238895	CCDS31894.2	12q24.11	2013-10-17	2013-10-17		ENSG00000187855	ENSG00000187855		"""Basic helix-loop-helix proteins"""	24311	protein-coding gene	gene with protein product		609155	"""achaete-scute complex-like 4 (Drosophila)"", ""achaete-scute complex homolog 4 (Drosophila)"""				Standard	NM_203436		Approved	HASH4, bHLHa44	uc001tmr.3	Q6XD76	OTTHUMG00000156964	ENST00000342331.4:c.12G>A	12.37:g.108169004G>A		Somatic		Capture	Illumina HiSeq	Phase_I	106693134	NM_203436	Q7RTS2	Silent	SNP	ENST00000342331.4	37	CCDS31894.2																																																																																				0.597	ASCL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346845.1	NM_203436	
FICD	11153	broad.mit.edu	37	12	108910974	108910974	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:108910974C>T	ENST00000552695.1	+	2	460	c.225C>T	c.(223-225)tgC>tgT	p.C75C	FICD_ENST00000552758.1_Silent_p.C75C|FICD_ENST00000361549.2_Silent_p.C75C	NM_007076.2	NP_009007.2	Q9BVA6	FICD_HUMAN	FIC domain containing	75					negative regulation of Rho GTPase activity (GO:0034259)|protein adenylylation (GO:0018117)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein adenylyltransferase activity (GO:0070733)	p.C75C(1)		NS(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|upper_aerodigestive_tract(2)	15						CCACCAAGTGCACCAGCCCGT	0.652																																					p.C75C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C225T	12						.						36.0	33.0	34.0					12																	108910974		2202	4299	6501	107435104	SO:0001819	synonymous_variant	11153	exon2			AF049611	CCDS9116.1	12q24.1	2007-12-05				ENSG00000198855			18416	protein-coding gene	gene with protein product	"""huntingtin interacting protein 13"", ""fic S-phase protein cell division homolog (E. coli)"""					9700202	Standard	NM_007076		Approved	HYPE, HIP13	uc001tmx.1	Q9BVA6		ENST00000552695.1:c.225C>T	12.37:g.108910974C>T		Somatic		Capture	Illumina HiSeq	Phase_I	107435104	NM_007076	O75406	Silent	SNP	ENST00000552695.1	37	CCDS9116.1	.	.	.	.	.	.	.	.	.	.	C	0.183	-1.060198	0.01950	.	.	ENSG00000198855	ENST00000549641	.	.	.	5.42	1.42	0.22433	.	.	.	.	.	T	0.21841	0.0526	.	.	.	0.09310	N	0.99999	.	.	.	.	.	.	T	0.21484	-1.0244	4	.	.	.	-5.8403	2.2112	0.03948	0.1346:0.5146:0.1306:0.2202	.	.	.	.	V	26	.	.	A	+	2	0	FICD	107435104	0.001000	0.12720	0.664000	0.29753	0.009000	0.06853	-0.019000	0.12546	0.270000	0.21984	-0.258000	0.10820	GCA		0.652	FICD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404842.1	NM_007076	
SELPLG	6404	broad.mit.edu	37	12	109017773	109017773	+	Missense_Mutation	SNP	G	G	A	rs147444406		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:109017773G>A	ENST00000550948.1	-	2	535	c.311C>T	c.(310-312)aCg>aTg	p.T104M	SELPLG_ENST00000388962.3_Missense_Mutation_p.T104M|SELPLG_ENST00000228463.6_Missense_Mutation_p.T120M			Q14242	SELPL_HUMAN	selectin P ligand	104					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.T104M(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						GGCCAGCTCCGTGGTCAGCTC	0.602													G|||	1	0.000199681	0.0	0.0014	5008	,	,		20585	0.0		0.0	False		,,,				2504	0.0				p.T104M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C311T	12						.	G	MET/THR,MET/THR	2,4404	4.2+/-10.8	0,2,2201	94.0	82.0	86.0		311,359	-7.6	0.0	12	dbSNP_134	86	12,8588	9.1+/-34.3	0,12,4288	yes	missense,missense	SELPLG	NM_003006.4,NM_001206609.1	81,81	0,14,6489	AA,AG,GG		0.1395,0.0454,0.1076	benign,benign	104/413,120/429	109017773	14,12992	2203	4300	6503	107541902	SO:0001583	missense	6404	exon2				CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.311C>T	12.37:g.109017773G>A	ENSP00000447752:p.Thr104Met	Somatic		Capture	Illumina HiSeq	Phase_I	107541902	NM_003006	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	37	CCDS31895.2	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	4.550	0.102060	0.08731	4.54E-4	0.001395	ENSG00000110876	ENST00000388962;ENST00000550948;ENST00000228463	T;T;T	0.35605	1.51;1.3;1.39	3.8	-7.59	0.01308	.	1.379380	0.05223	N	0.508925	T	0.11452	0.0279	N	0.03000	-0.44	0.09310	N	1	B;B	0.15473	0.013;0.013	B;B	0.14023	0.01;0.01	T	0.14980	-1.0453	10	0.26408	T	0.33	.	1.9049	0.03275	0.2565:0.0803:0.3219:0.3414	.	120;104	B7Z5C7;Q14242	.;SELPL_HUMAN	M	104;104;120	ENSP00000373614:T104M;ENSP00000447752:T104M;ENSP00000228463:T120M	ENSP00000228463:T120M	T	-	2	0	SELPLG	107541902	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.307000	0.08167	-1.934000	0.01051	-1.149000	0.01842	ACG		0.602	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
ACACB	32	broad.mit.edu	37	12	109610082	109610082	+	Silent	SNP	G	G	A	rs575445770		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:109610082G>A	ENST00000338432.7	+	6	1157	c.1038G>A	c.(1036-1038)gcG>gcA	p.A346A	ACACB_ENST00000377848.3_Silent_p.A346A|ACACB_ENST00000377854.5_Silent_p.A346A			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	346	Biotin carboxylation.				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.A346A(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)	GTTTGCAGGCGGTGTGGGCTG	0.527													G|||	1	0.000199681	0.0	0.0	5008	,	,		18797	0.001		0.0	False		,,,				2504	0.0				p.A346A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1038A	12						.						217.0	238.0	231.0					12																	109610082		2203	4300	6503	108094465	SO:0001819	synonymous_variant	32	exon5			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.1038G>A	12.37:g.109610082G>A		Somatic		Capture	Illumina HiSeq	Phase_I	108094465	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																				0.527	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
TCHP	84260	broad.mit.edu	37	12	110350854	110350854	+	Missense_Mutation	SNP	G	G	A	rs147052884		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:110350854G>A	ENST00000312777.5	+	10	1325	c.1111G>A	c.(1111-1113)Gca>Aca	p.A371T	TCHP_ENST00000405876.4_Missense_Mutation_p.A371T	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding									p.A371T(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						AGAGCGCAGCGCACGGGACAG	0.622													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16775	0.0		0.0	False		,,,				2504	0.0				p.A371T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1111A	12						.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	80.0	66.0	70.0		1111,1111	5.1	0.2	12	dbSNP_134	70	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	TCHP	NM_001143852.1,NM_032300.4	58,58	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	probably-damaging,probably-damaging	371/499,371/499	110350854	6,13000	2203	4300	6503	108835237	SO:0001583	missense	84260	exon10			AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"""mitostatin"""	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.1111G>A	12.37:g.110350854G>A	ENSP00000324404:p.Ala371Thr	Somatic		Capture	Illumina HiSeq	Phase_I	108835237	NM_001143852		Missense_Mutation	SNP	ENST00000312777.5	37	CCDS9137.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.003179	0.74932	0.0	6.98E-4	ENSG00000139437	ENST00000405876;ENST00000312777;ENST00000551627	T;T	0.10288	2.89;2.89	5.09	5.09	0.68999	.	0.054592	0.64402	D	0.000001	T	0.33760	0.0874	M	0.81497	2.545	0.58432	D	0.999992	D	0.89917	1.0	D	0.97110	1.0	T	0.07424	-1.0773	10	0.20046	T	0.44	-10.1881	16.342	0.83084	0.0:0.0:1.0:0.0	.	371	Q9BT92	TCHP_HUMAN	T	371;371;15	ENSP00000384520:A371T;ENSP00000324404:A371T	ENSP00000324404:A371T	A	+	1	0	TCHP	108835237	1.000000	0.71417	0.232000	0.24009	0.184000	0.23303	7.152000	0.77419	2.503000	0.84419	0.650000	0.86243	GCA		0.622	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300	
TCTN1	79600	broad.mit.edu	37	12	111078246	111078246	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:111078246G>A	ENST00000551590.1	+	8	1058	c.902G>A	c.(901-903)cGg>cAg	p.R301Q	HVCN1_ENST00000548312.1_Intron|TCTN1_ENST00000551555.2_3'UTR|TCTN1_ENST00000397655.3_Missense_Mutation_p.R287Q|TCTN1_ENST00000397659.4_Missense_Mutation_p.R301Q|TCTN1_ENST00000377654.3_Missense_Mutation_p.R123Q			Q2MV58	TECT1_HUMAN	tectonic family member 1	301					central nervous system interneuron axonogenesis (GO:0021956)|cilium morphogenesis (GO:0060271)|dorsal/ventral neural tube patterning (GO:0021904)|in utero embryonic development (GO:0001701)|neural tube formation (GO:0001841)|regulation of smoothened signaling pathway (GO:0008589)|somatic motor neuron differentiation (GO:0021523)|telencephalon development (GO:0021537)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)		p.R301Q(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|urinary_tract(1)	15						CTCACCCGACGGGAGGACACT	0.512																																					p.R301Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G902A	12						.						110.0	112.0	112.0					12																	111078246		2122	4257	6379	109562629	SO:0001583	missense	79600	exon8			AK055891	CCDS41833.1, CCDS41834.1, CCDS41835.1	12q24.11	2011-09-07			ENSG00000204852	ENSG00000204852		"""Tectonic proteins"""	26113	protein-coding gene	gene with protein product		609863				16357211	Standard	NM_001082537		Approved	FLJ21127, TECT1, JBTS13	uc001trn.4	Q2MV58	OTTHUMG00000150051	ENST00000551590.1:c.902G>A	12.37:g.111078246G>A	ENSP00000448735:p.Arg301Gln	Somatic		Capture	Illumina HiSeq	Phase_I	109562629	NM_001082537	A8MX11|Q49A60|Q6P5X1|Q6UXW2|Q8NAE9|Q96N72|Q9H798	Missense_Mutation	SNP	ENST00000551590.1	37	CCDS41835.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.808190	0.50421	.	.	ENSG00000204852	ENST00000397650;ENST00000551590;ENST00000397655;ENST00000377654;ENST00000548095;ENST00000397657;ENST00000397659;ENST00000397652	T;T;T;T	0.76316	-1.0;-0.99;-1.01;-0.99	5.79	0.273	0.15650	Domain of unknown function DUF1619 (1);	0.355527	0.27393	N	0.019574	T	0.49541	0.1563	N	0.04090	-0.28	0.09310	N	1	P;D;P;P;P	0.55385	0.913;0.971;0.892;0.776;0.772	B;B;B;B;B	0.40702	0.288;0.338;0.142;0.288;0.222	T	0.53627	-0.8412	10	0.29301	T	0.29	-11.8984	7.1238	0.25461	0.2244:0.0:0.2802:0.4954	.	301;287;301;241;245	Q2MV58;Q2MV58-3;Q2MV58-2;C9J1H5;C9J1H4	TECT1_HUMAN;.;.;.;.	Q	241;301;287;123;299;123;301;245	ENSP00000448735:R301Q;ENSP00000380775:R287Q;ENSP00000366882:R123Q;ENSP00000380779:R301Q	ENSP00000366882:R123Q	R	+	2	0	TCTN1	109562629	0.001000	0.12720	0.018000	0.16275	0.004000	0.04260	0.421000	0.21280	0.090000	0.17273	-0.283000	0.09986	CGG		0.512	TCTN1-001	KNOWN	non_canonical_TEC|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316016.2	NM_024549	
ATXN2	6311	broad.mit.edu	37	12	111954043	111954043	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:111954043C>T	ENST00000377617.3	-	10	1931	c.1770G>A	c.(1768-1770)tcG>tcA	p.S590S	ATXN2_ENST00000550104.1_Silent_p.S590S|ATXN2_ENST00000535949.1_Silent_p.S301S|ATXN2_ENST00000608853.1_Silent_p.S430S|ATXN2_ENST00000389153.4_Silent_p.S325S|ATXN2_ENST00000542287.2_Silent_p.S325S	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	590	Pro-rich.				cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)	p.S590S(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						TGGATGGCCGCGAGGGGGGCC	0.602																																					p.S590S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1770A	12						.						33.0	36.0	35.0					12																	111954043		2203	4300	6503	110438426	SO:0001819	synonymous_variant	6311	exon10			U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"""Ataxins"""	10555	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 13"""	601517	"""spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"""	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.1770G>A	12.37:g.111954043C>T		Somatic		Capture	Illumina HiSeq	Phase_I	110438426	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Silent	SNP	ENST00000377617.3	37	CCDS31902.1																																																																																				0.602	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973	
NAA25	80018	broad.mit.edu	37	12	112509782	112509782	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:112509782C>T	ENST00000261745.4	-	10	1201	c.953G>A	c.(952-954)cGc>cAc	p.R318H	Y_RNA_ENST00000363818.1_RNA	NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	318						cytoplasm (GO:0005737)		p.R318H(1)		autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						TCGGAGATGGCGAGAACTTTT	0.403																																					p.R318H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G953A	12						.						161.0	129.0	140.0					12																	112509782		2203	4300	6503	110994165	SO:0001583	missense	80018	exon10			AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"""N(alpha)-acetyltransferase subunits"""	25783	protein-coding gene	gene with protein product		612755	"""chromosome 12 open reading frame 30"""	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.953G>A	12.37:g.112509782C>T	ENSP00000261745:p.Arg318His	Somatic		Capture	Illumina HiSeq	Phase_I	110994165	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	37	CCDS9159.1	.	.	.	.	.	.	.	.	.	.	C	19.55	3.848157	0.71603	.	.	ENSG00000111300	ENST00000261745	T	0.44482	0.92	5.8	5.8	0.92144	.	0.056296	0.64402	D	0.000001	T	0.38799	0.1054	L	0.39898	1.24	0.58432	D	0.999999	B;B	0.26081	0.141;0.141	B;B	0.22880	0.042;0.042	T	0.08493	-1.0719	10	0.31617	T	0.26	-5.9151	20.0706	0.97721	0.0:1.0:0.0:0.0	.	318;318	A8K8X0;Q14CX7	.;NAA25_HUMAN	H	318	ENSP00000261745:R318H	ENSP00000261745:R318H	R	-	2	0	NAA25	110994165	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.087000	0.64480	2.744000	0.94065	0.655000	0.94253	CGC		0.403	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953	
HECTD4	283450	broad.mit.edu	37	12	112622318	112622318	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:112622318G>A	ENST00000430131.2	-	60	10331	c.9186C>T	c.(9184-9186)agC>agT	p.S3062S	HECTD4_ENST00000377560.5_Silent_p.S3312S|HECTD4_ENST00000550722.1_Silent_p.S3338S			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3062					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.S3312S(1)									AGGCGGAGGCGCTGATGCTCA	0.667																																					p.S3312S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9936T	12						.						23.0	34.0	31.0					12																	112622318		2197	4285	6482	111106701	SO:0001819	synonymous_variant	283450	exon60			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.9186C>T	12.37:g.112622318G>A		Somatic		Capture	Illumina HiSeq	Phase_I	111106701	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37																																																																																					0.667	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
HECTD4	283450	broad.mit.edu	37	12	112622740	112622740	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:112622740C>T	ENST00000430131.2	-	60	9909	c.8764G>A	c.(8764-8766)Gga>Aga	p.G2922R	HECTD4_ENST00000377560.5_Missense_Mutation_p.G3172R|HECTD4_ENST00000550722.1_Missense_Mutation_p.G3198R			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2922					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.G3172R(1)									TTGCTGCCTCCGATGCTGAGC	0.632																																					p.G3172R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G9514A	12						.						38.0	43.0	41.0					12																	112622740		2198	4294	6492	111107123	SO:0001583	missense	283450	exon60			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.8764G>A	12.37:g.112622740C>T	ENSP00000404379:p.Gly2922Arg	Somatic		Capture	Illumina HiSeq	Phase_I	111107123	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	37		.	.	.	.	.	.	.	.	.	.	C	21.1	4.092215	0.76756	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.52983	0.65;0.65;0.64	5.81	5.81	0.92471	.	.	.	.	.	T	0.44953	0.1318	N	0.19112	0.55	0.58432	D	0.999997	D	0.64830	0.994	P	0.47864	0.559	T	0.48990	-0.8985	9	0.87932	D	0	.	20.0858	0.97800	0.0:1.0:0.0:0.0	.	2922	Q9Y4D8	K0614_HUMAN	R	3172;2922;3198	ENSP00000366783:G3172R;ENSP00000404379:G2922R;ENSP00000449784:G3198R	ENSP00000366783:G3172R	G	-	1	0	C12orf51	111107123	0.998000	0.40836	1.000000	0.80357	0.893000	0.52053	5.174000	0.65015	2.753000	0.94483	0.650000	0.86243	GGA		0.632	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
HECTD4	283450	broad.mit.edu	37	12	112647856	112647856	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:112647856T>C	ENST00000430131.2	-	49	7709	c.6564A>G	c.(6562-6564)ccA>ccG	p.P2188P	HECTD4_ENST00000377560.5_Silent_p.P2438P|HECTD4_ENST00000550722.1_Silent_p.P2464P			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2188					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.P2438P(1)									TCCGGCATGGTGGCCCATGAG	0.542																																					p.P2438P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A7314G	12						.						48.0	50.0	49.0					12																	112647856		2145	4244	6389	111132239	SO:0001819	synonymous_variant	283450	exon49			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.6564A>G	12.37:g.112647856T>C		Somatic		Capture	Illumina HiSeq	Phase_I	111132239	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37		.	.	.	.	.	.	.	.	.	.	T	9.395	1.076513	0.20227	.	.	ENSG00000173064	ENST00000550968	.	.	.	5.39	-8.46	0.00942	.	.	.	.	.	T	0.32734	0.0839	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44726	-0.9309	4	.	.	.	.	1.1656	0.01814	0.2779:0.3185:0.1425:0.2611	.	.	.	.	R	355	.	.	H	-	2	0	C12orf51	111132239	0.001000	0.12720	0.715000	0.30552	0.961000	0.63080	-1.650000	0.01991	-0.940000	0.03705	-0.290000	0.09829	CAC		0.542	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
IQCD	115811	broad.mit.edu	37	12	113633674	113633674	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:113633674G>A	ENST00000416617.2	-	5	1246	c.1056C>T	c.(1054-1056)gaC>gaT	p.D352D	IQCD_ENST00000299732.2_Silent_p.D250D			Q96DY2	IQCD_HUMAN	IQ motif containing D	352								p.D250D(1)		endometrium(2)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						TGTGAACAGCGTCCAGATCCT	0.627																																					p.D250D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C750T	12						.						51.0	47.0	49.0					12																	113633674		2203	4300	6503	112118057	SO:0001819	synonymous_variant	115811	exon3			BC013151	CCDS9167.1	12q24.21	2014-07-18				ENSG00000166578			25168	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 10"""					23427265, 24804578	Standard	NM_138451		Approved	DRC10, CFAP84	uc001tuu.3	Q96DY2		ENST00000416617.2:c.1056C>T	12.37:g.113633674G>A		Somatic		Capture	Illumina HiSeq	Phase_I	112118057	NM_138451	Q6ZSU0	Silent	SNP	ENST00000416617.2	37																																																																																					0.627	IQCD-004	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000405327.1	NM_138451	
TPCN1	53373	broad.mit.edu	37	12	113710477	113710477	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:113710477T>C	ENST00000335509.6	+	8	1077	c.763T>C	c.(763-765)Tcc>Ccc	p.S255P	TPCN1_ENST00000550785.1_Missense_Mutation_p.S327P|TPCN1_ENST00000392569.4_Missense_Mutation_p.S187P|TPCN1_ENST00000541517.1_Missense_Mutation_p.S327P	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	255					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|voltage-gated calcium channel activity (GO:0005245)	p.S255P(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						CTACTTGTTCTCCCCTAACCC	0.478																																					p.S255P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T763C	12						.						308.0	284.0	292.0					12																	113710477		2203	4300	6503	112194860	SO:0001583	missense	53373	exon8			AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"""Voltage-gated ion channels / Two-pore channels"""	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.763T>C	12.37:g.113710477T>C	ENSP00000335300:p.Ser255Pro	Somatic		Capture	Illumina HiSeq	Phase_I	112194860	NM_017901	A7E258|Q86XS9|Q8NC20	Missense_Mutation	SNP	ENST00000335509.6	37	CCDS31908.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.744830	0.89663	.	.	ENSG00000186815	ENST00000335509;ENST00000550785;ENST00000541517;ENST00000392569	D;D;D;D	0.97505	-4.41;-4.41;-4.41;-4.41	5.73	5.73	0.89815	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97723	0.9253	L	0.51914	1.62	0.58432	D	0.999994	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.83275	0.996;0.977;0.987	D	0.98532	1.0628	10	0.59425	D	0.04	-35.6121	15.9985	0.80270	0.0:0.0:0.0:1.0	.	255;327;255	A5PKY2;Q9ULQ1-3;Q9ULQ1	.;.;TPC1_HUMAN	P	255;327;327;187	ENSP00000335300:S255P;ENSP00000448083:S327P;ENSP00000438125:S327P;ENSP00000376350:S187P	ENSP00000335300:S255P	S	+	1	0	TPCN1	112194860	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	5.894000	0.69806	2.183000	0.69458	0.459000	0.35465	TCC		0.478	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901	
SDSL	113675	broad.mit.edu	37	12	113873144	113873144	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:113873144G>A	ENST00000403593.4	+	6	716	c.454G>A	c.(454-456)Gcc>Acc	p.A152T	SDSL_ENST00000345635.4_Missense_Mutation_p.A152T			Q96GA7	SDSL_HUMAN	serine dehydratase-like	152					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.A152T(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)	15						GAAAGGCCACGCCAGCCTGGT	0.677																																					p.A152T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G454A	12						.						9.0	9.0	9.0					12																	113873144		2163	4235	6398	112357527	SO:0001583	missense	113675	exon7			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.454G>A	12.37:g.113873144G>A	ENSP00000385790:p.Ala152Thr	Somatic		Capture	Illumina HiSeq	Phase_I	112357527	NM_138432		Missense_Mutation	SNP	ENST00000403593.4	37	CCDS9170.1	.	.	.	.	.	.	.	.	.	.	G	3.209	-0.161980	0.06502	.	.	ENSG00000139410	ENST00000403593;ENST00000553248;ENST00000345635	D;D;D	0.96913	-4.17;-4.17;-4.17	4.49	2.62	0.31277	Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.188523	0.45126	D	0.000394	D	0.90717	0.7087	L	0.45051	1.395	0.38316	D	0.943384	P	0.40660	0.726	B	0.28916	0.096	D	0.86988	0.2108	10	0.51188	T	0.08	-1.325	6.3807	0.21533	0.1625:0.0:0.6891:0.1484	.	152	Q96GA7	SDSL_HUMAN	T	152;94;152	ENSP00000385790:A152T;ENSP00000448868:A94T;ENSP00000341117:A152T	ENSP00000341117:A152T	A	+	1	0	SDSL	112357527	0.004000	0.15560	0.138000	0.22173	0.135000	0.20990	0.014000	0.13333	0.430000	0.26230	0.462000	0.41574	GCC		0.677	SDSL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404782.1	NM_138432	
TBX3	6926	broad.mit.edu	37	12	115109673	115109673	+	Silent	SNP	C	C	T	rs142609038	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:115109673C>T	ENST00000257566.3	-	8	2594	c.2205G>A	c.(2203-2205)ccG>ccA	p.P735P	TBX3_ENST00000349155.2_Silent_p.P715P	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	735					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|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)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P735P(1)		breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		GGGACCTGTCCGGCTTGGCTT	0.587																																					p.P715P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2145A	12						.						11.0	10.0	10.0					12																	115109673		2189	4266	6455	113594056	SO:0001819	synonymous_variant	6926	exon7			BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.2205G>A	12.37:g.115109673C>T		Somatic		Capture	Illumina HiSeq	Phase_I	113594056	NM_005996	Q8TB20|Q9UKF8	Silent	SNP	ENST00000257566.3	37	CCDS9176.1																																																																																				0.587	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996	
TBX3	6926	broad.mit.edu	37	12	115112086	115112086	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:115112086C>T	ENST00000257566.3	-	7	2043	c.1654G>A	c.(1654-1656)Ggt>Agt	p.G552S	TBX3_ENST00000349155.2_Missense_Mutation_p.G532S	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	552	Transcription repression.				anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|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)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G552S(1)		breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		CCCGAGACACCGGTGGAGGCC	0.716																																					p.G532S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1594A	12						.						11.0	16.0	14.0					12																	115112086		2170	4255	6425	113596469	SO:0001583	missense	6926	exon6			BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.1654G>A	12.37:g.115112086C>T	ENSP00000257566:p.Gly552Ser	Somatic		Capture	Illumina HiSeq	Phase_I	113596469	NM_005996	Q8TB20|Q9UKF8	Missense_Mutation	SNP	ENST00000257566.3	37	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	C	32	5.167776	0.94768	.	.	ENSG00000135111	ENST00000349155;ENST00000257566	D;D	0.91521	-2.86;-2.83	5.26	5.26	0.73747	.	1.640980	0.04141	N	0.319622	D	0.95385	0.8502	M	0.72894	2.215	0.80722	D	1	D;D	0.76494	0.999;0.998	P;P	0.62382	0.901;0.875	D	0.87120	0.2190	10	0.37606	T	0.19	.	17.8586	0.88773	0.0:1.0:0.0:0.0	.	532;552	O15119-2;O15119	.;TBX3_HUMAN	S	532;552	ENSP00000257567:G532S;ENSP00000257566:G552S	ENSP00000257566:G552S	G	-	1	0	TBX3	113596469	1.000000	0.71417	0.419000	0.26584	0.845000	0.48019	5.633000	0.67825	2.441000	0.82636	0.650000	0.86243	GGT		0.716	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996	
MED13L	23389	broad.mit.edu	37	12	116424167	116424167	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:116424167G>A	ENST00000281928.3	-	19	4448	c.4242C>T	c.(4240-4242)ggC>ggT	p.G1414G		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1414						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.G1414G(1)		NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		CATCACGGTGGCCCCCATATG	0.517																																					p.G1414G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4242T	12						.						101.0	95.0	97.0					12																	116424167		2203	4300	6503	114908550	SO:0001819	synonymous_variant	23389	exon19			AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.4242C>T	12.37:g.116424167G>A		Somatic		Capture	Illumina HiSeq	Phase_I	114908550	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1																																																																																				0.517	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
MED13L	23389	broad.mit.edu	37	12	116457644	116457644	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:116457644C>T	ENST00000281928.3	-	6	965	c.759G>A	c.(757-759)tcG>tcA	p.S253S		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	253						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.S253S(2)		NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		CTTCCTCTTTCGATTCTTCTT	0.398																																					p.S253S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G759A	12						.						180.0	163.0	169.0					12																	116457644		2203	4300	6503	114942027	SO:0001819	synonymous_variant	23389	exon6			AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.759G>A	12.37:g.116457644C>T		Somatic		Capture	Illumina HiSeq	Phase_I	114942027	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1																																																																																				0.398	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
NOS1	4842	broad.mit.edu	37	12	117657907	117657907	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:117657907G>A	ENST00000338101.4	-	27	4249	c.4245C>T	c.(4243-4245)gaC>gaT	p.D1415D	NOS1_ENST00000317775.6_Silent_p.D1381D|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.D1381D(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		ATACGCCGGCGTCCTCTGCCG	0.577																																					p.D1381D	Esophageal Squamous(162;1748 2599 51982 52956)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4143T	12						.						96.0	108.0	104.0					12																	117657907		2143	4253	6396	116142290	SO:0001819	synonymous_variant	4842	exon27				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.4245C>T	12.37:g.117657907G>A		Somatic		Capture	Illumina HiSeq	Phase_I	116142290	NM_000620		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																				0.577	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
NOS1	4842	broad.mit.edu	37	12	117710231	117710231	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:117710231C>T	ENST00000338101.4	-	9	1802	c.1798G>A	c.(1798-1800)Gtc>Atc	p.V600I	NOS1_ENST00000317775.6_Missense_Mutation_p.V600I|NOS1_ENST00000344089.3_3'UTR			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)	p.V600I(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		TAGTCGCGGACACCAATCTCT	0.592																																					p.V600I	Esophageal Squamous(162;1748 2599 51982 52956)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1798A	12						.						70.0	79.0	76.0					12																	117710231		2198	4299	6497	116194614	SO:0001583	missense	4842	exon10				CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.1798G>A	12.37:g.117710231C>T	ENSP00000337459:p.Val600Ile	Somatic		Capture	Illumina HiSeq	Phase_I	116194614	NM_000620		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.542941	0.86022	.	.	ENSG00000089250	ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.45668	0.89;0.89	4.7	4.7	0.59300	Nitric oxide synthase, oxygenase domain (2);	0.000000	0.85682	D	0.000000	T	0.57301	0.2044	M	0.78049	2.395	0.80722	D	1	P	0.45428	0.858	P	0.49887	0.625	T	0.64110	-0.6484	10	0.59425	D	0.04	-46.1853	17.8477	0.88736	0.0:1.0:0.0:0.0	.	600	P29475	NOS1_HUMAN	I	600	ENSP00000320758:V600I;ENSP00000337459:V600I	ENSP00000320758:V600I	V	-	1	0	NOS1	116194614	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.841000	0.69409	2.437000	0.82529	0.655000	0.94253	GTC		0.592	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
SRRM4	84530	broad.mit.edu	37	12	119568587	119568587	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:119568587G>A	ENST00000267260.4	+	8	1107	c.719G>A	c.(718-720)cGc>cAc	p.R240H	SRRM4_ENST00000537597.1_3'UTR	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	240	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.R240H(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						CAGTCCAGTCGCCCGCCCAGT	0.647																																					p.R240H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G719A	12						.						25.0	30.0	28.0					12																	119568587		1941	4136	6077	118052970	SO:0001583	missense	84530	exon8			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.719G>A	12.37:g.119568587G>A	ENSP00000267260:p.Arg240His	Somatic		Capture	Illumina HiSeq	Phase_I	118052970	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	.	.	.	.	.	.	.	.	.	.	G	1.444	-0.566815	0.03910	.	.	ENSG00000139767	ENST00000267260	T	0.21361	2.01	5.07	-6.47	0.01902	.	0.859637	0.10382	N	0.681455	T	0.05364	0.0142	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39623	-0.9605	10	0.15066	T	0.55	-0.3204	6.6131	0.22763	0.3406:0.2692:0.3902:0.0	.	240	A7MD48	SRRM4_HUMAN	H	240	ENSP00000267260:R240H	ENSP00000267260:R240H	R	+	2	0	SRRM4	118052970	0.012000	0.17670	0.086000	0.20670	0.093000	0.18481	0.044000	0.13992	-1.513000	0.01789	-0.717000	0.03617	CGC		0.647	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286	
CCDC60	160777	broad.mit.edu	37	12	119942914	119942914	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:119942914G>A	ENST00000327554.2	+	7	1154	c.689G>A	c.(688-690)cGc>cAc	p.R230H	RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	230								p.R230H(2)		endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		GTCACCAACCGCAAACCAAGC	0.527																																					p.R230H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G689A	12						.						65.0	72.0	70.0					12																	119942914		2203	4300	6503	118427297	SO:0001583	missense	160777	exon7			BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.689G>A	12.37:g.119942914G>A	ENSP00000333374:p.Arg230His	Somatic		Capture	Illumina HiSeq	Phase_I	118427297	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	37	CCDS9190.1	.	.	.	.	.	.	.	.	.	.	G	6.667	0.491619	0.12702	.	.	ENSG00000183273	ENST00000327554	T	0.28255	1.62	5.07	2.26	0.28386	.	0.427916	0.19810	N	0.105546	T	0.21962	0.0529	L	0.42245	1.32	0.09310	N	1	B	0.21309	0.054	B	0.14023	0.01	T	0.19549	-1.0302	9	.	.	.	-3.5365	7.2921	0.26372	0.2797:0.0:0.7203:0.0	.	230	Q8IWA6	CCD60_HUMAN	H	230	ENSP00000333374:R230H	.	R	+	2	0	CCDC60	118427297	0.689000	0.27690	0.001000	0.08648	0.008000	0.06430	1.498000	0.35660	0.176000	0.19873	-0.142000	0.14014	CGC		0.527	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499	
CCDC60	160777	broad.mit.edu	37	12	119961555	119961555	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:119961555G>T	ENST00000327554.2	+	11	1626	c.1161G>T	c.(1159-1161)agG>agT	p.R387S	RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	387								p.R387S(1)		endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		ACACCATGAGGGCCAAGTTTT	0.498																																					p.R387S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1161T	12						.						113.0	93.0	99.0					12																	119961555		2203	4300	6503	118445938	SO:0001583	missense	160777	exon11			BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.1161G>T	12.37:g.119961555G>T	ENSP00000333374:p.Arg387Ser	Somatic		Capture	Illumina HiSeq	Phase_I	118445938	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	37	CCDS9190.1	.	.	.	.	.	.	.	.	.	.	G	13.47	2.246366	0.39697	.	.	ENSG00000183273	ENST00000327554	T	0.39997	1.05	4.16	3.17	0.36434	.	0.000000	0.53938	D	0.000048	T	0.57562	0.2062	M	0.76002	2.32	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.58284	-0.7663	9	.	.	.	-40.9912	6.0653	0.19860	0.1443:0.0:0.8557:0.0	.	387	Q8IWA6	CCD60_HUMAN	S	387	ENSP00000333374:R387S	.	R	+	3	2	CCDC60	118445938	1.000000	0.71417	1.000000	0.80357	0.077000	0.17291	0.769000	0.26604	2.156000	0.67533	0.655000	0.94253	AGG		0.498	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499	
CIT	11113	broad.mit.edu	37	12	120168426	120168426	+	Silent	SNP	G	G	A	rs138923592		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:120168426G>A	ENST00000261833.7	-	26	3286	c.3234C>T	c.(3232-3234)gcC>gcT	p.A1078A	CIT_ENST00000392521.2_Silent_p.A1120A|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1078					cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.A1078A(1)|p.A1121A(1)		breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		TCCGCTGATCGGCTCTCGCCC	0.587																																					p.A1078A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C3234T	12						.	G	,	0,4406		0,0,2203	49.0	44.0	46.0		3360,3234	-9.6	0.0	12	dbSNP_134	46	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	CIT	NM_001206999.1,NM_007174.2	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	1120/2070,1078/2028	120168426	2,13004	2203	4300	6503	118652809	SO:0001819	synonymous_variant	11113	exon26			AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.3234C>T	12.37:g.120168426G>A		Somatic		Capture	Illumina HiSeq	Phase_I	118652809	NM_007174	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.212878	0.39102	0.0	2.33E-4	ENSG00000122966	ENST00000392520	.	.	.	5.45	-9.62	0.00547	.	.	.	.	.	T	0.57607	0.2065	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66575	-0.5889	4	.	.	.	.	13.3535	0.60615	0.7444:0.0:0.1383:0.1173	.	.	.	.	L	706	.	.	P	-	2	0	CIT	118652809	0.000000	0.05858	0.037000	0.18230	0.929000	0.56500	-2.664000	0.00848	-1.795000	0.01255	-0.794000	0.03295	CCG		0.587	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
GCN1L1	10985	broad.mit.edu	37	12	120567133	120567133	+	Missense_Mutation	SNP	C	C	T	rs548401692		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:120567133C>T	ENST00000300648.6	-	57	7849	c.7837G>A	c.(7837-7839)Gac>Aac	p.D2613N		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	2613					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)	p.D2613N(1)		NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ATTGCCTGGTCGCTGTAGGCC	0.587													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16966	0.0		0.0	False		,,,				2504	0.0				p.D2613N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G7837A	12						.						168.0	167.0	167.0					12																	120567133		1937	4148	6085	119051516	SO:0001583	missense	10985	exon57			U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.7837G>A	12.37:g.120567133C>T	ENSP00000300648:p.Asp2613Asn	Somatic		Capture	Illumina HiSeq	Phase_I	119051516	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	37	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.422153	0.83559	.	.	ENSG00000089154	ENST00000300648	T	0.31769	1.48	5.48	5.48	0.80851	Armadillo-like helical (1);Armadillo-type fold (1);	0.117279	0.56097	D	0.000026	T	0.34716	0.0907	L	0.57536	1.79	0.80722	D	1	P	0.46578	0.88	B	0.39027	0.288	T	0.34079	-0.9843	10	0.87932	D	0	-16.5395	19.3583	0.94424	0.0:1.0:0.0:0.0	.	2613	Q92616	GCN1L_HUMAN	N	2613	ENSP00000300648:D2613N	ENSP00000300648:D2613N	D	-	1	0	GCN1L1	119051516	1.000000	0.71417	0.994000	0.49952	0.894000	0.52154	7.487000	0.81328	2.563000	0.86464	0.655000	0.94253	GAC		0.587	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
GCN1L1	10985	broad.mit.edu	37	12	120621398	120621398	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:120621398G>A	ENST00000300648.6	-	5	412	c.400C>T	c.(400-402)Cga>Tga	p.R134*		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	134					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)	p.R134*(1)		NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TCTCCTTGTCGCTTGGCTCTC	0.547																																					p.R134X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C400T	12						.						98.0	101.0	100.0					12																	120621398		2094	4235	6329	119105781	SO:0001587	stop_gained	10985	exon5			U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.400C>T	12.37:g.120621398G>A	ENSP00000300648:p.Arg134*	Somatic		Capture	Illumina HiSeq	Phase_I	119105781	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Nonsense_Mutation	SNP	ENST00000300648.6	37	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	G	35	5.578060	0.96565	.	.	ENSG00000089154	ENST00000300648	.	.	.	5.93	3.9	0.45041	.	0.119647	0.56097	D	0.000032	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	-3.5476	13.4693	0.61273	0.0:0.0:0.5101:0.4899	.	.	.	.	X	134	.	ENSP00000300648:R134X	R	-	1	2	GCN1L1	119105781	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.355000	0.34068	0.744000	0.32741	0.644000	0.83932	CGA		0.547	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
SIRT4	23409	broad.mit.edu	37	12	120741623	120741623	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:120741623C>A	ENST00000202967.4	+	2	318	c.259C>A	c.(259-261)Cgc>Agc	p.R87S		NM_012240.2	NP_036372.1			sirtuin 4									p.R87S(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCGCACTGACCGCAGGCCCAT	0.567																																					p.R87S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C259A	12						.						57.0	53.0	54.0					12																	120741623		2203	4300	6503	119226006	SO:0001583	missense	23409	exon2			AF083109	CCDS9194.1	12q24.31	2010-06-25	2010-06-25		ENSG00000089163	ENSG00000089163			14932	protein-coding gene	gene with protein product		604482	"""sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 4"", ""sirtuin (silent mating type information regulation 2 homolog) 4 (S. cerevisiae)"""			10381378	Standard	NM_012240		Approved	SIR2L4	uc001tyc.3	Q9Y6E7	OTTHUMG00000169028	ENST00000202967.4:c.259C>A	12.37:g.120741623C>A	ENSP00000202967:p.Arg87Ser	Somatic		Capture	Illumina HiSeq	Phase_I	119226006	NM_012240		Missense_Mutation	SNP	ENST00000202967.4	37	CCDS9194.1	.	.	.	.	.	.	.	.	.	.	C	15.72	2.916510	0.52546	.	.	ENSG00000089163	ENST00000536460;ENST00000202967	T;T	0.17370	2.28;2.28	5.39	4.49	0.54785	.	0.097314	0.64402	D	0.000002	T	0.14485	0.0350	L	0.29908	0.895	0.49213	D	0.999769	P	0.35844	0.524	B	0.37780	0.258	T	0.08472	-1.0720	10	0.25751	T	0.34	-22.2578	13.8149	0.63285	0.393:0.607:0.0:0.0	.	87	Q9Y6E7	SIRT4_HUMAN	S	28;87	ENSP00000444838:R28S;ENSP00000202967:R87S	ENSP00000202967:R87S	R	+	1	0	SIRT4	119226006	1.000000	0.71417	0.831000	0.32960	0.980000	0.70556	1.032000	0.30178	1.416000	0.47057	0.644000	0.83932	CGC		0.567	SIRT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402003.1	NM_012240	
RNF10	9921	broad.mit.edu	37	12	121001654	121001654	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:121001654C>T	ENST00000325954.4	+	10	2034	c.1573C>T	c.(1573-1575)Cgc>Tgc	p.R525C	RNF10_ENST00000413266.2_Missense_Mutation_p.R530C	NM_014868.4	NP_055683.3	Q8N5U6	RNF10_HUMAN	ring finger protein 10	525					negative regulation of Schwann cell proliferation (GO:0010626)|positive regulation of myelination (GO:0031643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autoubiquitination (GO:0051865)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription regulatory region DNA binding (GO:0044212)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R525C(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	27	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGTGAATGTGCGCTGCCTCGT	0.602																																					p.R525C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1573T	12						.						161.0	141.0	148.0					12																	121001654		2203	4300	6503	119486037	SO:0001583	missense	9921	exon10			AB027196	CCDS9201.1	12q23-q24	2013-01-09			ENSG00000022840	ENSG00000022840		"""RING-type (C3HC4) zinc fingers"""	10055	protein-coding gene	gene with protein product							Standard	NM_014868		Approved	KIAA0262, RIE2	uc001typ.4	Q8N5U6	OTTHUMG00000168999	ENST00000325954.4:c.1573C>T	12.37:g.121001654C>T	ENSP00000322242:p.Arg525Cys	Somatic		Capture	Illumina HiSeq	Phase_I	119486037	NM_014868	Q92550|Q9NPP8|Q9ULW4	Missense_Mutation	SNP	ENST00000325954.4	37	CCDS9201.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.810293	0.90707	.	.	ENSG00000022840	ENST00000325954;ENST00000458409;ENST00000413266;ENST00000540046	T;T;T	0.24350	1.86;1.86;1.86	5.85	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.55577	0.1929	M	0.85099	2.735	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.61422	-0.7066	10	0.87932	D	0	.	15.3754	0.74602	0.0:0.9322:0.0:0.0678	.	530;525	Q8N5U6-2;Q8N5U6	.;RNF10_HUMAN	C	525;525;530;69	ENSP00000322242:R525C;ENSP00000415682:R530C;ENSP00000439859:R69C	ENSP00000322242:R525C	R	+	1	0	RNF10	119486037	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	6.084000	0.71335	2.767000	0.95098	0.557000	0.71058	CGC		0.602	RNF10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401898.4		
P2RX4	5025	broad.mit.edu	37	12	121670890	121670890	+	Missense_Mutation	SNP	G	G	A	rs368547621		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:121670890G>A	ENST00000337233.4	+	11	1443	c.1135G>A	c.(1135-1137)Gag>Aag	p.E379K	P2RX4_ENST00000359949.7_Missense_Mutation_p.E395K|P2RX4_ENST00000543171.1_Missense_Mutation_p.E278K	NM_001261397.1|NM_001261398.1|NM_002560.2	NP_001248326.1|NP_001248327.1|NP_002551.2	Q99571	P2RX4_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 4	379					apoptotic signaling pathway (GO:0097190)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular response to ATP (GO:0071318)|endothelial cell activation (GO:0042118)|ion transmembrane transport (GO:0034220)|membrane depolarization (GO:0051899)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|neuronal action potential (GO:0019228)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction (GO:0055117)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sodium ion transport (GO:0002028)|relaxation of cardiac muscle (GO:0055119)|response to ATP (GO:0033198)|response to fluid shear stress (GO:0034405)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|tissue homeostasis (GO:0001894)|transport (GO:0006810)|vasodilation (GO:0042311)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadherin binding (GO:0045296)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)	p.E379K(1)		breast(1)|kidney(4)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GGAAGATTACGAGCAGGTAGG	0.552													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18747	0.0		0.0	False		,,,				2504	0.0				p.E379K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1135A	12						.	G	LYS/GLU	0,4406	2.1+/-5.4	0,0,2203	88.0	100.0	96.0		1135	4.6	0.9	12		96	1,8599	1.2+/-3.3	0,1,4299	no	missense	P2RX4	NM_002560.2	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	379/389	121670890	1,13005	2203	4300	6503	120155273	SO:0001583	missense	5025	exon11			Y07684	CCDS9214.1, CCDS58282.1	12q24.32	2012-01-17			ENSG00000135124	ENSG00000135124		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8535	protein-coding gene	gene with protein product		600846				9016352	Standard	NM_002560		Approved	P2X4	uc031qjt.1	Q99571	OTTHUMG00000169155	ENST00000337233.4:c.1135G>A	12.37:g.121670890G>A	ENSP00000336607:p.Glu379Lys	Somatic		Capture	Illumina HiSeq	Phase_I	120155273	NM_002560	E7EPF7|F6RU17|O00450|O14722|Q5U089|Q5U090|Q8N4N1|Q9UBG9	Missense_Mutation	SNP	ENST00000337233.4	37	CCDS9214.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.891401	0.52014	0.0	1.16E-4	ENSG00000135124	ENST00000337233;ENST00000359949;ENST00000543171;ENST00000542067	T;T;T;T	0.04049	3.72;3.72;3.72;3.72	5.48	4.58	0.56647	.	0.451330	0.26765	N	0.022611	T	0.03739	0.0106	N	0.26162	0.8	0.39840	D	0.973092	B;D;B	0.59357	0.077;0.985;0.094	B;B;B	0.39935	0.014;0.314;0.025	T	0.48317	-0.9046	10	0.07325	T	0.83	-11.5061	15.333	0.74229	0.0:0.1402:0.8598:0.0	.	352;395;379	F6RU17;E7EPF7;Q99571	.;.;P2RX4_HUMAN	K	379;395;278;352	ENSP00000336607:E379K;ENSP00000353032:E395K;ENSP00000438131:E278K;ENSP00000438329:E352K	ENSP00000336607:E379K	E	+	1	0	P2RX4	120155273	1.000000	0.71417	0.931000	0.37212	0.388000	0.30384	3.960000	0.56752	1.287000	0.44583	0.563000	0.77884	GAG		0.552	P2RX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402545.1	NM_175567	
KDM2B	84678	broad.mit.edu	37	12	121947730	121947730	+	Silent	SNP	G	G	A	rs78494968	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:121947730G>A	ENST00000377071.4	-	11	1359	c.1287C>T	c.(1285-1287)ggC>ggT	p.G429G	KDM2B_ENST00000536437.1_Silent_p.G312G|KDM2B_ENST00000538046.2_Silent_p.G339G|KDM2B_ENST00000377069.4_Silent_p.G398G|KDM2B_ENST00000542973.1_5'Flank	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	429	Glu-rich.				embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)	p.G68G(1)|p.G429G(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						CCCTGCCCTCGCcctcctcgt	0.642													G|||	113	0.0225639	0.0817	0.0072	5008	,	,		15219	0.0		0.0	False		,,,				2504	0.0				p.G429G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1287T	12						.	G	,	300,3838		10,280,1779	44.0	52.0	50.0		1194,1287	0.4	0.9	12	dbSNP_132	50	1,8359		0,1,4179	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	10,281,5958	AA,AG,GG		0.012,7.2499,2.4084	,	398/1266,429/1337	121947730	301,12197	2069	4180	6249	120432113	SO:0001819	synonymous_variant	84678	exon11			AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.1287C>T	12.37:g.121947730G>A		Somatic		Capture	Illumina HiSeq	Phase_I	120432113	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																				0.642	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
ORAI1	84876	broad.mit.edu	37	12	122079313	122079313	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:122079313G>A	ENST00000330079.7	+	2	869	c.676G>A	c.(676-678)Gtc>Atc	p.V226I		NM_032790.3	NP_116179	Q96D31	CRCM1_HUMAN	ORAI calcium release-activated calcium modulator 1	224					blood coagulation (GO:0007596)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|regulation of calcium ion transport (GO:0051924)|store-operated calcium entry (GO:0002115)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|store-operated calcium channel activity (GO:0015279)	p.V226I(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000415)|Epithelial(86;0.00148)		AGCAGCCAACGTCAGCACCAG	0.652																																					p.V226I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G676A	12						.						41.0	54.0	50.0					12																	122079313		2193	4291	6484	120563696	SO:0001583	missense	84876	exon2			AK027372		12q24.31	2014-09-17	2007-08-14	2007-08-14	ENSG00000182500	ENSG00000276045		"""ORAI calcium release-activated calcium modulators"""	25896	protein-coding gene	gene with protein product	"""calcium release-activated calcium modulator 1"""	610277	"""transmembrane protein 142A"""	TMEM142A		16582901	Standard	NM_032790		Approved	FLJ14466, CRACM1	uc021rff.1	Q96D31		ENST00000330079.7:c.676G>A	12.37:g.122079313G>A	ENSP00000328216:p.Val226Ile	Somatic		Capture	Illumina HiSeq	Phase_I	120563696	NM_032790	Q3MHV3|Q6DHX2|Q96BP7|Q96K71	Missense_Mutation	SNP	ENST00000330079.7	37	CCDS41851.1	.	.	.	.	.	.	.	.	.	.	G	1.807	-0.475694	0.04414	.	.	ENSG00000182500	ENST00000330079;ENST00000537188	T;T	0.42900	1.54;0.96	5.19	3.02	0.34903	.	1.325880	0.05029	N	0.474295	T	0.25158	0.0611	N	0.14661	0.345	0.09310	N	1	B	0.18741	0.03	B	0.17098	0.017	T	0.22103	-1.0226	10	0.32370	T	0.25	0.1102	2.3406	0.04259	0.2031:0.0:0.501:0.2958	.	224	Q96D31	CRCM1_HUMAN	I	226;121	ENSP00000328216:V226I;ENSP00000441198:V121I	ENSP00000328216:V226I	V	+	1	0	ORAI1	120563696	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	0.086000	0.14935	1.134000	0.42165	0.591000	0.81541	GTC		0.652	ORAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402151.1	NM_032790	
CLIP1	6249	broad.mit.edu	37	12	122757493	122757493	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:122757493G>A	ENST00000540338.1	-	25	4287	c.4246C>T	c.(4246-4248)Cgc>Tgc	p.R1416C	CLIP1_ENST00000545889.1_Missense_Mutation_p.R991C|CLIP1_ENST00000540539.1_Missense_Mutation_p.R95C|CLIP1_ENST00000537178.1_Missense_Mutation_p.R1370C|CLIP1_ENST00000536634.1_5'UTR|CLIP1_ENST00000302528.7_Missense_Mutation_p.R1405C|CLIP1_ENST00000358808.2_Missense_Mutation_p.R1405C|CLIP1_ENST00000361654.4_Missense_Mutation_p.R1294C			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	1416					microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.R1405C(1)		NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		CAGTATGGGCGTTCCTCACCC	0.542																																					p.R1370C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4108T	12						.						240.0	195.0	211.0					12																	122757493		2203	4300	6503	121323446	SO:0001583	missense	6249	exon24				CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"""restin"""	179838	"""restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"""	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.4246C>T	12.37:g.122757493G>A	ENSP00000439093:p.Arg1416Cys	Somatic		Capture	Illumina HiSeq	Phase_I	121323446	NM_198240	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	37	CCDS58285.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.173065	0.78452	.	.	ENSG00000130779	ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000392458;ENST00000537178;ENST00000540539;ENST00000540338	T;T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08;-1.08	5.86	5.86	0.93980	.	0.182057	0.46758	D	0.000275	D	0.89726	0.6798	M	0.83774	2.66	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	0.90165	0.4231	10	0.87932	D	0	-9.6838	20.2019	0.98263	0.0:0.0:1.0:0.0	.	1370;1405;1416	P30622-2;P30622-1;P30622	.;.;CLIP1_HUMAN	C	991;1405;1405;1137;449;1370;95;1416	ENSP00000438743:R991C;ENSP00000303585:R1405C;ENSP00000351665:R1405C;ENSP00000445531:R1370C;ENSP00000437617:R95C;ENSP00000439093:R1416C	ENSP00000303585:R1405C	R	-	1	0	CLIP1	121323446	1.000000	0.71417	0.967000	0.41034	0.983000	0.72400	5.951000	0.70273	2.776000	0.95493	0.655000	0.94253	CGC		0.542	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956	
LRP6	4040	broad.mit.edu	37	12	12334202	12334202	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:12334202G>A	ENST00000261349.4	-	6	1224	c.1148C>T	c.(1147-1149)gCc>gTc	p.A383V	LRP6_ENST00000543091.1_Missense_Mutation_p.A383V	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	383	Beta-propeller 2.				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.A383V(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)				ACGGCGTATGGCCCTCACTTC	0.468																																					p.A383V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1148T	12						.						217.0	181.0	193.0					12																	12334202		2203	4300	6503	12225469	SO:0001583	missense	4040	exon6			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.1148C>T	12.37:g.12334202G>A	ENSP00000261349:p.Ala383Val	Somatic		Capture	Illumina HiSeq	Phase_I	12225469	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.433600	0.83776	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.95885	-3.84;-3.84	5.82	5.82	0.92795	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	D	0.000010	D	0.95335	0.8486	L	0.41415	1.275	0.80722	D	1	D;P	0.54207	0.965;0.553	P;B	0.53266	0.722;0.302	D	0.93942	0.7224	10	0.32370	T	0.25	.	20.099	0.97865	0.0:0.0:1.0:0.0	.	383;383	F5H7J9;O75581	.;LRP6_HUMAN	V	383	ENSP00000261349:A383V;ENSP00000442472:A383V	ENSP00000261349:A383V	A	-	2	0	LRP6	12225469	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.752000	0.94435	0.655000	0.94253	GCC		0.468	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
PITPNM2	57605	broad.mit.edu	37	12	123489885	123489885	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:123489885G>A	ENST00000542749.1	-	5	917	c.854C>T	c.(853-855)cCg>cTg	p.P285L	PITPNM2_ENST00000451868.2_5'UTR|PITPNM2_ENST00000320201.4_Missense_Mutation_p.P285L|PITPNM2_ENST00000392428.1_Intron|PITPNM2_ENST00000280562.5_Missense_Mutation_p.P285L|PITPNM2_ENST00000546049.1_Missense_Mutation_p.P285L			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	285					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)	p.P285L(1)		NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		GCTGGGCTCCGGGGGCTCCCC	0.627																																					p.P285L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C854T	12						.						70.0	71.0	70.0					12																	123489885		2203	4300	6503	122055838	SO:0001583	missense	57605	exon6			AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.854C>T	12.37:g.123489885G>A	ENSP00000437611:p.Pro285Leu	Somatic		Capture	Illumina HiSeq	Phase_I	122055838	NM_020845	Q9P271	Missense_Mutation	SNP	ENST00000542749.1	37	CCDS9242.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.601755	0.46423	.	.	ENSG00000090975	ENST00000280562;ENST00000320201;ENST00000542749	T;T;T	0.35605	1.3;1.3;1.3	4.72	3.82	0.43975	.	0.876710	0.09822	N	0.751388	T	0.28732	0.0712	L	0.29908	0.895	0.35500	D	0.799685	B;B;B	0.26708	0.06;0.153;0.157	B;B;B	0.20577	0.011;0.03;0.013	T	0.21895	-1.0232	10	0.54805	T	0.06	-1.5014	11.3875	0.49793	0.0916:0.0:0.9084:0.0	.	285;285;285	A5D8U3;Q9BZ72-2;Q9BZ72	.;.;PITM2_HUMAN	L	285	ENSP00000280562:P285L;ENSP00000322218:P285L;ENSP00000437611:P285L	ENSP00000280562:P285L	P	-	2	0	PITPNM2	122055838	0.047000	0.20315	0.005000	0.12908	0.574000	0.36063	2.381000	0.44336	1.089000	0.41292	0.561000	0.74099	CCG		0.627	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845	
SBNO1	55206	broad.mit.edu	37	12	123815843	123815843	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:123815843G>A	ENST00000602398.1	-	8	1116	c.989C>T	c.(988-990)aCg>aTg	p.T330M	SBNO1_ENST00000267176.4_Missense_Mutation_p.T329M|SBNO1_ENST00000602750.1_Missense_Mutation_p.T329M|SBNO1_ENST00000420886.2_Missense_Mutation_p.T330M			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	330					regulation of transcription, DNA-templated (GO:0006355)			p.T329M(1)		NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TCCTGCTATCGTCCTTCCTTT	0.438																																					p.T329M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C986T	12						.						157.0	142.0	147.0					12																	123815843		2203	4300	6503	122381796	SO:0001583	missense	55206	exon7			AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"""sno, strawberry notch homolog 1 (Drosophila)"""				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.989C>T	12.37:g.123815843G>A	ENSP00000473665:p.Thr330Met	Somatic		Capture	Illumina HiSeq	Phase_I	122381796	NM_018183	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	.	.	.	.	.	.	.	.	.	.	G	32	5.115450	0.94339	.	.	ENSG00000139697	ENST00000420886;ENST00000267176;ENST00000442601	D;D	0.94092	-3.35;-3.35	5.83	5.83	0.93111	Helicase/UvrB domain (1);	0.000000	0.85682	D	0.000000	D	0.96846	0.8970	M	0.78637	2.42	0.80722	D	1	D;D;D	0.89917	0.987;0.986;1.0	P;P;D	0.85130	0.817;0.721;0.997	D	0.96590	0.9437	10	0.62326	D	0.03	-17.2227	20.1218	0.97964	0.0:0.0:1.0:0.0	.	330;329;328	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	M	330;329;329	ENSP00000387361:T330M;ENSP00000267176:T329M	ENSP00000267176:T329M	T	-	2	0	SBNO1	122381796	1.000000	0.71417	0.972000	0.41901	0.990000	0.78478	7.995000	0.88328	2.763000	0.94921	0.561000	0.74099	ACG		0.438	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
SETD8	387893	broad.mit.edu	37	12	123889532	123889532	+	Silent	SNP	C	C	T	rs529899431		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:123889532C>T	ENST00000402868.3	+	7	1185	c.759C>T	c.(757-759)acC>acT	p.T253T	SETD8_ENST00000330479.4_Silent_p.T253T			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	294					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.T253T(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)		TCGAGATCACCGACGCCAAGA	0.542													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18508	0.0		0.0	False		,,,				2504	0.0				p.T253T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C759T	12						.						70.0	63.0	65.0					12																	123889532		2203	4300	6503	122455485	SO:0001819	synonymous_variant	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.759C>T	12.37:g.123889532C>T		Somatic		Capture	Illumina HiSeq	Phase_I	122455485	NM_020382	A8K9D0|Q86W83|Q8TD09	Silent	SNP	ENST00000402868.3	37	CCDS9247.1																																																																																				0.542	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382	
DDX55	57696	broad.mit.edu	37	12	124099749	124099749	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:124099749A>T	ENST00000238146.4	+	9	892	c.842A>T	c.(841-843)gAa>gTa	p.E281V	DDX55_ENST00000421670.3_5'Flank|DDX55_ENST00000541259.1_3'UTR|SNORA9_ENST00000384170.1_RNA|DDX55_ENST00000538744.1_Missense_Mutation_p.E281V	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	281	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.E281V(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		GCCTGTGTGGAATACTATGGG	0.488																																					p.E281V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A842T	12						.						131.0	121.0	124.0					12																	124099749		2203	4300	6503	122665702	SO:0001583	missense	57696	exon9			AB046815	CCDS9251.1	12q24.31	2003-06-13			ENSG00000111364	ENSG00000111364		"""DEAD-boxes"""	20085	protein-coding gene	gene with protein product						10997877	Standard	NM_020936		Approved	KIAA1595	uc001ufi.3	Q8NHQ9	OTTHUMG00000168695	ENST00000238146.4:c.842A>T	12.37:g.124099749A>T	ENSP00000238146:p.Glu281Val	Somatic		Capture	Illumina HiSeq	Phase_I	122665702	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Missense_Mutation	SNP	ENST00000238146.4	37	CCDS9251.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.773682	0.90108	.	.	ENSG00000111364	ENST00000238146;ENST00000538449;ENST00000538744	T;D	0.93189	3.29;-3.18	5.75	5.75	0.90469	Helicase, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.96661	0.8910	M	0.81179	2.53	0.80722	D	1	B;P;D	0.89917	0.273;0.805;1.0	B;B;D	0.76575	0.15;0.358;0.988	D	0.97216	0.9874	10	0.87932	D	0	-21.7035	16.0591	0.80826	1.0:0.0:0.0:0.0	.	281;281;281	B4DVE4;Q8NHQ9;F5H5U2	.;DDX55_HUMAN;.	V	281	ENSP00000238146:E281V;ENSP00000443114:E281V	ENSP00000238146:E281V	E	+	2	0	DDX55	122665702	1.000000	0.71417	0.992000	0.48379	0.921000	0.55340	9.109000	0.94291	2.185000	0.69588	0.533000	0.62120	GAA		0.488	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		
DNAH10	196385	broad.mit.edu	37	12	124265683	124265683	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:124265683C>T	ENST00000409039.3	+	6	520	c.495C>T	c.(493-495)gtC>gtT	p.V165V		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	165	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.V165V(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CCGTGGGAGTCACATCTGGAG	0.433																																					p.V165V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C495T	12						.						107.0	117.0	114.0					12																	124265683		2203	4300	6503	122831636	SO:0001819	synonymous_variant	196385	exon6			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.495C>T	12.37:g.124265683C>T		Somatic		Capture	Illumina HiSeq	Phase_I	122831636	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																				0.433	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
DNAH10	196385	broad.mit.edu	37	12	124413887	124413887	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:124413887C>T	ENST00000409039.3	+	70	12043	c.12018C>T	c.(12016-12018)caC>caT	p.H4006H	DNAH10OS_ENST00000514254.2_3'UTR|CCDC92_ENST00000544798.1_Intron	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	4006	AAA 6. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.H4006H(1)|p.H2598H(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AGATCTCTCACGAAATGCTGG	0.522																																					p.H4006H												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C12018T	12						.						44.0	44.0	44.0					12																	124413887		2037	4201	6238	122979840	SO:0001819	synonymous_variant	196385	exon70			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.12018C>T	12.37:g.124413887C>T		Somatic		Capture	Illumina HiSeq	Phase_I	122979840	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	De_novo_Start_OutOfFrame	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																				0.522	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
NCOR2	9612	broad.mit.edu	37	12	124835175	124835175	+	Missense_Mutation	SNP	C	C	T	rs575622579		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:124835175C>T	ENST00000405201.1	-	28	3802	c.3802G>A	c.(3802-3804)Gtc>Atc	p.V1268I	NCOR2_ENST00000356219.3_Missense_Mutation_p.V1275I|NCOR2_ENST00000404121.2_Missense_Mutation_p.V829I|NCOR2_ENST00000397355.1_Missense_Mutation_p.V1259I|NCOR2_ENST00000404621.1_Missense_Mutation_p.V1258I|NCOR2_ENST00000429285.2_Missense_Mutation_p.V1258I			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1276					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|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 body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)	p.V1275I(1)		breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		TCGTAGATGACGTGGCCCTTG	0.642													C|||	1	0.000199681	0.0	0.0	5008	,	,		18803	0.001		0.0	False		,,,				2504	0.0				p.V1275I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3823A	12						.						101.0	108.0	105.0					12																	124835175		2177	4261	6438	123401128	SO:0001583	missense	9612	exon30			U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.3802G>A	12.37:g.124835175C>T	ENSP00000384018:p.Val1268Ile	Somatic		Capture	Illumina HiSeq	Phase_I	123401128	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	C	21.6	4.174600	0.78452	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.62364	1.06;1.32;1.05;1.32;1.11;1.33;0.03	4.84	4.84	0.62591	.	0.000000	0.64402	D	0.000001	T	0.78805	0.4341	M	0.69823	2.125	0.58432	D	0.999995	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.76071	0.985;0.972;0.987	T	0.81967	-0.0690	10	0.87932	D	0	-48.0659	17.9445	0.89035	0.0:1.0:0.0:0.0	.	1258;1259;1268	C9J0Q5;C9J239;C9JFD3	.;.;.	I	1268;1258;1275;1259;1267;829;1258;1276	ENSP00000384018:V1268I;ENSP00000384202:V1258I;ENSP00000348551:V1275I;ENSP00000380513:V1259I;ENSP00000385618:V829I;ENSP00000400281:V1258I;ENSP00000402808:V1276I	ENSP00000348551:V1275I	V	-	1	0	NCOR2	123401128	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	5.727000	0.68523	2.226000	0.72624	0.478000	0.44815	GTC		0.642	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
DDX47	51202	broad.mit.edu	37	12	12974224	12974224	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:12974224G>T	ENST00000358007.3	+	3	286	c.264G>T	c.(262-264)gaG>gaT	p.E88D	DDX47_ENST00000352940.4_Missense_Mutation_p.E88D|DDX47_ENST00000392155.2_3'UTR	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	88	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.E88D(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		CACTGCTGGAGACCCCGCAGC	0.512																																					p.E88D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G264T	12						.						137.0	135.0	136.0					12																	12974224		2203	4300	6503	12865491	SO:0001583	missense	51202	exon3			AK127712	CCDS8655.1, CCDS8656.1	12p13.2	2010-07-06			ENSG00000213782	ENSG00000213782		"""DEAD-boxes"""	18682	protein-coding gene	gene with protein product		615428					Standard	NM_016355		Approved	DKFZp564O176, FLJ30012, HQ0256, RRP3	uc001rax.3	Q9H0S4	OTTHUMG00000168709	ENST00000358007.3:c.264G>T	12.37:g.12974224G>T	ENSP00000350698:p.Glu88Asp	Somatic		Capture	Illumina HiSeq	Phase_I	12865491	NM_201224	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Missense_Mutation	SNP	ENST00000358007.3	37	CCDS8655.1	.	.	.	.	.	.	.	.	.	.	G	9.290	1.050332	0.19827	.	.	ENSG00000213782	ENST00000352940;ENST00000358007	T;T	0.17370	2.28;2.28	5.6	4.67	0.58626	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.178476	0.48767	D	0.000170	T	0.10680	0.0261	L	0.35542	1.07	0.46028	D	0.99882	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	0.18524	-1.0334	10	0.15499	T	0.54	-26.5803	6.1436	0.20273	0.1347:0.0:0.5916:0.2737	.	88;88;88;88	B4DYP6;Q9H4E3;G5E955;Q9H0S4	.;.;.;DDX47_HUMAN	D	88	ENSP00000319578:E88D;ENSP00000350698:E88D	ENSP00000319578:E88D	E	+	3	2	DDX47	12865491	0.997000	0.39634	1.000000	0.80357	0.906000	0.53458	0.406000	0.21032	2.642000	0.89623	0.555000	0.69702	GAG		0.512	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355	
NCOR2	9612	broad.mit.edu	37	12	124835269	124835269	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:124835269G>A	ENST00000405201.1	-	28	3708	c.3708C>T	c.(3706-3708)gaC>gaT	p.D1236D	NCOR2_ENST00000356219.3_Silent_p.D1243D|NCOR2_ENST00000404121.2_Silent_p.D797D|NCOR2_ENST00000397355.1_Silent_p.D1227D|NCOR2_ENST00000404621.1_Silent_p.D1226D|NCOR2_ENST00000429285.2_Silent_p.D1226D			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1244					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|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 body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)	p.D1243D(1)		breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		TGTACAGGACGTCAGCTGGCG	0.642																																					p.D1243D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3729T	12						.						53.0	58.0	56.0					12																	124835269		2193	4279	6472	123401222	SO:0001819	synonymous_variant	9612	exon30			U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.3708C>T	12.37:g.124835269G>A		Somatic		Capture	Illumina HiSeq	Phase_I	123401222	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																				0.642	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
TMEM132D	121256	broad.mit.edu	37	12	130184552	130184552	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:130184552G>A	ENST00000422113.2	-	2	1097	c.771C>T	c.(769-771)atC>atT	p.I257I	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	257					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.I257I(2)		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)		CGGACTCATCGATGTCACTGT	0.597																																					p.I257I												.	.	2	Substitution - coding silent(2)	large_intestine(1)|NS(1)	c.C771T	12						.						98.0	85.0	90.0					12																	130184552		2203	4300	6503	128750505	SO:0001819	synonymous_variant	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.771C>T	12.37:g.130184552G>A		Somatic		Capture	Illumina HiSeq	Phase_I	128750505	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																				0.597	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
STX2	2054	broad.mit.edu	37	12	131293187	131293187	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:131293187G>A	ENST00000392373.2	-	5	437	c.343C>T	c.(343-345)Cga>Tga	p.R115*	STX2_ENST00000261653.6_Nonsense_Mutation_p.R115*|RP11-989F5.3_ENST00000542821.1_lincRNA|RP11-989F5.1_ENST00000546264.1_lincRNA	NM_194356.2	NP_919337.1	P32856	STX2_HUMAN	syntaxin 2	115					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.R115*(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)		TGGGTTCTTCGTATCCGAAGA	0.363																																					p.R115X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C343T	12						.						217.0	228.0	224.0					12																	131293187		2203	4300	6503	129859140	SO:0001587	stop_gained	2054	exon5			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.343C>T	12.37:g.131293187G>A	ENSP00000376178:p.Arg115*	Somatic		Capture	Illumina HiSeq	Phase_I	129859140	NM_194356	Q86VW8	Nonsense_Mutation	SNP	ENST00000392373.2	37	CCDS9270.1	.	.	.	.	.	.	.	.	.	.	G	31	5.058930	0.93846	.	.	ENSG00000111450	ENST00000261653;ENST00000392373	.	.	.	4.37	4.37	0.52481	.	0.202003	0.44097	D	0.000499	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-36.1314	11.8642	0.52484	0.0:0.0:0.8129:0.1871	.	.	.	.	X	115	.	ENSP00000261653:R115X	R	-	1	2	STX2	129859140	1.000000	0.71417	0.719000	0.30619	0.612000	0.37316	6.515000	0.73751	2.262000	0.75019	0.561000	0.74099	CGA		0.363	STX2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399455.2	NM_194356	
EP400	57634	broad.mit.edu	37	12	132446241	132446241	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:132446241G>A	ENST00000333577.4	+	2	1186	c.1077G>A	c.(1075-1077)ccG>ccA	p.P359P	EP400_ENST00000330386.6_Silent_p.P359P|EP400_ENST00000389561.2_Silent_p.P359P|EP400_ENST00000389562.2_Silent_p.P359P|EP400_ENST00000332482.4_Silent_p.P359P			Q96L91	EP400_HUMAN	E1A binding protein p400	359					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.P359P(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)		CAGCCTCTCCGGAGATGGCAC	0.532																																					p.P359P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1077A	12						.						62.0	53.0	56.0					12																	132446241		2203	4300	6503	131012194	SO:0001819	synonymous_variant	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.1077G>A	12.37:g.132446241G>A		Somatic		Capture	Illumina HiSeq	Phase_I	131012194	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																					0.532	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
EP400	57634	broad.mit.edu	37	12	132464251	132464251	+	Missense_Mutation	SNP	G	G	A	rs147304028	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:132464251G>A	ENST00000333577.4	+	4	1565	c.1456G>A	c.(1456-1458)Gca>Aca	p.A486T	EP400_ENST00000330386.6_Missense_Mutation_p.A450T|EP400_ENST00000389561.2_Missense_Mutation_p.A450T|EP400_ENST00000389562.2_Missense_Mutation_p.A449T|EP400_ENST00000332482.4_Missense_Mutation_p.A449T			Q96L91	EP400_HUMAN	E1A binding protein p400	486					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.A449T(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)		GCAAGCCCTCGCAGGGAGCCT	0.493																																					p.A449T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1345A	12						.						47.0	48.0	48.0					12																	132464251		2203	4300	6503	131030204	SO:0001583	missense	57634	exon3			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.1456G>A	12.37:g.132464251G>A	ENSP00000333602:p.Ala486Thr	Somatic		Capture	Illumina HiSeq	Phase_I	131030204	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		.	.	.	.	.	.	.	.	.	.	G	12.14	1.849165	0.32699	.	.	ENSG00000183495	ENST00000537902;ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000423130;ENST00000541296;ENST00000542457	D;D;D;D;D	0.89810	-2.56;-2.31;-2.57;-2.57;-2.27	5.74	-4.11	0.03928	.	1.030140	0.07625	N	0.927659	T	0.61677	0.2366	N	0.01352	-0.895	0.09310	N	0.999999	B;B;B;B;B	0.13145	0.007;0.007;0.007;0.003;0.007	B;B;B;B;B	0.11329	0.001;0.001;0.001;0.006;0.001	T	0.61589	-0.7032	10	0.02654	T	1	.	4.2564	0.10719	0.5678:0.1047:0.2223:0.1052	.	450;450;449;486;449	Q96L91-2;Q96L91-4;Q96L91-5;F8WCN8;Q96L91-3	.;.;.;.;.	T	449;486;450;449;449;450;486;450;450	ENSP00000333602:A486T;ENSP00000374212:A450T;ENSP00000374213:A449T;ENSP00000331737:A449T;ENSP00000330620:A450T	ENSP00000330620:A450T	A	+	1	0	EP400	131030204	0.000000	0.05858	0.004000	0.12327	0.866000	0.49608	-0.274000	0.08537	-0.373000	0.07979	0.650000	0.86243	GCA		0.493	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
EP400	57634	broad.mit.edu	37	12	132551418	132551418	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:132551418G>A	ENST00000333577.4	+	50	8870	c.8761G>A	c.(8761-8763)Gtc>Atc	p.V2921I	EP400_ENST00000330386.6_Missense_Mutation_p.V2804I|EP400_ENST00000389561.2_Missense_Mutation_p.V2885I|EP400_ENST00000389562.2_Missense_Mutation_p.V2884I|EP400_ENST00000332482.4_Missense_Mutation_p.V2848I			Q96L91	EP400_HUMAN	E1A binding protein p400	2921					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.V2884I(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)		GGTGGTGTCCGTCCCGGCAGC	0.682																																					p.V2884I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8650A	12						.						36.0	38.0	37.0					12																	132551418		2203	4299	6502	131117371	SO:0001583	missense	57634	exon49			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.8761G>A	12.37:g.132551418G>A	ENSP00000333602:p.Val2921Ile	Somatic		Capture	Illumina HiSeq	Phase_I	131117371	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		.	.	.	.	.	.	.	.	.	.	G	14.77	2.633162	0.47049	.	.	ENSG00000183495	ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000541296	D;D;D;D;D	0.92199	-2.99;-2.99;-2.92;-2.97;-2.96	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	D	0.93145	0.7817	L	0.32530	0.975	0.39049	D	0.960288	D;D;D;D	0.76494	0.987;0.999;0.999;0.999	P;D;D;D	0.78314	0.897;0.991;0.991;0.991	D	0.92891	0.6331	10	0.33141	T	0.24	.	16.1317	0.81445	0.0:0.0:1.0:0.0	.	2921;2885;2804;2884	Q96L91;Q96L91-2;Q96L91-4;Q96L91-5	EP400_HUMAN;.;.;.	I	2921;2885;2884;2848;2804;2885	ENSP00000333602:V2921I;ENSP00000374212:V2885I;ENSP00000374213:V2884I;ENSP00000331737:V2848I;ENSP00000330620:V2804I	ENSP00000330620:V2804I	V	+	1	0	EP400	131117371	1.000000	0.71417	0.656000	0.29637	0.119000	0.20118	6.023000	0.70848	2.244000	0.73946	0.561000	0.74099	GTC		0.682	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
POLE	5426	broad.mit.edu	37	12	133254192	133254192	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:133254192C>T	ENST00000320574.5	-	7	735	c.692G>A	c.(691-693)cGc>cAc	p.R231H	POLE_ENST00000535270.1_Missense_Mutation_p.R204H	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	231			R -> H (found in a colorectal sample; somatic mutation). {ECO:0000269|PubMed:23263490}.		base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)	p.R231H(1)		NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	AATGGAGAGGCGGATGTGGTA	0.507								DNA polymerases (catalytic subunits)																													p.R231H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G692A	12						.						128.0	103.0	112.0					12																	133254192		2203	4300	6503	131764265	SO:0001583	missense	5426	exon7				CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.692G>A	12.37:g.133254192C>T	ENSP00000322570:p.Arg231His	Somatic		Capture	Illumina HiSeq	Phase_I	131764265	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	C	36	5.710510	0.96821	.	.	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270;ENST00000539006;ENST00000376577	T;T;T;T	0.18338	2.22;2.22;2.22;2.22	5.75	5.75	0.90469	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.55114	0.1900	M	0.92412	3.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.65274	-0.6208	10	0.87932	D	0	.	19.9577	0.97228	0.0:1.0:0.0:0.0	.	204;231	F5H1D6;Q07864	.;DPOE1_HUMAN	H	231;242;204;11;166	ENSP00000322570:R231H;ENSP00000406383:R242H;ENSP00000445753:R204H;ENSP00000442519:R11H	ENSP00000322570:R231H	R	-	2	0	POLE	131764265	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.770000	0.85390	2.714000	0.92807	0.563000	0.77884	CGC		0.507	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
CACNA2D4	93589	broad.mit.edu	37	12	1965240	1965240	+	Missense_Mutation	SNP	C	C	T	rs577055633		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:1965240C>T	ENST00000382722.5	-	22	2452	c.2090G>A	c.(2089-2091)cGg>cAg	p.R697Q	CACNA2D4_ENST00000585708.1_Missense_Mutation_p.R633Q|CACNA2D4_ENST00000587995.1_Missense_Mutation_p.R672Q|CACNA2D4_ENST00000539048.2_5'UTR|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.R697Q|CACNA2D4_ENST00000585732.1_Missense_Mutation_p.R558Q|CACNA2D4_ENST00000588077.1_Missense_Mutation_p.R633Q	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	697					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.R697Q(1)		endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		GCTGAGCTTCCGGTGGTCTGG	0.527													C|||	1	0.000199681	0.0008	0.0	5008	,	,		21198	0.0		0.0	False		,,,				2504	0.0				p.R697Q	Colon(2;101 179 21030 23310 28141)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2090A	12						.						73.0	81.0	79.0					12																	1965240		2021	4178	6199	1835501	SO:0001583	missense	93589	exon22			AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"""Calcium channel subunits"""	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.2090G>A	12.37:g.1965240C>T	ENSP00000372169:p.Arg697Gln	Somatic		Capture	Illumina HiSeq	Phase_I	1835501	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	37	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.262628	0.80358	.	.	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722	T	0.35421	1.31	4.2	3.31	0.37934	.	0.062781	0.64402	N	0.000003	T	0.56455	0.1986	M	0.76002	2.32	0.47778	D	0.999517	D;D	0.89917	1.0;1.0	D;D	0.85130	0.987;0.997	T	0.55854	-0.8075	10	0.42905	T	0.14	.	11.0744	0.48023	0.0:0.9051:0.0:0.0949	.	697;697	Q7Z3S7-2;Q7Z3S7	.;CA2D4_HUMAN	Q	633;697;697	ENSP00000372169:R697Q	ENSP00000280663:R697Q	R	-	2	0	CACNA2D4	1835501	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	4.628000	0.61282	0.896000	0.36366	0.462000	0.41574	CGG		0.527	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
TULP3	7289	broad.mit.edu	37	12	3047355	3047355	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:3047355G>A	ENST00000448120.2	+	10	1150	c.1099G>A	c.(1099-1101)Gtc>Atc	p.V367I	TULP3_ENST00000397132.2_Missense_Mutation_p.V367I	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	367					anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)	p.V367I(2)		endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			CAAGGCCCCCGTCTGGAACAG	0.483																																					p.V367I												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G1099A	12						.						122.0	113.0	116.0					12																	3047355		2203	4300	6503	2917616	SO:0001583	missense	7289	exon10			AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"""Intraflagellar transport homologs"""	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.1099G>A	12.37:g.3047355G>A	ENSP00000410051:p.Val367Ile	Somatic		Capture	Illumina HiSeq	Phase_I	2917616	NM_001160408	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	ENST00000448120.2	37	CCDS8519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	15.25|15.25	2.778744|2.778744	0.49891|0.49891	.|.	.|.	ENSG00000078246|ENSG00000078246	ENST00000541678;ENST00000538704|ENST00000228245;ENST00000544943;ENST00000542730;ENST00000448120;ENST00000397132	.|D;D;D	.|0.96365	.|-3.99;-3.99;-3.99	5.2|5.2	4.31|4.31	0.51392|0.51392	.|Tubby, C-terminal (4);	.|0.058039	.|0.64402	.|D	.|0.000002	D|D	0.93559|0.93559	0.7944|0.7944	L|L	0.58583|0.58583	1.82|1.82	0.58432|0.58432	D|D	0.999996|0.999996	.|B;B;P	.|0.40909	.|0.332;0.404;0.732	.|B;B;B	.|0.34418	.|0.106;0.104;0.182	D|D	0.91975|0.91975	0.5590|0.5590	5|10	.|0.40728	.|T	.|0.16	0.0435|0.0435	12.8065|12.8065	0.57616|0.57616	0.0788:0.0:0.9212:0.0|0.0788:0.0:0.9212:0.0	.|.	.|191;367;367	.|B7Z1E7;O75386;F8WBZ9	.|.;TULP3_HUMAN;.	H|I	43;32|367;94;191;367;367	.|ENSP00000442631:V94I;ENSP00000410051:V367I;ENSP00000380321:V367I	.|ENSP00000228245:V367I	R|V	+|+	2|1	0|0	TULP3|TULP3	2917616|2917616	1.000000|1.000000	0.71417|0.71417	0.213000|0.213000	0.23690|0.23690	0.687000|0.687000	0.40016|0.40016	8.026000|8.026000	0.88783|0.88783	1.184000|1.184000	0.42957|0.42957	0.651000|0.651000	0.88453|0.88453	CGT|GTC		0.483	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324	
C12orf4	57102	broad.mit.edu	37	12	4627386	4627386	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:4627386G>T	ENST00000261250.3	-	8	958	c.871C>A	c.(871-873)Ctg>Atg	p.L291M	C12orf4_ENST00000545746.1_Missense_Mutation_p.L291M	NM_020374.2	NP_065107.1	Q9NQ89	CL004_HUMAN	chromosome 12 open reading frame 4	291								p.L291M(1)		NS(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)	BRCA - Breast invasive adenocarcinoma(232;0.0281)		TCTGCTCTCAGCAATCTCAAA	0.423																																					p.L291M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C871A	12						.						132.0	135.0	134.0					12																	4627386		2203	4300	6503	4497647	SO:0001583	missense	57102	exon8			AJ272205	CCDS8528.1	12p13.3	2012-08-10			ENSG00000047621	ENSG00000047621			1184	protein-coding gene	gene with protein product							Standard	NM_020374		Approved		uc001qms.3	Q9NQ89	OTTHUMG00000168258	ENST00000261250.3:c.871C>A	12.37:g.4627386G>T	ENSP00000261250:p.Leu291Met	Somatic		Capture	Illumina HiSeq	Phase_I	4497647	NM_020374	D3DUQ8|Q6MZH5	Missense_Mutation	SNP	ENST00000261250.3	37	CCDS8528.1	.	.	.	.	.	.	.	.	.	.	G	11.10	1.538107	0.27475	.	.	ENSG00000047621	ENST00000261250;ENST00000545746;ENST00000541014	.	.	.	5.31	5.31	0.75309	.	0.126087	0.53938	D	0.000048	T	0.38665	0.1049	N	0.11756	0.17	0.52501	D	0.999956	B	0.18013	0.025	B	0.16289	0.015	T	0.20438	-1.0275	9	0.21540	T	0.41	.	14.2241	0.65848	0.0:0.0:0.8507:0.1493	.	291	Q9NQ89	CL004_HUMAN	M	291;291;118	.	ENSP00000261250:L291M	L	-	1	2	C12orf4	4497647	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.013000	0.40942	2.635000	0.89317	0.650000	0.86243	CTG		0.423	C12orf4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398992.1	NM_020374	
KCNA5	3741	broad.mit.edu	37	12	5154303	5154303	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:5154303G>A	ENST00000252321.3	+	1	1219	c.990G>A	c.(988-990)acG>acA	p.T330T		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	330					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|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 membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)	p.T330T(1)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	TGGAGACCACGTGCGTCATCT	0.652																																					p.T330T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G990A	12						.						86.0	78.0	81.0					12																	5154303		2203	4300	6503	5024564	SO:0001819	synonymous_variant	3741	exon1			M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.990G>A	12.37:g.5154303G>A		Somatic		Capture	Illumina HiSeq	Phase_I	5024564	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Silent	SNP	ENST00000252321.3	37	CCDS8536.1																																																																																				0.652	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234	
VWF	7450	broad.mit.edu	37	12	6103594	6103594	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:6103594C>T	ENST00000261405.5	-	36	6497	c.6243G>A	c.(6241-6243)acG>acA	p.T2081T		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2081	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)	p.T2081T(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	ACAGACCATACGTCTTTGAAG	0.428																																					p.T2081T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G6243A	12						.						299.0	254.0	269.0					12																	6103594		2203	4300	6503	5973855	SO:0001819	synonymous_variant	7450	exon36				CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.6243G>A	12.37:g.6103594C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5973855	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																				0.428	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
CHD4	1108	broad.mit.edu	37	12	6701669	6701669	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:6701669C>T	ENST00000357008.2	-	19	3001	c.2838G>A	c.(2836-2838)ctG>ctA	p.L946L	CHD4_ENST00000544484.1_Silent_p.L943L|CHD4_ENST00000544040.1_Silent_p.L939L|CHD4_ENST00000309577.6_Silent_p.L946L	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	946					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)	p.L946L(1)		central_nervous_system(2)	2						GCATGTCATGCAGTTTTTTTA	0.468																																					p.L946L	Colon(32;586 792 4568 16848 45314)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2838A	12						.						94.0	96.0	95.0					12																	6701669		2203	4300	6503	6571930	SO:0001819	synonymous_variant	1108	exon19			X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.2838G>A	12.37:g.6701669C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6571930	NM_001273	Q8IXZ5	Silent	SNP	ENST00000357008.2	37	CCDS8552.1																																																																																				0.468	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273	
LPAR5	57121	broad.mit.edu	37	12	6747504	6747504	+	5'Flank	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:6747504C>T	ENST00000329858.4	-	0	0				ACRBP_ENST00000414226.2_Missense_Mutation_p.V493I|ACRBP_ENST00000229243.2_Missense_Mutation_p.V526I|ACRBP_ENST00000542357.1_5'Flank|LPAR5_ENST00000540335.1_5'Flank	NM_020400.5	NP_065133.1	Q9H1C0	LPAR5_HUMAN	lysophosphatidic acid receptor 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V526I(1)		endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|skin(2)	7						CGAAGCACAACGTCCTCACTT	0.557																																					p.V526I	NSCLC(74;891 2312 37538)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1576A	12						.						135.0	109.0	118.0					12																	6747504		2203	4300	6503	6617765	SO:0001631	upstream_gene_variant	84519	exon10			AJ272207	CCDS8553.1	12p13.31	2012-08-08	2008-04-11	2008-04-11		ENSG00000184574		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	13307	protein-coding gene	gene with protein product		606926	"""G protein-coupled receptor 92"""	GPR93, GPR92		11062477, 11574155, 16774927, 16651401	Standard	NM_020400		Approved	KPG_010, LPA5	uc009zer.2	Q9H1C0			12.37:g.6747504C>T	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	6617765	NM_032489		Missense_Mutation	SNP	ENST00000329858.4	37	CCDS8553.1	.	.	.	.	.	.	.	.	.	.	C	0.686	-0.796423	0.02862	.	.	ENSG00000111644	ENST00000229243;ENST00000414226	T;T	0.44083	0.93;0.93	4.7	-9.4	0.00616	.	2.277090	0.01801	N	0.032918	T	0.19005	0.0456	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09707	-1.0662	10	0.18710	T	0.47	-10.7213	3.7466	0.08551	0.0807:0.1952:0.3506:0.3736	.	493;526	E7EP66;Q8NEB7	.;ACRBP_HUMAN	I	526;493	ENSP00000229243:V526I;ENSP00000402725:V493I	ENSP00000229243:V526I	V	-	1	0	ACRBP	6617765	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-1.600000	0.02083	-2.147000	0.00799	-2.075000	0.00382	GTT		0.557	LPAR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400699.1	NM_020400	
ING4	51147	broad.mit.edu	37	12	6761865	6761865	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:6761865G>T	ENST00000396807.4	-	5	501	c.463C>A	c.(463-465)Ccc>Acc	p.P155T	ING4_ENST00000341550.4_Missense_Mutation_p.P154T|ING4_ENST00000446105.2_Missense_Mutation_p.P151T|ING4_ENST00000486287.1_5'UTR|ING4_ENST00000423703.2_Missense_Mutation_p.P155T|ING4_ENST00000444704.2_Missense_Mutation_p.P131T|ING4_ENST00000412586.2_Missense_Mutation_p.P152T	NM_001127582.1|NM_001127585.1|NM_001127586.1|NM_016162.3	NP_001121054.1|NP_001121057.1|NP_001121058.1|NP_057246.2	Q9UNL4	ING4_HUMAN	inhibitor of growth family, member 4	155					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|protein acetylation (GO:0006473)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.P154T(1)		central_nervous_system(3)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	10						GCAGTCTTGGGGGCTTCTTCA	0.552																																					p.P155T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C463A	12						.						106.0	110.0	108.0					12																	6761865		2203	4300	6503	6632126	SO:0001583	missense	51147	exon5			AF063594	CCDS8555.1, CCDS44812.1, CCDS44813.1, CCDS44814.1, CCDS44815.1, CCDS44816.1	12p13.32	2013-01-28			ENSG00000111653	ENSG00000111653		"""Zinc fingers, PHD-type"""	19423	protein-coding gene	gene with protein product		608524				12750254	Standard	NM_001127582		Approved	p29ING4, my036	uc001qpw.4	Q9UNL4	OTTHUMG00000141274	ENST00000396807.4:c.463C>A	12.37:g.6761865G>T	ENSP00000380024:p.Pro155Thr	Somatic		Capture	Illumina HiSeq	Phase_I	6632126	NM_001127586	A4KYM4|A4KYM6|D3DUR8|Q0EF62|Q0EF63|Q4VBQ6|Q96E15|Q9H3J0	Missense_Mutation	SNP	ENST00000396807.4	37	CCDS44813.1	.	.	.	.	.	.	.	.	.	.	G	12.81	2.048476	0.36181	.	.	ENSG00000111653	ENST00000341550;ENST00000396807;ENST00000446105;ENST00000444704;ENST00000423703;ENST00000412586	T;T;T;T;T	0.43688	1.09;0.94;1.09;1.09;1.07	4.6	4.6	0.57074	.	0.131525	0.52532	D	0.000077	T	0.53610	0.1807	M	0.75615	2.305	0.47659	D	0.999487	P;P;B;B;P;B	0.52170	0.613;0.951;0.419;0.016;0.915;0.295	P;P;B;B;P;B	0.49597	0.543;0.548;0.168;0.06;0.616;0.081	T	0.59685	-0.7408	10	0.51188	T	0.08	-5.5517	15.7805	0.78257	0.0:0.0:1.0:0.0	.	131;155;151;152;155;154	Q9UNL4-3;A4KYM6;Q9UNL4-4;Q9UNL4-5;Q9UNL4;Q4VBQ6	.;.;.;.;ING4_HUMAN;.	T	154;155;151;131;155;152	ENSP00000343396:P154T;ENSP00000380024:P155T;ENSP00000415903:P151T;ENSP00000397343:P131T;ENSP00000412705:P152T	ENSP00000343396:P154T	P	-	1	0	ING4	6632126	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.828000	0.75308	2.390000	0.81377	0.561000	0.74099	CCC		0.552	ING4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280467.2	NM_198287	
ZNF384	171017	broad.mit.edu	37	12	6778353	6778353	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:6778353G>T	ENST00000396801.3	-	10	1383	c.1176C>A	c.(1174-1176)tcC>tcA	p.S392S	ZNF384_ENST00000319770.3_Silent_p.S315S|ZNF384_ENST00000396799.2_Silent_p.S331S|RP4-761J14.8_ENST00000589924.1_RNA|ZNF384_ENST00000355772.4_Silent_p.S276S|RP4-761J14.8_ENST00000586338.1_RNA|ZNF384_ENST00000361959.3_Silent_p.S392S|ZNF384_ENST00000396795.1_Silent_p.S331S	NM_001135734.2	NP_001129206.1	Q8TF68	ZN384_HUMAN	zinc finger protein 384	392					nucleocytoplasmic transport (GO:0006913)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)	p.S331S(1)|p.S392S(1)	EWSR1/ZNF384(4)	breast(3)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	18						GCCGTCTGTGGGACTGAGAAA	0.507			T	"""EWSR1, TAF15 """	ALL																																p.S392S			Dom	yes		12	12p13	171017	zinc finger protein 384 (CIZ/NMP4)		L	.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1176A	12						.						111.0	95.0	101.0					12																	6778353		2203	4300	6503	6648614	SO:0001819	synonymous_variant	171017	exon10			U80738	CCDS8557.1, CCDS31732.1, CCDS44817.1	12p12	2013-01-08	2002-05-23	2002-05-24		ENSG00000126746		"""Zinc fingers, C2H2-type"""	11955	protein-coding gene	gene with protein product		609951	"""trinucleotide repeat containing 1"""	TNRC1		9225980, 11149472	Standard	NM_001135734		Approved	CAGH1A, CIZ, NMP4, NP	uc010sfh.2	Q8TF68		ENST00000396801.3:c.1176C>A	12.37:g.6778353G>T		Somatic		Capture	Illumina HiSeq	Phase_I	6648614	NM_001135734	O15407|Q7Z722|Q8N938	Silent	SNP	ENST00000396801.3	37	CCDS44817.1																																																																																				0.507	ZNF384-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400712.1		
LAG3	3902	broad.mit.edu	37	12	6886507	6886507	+	Missense_Mutation	SNP	C	C	T	rs141308793		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:6886507C>T	ENST00000203629.2	+	6	1468	c.1135C>T	c.(1135-1137)Cgc>Tgc	p.R379C		NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	379	Ig-like C2-type 3.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell activation (GO:0050868)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|MHC class II protein binding (GO:0042289)|transmembrane signaling receptor activity (GO:0004888)	p.R379C(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						TGGACAAGAACGCTTTGTGTG	0.547																																					p.R379C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1135T	12						.	C	CYS/ARG	5,4401	9.9+/-24.2	0,5,2198	133.0	125.0	127.0		1135	1.4	0.0	12	dbSNP_134	127	0,8600		0,0,4300	yes	missense	LAG3	NM_002286.5	180	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	probably-damaging	379/526	6886507	5,13001	2203	4300	6503	6756768	SO:0001583	missense	3902	exon6				CCDS8561.1	12p13.3	2013-01-11			ENSG00000089692	ENSG00000089692		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6476	protein-coding gene	gene with protein product		153337					Standard	NM_002286		Approved	CD223	uc001qqt.4	P18627	OTTHUMG00000169197	ENST00000203629.2:c.1135C>T	12.37:g.6886507C>T	ENSP00000203629:p.Arg379Cys	Somatic		Capture	Illumina HiSeq	Phase_I	6756768	NM_002286	A8K7T9|Q7Z643	Missense_Mutation	SNP	ENST00000203629.2	37	CCDS8561.1	.	.	.	.	.	.	.	.	.	.	C	12.96	2.094084	0.36952	0.001135	0.0	ENSG00000089692	ENST00000203629	T	0.15603	2.41	4.76	1.44	0.22558	.	1.060030	0.07320	N	0.877481	T	0.11196	0.0273	L	0.32530	0.975	0.09310	N	1	P	0.44260	0.83	B	0.36666	0.23	T	0.25398	-1.0133	10	0.62326	D	0.03	-0.4596	2.9051	0.05718	0.2424:0.5072:0.152:0.0984	.	379	P18627	LAG3_HUMAN	C	379	ENSP00000203629:R379C	ENSP00000203629:R379C	R	+	1	0	LAG3	6756768	0.449000	0.25689	0.005000	0.12908	0.873000	0.50193	0.729000	0.26028	0.426000	0.26116	0.561000	0.74099	CGC		0.547	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1		
CDCA3	83461	broad.mit.edu	37	12	6958356	6958356	+	Missense_Mutation	SNP	G	G	A	rs148172476	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:6958356G>A	ENST00000538862.2	-	6	1559	c.658C>T	c.(658-660)Cgg>Tgg	p.R220W	USP5_ENST00000229268.8_5'Flank|CDCA3_ENST00000229265.6_Missense_Mutation_p.R195W|CDCA3_ENST00000540683.1_3'UTR|CDCA3_ENST00000422785.3_Intron|CDCA3_ENST00000535406.1_Missense_Mutation_p.R220W|USP5_ENST00000389231.5_5'Flank|CDCA3_ENST00000604599.1_5'Flank			Q99618	CDCA3_HUMAN	cell division cycle associated 3	220					mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)		p.R220W(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(1)|stomach(1)	8						GGTGAAGGCCGCTTACCCTGA	0.502																																					p.R220W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C658T	12						.	G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	76.0	67.0	70.0		658	2.3	1.0	12	dbSNP_134	70	5,8595	4.3+/-15.6	0,5,4295	yes	missense	CDCA3	NM_031299.4	101	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	benign	220/269	6958356	6,13000	2203	4300	6503	6828617	SO:0001583	missense	83461	exon6			BG354576	CCDS8565.1, CCDS73428.1	12p13.31	2010-07-20				ENSG00000111665			14624	protein-coding gene	gene with protein product	"""trigger of mitotic entry 1"""	607749				9074930, 12188893	Standard	XR_242988		Approved	TOME-1, GRCC8	uc001qrg.2	Q99618		ENST00000538862.2:c.658C>T	12.37:g.6958356G>A	ENSP00000442068:p.Arg220Trp	Somatic		Capture	Illumina HiSeq	Phase_I	6828617	NM_031299	A8K5V6|D3DUS6	Missense_Mutation	SNP	ENST00000538862.2	37	CCDS8565.1	.	.	.	.	.	.	.	.	.	.	G	8.434	0.849192	0.17034	2.27E-4	5.81E-4	ENSG00000111665	ENST00000229265;ENST00000538862;ENST00000535406	.	.	.	5.08	2.31	0.28768	.	0.632796	0.14913	N	0.291089	T	0.32010	0.0815	N	0.16307	0.4	0.80722	D	1	B	0.18968	0.032	B	0.17979	0.02	T	0.09729	-1.0661	9	0.52906	T	0.07	-32.2385	4.2926	0.10886	0.2468:0.0:0.5574:0.1958	.	220	Q99618	CDCA3_HUMAN	W	195;220;220	.	ENSP00000229265:R195W	R	-	1	2	CDCA3	6828617	1.000000	0.71417	1.000000	0.80357	0.111000	0.19643	1.015000	0.29963	0.342000	0.23796	-0.140000	0.14226	CGG		0.502	CDCA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401940.2	NM_031299	
PTPN6	5777	broad.mit.edu	37	12	7064426	7064426	+	Missense_Mutation	SNP	G	G	A	rs367551491		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:7064426G>A	ENST00000318974.9	+	5	873	c.629G>A	c.(628-630)cGg>cAg	p.R210Q	PTPN6_ENST00000447931.2_Missense_Mutation_p.R171Q|PTPN6_ENST00000456013.1_Missense_Mutation_p.R210Q|PTPN6_ENST00000399448.1_Missense_Mutation_p.R212Q	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	210	SH2 2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				abortive mitotic cell cycle (GO:0033277)|apoptotic process (GO:0006915)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|natural killer cell mediated cytotoxicity (GO:0042267)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of cell proliferation (GO:0008285)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein dephosphorylation (GO:0006470)|regulation of B cell differentiation (GO:0045577)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|type I interferon signaling pathway (GO:0060337)	alpha-beta T cell receptor complex (GO:0042105)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R210Q(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|prostate(3)	18						GTCTACCTGCGGCAGGTCAGG	0.607																																					p.R210Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G629A	12						.	G	GLN/ARG,GLN/ARG,GLN/ARG	1,3951		0,1,1975	88.0	95.0	93.0		629,635,629	4.3	1.0	12		93	1,8299		0,1,4149	no	missense,missense,missense	PTPN6	NM_002831.5,NM_080548.4,NM_080549.3	43,43,43	0,2,6124	AA,AG,GG		0.012,0.0253,0.0163	benign,benign,benign	210/596,212/598,210/625	7064426	2,12250	1976	4150	6126	6934687	SO:0001583	missense	5777	exon5				CCDS41744.1, CCDS44820.1, CCDS44821.1	12p13.31	2013-02-14			ENSG00000111679	ENSG00000111679		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9658	protein-coding gene	gene with protein product		176883				1639416	Standard	NM_080548		Approved	HCP, HCPH, PTP-1C, SHP-1, SHP1	uc001qsa.1	P29350	OTTHUMG00000168518	ENST00000318974.9:c.629G>A	12.37:g.7064426G>A	ENSP00000326010:p.Arg210Gln	Somatic		Capture	Illumina HiSeq	Phase_I	6934687	NM_002831	A8K306|G3V0F8|Q969V8|Q9UK67	Missense_Mutation	SNP	ENST00000318974.9	37	CCDS44820.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.125177	0.56721	2.53E-4	1.2E-4	ENSG00000111679	ENST00000399448;ENST00000447931;ENST00000318974;ENST00000456013	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	4.33	4.33	0.51752	SH2 motif (2);	0.161948	0.41001	D	0.000967	T	0.40815	0.1132	L	0.31578	0.945	0.37975	D	0.933424	P;P;P;B;P	0.44195	0.737;0.828;0.698;0.419;0.824	B;B;B;B;B	0.32583	0.047;0.046;0.138;0.045;0.148	T	0.44651	-0.9314	9	.	.	.	.	8.2207	0.31539	0.1923:0.0:0.8077:0.0	.	198;171;210;210;212	B4DPS0;P29350-2;G3V0F8;P29350;Q53XS4	.;.;.;PTN6_HUMAN;.	Q	212;171;210;210	ENSP00000382376:R212Q;ENSP00000415979:R171Q;ENSP00000326010:R210Q;ENSP00000391592:R210Q	.	R	+	2	0	PTPN6	6934687	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	2.718000	0.47236	2.115000	0.64714	0.491000	0.48974	CGG		0.607	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1	NM_002831	
CLSTN3	9746	broad.mit.edu	37	12	7310579	7310579	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:7310579G>A	ENST00000266546.6	+	18	3223	c.2773G>A	c.(2773-2775)Ggc>Agc	p.G925S	CLSTN3_ENST00000537408.1_Missense_Mutation_p.G937S|CLSTN3_ENST00000331148.5_3'UTR	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	925					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.G925S(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						GGCTGTTGGGGGCCAGCAGGA	0.622																																					p.G925S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2773A	12						.						58.0	50.0	53.0					12																	7310579		2130	4127	6257	7201846	SO:0001583	missense	9746	exon18			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.2773G>A	12.37:g.7310579G>A	ENSP00000266546:p.Gly925Ser	Somatic		Capture	Illumina HiSeq	Phase_I	7201846	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	37	CCDS8575.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.354313	0.61293	.	.	ENSG00000139182	ENST00000266546;ENST00000537408	T;T	0.33438	1.41;1.41	4.57	3.68	0.42216	.	0.465081	0.21426	N	0.074733	T	0.12646	0.0307	N	0.08118	0	0.28461	N	0.915859	B;B	0.12013	0.005;0.005	B;B	0.04013	0.001;0.001	T	0.26326	-1.0106	10	0.06757	T	0.87	-21.1413	8.7012	0.34327	0.1817:0.0:0.8183:0.0	.	937;925	Q5UE57;Q9BQT9	.;CSTN3_HUMAN	S	925;937	ENSP00000266546:G925S;ENSP00000440679:G937S	ENSP00000266546:G925S	G	+	1	0	CLSTN3	7201846	0.997000	0.39634	0.880000	0.34516	0.598000	0.36846	3.013000	0.49582	1.143000	0.42306	0.462000	0.41574	GGC		0.622	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718	
PHC1	1911	broad.mit.edu	37	12	9089804	9089804	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:9089804T>C	ENST00000543824.1	+	14	2842	c.2510T>C	c.(2509-2511)cTg>cCg	p.L837P	PHC1_ENST00000433083.2_Missense_Mutation_p.L792P|PHC1_ENST00000544916.1_Missense_Mutation_p.L837P|PHC1_ENST00000536844.1_Missense_Mutation_p.L443P			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	837					cellular response to retinoic acid (GO:0071300)|histone ubiquitination (GO:0016574)|multicellular organismal development (GO:0007275)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.L837P(1)		breast(2)|cervix(1)|endometrium(5)|large_intestine(8)|liver(2)|lung(3)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	27						CAGTTCCGGCTGAAGAGGAAA	0.498																																					p.L837P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2510C	12						.						46.0	44.0	45.0					12																	9089804		2203	4300	6503	8981071	SO:0001583	missense	1911	exon13			U89277	CCDS8597.1	12p13	2013-01-10	2006-09-12	2002-11-15	ENSG00000111752	ENSG00000111752		"""Sterile alpha motif (SAM) domain containing"""	3182	protein-coding gene	gene with protein product		602978	"""early development regulator 1 (homolog of polyhomeotic 1)"", ""polyhomeotic-like 1 (Drosophila)"""	EDR1		9121482	Standard	XM_005253334		Approved	HPH1, RAE28	uc001qvd.3	P78364	OTTHUMG00000168275	ENST00000543824.1:c.2510T>C	12.37:g.9089804T>C	ENSP00000440674:p.Leu837Pro	Somatic		Capture	Illumina HiSeq	Phase_I	8981071	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Missense_Mutation	SNP	ENST00000543824.1	37	CCDS8597.1	.	.	.	.	.	.	.	.	.	.	T	16.17	3.047796	0.55110	.	.	ENSG00000111752	ENST00000543824;ENST00000251757;ENST00000433083;ENST00000544916;ENST00000536844	T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75	5.58	5.58	0.84498	.	0.109569	0.39759	N	0.001280	T	0.60741	0.2292	L	0.55990	1.75	0.80722	D	1	D	0.61080	0.989	P	0.59115	0.852	T	0.64351	-0.6428	10	0.87932	D	0	-9.1751	15.4231	0.75028	0.0:0.0:0.0:1.0	.	837	P78364	PHC1_HUMAN	P	837;837;792;837;443	ENSP00000440674:L837P;ENSP00000251757:L837P;ENSP00000399194:L792P;ENSP00000437659:L837P;ENSP00000440488:L443P	ENSP00000251757:L837P	L	+	2	0	PHC1	8981071	0.995000	0.38212	0.999000	0.59377	0.999000	0.98932	2.507000	0.45442	2.121000	0.65114	0.533000	0.62120	CTG		0.498	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426	
GUCY2C	2984	broad.mit.edu	37	12	14804914	14804914	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:14804914delT	ENST00000261170.3	-	14	1720	c.1584delA	c.(1582-1584)aaafs	p.K528fs		NM_004963.3	NP_004954.2	P25092	GUC2C_HUMAN	guanylate cyclase 2C (heat stable enterotoxin receptor)	528	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of cell proliferation (GO:0042127)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|toxic substance binding (GO:0015643)	p.K528fs*4(1)		breast(3)|endometrium(7)|kidney(3)|large_intestine(9)|lung(17)|ovary(4)|skin(7)|urinary_tract(1)	51					Linaclotide(DB08890)	CTATCTTCTGTTTTTCAGTGA	0.368																																					p.K528fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1584delA	12						.						230.0	206.0	214.0					12																	14804914		2202	4300	6502	14696181	SO:0001589	frameshift_variant	2984	exon14				CCDS8664.1	12p12	2008-08-18			ENSG00000070019	ENSG00000070019			4688	protein-coding gene	gene with protein product		601330		GUC2C		8661067	Standard	NM_004963		Approved	STAR	uc001rcd.3	P25092	OTTHUMG00000168732	ENST00000261170.3:c.1584delA	12.37:g.14804914delT	ENSP00000261170:p.Lys528fs	Somatic		Capture	Illumina HiSeq	Phase_I	14696181	NM_004963	B2RMY6	Frame_Shift_Del	DEL	ENST00000261170.3	37	CCDS8664.1																																																																																				0.368	GUCY2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400835.1		
ERP27	121506	broad.mit.edu	37	12	15090958	15090958	+	Silent	SNP	C	C	T	rs367692738		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:15090958C>T	ENST00000266397.2	-	2	696	c.123G>A	c.(121-123)acG>acA	p.T41T		NM_152321.2	NP_689534.1	Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27	41	Thioredoxin.					endoplasmic reticulum (GO:0005783)		p.T41T(1)		breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(3)|prostate(2)|skin(1)	19						CTGTGAGCCACGTGGGTTCCT	0.512																																					p.T41T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G123A	12						.	C		0,4406		0,0,2203	97.0	97.0	97.0		123	0.9	0.0	12		97	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ERP27	NM_152321.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		41/274	15090958	2,13004	2203	4300	6503	14982225	SO:0001819	synonymous_variant	121506	exon2			AK056677	CCDS8670.1, CCDS73450.1	12p12.3	2011-10-19	2009-02-23	2007-03-26	ENSG00000139055	ENSG00000139055		"""Protein disulfide isomerases"""	26495	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 8"""	610642	"""chromosome 12 open reading frame 46"", ""endoplasmic reticulum protein 27 kDa"""	C12orf46		12975309, 16940051	Standard	XM_005253303		Approved	FLJ32115, ERp27, PDIA8	uc001rco.3	Q96DN0	OTTHUMG00000168741	ENST00000266397.2:c.123G>A	12.37:g.15090958C>T		Somatic		Capture	Illumina HiSeq	Phase_I	14982225	NM_152321		Silent	SNP	ENST00000266397.2	37	CCDS8670.1																																																																																				0.512	ERP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400868.1	NM_152321	
CAPZA3	93661	broad.mit.edu	37	12	18891664	18891664	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:18891664C>T	ENST00000317658.3	+	1	620	c.462C>T	c.(460-462)tgC>tgT	p.C154C	RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000447925.2_5'Flank|PLCZ1_ENST00000266505.7_5'Flank|PLCZ1_ENST00000539875.1_5'Flank|PLCZ1_ENST00000435379.1_5'Flank	NM_033328.2	NP_201585.1	Q96KX2	CAZA3_HUMAN	capping protein (actin filament) muscle Z-line, alpha 3	154					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cortical cytoskeleton (GO:0030863)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|nucleus (GO:0005634)|WASH complex (GO:0071203)		p.C154C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)	19	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)	Hepatocellular(102;0.194)				TGATAGCTTGCATTGAAGATC	0.388																																					p.C154C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C462T	12						.						93.0	88.0	90.0					12																	18891664		2203	4299	6502	18782931	SO:0001819	synonymous_variant	93661	exon1			AB053259	CCDS8681.1	12p12.3	2008-02-05			ENSG00000177938	ENSG00000177938			24205	protein-coding gene	gene with protein product		608722				12029070	Standard	NM_033328		Approved	Gsg3, CAPPA3	uc001rdy.3	Q96KX2	OTTHUMG00000169001	ENST00000317658.3:c.462C>T	12.37:g.18891664C>T		Somatic		Capture	Illumina HiSeq	Phase_I	18782931	NM_033328	Q969J0	Silent	SNP	ENST00000317658.3	37	CCDS8681.1																																																																																				0.388	CAPZA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401902.1	NM_033328	
GYS2	2998	broad.mit.edu	37	12	21757449	21757449	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:21757449C>A	ENST00000261195.2	-	1	332	c.78G>T	c.(76-78)gaG>gaT	p.E26D		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	26					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)	p.E26D(1)		NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GCAGTAACTCCTCCACAGGAA	0.502																																					p.E26D	Colon(149;9 1820 3690 10544 50424)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G78T	12						.						111.0	108.0	109.0					12																	21757449		2203	4299	6502	21648716	SO:0001583	missense	2998	exon1				CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.78G>T	12.37:g.21757449C>A	ENSP00000261195:p.Glu26Asp	Somatic		Capture	Illumina HiSeq	Phase_I	21648716	NM_021957	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	37	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.417615	0.42918	.	.	ENSG00000111713	ENST00000261195	T	0.64803	-0.12	5.28	-2.08	0.07254	.	0.051018	0.85682	N	0.000000	T	0.37892	0.1020	L	0.27053	0.805	0.45172	D	0.998188	B	0.02656	0.0	B	0.06405	0.002	T	0.02560	-1.1141	10	0.51188	T	0.08	-21.5348	1.7537	0.02977	0.1302:0.3508:0.1271:0.3918	.	26	P54840	GYS2_HUMAN	D	26	ENSP00000261195:E26D	ENSP00000261195:E26D	E	-	3	2	GYS2	21648716	0.051000	0.20477	0.151000	0.22473	0.981000	0.71138	-1.149000	0.03182	-0.652000	0.05408	0.655000	0.94253	GAG		0.502	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957	
LYRM5	144363	broad.mit.edu	37	12	25357077	25357077	+	Missense_Mutation	SNP	G	G	A	rs377621299		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:25357077G>A	ENST00000381356.4	+	3	263	c.104G>A	c.(103-105)cGt>cAt	p.R35H	LYRM5_ENST00000553788.1_Intron|LYRM5_ENST00000555711.1_3'UTR|LYRM5_ENST00000556351.1_Missense_Mutation_p.R33H|LYRM5_ENST00000556885.1_Missense_Mutation_p.R33H|LYRM5_ENST00000554266.1_3'UTR|LYRM5_ENST00000557540.2_Missense_Mutation_p.R33H|LYRM5_ENST00000556402.1_3'UTR|LYRM5_ENST00000556927.1_Missense_Mutation_p.R33H	NM_001001660.2	NP_001001660.2	Q6IPR1	LYRM5_HUMAN	LYR motif containing 5	35						mitochondrion (GO:0005739)		p.R35H(1)		large_intestine(3)	3	all_cancers(2;4.75e-35)|all_epithelial(2;1.91e-37)|all_lung(3;1.07e-23)|Lung NSC(3;5.49e-23)|Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.0016)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;2.21e-21)|Epithelial(3;8.04e-19)|all cancers(3;2.26e-16)|STAD - Stomach adenocarcinoma(2;0.00138)			TTTAAAAAGCGTTTGAAGAAC	0.328																																					p.R35H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G104A	12						.	G	HIS/ARG	0,3604		0,0,1802	30.0	27.0	28.0		104	5.9	1.0	12		28	2,8130		0,2,4064	no	missense	LYRM5	NM_001001660.2	29	0,2,5866	AA,AG,GG		0.0246,0.0,0.017	benign	35/91	25357077	2,11734	1802	4066	5868	25248344	SO:0001583	missense	144363	exon3			AK057730	CCDS53764.1	12p12.1	2006-09-19				ENSG00000205707		"""LYR motif containing"""	27052	protein-coding gene	gene with protein product							Standard	NM_001001660		Approved		uc001rgn.3	Q6IPR1		ENST00000381356.4:c.104G>A	12.37:g.25357077G>A	ENSP00000370761:p.Arg35His	Somatic		Capture	Illumina HiSeq	Phase_I	25248344	NM_001001660	J3KPI7	Missense_Mutation	SNP	ENST00000381356.4	37	CCDS53764.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.286801	0.80803	0.0	2.46E-4	ENSG00000205707	ENST00000557540;ENST00000381356;ENST00000556885;ENST00000556351;ENST00000556927;ENST00000556198	T;T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54;-0.54	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.85745	0.5768	.	.	.	0.80722	D	1	B;D	0.89917	0.151;1.0	B;D	0.87578	0.059;0.998	D	0.86646	0.1895	9	0.87932	D	0	.	19.2322	0.93845	0.0:0.0:1.0:0.0	.	33;33	Q6IPR1;G3V521	LYRM5_HUMAN;.	H	33;35;33;33;33;33	ENSP00000450584:R33H;ENSP00000370761:R35H;ENSP00000451494:R33H;ENSP00000452146:R33H;ENSP00000450443:R33H	ENSP00000370761:R35H	R	+	2	0	LYRM5	25248344	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.390000	0.97246	2.774000	0.95407	0.655000	0.94253	CGT		0.328	LYRM5-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001001660	
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		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.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(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)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12D	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,haematopoietic_and_lymphoid_tissue,NS,Substitution - Missense,0 	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35A	12						.						91.0	81.0	85.0					12																	25398284		2203	4300	6503	25289551	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.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp	Somatic		Capture	Illumina HiSeq	Phase_I	25289551	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
LMNTD1	160492	broad.mit.edu	37	12	25699336	25699336	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:25699336G>A	ENST00000282881.6	-	3	549	c.400C>T	c.(400-402)Ctt>Ttt	p.L134F	IFLTD1_ENST00000539744.1_Missense_Mutation_p.L37F|IFLTD1_ENST00000458174.2_Missense_Mutation_p.L155F|IFLTD1_ENST00000413632.2_Missense_Mutation_p.L155F|IFLTD1_ENST00000445693.1_Missense_Mutation_p.L71F	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		134					cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)	p.L134F(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					ACTTCTTCAAGAATCATAGAA	0.338																																					p.L71F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C211T	12						.						89.0	89.0	89.0					12																	25699336		2203	4298	6501	25590603	SO:0001583	missense	160492	exon2																														ENST00000282881.6:c.400C>T	12.37:g.25699336G>A	ENSP00000282881:p.Leu134Phe	Somatic		Capture	Illumina HiSeq	Phase_I	25590603	NM_001145727	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.930824	0.34096	.	.	ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000538178;ENST00000540106	T;T;T;T;T	0.19806	2.36;2.49;2.34;2.5;2.12	4.75	2.93	0.34026	.	.	.	.	.	T	0.30166	0.0756	L	0.29908	0.895	0.25720	N	0.985385	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.85130	0.974;0.974;0.997;0.984	T	0.06570	-1.0819	9	0.66056	D	0.02	.	6.6171	0.22782	0.0966:0.1818:0.7215:0.0	.	71;155;155;134	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9	.;.;.;ILFT1_HUMAN	F	134;37;155;71;155;109;109	ENSP00000282881:L134F;ENSP00000443132:L37F;ENSP00000407353:L155F;ENSP00000407043:L71F;ENSP00000393150:L155F	ENSP00000282881:L134F	L	-	1	0	IFLTD1	25590603	1.000000	0.71417	0.972000	0.41901	0.090000	0.18270	1.144000	0.31565	0.733000	0.32492	-0.121000	0.15023	CTT		0.338	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
ITPR2	3709	broad.mit.edu	37	12	26636737	26636737	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:26636737C>T	ENST00000381340.3	-	42	6322	c.5906G>A	c.(5905-5907)gGc>gAc	p.G1969D		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1969					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|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)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)	p.G1969D(1)	ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	CAGGCCCAGGCCACCGGTTGT	0.473																																					p.G1969D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5906A	12						.						176.0	169.0	171.0					12																	26636737		1880	4118	5998	26528004	SO:0001583	missense	3709	exon42			D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.5906G>A	12.37:g.26636737C>T	ENSP00000370744:p.Gly1969Asp	Somatic		Capture	Illumina HiSeq	Phase_I	26528004	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	.	.	.	.	.	.	.	.	.	.	c	29.3	4.993029	0.93167	.	.	ENSG00000123104	ENST00000381340	T	0.64991	-0.13	5.17	5.17	0.71159	RyR/IP3R Homology associated domain (1);	0.000000	0.85682	D	0.000000	D	0.82318	0.5011	M	0.88570	2.965	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.82356	-0.0498	10	0.35671	T	0.21	.	18.8599	0.92267	0.0:1.0:0.0:0.0	.	1969	Q14571	ITPR2_HUMAN	D	1969	ENSP00000370744:G1969D	ENSP00000370744:G1969D	G	-	2	0	ITPR2	26528004	1.000000	0.71417	0.996000	0.52242	0.967000	0.64934	7.590000	0.82653	2.671000	0.90904	0.586000	0.80456	GGC		0.473	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
FAR2	55711	broad.mit.edu	37	12	29450071	29450071	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:29450071G>A	ENST00000536681.3	+	4	729	c.483G>A	c.(481-483)aaG>aaA	p.K161K	RP11-996F15.2_ENST00000553105.1_RNA|FAR2_ENST00000547116.1_Silent_p.K64K|FAR2_ENST00000182377.4_Silent_p.K161K	NM_001271783.1|NM_001271784.1	NP_001258712.1|NP_001258713.1	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2	161					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)	p.K161K(1)		central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|prostate(1)|stomach(1)	29						GTAACCTGAAGCACATCGATG	0.448																																					p.K161K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G483A	12						.						140.0	146.0	144.0					12																	29450071		2203	4300	6503	29341338	SO:0001819	synonymous_variant	55711	exon4			AL136843	CCDS8717.1, CCDS61084.1	12p11.23	2013-07-30	2008-06-06	2008-06-06	ENSG00000064763	ENSG00000064763	1.2.1.-	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	25531	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 10E, member 2"""		"""male sterility domain containing 1"""	MLSTD1		15220348, 15220349, 19027726	Standard	NM_001271783		Approved	FLJ10462, SDR10E2	uc001ris.5	Q96K12	OTTHUMG00000169320	ENST00000536681.3:c.483G>A	12.37:g.29450071G>A		Somatic		Capture	Illumina HiSeq	Phase_I	29341338	NM_018099	F8VV73|Q9H0D5|Q9NVW8	Silent	SNP	ENST00000536681.3	37	CCDS8717.1																																																																																				0.448	FAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403479.2	NM_018099	
PKP2	5318	broad.mit.edu	37	12	33031092	33031092	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:33031092A>C	ENST00000070846.6	-	3	746	c.722T>G	c.(721-723)cTc>cGc	p.L241R	PKP2_ENST00000340811.4_Missense_Mutation_p.L241R	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	241					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)	p.L241R(1)		NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					GGGGTACGTGAGCAGGGCCGG	0.612																																					p.L241R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T722G	12						.						72.0	64.0	67.0					12																	33031092		2203	4298	6501	32922359	SO:0001583	missense	5318	exon3			X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"""Armadillo repeat containing"""	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.722T>G	12.37:g.33031092A>C	ENSP00000070846:p.Leu241Arg	Somatic		Capture	Illumina HiSeq	Phase_I	32922359	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	A	10.51	1.371793	0.24857	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.81415	-1.49;-1.47	5.29	4.12	0.48240	.	4.458510	0.00550	N	0.000248	T	0.74703	0.3751	L	0.50333	1.59	0.09310	N	1	P;P;P	0.37864	0.603;0.468;0.61	B;B;B	0.33521	0.165;0.08;0.125	T	0.58418	-0.7640	10	0.25106	T	0.35	-6.4718	4.6101	0.12399	0.6874:0.1868:0.1258:0.0	.	241;241;241	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	R	241	ENSP00000342800:L241R;ENSP00000070846:L241R	ENSP00000070846:L241R	L	-	2	0	PKP2	32922359	0.000000	0.05858	0.058000	0.19502	0.668000	0.39293	0.310000	0.19356	0.827000	0.34685	0.529000	0.55759	CTC		0.612	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572	
ADAMTS20	80070	broad.mit.edu	37	12	43824241	43824241	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:43824241G>A	ENST00000389420.3	-	23	3294	c.3295C>T	c.(3295-3297)Cga>Tga	p.R1099*	ADAMTS20_ENST00000395541.2_Nonsense_Mutation_p.R253*|ADAMTS20_ENST00000553158.1_Nonsense_Mutation_p.R1099*	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1099	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R1099*(1)		breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TTAACATCTCGCATCTGATAC	0.383																																					p.R1099X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C3295T	12						.						145.0	121.0	129.0					12																	43824241		2203	4300	6503	42110508	SO:0001587	stop_gained	80070	exon23			AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.3295C>T	12.37:g.43824241G>A	ENSP00000374071:p.Arg1099*	Somatic		Capture	Illumina HiSeq	Phase_I	42110508	NM_025003	A6NNC9|J3QT00	Nonsense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	g	40	8.209134	0.98706	.	.	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	.	.	.	5.3	5.3	0.74995	.	0.000000	0.52532	D	0.000064	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.8594	0.96778	0.0:0.0:1.0:0.0	.	.	.	.	X	1099;265;253;1099;1099	.	ENSP00000374068:R1099X	R	-	1	2	ADAMTS20	42110508	1.000000	0.71417	1.000000	0.80357	0.622000	0.37654	3.138000	0.50570	2.869000	0.98440	0.556000	0.70494	CGA		0.383	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
HDAC7	51564	broad.mit.edu	37	12	48179652	48179652	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:48179652C>T	ENST00000427332.2	-	23	2628	c.2472G>A	c.(2470-2472)acG>acA	p.T824T	HDAC7_ENST00000488927.1_5'Flank|AC004466.1_ENST00000599515.1_3'UTR|HDAC7_ENST00000354334.3_Silent_p.T826T|HDAC7_ENST00000552960.1_Silent_p.T846T|HDAC7_ENST00000380610.4_Silent_p.T880T|HDAC7_ENST00000080059.7_Silent_p.T863T			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	824	Histone deacetylase.				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.T824T(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)		TCAGTTGCTGCGTCATGTATC	0.602																																					p.T826T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2478A	12						.						43.0	38.0	40.0					12																	48179652		2203	4300	6503	46465919	SO:0001819	synonymous_variant	51564	exon22			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.2472G>A	12.37:g.48179652C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46465919	NM_001098416	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Silent	SNP	ENST00000427332.2	37		.	.	.	.	.	.	.	.	.	.	c	6.973	0.549524	0.13374	.	.	ENSG00000061273	ENST00000548080	.	.	.	4.78	-7.29	0.01451	.	.	.	.	.	T	0.50429	0.1615	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55604	-0.8115	4	.	.	.	.	9.9199	0.41457	0.0:0.2272:0.179:0.5939	.	.	.	.	H	256	.	.	R	-	2	0	HDAC7	46465919	0.000000	0.05858	0.749000	0.31150	0.846000	0.48090	-5.427000	0.00123	-1.578000	0.01648	-1.505000	0.00955	CGC		0.602	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2		
COL2A1	1280	broad.mit.edu	37	12	48379512	48379512	+	Splice_Site	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:48379512C>T	ENST00000380518.3	-	25	1843	c.1679G>A	c.(1678-1680)cGg>cAg	p.R560Q	COL2A1_ENST00000493991.1_5'UTR|COL2A1_ENST00000337299.6_Splice_Site_p.R491Q	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	560	Triple-helical region.				axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)	p.R491Q(1)|p.R560Q(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	GCTACTTACCCGGGCTCCAGG	0.662																																					p.R491Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1472A	12						.						44.0	42.0	42.0					12																	48379512		2203	4300	6503	46665779	SO:0001630	splice_region_variant	1280	exon24			X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"""Collagens"""	2200	protein-coding gene	gene with protein product		120140	"""collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)"", ""arthroophthalmopathy, progressive (Stickler syndrome)"""	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.1680+1G>A	12.37:g.48379512C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46665779	NM_033150	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Missense_Mutation	SNP	ENST00000380518.3	37	CCDS41778.1	.	.	.	.	.	.	.	.	.	.	C	34	5.377735	0.95945	.	.	ENSG00000139219	ENST00000380518;ENST00000395281;ENST00000337299	D;D	0.83755	-1.76;-1.76	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.86707	0.5997	L	0.33668	1.02	0.80722	D	1	D;D	0.89917	1.0;0.991	D;D	0.81914	0.995;0.932	D	0.86939	0.2078	10	0.49607	T	0.09	.	17.3421	0.87299	0.0:1.0:0.0:0.0	.	491;560	P02458-1;P02458	.;CO2A1_HUMAN	Q	560;491;491	ENSP00000369889:R560Q;ENSP00000338213:R491Q	ENSP00000338213:R491Q	R	-	2	0	COL2A1	46665779	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	3.860000	0.55995	2.629000	0.89072	0.609000	0.83330	CGG		0.662	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	Missense_Mutation
CCNT1	904	broad.mit.edu	37	12	49087817	49087817	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:49087817C>T	ENST00000261900.3	-	9	1402	c.1180G>A	c.(1180-1182)Gcg>Acg	p.A394T		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	394					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)	p.A394T(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						GCATGCTTCGCGCGGTATTCT	0.448																																					p.A394T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1180A	12						.						227.0	233.0	231.0					12																	49087817		2203	4300	6503	47374084	SO:0001583	missense	904	exon9			AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"""human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"""	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.1180G>A	12.37:g.49087817C>T	ENSP00000261900:p.Ala394Thr	Somatic		Capture	Illumina HiSeq	Phase_I	47374084	NM_001240	A9XU13|E7EX76|O60581	Missense_Mutation	SNP	ENST00000261900.3	37	CCDS8766.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.331979	0.81801	.	.	ENSG00000129315	ENST00000261900	T	0.52057	0.68	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.61060	0.2317	L	0.43923	1.385	0.80722	D	1	D	0.89917	1.0	D	0.65684	0.937	T	0.60439	-0.7263	10	0.51188	T	0.08	-11.6778	18.0305	0.89282	0.0:1.0:0.0:0.0	.	394	O60563	CCNT1_HUMAN	T	394	ENSP00000261900:A394T	ENSP00000261900:A394T	A	-	1	0	CCNT1	47374084	1.000000	0.71417	0.998000	0.56505	0.875000	0.50365	7.664000	0.83830	2.634000	0.89283	0.561000	0.74099	GCG		0.448	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240	
TROAP	10024	broad.mit.edu	37	12	49721073	49721073	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:49721073G>A	ENST00000257909.3	+	8	927	c.851G>A	c.(850-852)cGa>cAa	p.R284Q	TROAP_ENST00000551245.1_Missense_Mutation_p.R284Q|TROAP_ENST00000547923.1_5'UTR|RP11-161H23.9_ENST00000553259.1_RNA	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	284					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)		p.R284Q(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						CTGGCCCAGCGAGTACCATTA	0.507																																					p.R284Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G851A	12						.						121.0	108.0	112.0					12																	49721073		2203	4300	6503	48007340	SO:0001583	missense	10024	exon8			U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"""tastin"""	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.851G>A	12.37:g.49721073G>A	ENSP00000257909:p.Arg284Gln	Somatic		Capture	Illumina HiSeq	Phase_I	48007340	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Missense_Mutation	SNP	ENST00000257909.3	37	CCDS8784.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.799004	0.70567	.	.	ENSG00000135451	ENST00000551245;ENST00000550346;ENST00000257909;ENST00000547807	.	.	.	5.13	4.24	0.50183	.	0.139687	0.32624	N	0.005848	T	0.43919	0.1269	L	0.47190	1.495	0.80722	D	1	P;P	0.44877	0.845;0.845	B;B	0.39027	0.288;0.288	T	0.47005	-0.9150	9	0.59425	D	0.04	-5.867	10.3478	0.43916	0.0931:0.0:0.9069:0.0	.	284;284	F8W130;Q12815	.;TROAP_HUMAN	Q	284;167;284;278	.	ENSP00000257909:R284Q	R	+	2	0	TROAP	48007340	0.990000	0.36364	0.900000	0.35374	0.887000	0.51463	1.954000	0.40362	1.481000	0.48307	0.655000	0.94253	CGA		0.507	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480	
SPATS2	65244	broad.mit.edu	37	12	49888573	49888573	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:49888573G>A	ENST00000553127.1	+	8	827	c.314G>A	c.(313-315)gGc>gAc	p.G105D	SPATS2_ENST00000552557.1_3'UTR|SPATS2_ENST00000552918.1_Missense_Mutation_p.G105D|SPATS2_ENST00000321898.6_Missense_Mutation_p.G105D			Q86XZ4	SPAS2_HUMAN	spermatogenesis associated, serine-rich 2	105						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.G105D(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(1)|prostate(1)|urinary_tract(4)	21						CCAAGTAACGGCATCCCAGAT	0.393																																					p.G105D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G314A	12						.						47.0	42.0	43.0					12																	49888573		2203	4300	6503	48174840	SO:0001583	missense	65244	exon7			AK023179	CCDS31794.1	12q13.12	2009-06-12							18650	protein-coding gene	gene with protein product		611667				11944913, 17989879	Standard	NM_023071		Approved	SPATA10, SCR59, FLJ13117	uc001rud.2	Q86XZ4		ENST00000553127.1:c.314G>A	12.37:g.49888573G>A	ENSP00000448228:p.Gly105Asp	Somatic		Capture	Illumina HiSeq	Phase_I	48174840	NM_023071	A8K8G9|Q9H7D4|Q9H8Y7|Q9H8Z8	Missense_Mutation	SNP	ENST00000553127.1	37	CCDS31794.1	.	.	.	.	.	.	.	.	.	.	G	5.563	0.288800	0.10513	.	.	ENSG00000123352	ENST00000553127;ENST00000321898;ENST00000552918;ENST00000395063	.	.	.	5.03	1.98	0.26296	.	0.421155	0.29579	N	0.011742	T	0.13372	0.0324	N	0.03608	-0.345	0.20307	N	0.999918	B	0.20164	0.042	B	0.25506	0.061	T	0.22906	-1.0203	8	.	.	.	-4.2015	4.6615	0.12645	0.1987:0.3526:0.4488:0.0	.	105	Q86XZ4	SPAS2_HUMAN	D	105	.	.	G	+	2	0	SPATS2	48174840	0.003000	0.15002	0.703000	0.30354	0.778000	0.44026	0.934000	0.28910	0.701000	0.31803	0.655000	0.94253	GGC		0.393	SPATS2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404023.1	NM_023071	
PRPF40B	25766	broad.mit.edu	37	12	50026386	50026386	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:50026386C>T	ENST00000380281.1	+	4	300	c.236C>T	c.(235-237)cCg>cTg	p.P79L	PRPF40B_ENST00000261897.1_Missense_Mutation_p.P73L|PRPF40B_ENST00000548825.2_Missense_Mutation_p.P101L			Q6NWY9	PR40B_HUMAN	PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)	79					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)		p.P79L(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34						CAGACGGCTCCGGGTGCGGAC	0.697																																					p.P79L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C236T	12						.						58.0	66.0	63.0					12																	50026386		2203	4299	6502	48312653	SO:0001583	missense	25766	exon4			AF049525	CCDS31796.1, CCDS31796.2	12q13.12	2014-09-17	2006-04-04			ENSG00000110844			25031	protein-coding gene	gene with protein product	"""Huntingtin interacting protein C"""		"""PRP40 pre-mRNA processing factor 40 homolog B (yeast)"""			9700202	Standard	NM_001031698		Approved	HYPC	uc001rus.2	Q6NWY9		ENST00000380281.1:c.236C>T	12.37:g.50026386C>T	ENSP00000369634:p.Pro79Leu	Somatic		Capture	Illumina HiSeq	Phase_I	48312653	NM_001031698	O75401|Q6PI09|Q6ZWB3|Q8NCZ1|Q9H5G4|Q9NT95	Missense_Mutation	SNP	ENST00000380281.1	37		.	.	.	.	.	.	.	.	.	.	C	13.90	2.374969	0.42105	.	.	ENSG00000110844	ENST00000548825;ENST00000261897;ENST00000380281	T;T;T	0.30981	1.54;1.54;1.51	4.99	4.99	0.66335	.	0.216556	0.32231	N	0.006392	T	0.46112	0.1376	L	0.39898	1.24	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.79108	0.982;0.992;0.992	T	0.14643	-1.0465	9	.	.	.	-20.8841	16.156	0.81666	0.0:1.0:0.0:0.0	.	79;73;79	Q6NWY9;Q6NWY9-2;Q6NWY9-3	PR40B_HUMAN;.;.	L	101;73;79	ENSP00000448073:P101L;ENSP00000261897:P73L;ENSP00000369634:P79L	.	P	+	2	0	PRPF40B	48312653	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.479000	0.45197	2.764000	0.94973	0.561000	0.74099	CCG		0.697	PRPF40B-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000404838.1	NM_012272	
ASIC1	41	broad.mit.edu	37	12	50471048	50471048	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:50471048G>A	ENST00000447966.2	+	4	840	c.611G>A	c.(610-612)cGg>cAg	p.R204Q	ASIC1_ENST00000228468.4_Missense_Mutation_p.R204Q|ASIC1_ENST00000552438.1_Missense_Mutation_p.R238Q	NM_001095.3	NP_001086.2	P78348	ASIC1_HUMAN	acid-sensing (proton-gated) ion channel 1	204					associative learning (GO:0008306)|calcium ion transmembrane transport (GO:0070588)|cellular response to pH (GO:0071467)|ion transmembrane transport (GO:0034220)|memory (GO:0007613)|negative regulation of neurotransmitter secretion (GO:0046929)|protein homotrimerization (GO:0070207)|regulation of membrane potential (GO:0042391)|response to acidic pH (GO:0010447)|response to pH (GO:0009268)|sensory perception of sour taste (GO:0050915)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acid-sensing ion channel activity (GO:0044736)|ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)	p.R204Q(1)								Amiloride(DB00594)|Diclofenac(DB00586)	CGAGATGGGCGGCCGCGGCTG	0.607																																					p.R204Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G611A	12						.						82.0	70.0	74.0					12																	50471048		2203	4300	6503	48757315	SO:0001583	missense	41	exon4			U78181	CCDS8796.1, CCDS44876.1, CCDS58228.1	12q12	2012-02-23	2012-02-22	2012-02-22		ENSG00000110881		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	100	protein-coding gene	gene with protein product		602866	"""amiloride-sensitive cation channel 2, neuronal"""	ACCN2		9037075	Standard	NM_001095		Approved	BNaC2, hBNaC2	uc001rvv.4	P78348	OTTHUMG00000169812	ENST00000447966.2:c.611G>A	12.37:g.50471048G>A	ENSP00000400228:p.Arg204Gln	Somatic		Capture	Illumina HiSeq	Phase_I	48757315	NM_020039	A3KN86|E5KBL7|P78349|Q96CV2	Missense_Mutation	SNP	ENST00000447966.2	37	CCDS44876.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.33|12.33	1.906934|1.906934	0.33628|0.33628	.|.	.|.	ENSG00000110881|ENSG00000110881	ENST00000453327|ENST00000228468;ENST00000447966;ENST00000552438	.|T;T;T	.|0.61980	.|0.06;0.06;0.06	4.03|4.03	4.03|4.03	0.46877|0.46877	.|.	.|0.000000	.|0.64402	.|D	.|0.000005	T|T	0.39410|0.39410	0.1077|0.1077	N|N	0.13235|0.13235	0.315|0.315	0.33523|0.33523	D|D	0.592623|0.592623	.|B;B	.|0.17465	.|0.003;0.022	.|B;B	.|0.13407	.|0.009;0.009	T|T	0.44390|0.44390	-0.9331|-0.9331	5|10	.|0.19590	.|T	.|0.45	-22.1995|-22.1995	8.2025|8.2025	0.31432|0.31432	0.1514:0.0:0.8486:0.0|0.1514:0.0:0.8486:0.0	.|.	.|204;204	.|P78348;P78348-1	.|ACCN2_HUMAN;.	S|Q	72|204;204;238	.|ENSP00000228468:R204Q;ENSP00000400228:R204Q;ENSP00000450247:R238Q	.|ENSP00000228468:R204Q	G|R	+|+	1|2	0|0	ACCN2|ACCN2	48757315|48757315	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	4.058000|4.058000	0.57463|0.57463	2.258000|2.258000	0.74832|0.74832	0.561000|0.561000	0.74099|0.74099	GGC|CGG		0.607	ASIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406004.2	NM_020039	
FIGNL2	401720	broad.mit.edu	37	12	52215925	52215925	+	lincRNA	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:52215925G>A	ENST00000562343.2	+	0	4188				RP11-923I11.4_ENST00000567167.1_lincRNA																							CCCCTTTGGCGCCGTTGAGGA	0.662																																					p.G91G												.	.	0			c.C273T	12						.						27.0	29.0	29.0					12																	52215925		1928	4098	6026	50502192			401720	exon1																															12.37:g.52215925G>A		Somatic		Capture	Illumina HiSeq	Phase_I	50502192	NM_001013690		Silent	SNP	ENST00000562343.2	37																																																																																					0.662	RP11-923I11.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000430848.2		
KRT84	3890	broad.mit.edu	37	12	52779212	52779212	+	Missense_Mutation	SNP	C	C	T	rs143172691		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:52779212C>T	ENST00000257951.3	-	1	224	c.158G>A	c.(157-159)cGg>cAg	p.R53Q	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	53	Head.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)	p.R53Q(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GATGACACTCCGACTACCAAA	0.582																																					p.R53Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G158A	12						.	C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	80.0	83.0	82.0		158	4.2	1.0	12	dbSNP_134	82	0,8600		0,0,4300	no	missense	KRT84	NM_033045.3	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	53/601	52779212	1,13005	2203	4300	6503	51065479	SO:0001583	missense	3890	exon1			Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.158G>A	12.37:g.52779212C>T	ENSP00000257951:p.Arg53Gln	Somatic		Capture	Illumina HiSeq	Phase_I	51065479	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.856105	0.51376	2.27E-4	0.0	ENSG00000161849	ENST00000257951	T	0.75260	-0.92	5.06	4.16	0.48862	.	0.345102	0.21430	N	0.074663	T	0.73473	0.3591	M	0.79926	2.475	0.29074	N	0.883081	B	0.25312	0.123	B	0.13407	0.009	T	0.71689	-0.4517	10	0.62326	D	0.03	.	11.3836	0.49771	0.0:0.8517:0.0:0.1483	.	53	Q9NSB2	KRT84_HUMAN	Q	53	ENSP00000257951:R53Q	ENSP00000257951:R53Q	R	-	2	0	KRT84	51065479	0.012000	0.17670	0.998000	0.56505	0.360000	0.29518	0.714000	0.25808	1.483000	0.48342	0.543000	0.68304	CGG		0.582	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
KRT75	9119	broad.mit.edu	37	12	52818502	52818502	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:52818502G>A	ENST00000252245.5	-	9	1675	c.1455C>T	c.(1453-1455)agC>agT	p.S485S	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	485	Tail.		S -> R (in dbSNP:rs298104). {ECO:0000269|PubMed:10692104, ECO:0000269|PubMed:9856802}.		hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.S485S(2)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		TGCTGCTGCCGCTTCCATAGC	0.607																																					p.S485S												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C1455T	12						.						56.0	59.0	58.0					12																	52818502		2203	4300	6503	51104769	SO:0001819	synonymous_variant	9119	exon9			Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.1455C>T	12.37:g.52818502G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51104769	NM_004693	B4DQU4|Q9NSA9	Silent	SNP	ENST00000252245.5	37	CCDS8827.1																																																																																				0.607	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
KRT75	9119	broad.mit.edu	37	12	52824362	52824362	+	Missense_Mutation	SNP	C	C	T	rs138832844	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:52824362C>T	ENST00000252245.5	-	5	1218	c.998G>A	c.(997-999)cGc>cAc	p.R333H	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	333	Coil 2.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R333H(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		GGCCCGGCTGCGGTTGGCAAT	0.557																																					p.R333H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G998A	12						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	188.0	165.0	173.0		998	4.8	1.0	12	dbSNP_134	173	2,8598	2.2+/-6.3	0,2,4298	yes	missense	KRT75	NM_004693.2	29	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	probably-damaging	333/552	52824362	3,13003	2203	4300	6503	51110629	SO:0001583	missense	9119	exon5			Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.998G>A	12.37:g.52824362C>T	ENSP00000252245:p.Arg333His	Somatic		Capture	Illumina HiSeq	Phase_I	51110629	NM_004693	B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	37	CCDS8827.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.465102	0.84425	2.27E-4	2.33E-4	ENSG00000170454	ENST00000252245	T	0.75477	-0.94	5.73	4.83	0.62350	Prefoldin (1);Filament (1);	0.000000	0.56097	D	0.000039	T	0.76463	0.3991	M	0.64080	1.96	0.36015	D	0.838335	P	0.51537	0.946	P	0.52758	0.708	T	0.81822	-0.0756	10	0.66056	D	0.02	.	7.3859	0.26882	0.1365:0.7285:0.0:0.1351	.	333	O95678	K2C75_HUMAN	H	333	ENSP00000252245:R333H	ENSP00000252245:R333H	R	-	2	0	KRT75	51110629	0.989000	0.36119	1.000000	0.80357	0.994000	0.84299	0.597000	0.24059	2.706000	0.92434	0.655000	0.94253	CGC		0.557	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
KRT78	196374	broad.mit.edu	37	12	53240585	53240585	+	Missense_Mutation	SNP	C	C	T	rs368302097		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:53240585C>T	ENST00000304620.4	-	3	686	c.623G>A	c.(622-624)cGt>cAt	p.R208H	KRT78_ENST00000359499.4_Missense_Mutation_p.R98H	NM_173352.2	NP_775487.2	Q8N1N4	K2C78_HUMAN	keratin 78	208	Coil 1B.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R208H(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18						AAGTGTGGCACGCCTGTGGGC	0.572																																					p.R208H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G623A	12						.	C	HIS/ARG	0,4406		0,0,2203	87.0	64.0	72.0		623	-2.1	0.0	12		72	1,8599	1.2+/-3.3	0,1,4299	no	missense	KRT78	NM_173352.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	208/521	53240585	1,13005	2203	4300	6503	51526852	SO:0001583	missense	196374	exon3			AK096419	CCDS8840.1, CCDS73473.1	12q13.13	2013-06-25			ENSG00000170423	ENSG00000170423		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28926	protein-coding gene	gene with protein product		611159				16831889	Standard	XM_005268695		Approved	K5B	uc001sbc.1	Q8N1N4	OTTHUMG00000169880	ENST00000304620.4:c.623G>A	12.37:g.53240585C>T	ENSP00000306261:p.Arg208His	Somatic		Capture	Illumina HiSeq	Phase_I	51526852	NM_173352	A8K4D6|Q5HYM7|Q7RTT2	Missense_Mutation	SNP	ENST00000304620.4	37	CCDS8840.1	.	.	.	.	.	.	.	.	.	.	C	12.23	1.874979	0.33162	0.0	1.16E-4	ENSG00000170423	ENST00000359499;ENST00000304620	D;D	0.89939	-2.59;-2.59	4.26	-2.13	0.07144	Filament (1);	0.807228	0.09930	N	0.737302	D	0.83788	0.5330	M	0.68952	2.095	0.09310	N	1	B	0.28258	0.205	B	0.22601	0.04	T	0.72283	-0.4339	10	0.62326	D	0.03	.	4.4893	0.11806	0.1548:0.3045:0.0:0.5407	.	208	Q8N1N4	K2C78_HUMAN	H	98;208	ENSP00000352479:R98H;ENSP00000306261:R208H	ENSP00000306261:R208H	R	-	2	0	KRT78	51526852	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	-0.076000	0.11412	-0.404000	0.07610	-0.300000	0.09419	CGT		0.572	KRT78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406380.1	NM_173352	
KRT8	3856	broad.mit.edu	37	12	53292614	53292614	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:53292614C>T	ENST00000552551.1	-	7	1483	c.1051G>A	c.(1051-1053)Gcc>Acc	p.A351T	KRT8_ENST00000293308.6_Missense_Mutation_p.A351T|KRT8_ENST00000546897.1_Missense_Mutation_p.A351T|KRT8_ENST00000552150.1_Missense_Mutation_p.A379T			P05787	K2C8_HUMAN	keratin 8	351	Coil 2.|Necessary for interaction with PNN.|Rod.				cell differentiation involved in embryonic placenta development (GO:0060706)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatocyte apoptotic process (GO:0097284)|response to hydrostatic pressure (GO:0051599)|response to other organism (GO:0051707)|sarcomere organization (GO:0045214)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	scaffold protein binding (GO:0097110)|structural molecule activity (GO:0005198)	p.A351T(1)		endometrium(5)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(357;0.108)	Tenecteplase(DB00031)	GACAACTTGGCGTTGGCATCC	0.637																																					p.A351T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1051A	12						.						50.0	49.0	49.0					12																	53292614		2203	4300	6503	51578881	SO:0001583	missense	3856	exon6			BC000654	CCDS8841.1, CCDS58234.1	12q13.13	2013-01-16			ENSG00000170421	ENSG00000170421		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6446	protein-coding gene	gene with protein product		148060				2434381, 1705144, 16831889	Standard	NM_002273		Approved	CARD2, K8, CK8, CYK8, K2C8, KO	uc009zmk.1	P05787	OTTHUMG00000169881	ENST00000552551.1:c.1051G>A	12.37:g.53292614C>T	ENSP00000447566:p.Ala351Thr	Somatic		Capture	Illumina HiSeq	Phase_I	51578881	NM_002273	A8K4H3|B0AZN5|F8VXB4|Q14099|Q14716|Q14717|Q53GJ0|Q6DHW5|Q6GMY0|Q6P4C7|Q96J60	Missense_Mutation	SNP	ENST00000552551.1	37	CCDS8841.1	.	.	.	.	.	.	.	.	.	.	C	4.137	0.023713	0.08006	.	.	ENSG00000170421	ENST00000552551;ENST00000293308;ENST00000546897;ENST00000552150	T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03	3.85	0.504	0.16946	Filament (1);	0.741337	0.12546	N	0.459495	T	0.66237	0.2769	L	0.49699	1.58	0.09310	N	1	B;B	0.15473	0.011;0.013	B;B	0.15052	0.012;0.012	T	0.52170	-0.8611	10	0.33940	T	0.23	.	3.7344	0.08504	0.1673:0.3997:0.0:0.433	.	379;351	F8VXB4;P05787	.;K2C8_HUMAN	T	351;351;351;379	ENSP00000447566:A351T;ENSP00000293308:A351T;ENSP00000447402:A351T;ENSP00000449404:A379T	ENSP00000293308:A351T	A	-	1	0	KRT8	51578881	0.000000	0.05858	0.067000	0.19924	0.003000	0.03518	-0.122000	0.10627	-0.035000	0.13691	0.561000	0.74099	GCC		0.637	KRT8-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406385.1	NM_002273	
SOAT2	8435	broad.mit.edu	37	12	53509275	53509275	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:53509275A>G	ENST00000301466.3	+	6	605	c.545A>G	c.(544-546)tAc>tGc	p.Y182C		NM_003578.3	NP_003569.1	O75908	SOAT2_HUMAN	sterol O-acyltransferase 2	182					cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|intestinal cholesterol absorption (GO:0030299)|macrophage derived foam cell differentiation (GO:0010742)|very-low-density lipoprotein particle assembly (GO:0034379)	brush border (GO:0005903)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|transferase activity, transferring acyl groups (GO:0016746)	p.Y182C(1)		endometrium(5)|kidney(3)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	18					Hesperetin(DB01094)	TTGGCGCCGTACCAGGCCCTA	0.677																																					p.Y182C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A545G	12						.						41.0	40.0	40.0					12																	53509275		2203	4300	6503	51795542	SO:0001583	missense	8435	exon6			AF059203	CCDS8847.1	12q13.13	2012-09-20			ENSG00000167780	ENSG00000167780	2.3.1.26		11178	protein-coding gene	gene with protein product		601311				9756920	Standard	NM_003578		Approved	ACAT2	uc001sbv.3	O75908	OTTHUMG00000169774	ENST00000301466.3:c.545A>G	12.37:g.53509275A>G	ENSP00000301466:p.Tyr182Cys	Somatic		Capture	Illumina HiSeq	Phase_I	51795542	NM_003578	F5H7W4|I6L9H9|Q4VB99|Q4VBA1|Q96TD4|Q9UNR2	Missense_Mutation	SNP	ENST00000301466.3	37	CCDS8847.1	.	.	.	.	.	.	.	.	.	.	A	18.82	3.704767	0.68615	.	.	ENSG00000167780	ENST00000551896;ENST00000301466	T;T	0.74526	2.08;-0.85	5.61	5.61	0.85477	.	0.064326	0.64402	D	0.000005	D	0.87649	0.6230	M	0.87971	2.92	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.89745	0.3936	10	0.87932	D	0	-26.2703	15.101	0.72276	1.0:0.0:0.0:0.0	.	182	O75908	SOAT2_HUMAN	C	162;182	ENSP00000450120:Y162C;ENSP00000301466:Y182C	ENSP00000301466:Y182C	Y	+	2	0	SOAT2	51795542	1.000000	0.71417	1.000000	0.80357	0.640000	0.38277	4.447000	0.60020	2.281000	0.76405	0.533000	0.62120	TAC		0.677	SOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405817.1		
ITGB7	3695	broad.mit.edu	37	12	53586536	53586536	+	Missense_Mutation	SNP	C	C	T	rs61754162	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:53586536C>T	ENST00000267082.5	-	13	2116	c.1885G>A	c.(1885-1887)Ggc>Agc	p.G629S	ITGB7_ENST00000338737.4_Intron|ITGB7_ENST00000422257.3_Missense_Mutation_p.G629S|ITGB7_ENST00000550743.2_Intron	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	629	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)	p.G629S(1)		NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CCATAGTAGCCGTCCAAGCAC	0.597													C|||	44	0.00878594	0.0015	0.0245	5008	,	,		22482	0.0		0.0089	False		,,,				2504	0.0164				p.G629S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1885A	12						.	C	SER/GLY	3,4403	6.2+/-15.9	0,3,2200	114.0	93.0	100.0		1885	5.1	1.0	12	dbSNP_129	100	25,8575	17.9+/-57.8	0,25,4275	yes	missense	ITGB7	NM_000889.1	56	0,28,6475	TT,TC,CC		0.2907,0.0681,0.2153	probably-damaging	629/799	53586536	28,12978	2203	4300	6503	51872803	SO:0001583	missense	3695	exon13				CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"""Integrins"""	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.1885G>A	12.37:g.53586536C>T	ENSP00000267082:p.Gly629Ser	Somatic		Capture	Illumina HiSeq	Phase_I	51872803	NM_000889	Q9UCP7|Q9UCS7	Missense_Mutation	SNP	ENST00000267082.5	37	CCDS8849.1	22	0.010073260073260074	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	7	0.009234828496042216	C	16.57	3.160414	0.57368	6.81E-4	0.002907	ENSG00000139626	ENST00000422257;ENST00000267082	D;D	0.94793	-3.52;-3.52	5.13	5.13	0.70059	EGF, extracellular (1);	0.000000	0.43579	D	0.000557	D	0.89708	0.6793	M	0.72576	2.205	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.88629	0.3168	10	0.38643	T	0.18	.	17.828	0.88672	0.0:1.0:0.0:0.0	rs61754162	629	P26010	ITB7_HUMAN	S	629	ENSP00000408741:G629S;ENSP00000267082:G629S	ENSP00000267082:G629S	G	-	1	0	ITGB7	51872803	0.784000	0.28713	0.953000	0.39169	0.039000	0.13416	1.984000	0.40658	2.579000	0.87056	0.556000	0.70494	GGC		0.597	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2		
ITGB7	3695	broad.mit.edu	37	12	53588114	53588114	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:53588114G>A	ENST00000267082.5	-	10	1407	c.1176C>T	c.(1174-1176)acC>acT	p.T392T	ITGB7_ENST00000338737.4_Silent_p.T392T|ITGB7_ENST00000422257.3_Silent_p.T392T|ITGB7_ENST00000550743.2_Silent_p.T392T	NM_000889.1	NP_000880.1	P26010	ITB7_HUMAN	integrin, beta 7	392					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte tethering or rolling (GO:0050901)|multicellular organismal development (GO:0007275)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alpha4-beta7 complex (GO:0034669)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)	p.T392T(1)		NS(2)|breast(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CAAGGGTCACGGTGGAAGACA	0.537																																					p.T392T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1176T	12						.						114.0	94.0	101.0					12																	53588114		2203	4300	6503	51874381	SO:0001819	synonymous_variant	3695	exon10				CCDS8849.1	12q13.1	2010-03-23				ENSG00000139626		"""Integrins"""	6162	protein-coding gene	gene with protein product		147559				2040616	Standard	XM_005268851		Approved		uc001scc.3	P26010		ENST00000267082.5:c.1176C>T	12.37:g.53588114G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51874381	NM_000889	Q9UCP7|Q9UCS7	Silent	SNP	ENST00000267082.5	37	CCDS8849.1																																																																																				0.537	ITGB7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405821.2		
RARG	5916	broad.mit.edu	37	12	53607428	53607428	+	Silent	SNP	G	G	A	rs201815743		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:53607428G>A	ENST00000425354.2	-	8	1357	c.870C>T	c.(868-870)gaC>gaT	p.D290D	RARG_ENST00000327550.3_Silent_p.D218D|RARG_ENST00000543762.1_5'UTR|RARG_ENST00000394426.1_Silent_p.D290D|RARG_ENST00000338561.5_Silent_p.D279D|RARG_ENST00000543726.1_Silent_p.D268D	NM_000966.5	NP_000957.1	P13631	RARG_HUMAN	retinoic acid receptor, gamma	290	Ligand-binding.				anterior/posterior pattern specification (GO:0009952)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|embryonic camera-type eye development (GO:0031076)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|face development (GO:0060324)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage chondrocyte growth (GO:0003430)|Harderian gland development (GO:0070384)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of programmed cell death (GO:0043068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of cell size (GO:0008361)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|retinal pigment epithelium development (GO:0003406)|retinoic acid receptor signaling pathway (GO:0048384)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)	integral component of membrane (GO:0016021)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|retinoic acid receptor activity (GO:0003708)|retinoid X receptor binding (GO:0046965)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.D290D(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tazarotene(DB00799)|Tretinoin(DB00755)	GGGTCAGCCCGTCGGAGAAGG	0.617											OREG0021862	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D290D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C870T	12						.						105.0	92.0	96.0					12																	53607428		2203	4300	6503	51893695	SO:0001819	synonymous_variant	5916	exon8			M57707	CCDS8850.1, CCDS41790.1, CCDS58236.1, CCDS58237.1	12q13	2013-01-16			ENSG00000172819	ENSG00000172819		"""Nuclear hormone receptors"""	9866	protein-coding gene	gene with protein product		180190				1849262	Standard	NM_001042728		Approved	RARC, NR1B3	uc001scf.3	P13631	OTTHUMG00000048077	ENST00000425354.2:c.870C>T	12.37:g.53607428G>A		Somatic	993	Capture	Illumina HiSeq	Phase_I	51893695	NM_000966	B7Z492|B7Z4F1|B7ZAE4|J3KNP6|P22932|Q15281|Q52LZ8|Q9BYX8|Q9H1I3|Q9UJ38	Silent	SNP	ENST00000425354.2	37	CCDS8850.1																																																																																				0.617	RARG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109404.2	NM_000966	
ESPL1	9700	broad.mit.edu	37	12	53663626	53663626	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:53663626G>A	ENST00000257934.4	+	3	991	c.900G>A	c.(898-900)ctG>ctA	p.L300L	ESPL1_ENST00000552462.1_Silent_p.L300L	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	300					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)	p.L300L(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						GGGTTAAGCTGCTGCAGGTTG	0.552																																					p.L300L	Colon(53;1069 1201 2587 5382)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G900A	12						.						86.0	67.0	74.0					12																	53663626		2203	4300	6503	51949893	SO:0001819	synonymous_variant	9700	exon3			D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.900G>A	12.37:g.53663626G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51949893	NM_012291		Silent	SNP	ENST00000257934.4	37	CCDS8852.1																																																																																				0.552	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
ESPL1	9700	broad.mit.edu	37	12	53684700	53684700	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:53684700G>T	ENST00000257934.4	+	25	5531	c.5440G>T	c.(5440-5442)Ggc>Tgc	p.G1814C	ESPL1_ENST00000552462.1_Missense_Mutation_p.G1814C	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1814					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)	p.G1814C(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						TGAGGAGCCCGGCCCTGCCCA	0.607																																					p.G1814C	Colon(53;1069 1201 2587 5382)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5440T	12						.						23.0	22.0	23.0					12																	53684700		2203	4298	6501	51970967	SO:0001583	missense	9700	exon25			D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.5440G>T	12.37:g.53684700G>T	ENSP00000257934:p.Gly1814Cys	Somatic		Capture	Illumina HiSeq	Phase_I	51970967	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	.	.	.	.	.	.	.	.	.	.	g	13.85	2.361326	0.41801	.	.	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.12569	2.67;2.67	4.78	-2.95	0.05564	.	0.890338	0.09943	N	0.735723	T	0.19886	0.0478	L	0.58101	1.795	0.09310	N	1	P	0.43169	0.8	P	0.48425	0.577	T	0.27468	-1.0073	10	0.56958	D	0.05	.	10.8846	0.46960	0.5789:0.0:0.4211:0.0	.	1814	Q14674	ESPL1_HUMAN	C	1814;1489;1814	ENSP00000257934:G1814C;ENSP00000449831:G1814C	ENSP00000257934:G1814C	G	+	1	0	ESPL1	51970967	0.000000	0.05858	0.004000	0.12327	0.713000	0.41058	-0.137000	0.10389	-0.458000	0.07023	-1.785000	0.00643	GGC		0.607	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
MAP3K12	7786	broad.mit.edu	37	12	53875837	53875837	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:53875837T>C	ENST00000267079.2	-	14	2594	c.2369A>G	c.(2368-2370)gAc>gGc	p.D790G	MAP3K12_ENST00000547035.1_Missense_Mutation_p.D823G|MAP3K12_ENST00000547488.1_Missense_Mutation_p.D823G	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	790					histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)	p.D790G(1)		NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						GGAGCACATGTCATCAGACCG	0.587											OREG0021873	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D823G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2468G	12						.						148.0	131.0	137.0					12																	53875837		2203	4300	6503	52162104	SO:0001583	missense	7786	exon13			U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6851	protein-coding gene	gene with protein product	"""dual leucine zipper kinase DLK"""	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.2369A>G	12.37:g.53875837T>C	ENSP00000267079:p.Asp790Gly	Somatic	996	Capture	Illumina HiSeq	Phase_I	52162104	NM_001193511	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Missense_Mutation	SNP	ENST00000267079.2	37	CCDS8860.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.516624	0.85495	.	.	ENSG00000139625	ENST00000267079;ENST00000547488;ENST00000547035	T;T;T	0.55760	0.5;0.5;0.5	4.37	4.37	0.52481	.	0.000000	0.48767	D	0.000180	T	0.66645	0.2810	L	0.55481	1.735	0.58432	D	0.999995	D;D	0.63880	0.988;0.993	D;D	0.77557	0.99;0.977	T	0.69738	-0.5064	10	0.72032	D	0.01	.	13.4934	0.61408	0.0:0.0:0.0:1.0	.	823;790	G3V1Y2;Q12852	.;M3K12_HUMAN	G	790;823;823	ENSP00000267079:D790G;ENSP00000449038:D823G;ENSP00000448689:D823G	ENSP00000267079:D790G	D	-	2	0	MAP3K12	52162104	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.142000	0.77339	2.197000	0.70478	0.402000	0.26972	GAC		0.587	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301	
HOXC12	3228	broad.mit.edu	37	12	54348853	54348853	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:54348853G>A	ENST00000243103.3	+	1	236	c.140G>A	c.(139-141)cGc>cAc	p.R47H	AC012531.23_ENST00000603432.1_lincRNA	NM_173860.1	NP_776272.1	P31275	HXC12_HUMAN	homeobox C12	47					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.R47H(1)		large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	12						TACCCACGCCGCGACAACGTG	0.672																																					p.R47H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G140A	12						.						26.0	26.0	26.0					12																	54348853		2201	4299	6500	52635120	SO:0001583	missense	3228	exon1			AF328962	CCDS8866.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123407	ENSG00000123407		"""Homeoboxes / ANTP class : HOXL subclass"""	5124	protein-coding gene	gene with protein product		142975	"""homeo box C12"""	HOX3, HOX3F, HOC3F		1973146, 1358459	Standard	NM_173860		Approved		uc010soq.2	P31275	OTTHUMG00000160010	ENST00000243103.3:c.140G>A	12.37:g.54348853G>A	ENSP00000243103:p.Arg47His	Somatic		Capture	Illumina HiSeq	Phase_I	52635120	NM_173860	Q9BXJ6	Missense_Mutation	SNP	ENST00000243103.3	37	CCDS8866.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.373374	0.82573	.	.	ENSG00000123407	ENST00000243103	D	0.94497	-3.44	2.58	2.58	0.30949	.	0.000000	0.85682	D	0.000000	D	0.96965	0.9009	M	0.86651	2.83	0.58432	D	0.999996	D	0.89917	1.0	D	0.70716	0.97	D	0.97143	0.9826	10	0.66056	D	0.02	.	12.9591	0.58447	0.0:0.0:1.0:0.0	.	47	P31275	HXC12_HUMAN	H	47	ENSP00000243103:R47H	ENSP00000243103:R47H	R	+	2	0	HOXC12	52635120	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.867000	0.63013	1.757000	0.51966	0.455000	0.32223	CGC		0.672	HOXC12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358868.2	NM_173860	
TESPA1	9840	broad.mit.edu	37	12	55356832	55356832	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:55356832G>A	ENST00000449076.1	-	9	982	c.850C>T	c.(850-852)Cgg>Tgg	p.R284W	TESPA1_ENST00000316577.8_Missense_Mutation_p.R284W|TESPA1_ENST00000531122.1_Missense_Mutation_p.R146W|TESPA1_ENST00000532804.1_Missense_Mutation_p.R146W|TESPA1_ENST00000524959.1_5'Flank|TESPA1_ENST00000524622.1_Missense_Mutation_p.R146W	NM_001136030.2	NP_001129502.1	A2RU30	TESP1_HUMAN	thymocyte expressed, positive selection associated 1	284					COP9 signalosome assembly (GO:0010387)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.R146W(1)									ATGGCTTTCCGAAGGCGGTCT	0.547																																					p.R284W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C850T	12						.						71.0	72.0	71.0					12																	55356832		1950	4138	6088	53643099	SO:0001583	missense	9840	exon9			AB018291	CCDS44913.1, CCDS58240.1	12q13.2	2012-03-21	2012-03-21	2012-03-21	ENSG00000135426	ENSG00000135426			29109	protein-coding gene	gene with protein product		615664	"""KIAA0748"""	KIAA0748		9872452	Standard	NM_001136030		Approved		uc001sgn.4	A2RU30	OTTHUMG00000165407	ENST00000449076.1:c.850C>T	12.37:g.55356832G>A	ENSP00000400892:p.Arg284Trp	Somatic		Capture	Illumina HiSeq	Phase_I	53643099	NM_001098815	B4DPM3|B4E048|B7Z9K7|O94849|Q4G0P2|Q9P0C4	Missense_Mutation	SNP	ENST00000449076.1	37	CCDS44913.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.355419	0.82243	.	.	ENSG00000135426	ENST00000524622;ENST00000532804;ENST00000449076;ENST00000316577;ENST00000531122	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.49	4.57	0.56435	.	0.073564	0.52532	D	0.000064	T	0.65883	0.2734	N	0.22421	0.69	0.39255	D	0.964105	D	0.89917	1.0	D	0.76071	0.987	T	0.70978	-0.4725	10	0.66056	D	0.02	-4.4437	11.6938	0.51532	0.0:0.0:0.823:0.177	.	284	A2RU30	K0748_HUMAN	W	146;146;284;284;146	ENSP00000435622:R146W;ENSP00000432030:R146W;ENSP00000400892:R284W;ENSP00000312679:R284W;ENSP00000433098:R146W	ENSP00000312679:R284W	R	-	1	2	KIAA0748	53643099	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.055000	0.49916	1.395000	0.46643	0.655000	0.94253	CGG		0.547	TESPA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383822.1	NM_001098815	
OR6C1	390321	broad.mit.edu	37	12	55715023	55715023	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:55715023C>T	ENST00000379668.2	+	1	678	c.640C>T	c.(640-642)Ctg>Ttg	p.L214L		NM_001005182.1	NP_001005182.1	Q96RD1	OR6C1_HUMAN	olfactory receptor, family 6, subfamily C, member 1	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L214L(1)		endometrium(3)|large_intestine(5)|liver(2)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)	25						ATTAATATTTCTGTCCTACAT	0.388																																					p.L214L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C640T	12						.						85.0	75.0	79.0					12																	55715023		2203	4300	6503	54001290	SO:0001819	synonymous_variant	390321	exon1			AF399506	CCDS31818.1	12q13.13	2012-08-09			ENSG00000205330	ENSG00000205330		"""GPCR / Class A : Olfactory receptors"""	8355	protein-coding gene	gene with protein product							Standard	NM_001005182		Approved	OST267	uc010spi.2	Q96RD1	OTTHUMG00000168102	ENST00000379668.2:c.640C>T	12.37:g.55715023C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54001290	NM_001005182	B2RNM0	Silent	SNP	ENST00000379668.2	37	CCDS31818.1																																																																																				0.388	OR6C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398152.1	NM_001005182	
OR6C70	390327	broad.mit.edu	37	12	55863004	55863005	+	Frame_Shift_Del	DEL	AT	AT	-	rs545618554		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	AT	AT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:55863004_55863005delAT	ENST00000327335.4	-	1	917_918	c.918_919delAT	c.(916-921)atatttfs	p.F307fs	RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000555146.1_RNA	NM_001005499.1	NP_001005499.1	A6NIJ9	O6C70_HUMAN	olfactory receptor, family 6, subfamily C, member 70	307						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S308fs*>5(1)		autonomic_ganglia(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	18						GAAGCAGAAAATATCTTTCTAA	0.317																																					p.306_307del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.918_919del	12						.																																			54149272	SO:0001589	frameshift_variant	390327	exon1				CCDS31825.1	12q13.2	2013-09-23			ENSG00000184954	ENSG00000184954		"""GPCR / Class A : Olfactory receptors"""	31299	protein-coding gene	gene with protein product							Standard	NM_001005499		Approved		uc010spn.2	A6NIJ9	OTTHUMG00000171127	ENST00000327335.4:c.918_919delAT	12.37:g.55863006_55863007delAT	ENSP00000329153:p.Phe307fs	Somatic		Capture	Illumina HiSeq	Phase_I	54149271	NM_001005499		Frame_Shift_Del	DEL	ENST00000327335.4	37	CCDS31825.1																																																																																				0.317	OR6C70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411820.1		
ITGA7	3679	broad.mit.edu	37	12	56092685	56092685	+	Silent	SNP	C	C	T	rs199699185	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:56092685C>T	ENST00000555728.1	-	7	967	c.939G>A	c.(937-939)tcG>tcA	p.S313S	ITGA7_ENST00000553804.1_Silent_p.S273S|ITGA7_ENST00000257879.6_Silent_p.S269S|ITGA7_ENST00000452168.2_Silent_p.S176S|ITGA7_ENST00000347027.6_Silent_p.S269S|ITGA7_ENST00000394229.2_Silent_p.S269S|ITGA7_ENST00000257880.7_Silent_p.S313S|ITGA7_ENST00000394230.2_Silent_p.S273S			Q13683	ITA7_HUMAN	integrin, alpha 7	313					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)	p.S269S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GACCTTTCCCCGAGTCAATAG	0.622													C|||	2	0.000399361	0.0	0.0	5008	,	,		15925	0.001		0.0	False		,,,				2504	0.001				p.S176S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G528A	12						.						18.0	19.0	19.0					12																	56092685		2203	4300	6503	54378952	SO:0001819	synonymous_variant	3679	exon6				CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"""Integrins"""	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.939G>A	12.37:g.56092685C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54378952	NM_001144997	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Silent	SNP	ENST00000555728.1	37																																																																																					0.622	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206	
CDK2	1017	broad.mit.edu	37	12	56362585	56362585	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:56362585G>T	ENST00000266970.4	+	4	579	c.339G>T	c.(337-339)caG>caT	p.Q113H	PMEL_ENST00000360714.4_5'Flank|PMEL_ENST00000550464.1_5'Flank|PMEL_ENST00000536427.1_5'Flank|PMEL_ENST00000548493.1_5'Flank|PMEL_ENST00000550447.1_5'Flank|CDK2_ENST00000556656.1_3'UTR|PMEL_ENST00000548747.1_5'Flank|CDK2_ENST00000440311.2_Missense_Mutation_p.Q87H|RP11-973D8.4_ENST00000554022.1_RNA|PMEL_ENST00000539511.1_5'Flank|PMEL_ENST00000449260.2_5'Flank|PMEL_ENST00000548689.1_5'Flank|CDK2_ENST00000354056.4_Missense_Mutation_p.Q113H|CDK2_ENST00000553376.1_Missense_Mutation_p.Q113H|PMEL_ENST00000552882.1_5'Flank	NM_001798.3	NP_001789.2	P24941	CDK2_HUMAN	cyclin-dependent kinase 2	113	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|blood coagulation (GO:0007596)|cellular response to nitric oxide (GO:0071732)|centrosome duplication (GO:0051298)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|histone phosphorylation (GO:0016572)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|mitotic nuclear division (GO:0007067)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transport (GO:0006813)|Ras protein signal transduction (GO:0007265)|regulation of gene silencing (GO:0060968)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	Cajal body (GO:0015030)|centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|condensed chromosome (GO:0000793)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|X chromosome (GO:0000805)|Y chromosome (GO:0000806)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|metal ion binding (GO:0046872)	p.Q113H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	18			UCEC - Uterine corpus endometrioid carcinoma (6;0.123)|OV - Ovarian serous cystadenocarcinoma(18;0.235)		Bosutinib(DB06616)	AGCTGCTCCAGGGCCTAGCTT	0.502																																					p.Q113H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G339T	12						.						121.0	112.0	115.0					12																	56362585		2203	4300	6503	54648852	SO:0001583	missense	1017	exon4			M68520	CCDS8898.1, CCDS8899.1	12q13	2011-11-08				ENSG00000123374		"""Cyclin-dependent kinases"""	1771	protein-coding gene	gene with protein product		116953				1717994, 8275715	Standard	NM_001798		Approved		uc001sit.4	P24941		ENST00000266970.4:c.339G>T	12.37:g.56362585G>T	ENSP00000266970:p.Gln113His	Somatic		Capture	Illumina HiSeq	Phase_I	54648852	NM_052827	A8K7C6|O75100	Missense_Mutation	SNP	ENST00000266970.4	37	CCDS8898.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.356525	0.41700	.	.	ENSG00000123374	ENST00000266970;ENST00000553376;ENST00000440311;ENST00000354056	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	4.53	1.56	0.23342	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	0.56645	0.1999	L	0.52573	1.65	0.58432	D	0.999998	B;B;B	0.18013	0.025;0.016;0.015	B;B;B	0.23852	0.049;0.022;0.017	T	0.51196	-0.8736	10	0.56958	D	0.05	-14.1454	7.1972	0.25860	0.3954:0.0:0.6046:0.0	.	87;113;113	E7ESI2;P24941-2;P24941	.;.;CDK2_HUMAN	H	113;113;87;113	ENSP00000266970:Q113H;ENSP00000452514:Q113H;ENSP00000393605:Q87H;ENSP00000243067:Q113H	ENSP00000266970:Q113H	Q	+	3	2	CDK2	54648852	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	1.753000	0.38359	0.219000	0.20840	0.462000	0.41574	CAG		0.502	CDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409650.1		
ERBB3	2065	broad.mit.edu	37	12	56478852	56478852	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:56478852G>A	ENST00000267101.3	+	3	748	c.308G>A	c.(307-309)cGc>cAc	p.R103H	ERBB3_ENST00000450146.2_Intron|ERBB3_ENST00000415288.2_Missense_Mutation_p.R44H|ERBB3_ENST00000411731.2_Missense_Mutation_p.R103H	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	103					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)	p.R103H(1)		central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			CCCAACCTCCGCGTGGTGCGA	0.517																																					p.R103H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G308A	12						.						183.0	157.0	166.0					12																	56478852		2203	4300	6503	54765119	SO:0001583	missense	2065	exon3			M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"""lethal congenital contracture syndrome 2"""	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.308G>A	12.37:g.56478852G>A	ENSP00000267101:p.Arg103His	Somatic		Capture	Illumina HiSeq	Phase_I	54765119	NM_001005915	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Missense_Mutation	SNP	ENST00000267101.3	37	CCDS31833.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.109161	0.77096	.	.	ENSG00000065361	ENST00000549282;ENST00000549061;ENST00000267101;ENST00000394099;ENST00000411731;ENST00000549672;ENST00000415288	T;D;D;T;D;D	0.84944	-1.47;-1.92;-1.92;-1.47;-1.92;-1.92	5.82	5.82	0.92795	EGF receptor, L domain (1);	0.101624	0.42172	D	0.000748	D	0.94076	0.8101	M	0.90705	3.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.94635	0.7825	10	0.87932	D	0	.	18.8728	0.92322	0.0:0.0:1.0:0.0	.	103;103	P21860;P21860-2	ERBB3_HUMAN;.	H	103;44;103;103;103;44;44	ENSP00000448636:R103H;ENSP00000449138:R44H;ENSP00000267101:R103H;ENSP00000415753:R103H;ENSP00000449713:R44H;ENSP00000408340:R44H	ENSP00000267101:R103H	R	+	2	0	ERBB3	54765119	1.000000	0.71417	0.967000	0.41034	0.084000	0.17831	9.282000	0.95840	2.748000	0.94277	0.655000	0.94253	CGC		0.517	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3		
ESYT1	23344	broad.mit.edu	37	12	56528163	56528163	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:56528163C>T	ENST00000394048.5	+	15	1847	c.1583C>T	c.(1582-1584)gCg>gTg	p.A528V	ESYT1_ENST00000267113.4_Missense_Mutation_p.A538V|ESYT1_ENST00000541590.1_Missense_Mutation_p.A538V	NM_001184796.1|NM_015292.2	NP_001171725.1|NP_056107.1	Q9BSJ8	ESYT1_HUMAN	extended synaptotagmin-like protein 1	528	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid transport (GO:0006869)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)	p.A528V(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(10)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	28						TGGGAGGAAGCGTTCCGGTTC	0.507																																					p.A528V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1583T	12						.						186.0	166.0	173.0					12																	56528163		2203	4300	6503	54814430	SO:0001583	missense	23344	exon15			AK074368	CCDS8904.1, CCDS53801.1	12q13.2	2014-07-02	2009-06-23	2009-06-23		ENSG00000139641		"""Synaptotagmins"""	29534	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member A"""	FAM62A		9872452, 10350628, 17672888	Standard	NM_015292		Approved	MBC2, KIAA0747	uc001sjr.3	Q9BSJ8		ENST00000394048.5:c.1583C>T	12.37:g.56528163C>T	ENSP00000377612:p.Ala528Val	Somatic		Capture	Illumina HiSeq	Phase_I	54814430	NM_015292	A0FGR7|A8K2S2|O94848|Q6PJN4|Q9H6J1|Q9H6W2|Q9Y416	Missense_Mutation	SNP	ENST00000394048.5	37	CCDS8904.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.952250	0.73787	.	.	ENSG00000139641	ENST00000394048;ENST00000402331;ENST00000267113;ENST00000541590	T;T;T	0.68903	-0.36;-0.36;-0.36	5.28	5.28	0.74379	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.050689	0.85682	D	0.000000	T	0.73916	0.3648	L	0.42245	1.32	0.58432	D	0.999993	D;D	0.76494	0.999;0.999	D;D	0.67548	0.952;0.93	T	0.68788	-0.5316	10	0.23891	T	0.37	-17.4297	16.2109	0.82158	0.0:1.0:0.0:0.0	.	538;528	Q9BSJ8-2;Q9BSJ8	.;ESYT1_HUMAN	V	528;482;538;538	ENSP00000377612:A528V;ENSP00000267113:A538V;ENSP00000445952:A538V	ENSP00000267113:A538V	A	+	2	0	ESYT1	54814430	0.968000	0.33430	0.999000	0.59377	0.952000	0.60782	3.468000	0.53086	2.633000	0.89246	0.655000	0.94253	GCG		0.507	ESYT1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000407906.1	NM_015292	
SLC39A5	283375	broad.mit.edu	37	12	56629416	56629416	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:56629416G>A	ENST00000266980.4	+	6	1170	c.877G>A	c.(877-879)Gga>Aga	p.G293R	SLC39A5_ENST00000454355.2_Missense_Mutation_p.G293R|ANKRD52_ENST00000548241.1_5'Flank	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	293					cellular response to zinc ion starvation (GO:0034224)|G1 to G0 transition involved in cell differentiation (GO:0070315)|neural precursor cell proliferation (GO:0061351)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)	p.G292R(2)		NS(1)|cervix(6)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GTCAGTGCTCGGAGGCCTCTT	0.617																																					p.G293R												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G877A	12						.						148.0	155.0	153.0					12																	56629416		2203	4300	6503	54915683	SO:0001583	missense	283375	exon6				CCDS8912.2	12q13.3	2013-07-17	2013-07-17		ENSG00000139540	ENSG00000139540		"""Solute carriers"""	20502	protein-coding gene	gene with protein product		608730	"""solute carrier family 39 (metal ion transporter), member 5"""				Standard	NM_173596		Approved		uc010sqj.2	Q6ZMH5	OTTHUMG00000156962	ENST00000266980.4:c.877G>A	12.37:g.56629416G>A	ENSP00000266980:p.Gly293Arg	Somatic		Capture	Illumina HiSeq	Phase_I	54915683	NM_001135195	B2R808|Q8N6Y3	Missense_Mutation	SNP	ENST00000266980.4	37	CCDS8912.2	.	.	.	.	.	.	.	.	.	.	G	19.86	3.905464	0.72868	.	.	ENSG00000139540	ENST00000454355;ENST00000266980	T;T	0.53857	0.6;0.6	3.7	3.7	0.42460	.	0.000000	0.49916	D	0.000126	T	0.75295	0.3830	M	0.90870	3.155	0.48696	D	0.999698	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.985	T	0.80410	-0.1394	10	0.87932	D	0	-9.8824	11.2733	0.49153	0.0:0.0:1.0:0.0	.	293;184	Q6ZMH5;B4DPG8	S39A5_HUMAN;.	R	293	ENSP00000405360:G293R;ENSP00000266980:G293R	ENSP00000266980:G293R	G	+	1	0	SLC39A5	54915683	1.000000	0.71417	0.982000	0.44146	0.689000	0.40095	5.380000	0.66202	2.372000	0.80975	0.655000	0.94253	GGA		0.617	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346834.1	NM_173596	
ANKRD52	283373	broad.mit.edu	37	12	56649628	56649628	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:56649628G>A	ENST00000267116.7	-	5	523	c.402C>T	c.(400-402)aaC>aaT	p.N134N		NM_173595.3	NP_775866.2	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	134								p.N134N(1)		endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1)	29						TGTCAGCCACGTTGAGGCTGC	0.632																																					p.N134N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C402T	12						.						14.0	16.0	15.0					12																	56649628		2036	4170	6206	54935895	SO:0001819	synonymous_variant	283373	exon5			AK091555	CCDS44920.1	12q13.3	2013-01-10			ENSG00000139645	ENSG00000139645		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	26614	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit C"""						Standard	NM_173595		Approved	FLJ34236, PP6-ARS-C	uc001skm.4	Q8NB46	OTTHUMG00000170329	ENST00000267116.7:c.402C>T	12.37:g.56649628G>A		Somatic		Capture	Illumina HiSeq	Phase_I	54935895	NM_173595	A6NE79|B1Q2K2	Silent	SNP	ENST00000267116.7	37	CCDS44920.1																																																																																				0.632	ANKRD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408539.1	NM_173595	
SPRYD4	283377	broad.mit.edu	37	12	56863100	56863100	+	Silent	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:56863100C>A	ENST00000338146.5	+	2	438	c.363C>A	c.(361-363)tcC>tcA	p.S121S	MIP_ENST00000555551.1_5'Flank	NM_207344.3	NP_997227	Q8WW59	SPRY4_HUMAN	SPRY domain containing 4	121	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.S121S(1)		kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)	7						ATGATCGTTCCTGGGTGTTCA	0.562																																					p.S121S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C363A	12						.						162.0	151.0	155.0					12																	56863100		2203	4300	6503	55149367	SO:0001819	synonymous_variant	283377	exon2			AL832247	CCDS8920.1	12q13.3	2006-03-09				ENSG00000176422			27468	protein-coding gene	gene with protein product							Standard	NM_207344		Approved	DKFZp686N0877	uc001sli.4	Q8WW59		ENST00000338146.5:c.363C>A	12.37:g.56863100C>A		Somatic		Capture	Illumina HiSeq	Phase_I	55149367	NM_207344	A8K7A5	Silent	SNP	ENST00000338146.5	37	CCDS8920.1																																																																																				0.562	SPRYD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_207344	
NACA	4666	broad.mit.edu	37	12	57114335	57114335	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:57114335C>A	ENST00000454682.1	-	3	1260	c.979G>T	c.(979-981)Ggt>Tgt	p.G327C	NACA_ENST00000552540.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.G327C|NACA_ENST00000551793.1_Intron|NACA_ENST00000548563.1_Intron|NACA_ENST00000546392.1_Intron|NACA_ENST00000393891.4_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	327	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.G327C(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						GCACTAGGACCTGTTTGACCT	0.473			T	BCL6	NHL																																p.G327C			Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G979T	12						.						70.0	63.0	65.0					12																	57114335		1568	3582	5150	55400602	SO:0001583	missense	4666	exon3			X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.979G>T	12.37:g.57114335C>A	ENSP00000403817:p.Gly327Cys	Somatic		Capture	Illumina HiSeq	Phase_I	55400602	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	37		.	.	.	.	.	.	.	.	.	.	C	8.531	0.870913	0.17322	.	.	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.70399	-0.48;0.62	3.13	-0.167	0.13347	.	.	.	.	.	T	0.45115	0.1326	N	0.08118	0	0.09310	N	1	B;B	0.19445	0.036;0.0	B;B	0.18561	0.022;0.006	T	0.35847	-0.9772	9	0.87932	D	0	.	3.1624	0.06524	0.2021:0.5381:0.0:0.2598	.	327;327	E9PAV3;F8VU71	.;.	C	327	ENSP00000403817:G327C;ENSP00000448035:G327C	ENSP00000403817:G327C	G	-	1	0	NACA	55400602	0.000000	0.05858	0.008000	0.14137	0.001000	0.01503	-0.011000	0.12721	0.029000	0.15352	-1.225000	0.01585	GGT		0.473	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
GPR182	11318	broad.mit.edu	37	12	57389041	57389041	+	Silent	SNP	C	C	T	rs565165510		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:57389041C>T	ENST00000300098.1	+	2	267	c.48C>T	c.(46-48)acC>acT	p.T16T	RP11-474N8.5_ENST00000556850.1_RNA|HBCBP_ENST00000600202.1_5'Flank	NM_007264.3	NP_009195.1	O15218	GP182_HUMAN	G protein-coupled receptor 182	16					cell surface receptor signaling pathway (GO:0007166)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)	p.T16T(1)		endometrium(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	15						AGGGGGTCACCGCAGTGCCTA	0.592													C|||	1	0.000199681	0.0	0.0	5008	,	,		16661	0.0		0.0	False		,,,				2504	0.001				p.T16T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C48T	12						.						121.0	117.0	118.0					12																	57389041		2203	4300	6503	55675308	SO:0001819	synonymous_variant	11318	exon2			Y13583	CCDS8927.1	12q13.3	2012-08-21	2007-09-24	2007-09-24		ENSG00000166856		"""GPCR / Class A : Orphans"""	13708	protein-coding gene	gene with protein product		605307	"""adrenomedullin receptor"""	ADMR		9367907, 9535752	Standard	NM_007264		Approved	hrhAMR, G10D, AM-R	uc001smk.3	O15218		ENST00000300098.1:c.48C>T	12.37:g.57389041C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55675308	NM_007264		Silent	SNP	ENST00000300098.1	37	CCDS8927.1																																																																																				0.592	GPR182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411212.1	NM_007264	
NAB2	4665	broad.mit.edu	37	12	57485187	57485187	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:57485187C>T	ENST00000300131.3	+	2	741	c.363C>T	c.(361-363)ccC>ccT	p.P121P	NAB2_ENST00000342556.6_Silent_p.P121P|NAB2_ENST00000554718.1_3'UTR|NAB2_ENST00000357680.4_Silent_p.P121P	NM_005967.3	NP_005958.1	Q15742	NAB2_HUMAN	NGFI-A binding protein 2 (EGR1 binding protein 2)	121					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.P121P(2)		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						CTGCTGTTCCCGTCTCCAGCA	0.617																																					p.P121P												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C363T	12						.						75.0	82.0	80.0					12																	57485187		2203	4300	6503	55771454	SO:0001819	synonymous_variant	4665	exon2			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.363C>T	12.37:g.57485187C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55771454	NM_005967	B2RAK3|O76006|Q14797	Silent	SNP	ENST00000300131.3	37	CCDS8930.1																																																																																				0.617	NAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412222.1	NM_005967	
NAB2	4665	broad.mit.edu	37	12	57486939	57486939	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:57486939G>A	ENST00000300131.3	+	5	1615	c.1237G>A	c.(1237-1239)Gcc>Acc	p.A413T	NAB2_ENST00000342556.6_Missense_Mutation_p.A413T|NAB2_ENST00000357680.4_3'UTR	NM_005967.3	NP_005958.1	Q15742	NAB2_HUMAN	NGFI-A binding protein 2 (EGR1 binding protein 2)	413					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.A413T(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						GGAGGACAGCGCCAGCCTGTC	0.597																																					p.A413T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1237A	12						.						74.0	82.0	79.0					12																	57486939		2203	4300	6503	55773206	SO:0001583	missense	4665	exon5			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.1237G>A	12.37:g.57486939G>A	ENSP00000300131:p.Ala413Thr	Somatic		Capture	Illumina HiSeq	Phase_I	55773206	NM_005967	B2RAK3|O76006|Q14797	Missense_Mutation	SNP	ENST00000300131.3	37	CCDS8930.1	.	.	.	.	.	.	.	.	.	.	G	19.82	3.898102	0.72639	.	.	ENSG00000166886	ENST00000300131;ENST00000342556	.	.	.	4.98	4.98	0.66077	.	0.170614	0.37761	N	0.001952	T	0.28599	0.0708	N	0.08118	0	0.80722	D	1	D	0.57571	0.98	B	0.41860	0.368	T	0.07177	-1.0786	9	0.20519	T	0.43	-10.9252	16.1226	0.81369	0.0:0.0:1.0:0.0	.	413	Q15742	NAB2_HUMAN	T	413	.	ENSP00000300131:A413T	A	+	1	0	NAB2	55773206	1.000000	0.71417	0.992000	0.48379	0.989000	0.77384	5.143000	0.64826	2.755000	0.94549	0.655000	0.94253	GCC		0.597	NAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412222.1	NM_005967	
LRP1	4035	broad.mit.edu	37	12	57595353	57595353	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:57595353C>T	ENST00000243077.3	+	66	10885	c.10419C>T	c.(10417-10419)tgC>tgT	p.C3473C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3473	LDL-receptor class A 24. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)	p.C3473C(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	TCTGGGTCTGCGACCGGGACA	0.632																																					p.C3473C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C10419T	12						.						82.0	75.0	77.0					12																	57595353		2203	4300	6503	55881620	SO:0001819	synonymous_variant	4035	exon66			X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.10419C>T	12.37:g.57595353C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55881620	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																				0.632	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
R3HDM2	22864	broad.mit.edu	37	12	57662832	57662832	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:57662832G>A	ENST00000347140.3	-	17	2096	c.1706C>T	c.(1705-1707)gCg>gTg	p.A569V	R3HDM2_ENST00000358907.2_Missense_Mutation_p.A569V|R3HDM2_ENST00000402412.1_Missense_Mutation_p.A583V|R3HDM2_ENST00000413953.2_Missense_Mutation_p.A296V|R3HDM2_ENST00000546843.1_5'Flank|RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000403821.2_Missense_Mutation_p.A603V|R3HDM2_ENST00000441731.2_Missense_Mutation_p.A264V			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	569	Gln-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.A230V(1)|p.A569V(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	22						TTGGTAAGCCGCCTGCTGCTG	0.532																																					p.A569V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1706T	12						.						96.0	94.0	95.0					12																	57662832		2203	4300	6503	55949099	SO:0001583	missense	22864	exon15			AB023219	CCDS8937.2	12q13.3	2012-11-19			ENSG00000179912	ENSG00000179912			29167	protein-coding gene	gene with protein product							Standard	NM_014925		Approved	KIAA1002	uc009zpm.1	Q9Y2K5	OTTHUMG00000171568	ENST00000347140.3:c.1706C>T	12.37:g.57662832G>A	ENSP00000317903:p.Ala569Val	Somatic		Capture	Illumina HiSeq	Phase_I	55949099	NM_014925	Q2M1T9|Q3ZCT5	Missense_Mutation	SNP	ENST00000347140.3	37	CCDS8937.2	.	.	.	.	.	.	.	.	.	.	G	19.17	3.775356	0.70107	.	.	ENSG00000179912	ENST00000413953;ENST00000393811;ENST00000347140;ENST00000402412;ENST00000358907;ENST00000441731;ENST00000429355;ENST00000403821	T;T;T;T;T;T;T;T	0.45276	0.9;0.9;1.92;1.92;1.92;0.91;1.5;1.91	5.07	5.07	0.68467	.	0.122723	0.37623	N	0.002008	T	0.19446	0.0467	N	0.08118	0	0.34345	D	0.689203	P;P;P;B	0.40083	0.702;0.569;0.569;0.021	B;B;B;B	0.23852	0.049;0.049;0.049;0.016	T	0.22277	-1.0221	10	0.15952	T	0.53	-3.5994	17.7673	0.88482	0.0:0.0:1.0:0.0	.	603;583;569;296	B5MCG9;B5MCU0;Q9Y2K5;E9PAL1	.;.;R3HD2_HUMAN;.	V	296;296;569;583;569;264;334;603	ENSP00000409146:A296V;ENSP00000377400:A296V;ENSP00000317903:A569V;ENSP00000385839:A583V;ENSP00000351784:A569V;ENSP00000408536:A264V;ENSP00000394676:A334V;ENSP00000385169:A603V	ENSP00000317903:A569V	A	-	2	0	R3HDM2	55949099	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	5.531000	0.67148	2.805000	0.96524	0.655000	0.94253	GCG		0.532	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925	
INHBC	3626	broad.mit.edu	37	12	57843559	57843559	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:57843559C>T	ENST00000309668.2	+	2	940	c.813C>T	c.(811-813)taC>taT	p.Y271Y		NM_005538.2	NP_005529.1	P55103	INHBC_HUMAN	inhibin, beta C	271					growth (GO:0040007)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	transforming growth factor beta receptor binding (GO:0005160)	p.Y271Y(2)		breast(2)|endometrium(1)|large_intestine(6)|liver(2)|lung(4)|prostate(1)	16						CTGAGGGCTACGCCATGAACT	0.542																																					p.Y271Y												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C813T	12						.						93.0	77.0	82.0					12																	57843559		2203	4300	6503	56129826	SO:0001819	synonymous_variant	3626	exon2				CCDS8938.1	12q13	2008-02-05				ENSG00000175189			6068	protein-coding gene	gene with protein product		601233				7826378	Standard	NM_005538		Approved		uc001snv.1	P55103	OTTHUMG00000169994	ENST00000309668.2:c.813C>T	12.37:g.57843559C>T		Somatic		Capture	Illumina HiSeq	Phase_I	56129826	NM_005538	A1L3Y2	Silent	SNP	ENST00000309668.2	37	CCDS8938.1																																																																																				0.542	INHBC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406770.1	NM_005538	
GRIP1	23426	broad.mit.edu	37	12	66800084	66800084	+	Missense_Mutation	SNP	G	G	A	rs201662071		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:66800084G>A	ENST00000398016.3	-	15	1875	c.1807C>T	c.(1807-1809)Cgc>Tgc	p.R603C	GRIP1_ENST00000359742.4_Missense_Mutation_p.R655C|GRIP1_ENST00000542021.1_5'UTR|GRIP1_ENST00000286445.7_Missense_Mutation_p.R655C	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)	p.R603S(1)|p.R603C(1)		NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		TCATCTTTGCGGATTTTGAGC	0.393																																					p.R603C												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C1807T	12						.						131.0	122.0	125.0					12																	66800084		1896	4124	6020	65086351	SO:0001583	missense	23426	exon15			AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.1807C>T	12.37:g.66800084G>A	ENSP00000381098:p.Arg603Cys	Somatic		Capture	Illumina HiSeq	Phase_I	65086351	NM_001178074	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	37	CCDS41807.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.027953	0.93518	.	.	ENSG00000155974	ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215	T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6	5.38	5.38	0.77491	PDZ/DHR/GLGF (4);	0.049933	0.85682	D	0.000000	T	0.64560	0.2609	M	0.90082	3.085	0.80722	D	1	P;P;D;D	0.76494	0.465;0.683;0.998;0.999	B;B;D;D	0.71414	0.232;0.38;0.932;0.973	T	0.71006	-0.4717	9	.	.	.	-14.5406	19.5067	0.95121	0.0:0.0:1.0:0.0	.	603;655;603;655	F5H4N6;Q9Y3R0;Q9Y3R0-3;Q9Y3R0-2	.;GRIP1_HUMAN;.;.	C	603;655;655;603;547;495	ENSP00000381098:R603C;ENSP00000352780:R655C;ENSP00000286445:R655C;ENSP00000446047:R603C;ENSP00000446024:R547C;ENSP00000446011:R495C	.	R	-	1	0	GRIP1	65086351	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.992000	0.88273	2.682000	0.91365	0.491000	0.48974	CGC		0.393	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2		
PTPRB	5787	broad.mit.edu	37	12	70964983	70964983	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:70964983C>T	ENST00000261266.5	-	11	2568	c.2539G>A	c.(2539-2541)Gac>Aac	p.D847N	PTPRB_ENST00000451516.2_Missense_Mutation_p.D757N|PTPRB_ENST00000551525.1_Missense_Mutation_p.D1064N|PTPRB_ENST00000550857.1_Missense_Mutation_p.D757N|PTPRB_ENST00000538708.1_Missense_Mutation_p.D847N|PTPRB_ENST00000550358.1_Missense_Mutation_p.D977N|PTPRB_ENST00000334414.6_Missense_Mutation_p.D1065N	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	847	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.D1065N(1)|p.D847N(1)		breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			TCATATTGGTCGACATCCCCA	0.448																																					p.D1065N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3193A	12						.						96.0	91.0	93.0					12																	70964983		1997	4166	6163	69251250	SO:0001583	missense	5787	exon13			X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.2539G>A	12.37:g.70964983C>T	ENSP00000261266:p.Asp847Asn	Somatic		Capture	Illumina HiSeq	Phase_I	69251250	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.856099	0.91355	.	.	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3;0.3;0.3	5.75	5.75	0.90469	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.75910	0.3914	M	0.73217	2.22	0.80722	D	1	D;D;D;P;D;D;D	0.89917	1.0;1.0;1.0;0.921;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;0.999;0.943;1.0;1.0;1.0	T	0.70970	-0.4727	10	0.28530	T	0.3	.	19.9662	0.97271	0.0:1.0:0.0:0.0	.	757;847;944;1064;1065;847;977	P23467-2;F5H3G6;Q6ZR19;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;.;PTPRB_HUMAN;.	N	1065;757;977;847;757;847;1064;944	ENSP00000334928:D1065N;ENSP00000393028:D757N;ENSP00000448058:D977N;ENSP00000438927:D847N;ENSP00000447302:D757N;ENSP00000261266:D847N;ENSP00000448349:D1064N;ENSP00000446982:D944N	ENSP00000261266:D847N	D	-	1	0	PTPRB	69251250	1.000000	0.71417	0.957000	0.39632	0.772000	0.43724	7.456000	0.80751	2.701000	0.92244	0.650000	0.86243	GAC		0.448	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
ZFC3H1	196441	broad.mit.edu	37	12	72021607	72021607	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:72021607C>T	ENST00000378743.3	-	21	4412	c.4054G>A	c.(4054-4056)Gca>Aca	p.A1352T		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1352					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.A1352T(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						AGCACACTTGCTTCTAAATTA	0.398																																					p.A1352T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4054A	12						.						130.0	117.0	121.0					12																	72021607		1883	4120	6003	70307874	SO:0001583	missense	196441	exon21			AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.4054G>A	12.37:g.72021607C>T	ENSP00000368017:p.Ala1352Thr	Somatic		Capture	Illumina HiSeq	Phase_I	70307874	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	37	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.946079	0.73672	.	.	ENSG00000133858	ENST00000378743	T	0.33865	1.39	5.6	5.6	0.85130	Tetratricopeptide-like helical (1);	0.059520	0.64402	D	0.000004	T	0.28928	0.0718	L	0.27053	0.805	0.80722	D	1	B	0.18863	0.031	B	0.15870	0.014	T	0.06807	-1.0806	10	0.17369	T	0.5	.	19.6014	0.95563	0.0:1.0:0.0:0.0	.	1352	O60293	ZC3H1_HUMAN	T	1352	ENSP00000368017:A1352T	ENSP00000368017:A1352T	A	-	1	0	ZFC3H1	70307874	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.071000	0.50041	2.635000	0.89317	0.655000	0.94253	GCA		0.398	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982	
NAV3	89795	broad.mit.edu	37	12	78401200	78401200	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:78401200G>A	ENST00000397909.2	+	8	2055	c.1882G>A	c.(1882-1884)Gcg>Acg	p.A628T	NAV3_ENST00000536525.2_Missense_Mutation_p.A628T|NAV3_ENST00000228327.6_Missense_Mutation_p.A628T|NAV3_ENST00000266692.7_Missense_Mutation_p.A628T			Q8IVL0	NAV3_HUMAN	neuron navigator 3	628						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.A628T(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						CCCGAATACCGCGACAGTGGC	0.488										HNSCC(70;0.22)																											p.A628T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1882A	12						.						116.0	113.0	114.0					12																	78401200		2053	4198	6251	76925331	SO:0001583	missense	89795	exon8			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.1882G>A	12.37:g.78401200G>A	ENSP00000381007:p.Ala628Thr	Somatic		Capture	Illumina HiSeq	Phase_I	76925331	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.	.	.	.	.	.	.	.	.	.	G	21.4	4.136981	0.77775	.	.	ENSG00000067798	ENST00000549464;ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692	T;T;T;T;T	0.15603	2.41;2.41;2.41;2.41;2.41	4.84	4.84	0.62591	.	0.181717	0.25628	U	0.029369	T	0.41073	0.1143	M	0.61703	1.905	0.80722	D	1	D;D	0.76494	0.996;0.999	P;D	0.80764	0.652;0.994	T	0.30001	-0.9993	10	0.62326	D	0.03	-7.8341	17.9357	0.89011	0.0:0.0:1.0:0.0	.	628;628	Q8IVL0;Q8IVL0-2	NAV3_HUMAN;.	T	628	ENSP00000446628:A628T;ENSP00000446132:A628T;ENSP00000381007:A628T;ENSP00000228327:A628T;ENSP00000266692:A628T	ENSP00000228327:A628T	A	+	1	0	NAV3	76925331	1.000000	0.71417	0.936000	0.37596	0.357000	0.29423	9.624000	0.98398	2.243000	0.73865	0.555000	0.69702	GCG		0.488	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
PPP1R12A	4659	broad.mit.edu	37	12	80180204	80180204	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:80180204T>C	ENST00000450142.2	-	22	3123	c.2857A>G	c.(2857-2859)Aca>Gca	p.T953A	PPP1R12A_ENST00000550107.1_Missense_Mutation_p.T897A|PPP1R12A_ENST00000437004.2_Intron|PPP1R12A_ENST00000261207.5_Missense_Mutation_p.T953A|PPP1R12A_ENST00000546369.1_Missense_Mutation_p.T866A	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	953					centrosome organization (GO:0051297)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of catalytic activity (GO:0043086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)|regulation of nucleocytoplasmic transport (GO:0046822)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|PTW/PP1 phosphatase complex (GO:0072357)	14-3-3 protein binding (GO:0071889)|enzyme inhibitor activity (GO:0004857)|phosphatase regulator activity (GO:0019208)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.T953A(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|liver(1)|lung(4)|ovary(2)|skin(1)	29						TCCATATTTGTATCATGTAGC	0.333																																					p.T866A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2596G	12						.						135.0	130.0	132.0					12																	80180204		1806	4070	5876	78704335	SO:0001583	missense	4659	exon22			D87930	CCDS44947.1, CCDS44948.1, CCDS58259.1, CCDS58260.1	12q15-q21	2013-01-18	2011-10-04	2001-08-10	ENSG00000058272	ENSG00000058272		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	7618	protein-coding gene	gene with protein product	"""myosin phosphatase-targeting subunit 1"", ""myosin binding subunit"""	602021	"""protein phosphatase 1, regulatory (inhibitor) subunit 12A"""	MYPT1		9286714	Standard	NM_002480		Approved	MBS, M130	uc001syz.3	O14974	OTTHUMG00000170100	ENST00000450142.2:c.2857A>G	12.37:g.80180204T>C	ENSP00000389168:p.Thr953Ala	Somatic		Capture	Illumina HiSeq	Phase_I	78704335	NM_001143886	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Missense_Mutation	SNP	ENST00000450142.2	37	CCDS44947.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.91|16.91	3.252798|3.252798	0.59212|0.59212	.|.	.|.	ENSG00000058272|ENSG00000058272	ENST00000550299|ENST00000261207;ENST00000546189;ENST00000341878;ENST00000312727;ENST00000450142;ENST00000546369;ENST00000550107	.|T;T;T;T	.|0.36340	.|1.31;1.31;1.33;1.26	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.35624|0.35624	0.0938|0.0938	N|N	0.11560|0.11560	0.145|0.145	0.80722|0.80722	D|D	1|1	.|B;D	.|0.58970	.|0.135;0.984	.|B;D	.|0.68192	.|0.355;0.956	T|T	0.13202|0.13202	-1.0518|-1.0518	5|10	.|0.02654	.|T	.|1	.|.	16.0023|16.0023	0.80306|0.80306	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|897;953	.|O14974-3;O14974	.|.;MYPT1_HUMAN	M|A	135|953;953;897;894;953;866;897	.|ENSP00000261207:T953A;ENSP00000389168:T953A;ENSP00000449514:T866A;ENSP00000446855:T897A	.|ENSP00000261207:T953A	I|T	-|-	3|1	3|0	PPP1R12A|PPP1R12A	78704335|78704335	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.477000|7.477000	0.81069|0.81069	2.177000|2.177000	0.69029|0.69029	0.533000|0.533000	0.62120|0.62120	ATA|ACA		0.333	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480	
ALX1	8092	broad.mit.edu	37	12	85674186	85674186	+	Silent	SNP	C	C	T	rs141968055		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:85674186C>T	ENST00000316824.3	+	1	302	c.147C>T	c.(145-147)tgC>tgT	p.C49C		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	49					anterior/posterior pattern specification (GO:0009952)|brain development (GO:0007420)|cartilage condensation (GO:0001502)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|mesenchymal cell development (GO:0014031)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.C49C(1)		breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|ovary(1)	26				GBM - Glioblastoma multiforme(134;0.134)		CAGGCAAATGCGTGCAGGCCT	0.607																																					p.C49C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C147T	12						.	C		1,4405	2.1+/-5.4	0,1,2202	50.0	50.0	50.0		147	3.6	1.0	12	dbSNP_134	50	0,8600		0,0,4300	no	coding-synonymous	ALX1	NM_006982.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		49/327	85674186	1,13005	2203	4300	6503	84198317	SO:0001819	synonymous_variant	8092	exon1			U31986	CCDS9028.1	12q21.31	2011-06-20	2007-07-26	2007-07-26		ENSG00000180318		"""Homeoboxes / PRD class"""	1494	protein-coding gene	gene with protein product		601527	"""cartilage paired-class homeoprotein 1"""	CART1		8756334, 7592751	Standard	NM_006982		Approved		uc001tae.4	Q15699	OTTHUMG00000169820	ENST00000316824.3:c.147C>T	12.37:g.85674186C>T		Somatic		Capture	Illumina HiSeq	Phase_I	84198317	NM_006982	Q546C8|Q96FH4	Silent	SNP	ENST00000316824.3	37	CCDS9028.1																																																																																				0.607	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982	
CEP290	80184	broad.mit.edu	37	12	88524335	88524335	+	Missense_Mutation	SNP	C	C	T	rs200063017		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:88524335C>T	ENST00000552810.1	-	8	846	c.503G>A	c.(502-504)cGt>cAt	p.R168H	CEP290_ENST00000309041.7_Missense_Mutation_p.R168H|CEP290_ENST00000397838.3_5'Flank	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	168					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)		p.R168H(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TTTCTTTAGACGTTTGTTCTA	0.279																																					p.R168H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G503A	12						.	C	HIS/ARG	1,3587		0,1,1793	77.0	67.0	70.0		503	4.7	1.0	12		70	0,8128		0,0,4064	yes	missense	CEP290	NM_025114.3	29	0,1,5857	TT,TC,CC		0.0,0.0279,0.0085	probably-damaging	168/2480	88524335	1,11715	1794	4064	5858	87048466	SO:0001583	missense	80184	exon8			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.503G>A	12.37:g.88524335C>T	ENSP00000448012:p.Arg168His	Somatic		Capture	Illumina HiSeq	Phase_I	87048466	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	C	14.97	2.693650	0.48202	2.79E-4	0.0	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139;ENST00000550962	T;T;D	0.87412	-0.17;-0.17;-2.25	5.77	4.7	0.59300	.	0.228428	0.38272	N	0.001759	T	0.75110	0.3805	N	0.14661	0.345	0.80722	D	1	B	0.21381	0.055	B	0.14578	0.011	T	0.71659	-0.4526	10	0.51188	T	0.08	.	9.3954	0.38399	0.133:0.7458:0.0:0.1212	.	168	O15078	CE290_HUMAN	H	168;168;168;70;150	ENSP00000448012:R168H;ENSP00000308021:R168H;ENSP00000447623:R150H	ENSP00000308021:R168H	R	-	2	0	CEP290	87048466	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	0.316000	0.19469	2.728000	0.93425	0.650000	0.86243	CGT		0.279	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
USP44	84101	broad.mit.edu	37	12	95927429	95927429	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:95927429T>C	ENST00000258499.3	-	2	892	c.604A>G	c.(604-606)Aaa>Gaa	p.K202E	USP44_ENST00000537435.2_Missense_Mutation_p.K202E|USP44_ENST00000552440.1_Missense_Mutation_p.K202E|USP44_ENST00000393091.2_Missense_Mutation_p.K202E	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	202					mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.K202E(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						AATTCTGCTTTAACTTGATAC	0.383																																					p.K202E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A604G	12						.						101.0	93.0	96.0					12																	95927429		2203	4300	6503	94451560	SO:0001583	missense	84101	exon2			AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"""Ubiquitin-specific peptidases"""	20064	protein-coding gene	gene with protein product		610993	"""ubiquitin specific protease 44"""			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.604A>G	12.37:g.95927429T>C	ENSP00000258499:p.Lys202Glu	Somatic		Capture	Illumina HiSeq	Phase_I	94451560	NM_001042403	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	37	CCDS9053.1	.	.	.	.	.	.	.	.	.	.	T	9.059	0.993978	0.19043	.	.	ENSG00000136014	ENST00000258499;ENST00000393091;ENST00000552440;ENST00000537435	T;T;T;T	0.14391	3.74;3.74;2.51;3.74	5.0	5.0	0.66597	.	0.213249	0.47852	D	0.000220	T	0.12732	0.0309	L	0.51422	1.61	0.44061	D	0.996804	B	0.10296	0.003	B	0.10450	0.005	T	0.06162	-1.0842	10	0.02654	T	1	.	15.0053	0.71507	0.0:0.0:0.0:1.0	.	202	Q9H0E7	UBP44_HUMAN	E	202	ENSP00000258499:K202E;ENSP00000376806:K202E;ENSP00000448670:K202E;ENSP00000442629:K202E	ENSP00000258499:K202E	K	-	1	0	USP44	94451560	0.996000	0.38824	0.908000	0.35775	0.603000	0.37013	3.176000	0.50863	2.002000	0.58637	0.459000	0.35465	AAA		0.383	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147	
ANKS1B	56899	broad.mit.edu	37	12	100200244	100200244	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:100200244G>A	ENST00000547776.2	-	4	606	c.607C>T	c.(607-609)Cgc>Tgc	p.R203C	ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000329257.7_Missense_Mutation_p.R203C	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	203						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)	p.R203C(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		TGGCCATTGCGCGCAGCAAGG	0.493																																					p.R203C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C607T	12						.						88.0	88.0	88.0					12																	100200244		2166	4266	6432	98724375	SO:0001583	missense	56899	exon4			AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.607C>T	12.37:g.100200244G>A	ENSP00000449629:p.Arg203Cys	Somatic		Capture	Illumina HiSeq	Phase_I	98724375	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	37	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.935422	0.92458	.	.	ENSG00000185046	ENST00000547776;ENST00000329257;ENST00000549866	T;T;T	0.65732	0.55;0.55;-0.17	5.54	5.54	0.83059	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.73313	0.3571	L	0.39514	1.22	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.70088	-0.4968	9	.	.	.	-8.2021	19.4821	0.95014	0.0:0.0:1.0:0.0	.	203;203	F8VVQ4;Q7Z6G8	.;ANS1B_HUMAN	C	203	ENSP00000449629:R203C;ENSP00000331381:R203C;ENSP00000449894:R203C	.	R	-	1	0	ANKS1B	98724375	1.000000	0.71417	0.948000	0.38648	0.923000	0.55619	9.848000	0.99507	2.591000	0.87537	0.557000	0.71058	CGC		0.493	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
UHRF1BP1L	23074	broad.mit.edu	37	12	100452833	100452833	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:100452833G>A	ENST00000279907.7	-	14	2434	c.2222C>T	c.(2221-2223)cCg>cTg	p.P741L	UHRF1BP1L_ENST00000545232.2_Missense_Mutation_p.P391L	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	741								p.P741L(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						ACAAGTCTGCGGCTCTTTTTG	0.403																																					p.P741L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2222T	12						.																																			98976964	SO:0001583	missense	23074	exon14				CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.2222C>T	12.37:g.100452833G>A	ENSP00000279907:p.Pro741Leu	Somatic		Capture	Illumina HiSeq	Phase_I	98976964	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	37	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.523262	0.00149	.	.	ENSG00000111647	ENST00000279907;ENST00000545232	T;T	0.08807	3.06;3.05	6.02	-0.336	0.12658	.	0.787648	0.12193	N	0.490964	T	0.01940	0.0061	N	0.01705	-0.755	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.43540	-0.9385	10	0.02654	T	1	3.2458	1.3362	0.02145	0.3655:0.254:0.2576:0.1229	.	741	A0JNW5	UH1BL_HUMAN	L	741;391	ENSP00000279907:P741L;ENSP00000444824:P391L	ENSP00000279907:P741L	P	-	2	0	UHRF1BP1L	98976964	0.040000	0.19996	0.019000	0.16419	0.295000	0.27426	1.585000	0.36600	-0.066000	0.12998	-0.312000	0.09012	CCG		0.403	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947	
UHRF1BP1L	23074	broad.mit.edu	37	12	100492155	100492155	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:100492155C>T	ENST00000279907.7	-	5	715	c.503G>A	c.(502-504)cGt>cAt	p.R168H	UHRF1BP1L_ENST00000356828.3_Missense_Mutation_p.R168H	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	168								p.R168H(2)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(21)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	50						ATCCTGAATACGAGTAAATCT	0.348																																					p.R168H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G503A	12						.						107.0	101.0	103.0					12																	100492155		2203	4300	6503	99016286	SO:0001583	missense	23074	exon5				CCDS31882.1, CCDS31883.1	12q23.1	2011-04-15	2008-08-15		ENSG00000111647	ENSG00000111647			29102	protein-coding gene	gene with protein product							Standard	XM_005268737		Approved	KIAA0701	uc001tgq.3	A0JNW5	OTTHUMG00000170195	ENST00000279907.7:c.503G>A	12.37:g.100492155C>T	ENSP00000279907:p.Arg168His	Somatic		Capture	Illumina HiSeq	Phase_I	99016286	NM_001006947	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	37	CCDS31882.1	.	.	.	.	.	.	.	.	.	.	C	33	5.220451	0.95139	.	.	ENSG00000111647	ENST00000279907;ENST00000356828	T;T	0.40225	2.25;1.04	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.68641	0.3023	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.994;0.999	T	0.73084	-0.4094	10	0.87932	D	0	-11.8898	19.0677	0.93119	0.0:1.0:0.0:0.0	.	168;168	A0JNW5-2;A0JNW5	.;UH1BL_HUMAN	H	168	ENSP00000279907:R168H;ENSP00000349285:R168H	ENSP00000279907:R168H	R	-	2	0	UHRF1BP1L	99016286	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.723000	0.84788	2.514000	0.84764	0.591000	0.81541	CGT		0.348	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947	
RPLP0	6175	broad.mit.edu	37	12	120634582	120634583	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	AA	AA	AA	-	AA	AA	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:120634582_120634583delAA	ENST00000551150.1	-	7	1262_1263	c.947_948delTT	c.(946-948)tttfs	p.F316fs	RPLP0_ENST00000313104.5_Frame_Shift_Del_p.F254fs|RPLP0_ENST00000546989.1_Frame_Shift_Del_p.F280fs|RPLP0_ENST00000392514.4_Frame_Shift_Del_p.F316fs|RPLP0_ENST00000552292.1_Frame_Shift_Del_p.F106fs|RPLP0_ENST00000228306.4_Frame_Shift_Del_p.F316fs|RPLP0_ENST00000550296.1_5'Flank|GCN1L1_ENST00000300648.6_5'Flank			P05388	RLA0_HUMAN	ribosomal protein, large, P0	316					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.F316fs*1(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GTGATTAGTCAAAGAGACCAAA	0.45																																					p.316_316del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.947_948del	12						.																																			119118966	SO:0001589	frameshift_variant	6175	exon8			AB007187	CCDS9193.1	12q24.2	2011-07-29			ENSG00000089157	ENSG00000089157		"""L ribosomal proteins"""	10371	protein-coding gene	gene with protein product	"""acidic ribosomal phosphoprotein P0"""	180510				9582194	Standard	NM_053275		Approved	PRLP0, P0, L10E, RPP0, LP0	uc001txq.3	P05388	OTTHUMG00000169317	ENST00000551150.1:c.947_948delTT	12.37:g.120634582_120634583delAA	ENSP00000449328:p.Phe316fs	Somatic		Capture	Illumina HiSeq	Phase_I	119118965	NM_001002	Q3B7A4|Q9BVK4	Frame_Shift_Del	DEL	ENST00000551150.1	37	CCDS9193.1																																																																																				0.450	RPLP0-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403448.3	NM_053275	
ZNF26	7574	broad.mit.edu	37	12	133587170	133587170	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr12:133587170C>T	ENST00000328654.5	+	4	1082	c.705C>T	c.(703-705)tgC>tgT	p.C235C	ZNF26_ENST00000534834.1_Silent_p.C215C	NM_019591.3	NP_062537.2	P17031	ZNF26_HUMAN	zinc finger protein 26	235					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.C235C(1)		autonomic_ganglia(1)|large_intestine(7)|lung(2)|prostate(1)|skin(2)	13	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.24e-11)|all_epithelial(31;1.21e-08)|Lung NSC(355;0.000431)		OV - Ovarian serous cystadenocarcinoma(86;9.53e-09)|Epithelial(86;2.63e-07)|all cancers(50;1.14e-05)		GTAGTGAGTGCGAGAAGGTCT	0.448																																					p.C235C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C705T	12						.						0.0	0.0	0.0					12																	133587170		0	0	0	132097243	SO:0001819	synonymous_variant	7574	exon4			X52351	CCDS31939.1	12q24.33	2013-01-08	2006-05-10		ENSG00000198393	ENSG00000198393		"""Zinc fingers, C2H2-type"", ""-"""	13053	protein-coding gene	gene with protein product		194537	"""zinc finger protein 26 (KOX 20)"""				Standard	NM_001256279		Approved	KOX20, FLJ20755	uc031qkj.1	P17031	OTTHUMG00000167936	ENST00000328654.5:c.705C>T	12.37:g.133587170C>T		Somatic		Capture	Illumina HiSeq	Phase_I	132097243	NM_019591	Q86X57|Q9NWL3	Silent	SNP	ENST00000328654.5	37	CCDS31939.1																																																																																				0.448	ZNF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397145.2	NM_019591	
TMTC4	84899	broad.mit.edu	37	13	101315319	101315319	+	Missense_Mutation	SNP	C	C	T	rs577395138		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:101315319C>T	ENST00000376234.3	-	4	583	c.394G>A	c.(394-396)Ggc>Agc	p.G132S	TMTC4_ENST00000328767.5_Intron|TMTC4_ENST00000342624.5_Missense_Mutation_p.G151S	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	132						integral component of membrane (GO:0016021)		p.G151S(1)		breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					TACTGCAGGCCGCCAAACAGA	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		17707	0.0		0.0	False		,,,				2504	0.001				p.G151S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G451A	13						.						65.0	73.0	70.0					13																	101315319		2114	4234	6348	100113320	SO:0001583	missense	84899	exon5				CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.394G>A	13.37:g.101315319C>T	ENSP00000365408:p.Gly132Ser	Somatic		Capture	Illumina HiSeq	Phase_I	100113320	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Missense_Mutation	SNP	ENST00000376234.3	37	CCDS41904.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.738128	0.69304	.	.	ENSG00000125247	ENST00000376234;ENST00000342624	T;T	0.41400	1.0;1.0	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.35008	0.0917	L	0.55103	1.725	0.80722	D	1	P;B	0.42871	0.792;0.449	B;B	0.32090	0.14;0.119	T	0.27739	-1.0065	10	0.10902	T	0.67	.	19.2569	0.93949	0.0:1.0:0.0:0.0	.	132;151	Q5T4D3;Q5T4D3-3	TMTC4_HUMAN;.	S	132;151	ENSP00000365408:G132S;ENSP00000343871:G151S	ENSP00000343871:G151S	G	-	1	0	TMTC4	100113320	1.000000	0.71417	0.958000	0.39756	0.389000	0.30415	7.487000	0.81328	2.561000	0.86390	0.561000	0.74099	GGC		0.632	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
TEX30	93081	broad.mit.edu	37	13	103420636	103420636	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:103420636T>C	ENST00000376032.4	-	4	461	c.272A>G	c.(271-273)tAc>tGc	p.Y91C	TEX30_ENST00000487260.1_5'UTR|TEX30_ENST00000376027.1_Missense_Mutation_p.Y91C|TEX30_ENST00000376019.1_Missense_Mutation_p.Y50C|TEX30_ENST00000376022.1_Missense_Mutation_p.Y50C|TEX30_ENST00000376029.3_Missense_Mutation_p.Y91C|TEX30_ENST00000376021.4_Missense_Mutation_p.Y50C	NM_138779.3	NP_620134.3	Q5JUR7	TEX30_HUMAN	testis expressed 30	91								p.Y50C(2)		lung(1)|urinary_tract(1)	2						TGCAAGTTTGTATTCTCCTGA	0.299																																					p.Y91C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A272G	13						.						71.0	81.0	78.0					13																	103420636		2201	4294	6495	102218637	SO:0001583	missense	93081	exon4			AF070559	CCDS9503.2, CCDS66577.1, CCDS66578.1	13q33.1	2012-02-09	2012-02-09	2012-02-09	ENSG00000151287	ENSG00000151287			25188	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 27"""	C13orf27			Standard	XM_005254097		Approved		uc001vpo.3	Q5JUR7	OTTHUMG00000017306	ENST00000376032.4:c.272A>G	13.37:g.103420636T>C	ENSP00000365200:p.Tyr91Cys	Somatic		Capture	Illumina HiSeq	Phase_I	102218637	NM_138779	Q5JUR8|Q96KZ8	Missense_Mutation	SNP	ENST00000376032.4	37	CCDS9503.2	.	.	.	.	.	.	.	.	.	.	T	19.36	3.812553	0.70912	.	.	ENSG00000151287	ENST00000376027;ENST00000376019;ENST00000376022;ENST00000376021;ENST00000376032;ENST00000376029	.	.	.	4.95	4.95	0.65309	.	0.178036	0.50627	D	0.000108	T	0.74359	0.3706	L	0.59436	1.845	0.47511	D	0.999442	D	0.76494	0.999	D	0.68192	0.956	T	0.75342	-0.3351	9	0.46703	T	0.11	-21.2603	14.9013	0.70681	0.0:0.0:0.0:1.0	.	91	Q5JUR7	CM027_HUMAN	C	91;50;50;50;91;91	.	ENSP00000365187:Y50C	Y	-	2	0	C13orf27	102218637	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.737000	0.55060	1.959000	0.56917	0.455000	0.32223	TAC		0.299	TEX30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045691.4	NM_138779	
LIG4	3981	broad.mit.edu	37	13	108861787	108861787	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:108861787G>A	ENST00000356922.4	-	2	2102	c.1830C>T	c.(1828-1830)ctC>ctT	p.L610L	LIG4_ENST00000442234.1_Silent_p.L610L|LIG4_ENST00000405925.1_Silent_p.L610L	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	610					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.L610L(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					GTTTAGATGCGAGCTTACCAG	0.428								Non-homologous end-joining																													p.L610L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1830T	13						.						93.0	92.0	92.0					13																	108861787		2203	4300	6503	107659788	SO:0001819	synonymous_variant	3981	exon2			X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"""polydeoxyribonucleotide synthase [ATP] 4"", ""polynucleotide ligase"", ""sealase"", ""DNA repair enzyme"", ""DNA joinase"""	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.1830C>T	13.37:g.108861787G>A		Somatic		Capture	Illumina HiSeq	Phase_I	107659788	NM_002312	Q8IY66|Q8TEU5	Silent	SNP	ENST00000356922.4	37	CCDS9508.1																																																																																				0.428	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312	
MYO16	23026	broad.mit.edu	37	13	109318490	109318490	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:109318490C>T	ENST00000357550.2	+	1	260	c.219C>T	c.(217-219)gaC>gaT	p.D73D	MYO16_ENST00000356711.2_Silent_p.D73D|MYO16_ENST00000251041.5_Silent_p.D73D	NM_001198950.1	NP_001185879.1			myosin XVI									p.D73D(1)		NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			ACCACAATGACAAAGAAGGTA	0.423																																					p.D95D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C285T	13						.						41.0	37.0	38.0					13																	109318490		2203	4300	6503	108116491	SO:0001819	synonymous_variant	23026	exon2				CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"""Myosins / Myosin superfamily : Class XVI"", ""Ankyrin repeat domain containing"""	29822	protein-coding gene	gene with protein product	"""neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3"", ""protein phosphatase 1, regulatory subunit 107"""	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.219C>T	13.37:g.109318490C>T		Somatic		Capture	Illumina HiSeq	Phase_I	108116491	NM_001198950		Silent	SNP	ENST00000357550.2	37	CCDS32008.1																																																																																				0.423	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
COL4A1	1282	broad.mit.edu	37	13	110864798	110864798	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:110864798C>T	ENST00000375820.4	-	6	474	c.353G>A	c.(352-354)gGc>gAc	p.G118D	COL4A1_ENST00000543140.1_Missense_Mutation_p.G118D	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	118					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.G118D(2)		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)			ACCTGGGGGGCCTGGCGGGCC	0.448																																					p.G118D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G353A	13						.						127.0	151.0	143.0					13																	110864798		2203	4300	6503	109662799	SO:0001583	missense	1282	exon6			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.353G>A	13.37:g.110864798C>T	ENSP00000364979:p.Gly118Asp	Somatic		Capture	Illumina HiSeq	Phase_I	109662799	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	37	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	C	17.29	3.352541	0.61293	.	.	ENSG00000187498	ENST00000375815;ENST00000375820;ENST00000397198;ENST00000543140	D;D	0.99353	-5.77;-5.77	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	D	0.99687	0.9882	H	0.98068	4.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97214	0.9873	10	0.87932	D	0	.	18.3564	0.90358	0.0:1.0:0.0:0.0	.	118;118	F5H5K0;P02462	.;CO4A1_HUMAN	D	118	ENSP00000364979:G118D;ENSP00000443348:G118D	ENSP00000364973:G118D	G	-	2	0	COL4A1	109662799	1.000000	0.71417	0.825000	0.32803	0.485000	0.33311	6.688000	0.74557	2.394000	0.81467	0.643000	0.83706	GGC		0.448	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
CARKD	55739	broad.mit.edu	37	13	111287049	111287049	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:111287049G>A	ENST00000309957.2	+	7	591	c.577G>A	c.(577-579)Gcc>Acc	p.A193T	CARKD_ENST00000424185.2_Missense_Mutation_p.A83T|CARKD_ENST00000470164.2_3'UTR|CARKD_ENST00000458711.2_Missense_Mutation_p.A62T|CARKD_ENST00000397191.4_3'UTR	NM_001242881.1|NM_018210.3	NP_001229810.1|NP_060680.2			carbohydrate kinase domain containing									p.A193T(1)		NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	15						TCAGCAGCCGGCCCTCATCCA	0.622																																					p.A193T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G577A	13						.						66.0	59.0	62.0					13																	111287049		2203	4300	6503	110085050	SO:0001583	missense	55739	exon7			AF151071	CCDS9513.1, CCDS55903.1	13q34	2008-12-19			ENSG00000213995	ENSG00000213995			25576	protein-coding gene	gene with protein product		615910					Standard	NM_018210		Approved	LP3298, FLJ10769	uc001vrc.3	Q8IW45	OTTHUMG00000017345	ENST00000309957.2:c.577G>A	13.37:g.111287049G>A	ENSP00000311984:p.Ala193Thr	Somatic		Capture	Illumina HiSeq	Phase_I	110085050	NM_018210		Missense_Mutation	SNP	ENST00000309957.2	37	CCDS9513.1	.	.	.	.	.	.	.	.	.	.	G	12.48	1.951177	0.34471	.	.	ENSG00000213995	ENST00000458711;ENST00000424185;ENST00000439607;ENST00000309957	T;T;T	0.22336	1.96;1.96;1.96	5.0	1.88	0.25563	Uncharacterised domain, carbohydrate kinase-related (3);	0.304024	0.37012	N	0.002288	T	0.19005	0.0456	M	0.69358	2.11	0.80722	D	1	B;B;B;B;B	0.22003	0.063;0.04;0.049;0.049;0.022	B;B;B;B;B	0.22386	0.038;0.021;0.035;0.039;0.021	T	0.05178	-1.0901	10	0.34782	T	0.22	-11.3778	4.464	0.11680	0.214:0.0:0.332:0.454	.	62;83;175;193;193	B4DQR1;Q8IW45-4;B4DKX7;Q8IW45-2;Q8IW45	.;.;.;.;CARKD_HUMAN	T	62;83;175;193	ENSP00000412789:A62T;ENSP00000413191:A83T;ENSP00000311984:A193T	ENSP00000311984:A193T	A	+	1	0	CARKD	110085050	0.976000	0.34144	0.048000	0.18961	0.751000	0.42716	1.974000	0.40559	0.065000	0.16485	0.655000	0.94253	GCC		0.622	CARKD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045764.1	NM_018210	
MCF2L	23263	broad.mit.edu	37	13	113679017	113679017	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:113679017G>A	ENST00000375608.3	+	4	371	c.313G>A	c.(313-315)Gag>Aag	p.E105K	MCF2L_ENST00000434480.2_Missense_Mutation_p.E81K|MCF2L_ENST00000375604.2_Missense_Mutation_p.E132K|MCF2L_ENST00000535094.2_Missense_Mutation_p.E75K|MCF2L_ENST00000442652.2_Missense_Mutation_p.E105K|MCF2L_ENST00000375597.4_Missense_Mutation_p.E73K|MCF2L_ENST00000423482.2_Missense_Mutation_p.E73K|MCF2L_ENST00000421756.1_Missense_Mutation_p.E79K|MCF2L_ENST00000397024.1_Missense_Mutation_p.E73K|MCF2L_ENST00000397030.1_Missense_Mutation_p.E108K|MCF2L_ENST00000375601.3_Missense_Mutation_p.E79K			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	105	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				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.E79K(1)|p.E73K(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)				GGCCTTCAGCGAGATTCCGGA	0.622																																					p.E79K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G235A	13						.						76.0	72.0	74.0					13																	113679017		2203	4300	6503	112727018	SO:0001583	missense	23263	exon3			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.313G>A	13.37:g.113679017G>A	ENSP00000364758:p.Glu105Lys	Somatic		Capture	Illumina HiSeq	Phase_I	112727018	NM_024979	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	37		.	.	.	.	.	.	.	.	.	.	G	26.7	4.765101	0.90020	.	.	ENSG00000126217	ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000430480;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000433807;ENST00000434480;ENST00000409954;ENST00000423482;ENST00000375597;ENST00000397024	D;D;D;D;D;D;D;D;T;D;D	0.82984	-1.67;-1.67;-1.67;-1.67;-1.67;-1.67;-1.67;-1.67;1.5;-1.67;-1.67	4.16	4.16	0.48862	Cellular retinaldehyde-binding/triple function, C-terminal (2);	0.269286	0.34676	N	0.003761	D	0.87830	0.6276	L	0.60455	1.87	0.52501	D	0.999955	D;D;D;D;D	0.69078	0.994;0.994;0.997;0.97;0.997	P;P;P;B;D	0.65874	0.863;0.793;0.899;0.439;0.939	D	0.86348	0.1709	10	0.30078	T	0.28	.	15.586	0.76482	0.0:0.0:1.0:0.0	.	73;75;132;73;105	E9PDN8;O15068-9;G5E9A1;O15068-4;O15068	.;.;.;.;MCF2L_HUMAN	K	105;105;132;108;75;75;79;79;81;81;46;73;73;73	ENSP00000364758:E105K;ENSP00000401422:E105K;ENSP00000364754:E132K;ENSP00000380225:E108K;ENSP00000440374:E75K;ENSP00000397285:E79K;ENSP00000364751:E79K;ENSP00000407722:E81K;ENSP00000386551:E46K;ENSP00000405639:E73K;ENSP00000364747:E73K	ENSP00000364747:E73K	E	+	1	0	MCF2L	112727018	1.000000	0.71417	0.999000	0.59377	0.947000	0.59692	4.385000	0.59613	2.037000	0.60232	0.462000	0.41574	GAG		0.622	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
PROZ	8858	broad.mit.edu	37	13	113826077	113826077	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:113826077C>T	ENST00000375547.2	+	8	868	c.861C>T	c.(859-861)ttC>ttT	p.F287F	PROZ_ENST00000342783.4_Silent_p.F309F	NM_003891.2	NP_003882.1	P22891	PROZ_HUMAN	protein Z, vitamin K-dependent plasma glycoprotein	287	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)	p.F287F(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(2)|skin(2)	16	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;0.216)	all cancers(43;0.104)		Menadione(DB00170)	AGAAAGACTTCGCTGAGCACC	0.672																																					p.F287F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C861T	13						.						67.0	64.0	65.0					13																	113826077		2203	4300	6503	112874078	SO:0001819	synonymous_variant	8858	exon8			M55670	CCDS9531.1, CCDS58300.1	13q34	2008-07-18			ENSG00000126231	ENSG00000126231			9460	protein-coding gene	gene with protein product		176895				2244898, 2403355	Standard	NM_001256134		Approved	PZ	uc010agr.2	P22891	OTTHUMG00000017376	ENST00000375547.2:c.861C>T	13.37:g.113826077C>T		Somatic		Capture	Illumina HiSeq	Phase_I	112874078	NM_003891	A6NMB4|Q15213|Q5JVF5|Q5JVF6	Silent	SNP	ENST00000375547.2	37	CCDS9531.1																																																																																				0.672	PROZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045845.1	NM_003891	
ZMYM2	7750	broad.mit.edu	37	13	20605499	20605499	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:20605499C>T	ENST00000382874.2	+	11	2082	c.1892C>T	c.(1891-1893)gCg>gTg	p.A631V	ZMYM2_ENST00000382883.3_Missense_Mutation_p.A113V|ZMYM2_ENST00000382871.2_Missense_Mutation_p.A631V|ZMYM2_ENST00000382869.3_Missense_Mutation_p.A631V	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	631					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)	p.A631V(2)		large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		CAGTTTGTAGCGCCAAGTGAT	0.363																																					p.A631V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1892T	13						.						107.0	98.0	101.0					13																	20605499		1851	4099	5950	19503499	SO:0001583	missense	7750	exon10			AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"""Zinc fingers, MYM type"""	12989	protein-coding gene	gene with protein product		602221	"""zinc finger protein 198"""	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.1892C>T	13.37:g.20605499C>T	ENSP00000372327:p.Ala631Val	Somatic		Capture	Illumina HiSeq	Phase_I	19503499	NM_197968	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Missense_Mutation	SNP	ENST00000382874.2	37	CCDS45016.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.604395	0.66445	.	.	ENSG00000121741	ENST00000382869;ENST00000456228;ENST00000382874;ENST00000382871;ENST00000382883;ENST00000382870	T;T;T;T	0.46063	2.15;2.15;2.15;0.88	5.42	4.58	0.56647	.	0.349460	0.32081	N	0.006615	T	0.28400	0.0702	N	0.22421	0.69	0.35463	D	0.796678	B	0.30973	0.302	B	0.22601	0.04	T	0.32508	-0.9904	10	0.39692	T	0.17	-4.5641	13.8835	0.63696	0.0:0.9264:0.0:0.0736	.	631	Q9UBW7	ZMYM2_HUMAN	V	631;631;631;631;113;11	ENSP00000372322:A631V;ENSP00000372327:A631V;ENSP00000372324:A631V;ENSP00000372336:A113V	ENSP00000372322:A631V	A	+	2	0	ZMYM2	19503499	0.960000	0.32886	0.978000	0.43139	0.990000	0.78478	1.399000	0.34566	1.279000	0.44446	0.655000	0.94253	GCG		0.363	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453	
TNFRSF19	55504	broad.mit.edu	37	13	24243025	24243025	+	Missense_Mutation	SNP	C	C	T	rs115520634	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:24243025C>T	ENST00000382258.4	+	9	1238	c.1034C>T	c.(1033-1035)aCg>aTg	p.T345M	TNFRSF19_ENST00000382263.3_Missense_Mutation_p.T345M|TNFRSF19_ENST00000248484.4_Missense_Mutation_p.T345M|TNFRSF19_ENST00000403372.2_Missense_Mutation_p.T213M	NM_018647.3	NP_061117.2	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily, member 19	345					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.T345M(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)		GAAAGCTCAACGTCTTTGGAT	0.413													C|||	2	0.000399361	0.0008	0.0	5008	,	,		20758	0.0		0.0	False		,,,				2504	0.001				p.T345M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1034T	13						.						166.0	162.0	163.0					13																	24243025		2203	4300	6503	23141025	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.1034C>T	13.37:g.24243025C>T	ENSP00000371693:p.Thr345Met	Somatic		Capture	Illumina HiSeq	Phase_I	23141025	NM_148957	A8KA09|A8KA26|B1AM40|B1AM41|B4E2I6|Q9BXZ9|Q9BY00|Q9NZV2	Missense_Mutation	SNP	ENST00000382258.4	37	CCDS9302.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	15.66	2.899311	0.52227	.	.	ENSG00000127863	ENST00000248484;ENST00000403372;ENST00000382258;ENST00000382263	T;T;T;T	0.78816	-1.2;1.4;-1.21;-1.2	5.81	2.18	0.27775	.	1.616700	0.03287	N	0.187038	T	0.77191	0.4094	N	0.22421	0.69	0.09310	N	1	D;D;D	0.65815	0.983;0.995;0.995	P;P;P	0.53861	0.578;0.736;0.736	T	0.63594	-0.6602	10	0.87932	D	0	3.3154	9.0884	0.36596	0.0:0.7156:0.0:0.2844	.	213;345;345	B4E2I6;Q9NS68;Q9NS68-2	.;TNR19_HUMAN;.	M	345;213;345;345	ENSP00000248484:T345M;ENSP00000385408:T213M;ENSP00000371693:T345M;ENSP00000371698:T345M	ENSP00000248484:T345M	T	+	2	0	TNFRSF19	23141025	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.004000	0.12878	0.092000	0.17331	0.655000	0.94253	ACG		0.413	TNFRSF19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044156.2	NM_018647	
MIPEP	4285	broad.mit.edu	37	13	24330743	24330743	+	Missense_Mutation	SNP	C	C	T	rs79151541	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:24330743C>T	ENST00000382172.3	-	18	2083	c.1985G>A	c.(1984-1986)cGc>cAc	p.R662H		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	662					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.R662H(1)		breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		CCTGCGATAGCGCTCCCCGGC	0.522													C|||	9	0.00179712	0.0053	0.0029	5008	,	,		16129	0.0		0.0	False		,,,				2504	0.0				p.R662H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1985A	13						.	C	HIS/ARG	26,4380	31.7+/-61.6	0,26,2177	81.0	79.0	80.0		1985	5.5	1.0	13	dbSNP_131	80	0,8600		0,0,4300	yes	missense	MIPEP	NM_005932.3	29	0,26,6477	TT,TC,CC		0.0,0.5901,0.1999	probably-damaging	662/714	24330743	26,12980	2203	4300	6503	23228743	SO:0001583	missense	4285	exon18				CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.1985G>A	13.37:g.24330743C>T	ENSP00000371607:p.Arg662His	Somatic		Capture	Illumina HiSeq	Phase_I	23228743	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	3|3	0.0013736263736263737|0.0013736263736263737	2|2	0.0040650406504065045|0.0040650406504065045	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	26.2|26.2	4.718623|4.718623	0.89205|0.89205	0.005901|0.005901	0.0|0.0	ENSG00000027001|ENSG00000027001	ENST00000433710|ENST00000382172	.|T	.|0.13307	.|2.6	5.49|5.49	5.49|5.49	0.81192|0.81192	.|Neurolysin/Thimet oligopeptidase, domain 2 (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.26048|0.26048	0.0635|0.0635	M|M	0.74647|0.74647	2.275|2.275	0.58432|0.58432	D|D	0.999991|0.999991	.|D	.|0.71674	.|0.998	.|P	.|0.62885	.|0.908	T|T	0.01561|0.01561	-1.1324|-1.1324	6|10	0.87932|0.62326	D|D	0|0.03	.|.	12.2882|12.2882	0.54803|0.54803	0.0:0.9183:0.0:0.0817|0.0:0.9183:0.0:0.0817	.|.	.|662	.|Q99797	.|MIPEP_HUMAN	T|H	60|662	.|ENSP00000371607:R662H	ENSP00000397404:A60T|ENSP00000371607:R662H	A|R	-|-	1|2	0|0	MIPEP|MIPEP	23228743|23228743	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	5.692000|5.692000	0.68256|0.68256	2.574000|2.574000	0.86865|0.86865	0.585000|0.585000	0.79938|0.79938	GCT|CGC		0.522	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1		
ATP12A	479	broad.mit.edu	37	13	25264762	25264762	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:25264762G>A	ENST00000381946.3	+	7	869	c.702G>A	c.(700-702)acG>acA	p.T234T	ATP12A_ENST00000218548.6_Silent_p.T234T			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	234					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)	p.T234T(1)		breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		CATCTCTCACGGGGGAGTCTG	0.507																																					p.T234T	Pancreas(156;1582 1935 18898 22665 26498)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G702A	13						.						115.0	130.0	125.0					13																	25264762		2203	4300	6503	24162762	SO:0001819	synonymous_variant	479	exon7			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.702G>A	13.37:g.25264762G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24162762	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																				0.507	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
ATP12A	479	broad.mit.edu	37	13	25274947	25274947	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:25274947G>A	ENST00000381946.3	+	13	1935	c.1768G>A	c.(1768-1770)Gct>Act	p.A590T	RNY1P7_ENST00000384743.1_RNA|ATP12A_ENST00000218548.6_Missense_Mutation_p.A596T			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	590					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)	p.A590T(1)		breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TGACATAGACGCTATGAACTT	0.478																																					p.A596T	Pancreas(156;1582 1935 18898 22665 26498)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1786A	13						.						147.0	133.0	138.0					13																	25274947		2203	4300	6503	24172947	SO:0001583	missense	479	exon13			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1768G>A	13.37:g.25274947G>A	ENSP00000371372:p.Ala590Thr	Somatic		Capture	Illumina HiSeq	Phase_I	24172947	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	G	7.845	0.722717	0.15439	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	T;T	0.79033	-1.23;-1.23	6.17	-12.3	0.00002	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	1.172930	0.06057	N	0.657719	T	0.50820	0.1638	N	0.04705	-0.18	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.50162	-0.8860	10	0.46703	T	0.11	.	10.3644	0.44015	0.2931:0.0:0.5374:0.1695	.	596;590	P54707-2;P54707	.;AT12A_HUMAN	T	596;590	ENSP00000218548:A596T;ENSP00000371372:A590T	ENSP00000218548:A596T	A	+	1	0	ATP12A	24172947	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.029000	0.13666	-2.510000	0.00504	-0.768000	0.03414	GCT		0.478	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
ATP8A2	51761	broad.mit.edu	37	13	26163805	26163805	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:26163805G>A	ENST00000381655.2	+	24	2321	c.2179G>A	c.(2179-2181)Gcc>Acc	p.A727T	ATP8A2_ENST00000255283.8_Missense_Mutation_p.A687T|ATP8A2_ENST00000491840.1_3'UTR	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	687					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|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.A727T(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		GCAGAATATGGCCCTTATCCT	0.383																																					p.A727T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2179A	13						.						172.0	162.0	165.0					13																	26163805		1866	4096	5962	25061805	SO:0001583	missense	51761	exon24			AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"""ATPases / P-type"""	13533	protein-coding gene	gene with protein product		605870	"""ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2"", ""ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"""			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.2179G>A	13.37:g.26163805G>A	ENSP00000371070:p.Ala727Thr	Somatic		Capture	Illumina HiSeq	Phase_I	25061805	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Missense_Mutation	SNP	ENST00000381655.2	37	CCDS41873.1	.	.	.	.	.	.	.	.	.	.	G	10.67	1.414356	0.25465	.	.	ENSG00000132932	ENST00000381655;ENST00000255283;ENST00000544544	T;T	0.63744	-0.06;-0.06	5.73	3.82	0.43975	HAD-like domain (2);	0.264699	0.38663	N	0.001603	T	0.29783	0.0744	N	0.02213	-0.635	0.37077	D	0.898787	B;B;B	0.13594	0.008;0.006;0.008	B;B;B	0.19666	0.026;0.015;0.026	T	0.17653	-1.0362	10	0.10377	T	0.69	.	6.4207	0.21742	0.0949:0.0:0.6066:0.2986	.	687;507;687	B7Z880;F5GZN5;Q9NTI2	.;.;AT8A2_HUMAN	T	727;687;507	ENSP00000371070:A727T;ENSP00000255283:A687T	ENSP00000255283:A687T	A	+	1	0	ATP8A2	25061805	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	4.088000	0.57678	1.440000	0.47531	0.655000	0.94253	GCC		0.383	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529	
RNF6	6049	broad.mit.edu	37	13	26789265	26789265	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:26789265G>A	ENST00000381588.4	-	5	1506	c.754C>T	c.(754-756)Cgc>Tgc	p.R252C	RNF6_ENST00000468480.1_Intron|RNF6_ENST00000381570.3_Missense_Mutation_p.R252C|RNF6_ENST00000346166.3_Missense_Mutation_p.R252C|RNF6_ENST00000399762.2_Intron	NM_005977.3	NP_005968.1	Q9Y252	RNF6_HUMAN	ring finger protein (C3H2C3 type) 6	252					negative regulation of axon extension (GO:0030517)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K27-linked ubiquitination (GO:0044314)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R252C(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(3)|ovary(2)|prostate(2)|skin(2)	23	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245)		AAATTAGTGCGTGAAGCGTTA	0.493																																					p.R252C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C754T	13						.						126.0	116.0	119.0					13																	26789265		2203	4300	6503	25687265	SO:0001583	missense	6049	exon5			AJ010346	CCDS9316.1	13q12.2	2013-01-09			ENSG00000127870	ENSG00000127870		"""RING-type (C3HC4) zinc fingers"""	10069	protein-coding gene	gene with protein product	"""RING-H2 protein RNF-6"""	604242				10331950	Standard	NM_005977		Approved	DKFZp686P0776	uc001uqq.3	Q9Y252	OTTHUMG00000016614	ENST00000381588.4:c.754C>T	13.37:g.26789265G>A	ENSP00000371000:p.Arg252Cys	Somatic		Capture	Illumina HiSeq	Phase_I	25687265	NM_005977	B4DDP0|Q5W0H0|Q9BZP5|Q9UF41	Missense_Mutation	SNP	ENST00000381588.4	37	CCDS9316.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.227494	0.39399	.	.	ENSG00000127870	ENST00000346166;ENST00000381588;ENST00000381570	T;T;T	0.07908	3.15;3.15;3.15	5.16	0.939	0.19506	.	1.757910	0.02677	N	0.109210	T	0.11239	0.0274	L	0.46157	1.445	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.40683	-0.9550	10	0.87932	D	0	0.0269	9.3764	0.38286	0.0711:0.0:0.476:0.4529	.	252	Q9Y252	RNF6_HUMAN	C	252	ENSP00000342121:R252C;ENSP00000371000:R252C;ENSP00000370982:R252C	ENSP00000342121:R252C	R	-	1	0	RNF6	25687265	0.002000	0.14202	0.000000	0.03702	0.014000	0.08584	1.217000	0.32455	0.291000	0.22468	0.557000	0.71058	CGC		0.493	RNF6-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044246.2	NM_005977	
FLT3	2322	broad.mit.edu	37	13	28589369	28589369	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:28589369G>A	ENST00000241453.7	-	22	2759	c.2678C>T	c.(2677-2679)cCg>cTg	p.P893L	FLT3_ENST00000469894.1_5'Flank|FLT3_ENST00000537084.1_Missense_Mutation_p.P852L|FLT3_ENST00000380982.4_Missense_Mutation_p.P896L	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	893	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.P893L(1)|p.G885fs*4(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGCATCAACCGGAATGCCAGG	0.343			"""Mis, O"""		"""AML, ALL"""																																p.P893L			Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.C2678T	13						.						74.0	67.0	69.0					13																	28589369		2203	4300	6503	27487369	SO:0001583	missense	2322	exon22			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.2678C>T	13.37:g.28589369G>A	ENSP00000241453:p.Pro893Leu	Somatic		Capture	Illumina HiSeq	Phase_I	27487369	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	37	CCDS31953.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.194370	0.58017	.	.	ENSG00000122025	ENST00000241453;ENST00000380982;ENST00000537084	D;D;D	0.89196	-2.48;-2.48;-2.48	5.3	3.44	0.39384	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.228544	0.31673	N	0.007260	T	0.81389	0.4812	L	0.28274	0.84	0.44736	D	0.997735	P;D	0.64830	0.924;0.994	B;P	0.47470	0.334;0.548	T	0.79371	-0.1831	10	0.02654	T	1	.	11.9201	0.52787	0.0:0.0:0.4664:0.5336	.	852;893	P36888-2;P36888	.;FLT3_HUMAN	L	893;896;852	ENSP00000241453:P893L;ENSP00000370369:P896L;ENSP00000438139:P852L	ENSP00000241453:P893L	P	-	2	0	FLT3	27487369	0.995000	0.38212	0.043000	0.18650	0.987000	0.75469	2.368000	0.44222	1.205000	0.43262	0.655000	0.94253	CCG		0.343	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2		
PAN3	255967	broad.mit.edu	37	13	28841485	28841485	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:28841485G>A	ENST00000380958.3	+	12	1891	c.1739G>A	c.(1738-1740)aGc>aAc	p.S580N	PAN3_ENST00000399613.1_Missense_Mutation_p.S380N|PAN3_ENST00000282391.5_Missense_Mutation_p.S268N	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit									p.S380N(2)		endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		ACTATGATGAGCAGACACTTT	0.368																																					p.S580N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1739A	13						.						134.0	125.0	128.0					13																	28841485		2203	4300	6503	27739485	SO:0001583	missense	255967	exon12			AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520			29991	protein-coding gene	gene with protein product			"""PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"""			14583602	Standard	NM_175854		Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.1739G>A	13.37:g.28841485G>A	ENSP00000370345:p.Ser580Asn	Somatic		Capture	Illumina HiSeq	Phase_I	27739485	NM_175854		Missense_Mutation	SNP	ENST00000380958.3	37	CCDS9329.2	.	.	.	.	.	.	.	.	.	.	G	13.63	2.295351	0.40594	.	.	ENSG00000152520	ENST00000380958;ENST00000399613;ENST00000282391	T;T;T	0.20069	2.1;2.1;2.1	5.56	4.72	0.59763	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.115505	0.85682	N	0.000000	T	0.16599	0.0399	L	0.28344	0.845	0.80722	D	1	B;B;B;B	0.31790	0.34;0.314;0.015;0.112	B;B;B;B	0.33846	0.171;0.075;0.009;0.048	T	0.05666	-1.0871	10	0.22706	T	0.39	-4.8908	14.5814	0.68295	0.0704:0.0:0.9296:0.0	.	580;580;268;526	Q58A45-4;Q58A45;Q58A45-2;Q58A45-3	.;PAN3_HUMAN;.;.	N	580;380;268	ENSP00000370345:S580N;ENSP00000382522:S380N;ENSP00000282391:S268N	ENSP00000282391:S268N	S	+	2	0	PAN3	27739485	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	1.359000	0.45940	-0.157000	0.13467	AGC		0.368	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854	
FLT1	2321	broad.mit.edu	37	13	28903855	28903855	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:28903855C>T	ENST00000282397.4	-	19	2855	c.2604G>A	c.(2602-2604)acG>acA	p.T868T	FLT1_ENST00000540678.1_Silent_p.T86T	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	868	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|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 MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)	p.T868T(1)		NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ACTCGCTGGCCGTGGCCCCCT	0.562																																					p.T868T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2604A	13						.						107.0	93.0	97.0					13																	28903855		2203	4300	6503	27801855	SO:0001819	synonymous_variant	2321	exon19			AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3763	protein-coding gene	gene with protein product	"""vascular endothelial growth factor receptor 1"", ""vascular permeability factor receptor"""	165070	"""fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"""	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.2604G>A	13.37:g.28903855C>T		Somatic		Capture	Illumina HiSeq	Phase_I	27801855	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	37	CCDS9330.1																																																																																				0.562	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1		
MTUS2	23281	broad.mit.edu	37	13	29599559	29599559	+	Missense_Mutation	SNP	C	C	T	rs201979907	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:29599559C>T	ENST00000431530.3	+	1	812	c.754C>T	c.(754-756)Cgt>Tgt	p.R252C		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	242						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.R252C(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						AAAGAGTGTGCGTCATCCTAA	0.567													C|||	4	0.000798722	0.003	0.0	5008	,	,		18237	0.0		0.0	False		,,,				2504	0.0				p.R252C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C754T	13						.	C	CYS/ARG	12,4386	17.9+/-39.9	0,12,2187	43.0	43.0	43.0		754	-5.3	0.0	13		43	0,8600		0,0,4300	yes	missense	MTUS2	NM_001033602.2	180	0,12,6487	TT,TC,CC		0.0,0.2729,0.0923	benign	252/1380	29599559	12,12986	2199	4300	6499	28497559	SO:0001583	missense	23281	exon1			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.754C>T	13.37:g.29599559C>T	ENSP00000392057:p.Arg252Cys	Somatic		Capture	Illumina HiSeq	Phase_I	28497559	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	37	CCDS45022.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	c	8.051	0.765942	0.15983	0.002729	0.0	ENSG00000132938	ENST00000431530	T	0.11385	2.78	4.96	-5.27	0.02763	.	2.018660	0.02014	N	0.047233	T	0.04003	0.0112	N	0.03115	-0.41	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.33752	-0.9856	9	.	.	.	.	4.3278	0.11048	0.1044:0.2328:0.104:0.5587	.	242	Q5JR59	MTUS2_HUMAN	C	252	ENSP00000392057:R252C	.	R	+	1	0	MTUS2	28497559	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.800000	0.04555	-1.108000	0.03000	-1.288000	0.01363	CGT		0.567	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270	
MTUS2	23281	broad.mit.edu	37	13	29600529	29600529	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:29600529C>T	ENST00000431530.3	+	1	1782	c.1724C>T	c.(1723-1725)gCg>gTg	p.A575V		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	565						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.A575V(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						GGTATGGATGCGGGGTCCCCC	0.552																																					p.A575V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1724T	13						.						104.0	107.0	106.0					13																	29600529		2031	4196	6227	28498529	SO:0001583	missense	23281	exon1			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.1724C>T	13.37:g.29600529C>T	ENSP00000392057:p.Ala575Val	Somatic		Capture	Illumina HiSeq	Phase_I	28498529	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	37	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	c	9.201	1.028544	0.19512	.	.	ENSG00000132938	ENST00000431530	T	0.12984	2.63	5.53	0.673	0.17941	.	1.669770	0.03413	N	0.205075	T	0.11750	0.0286	L	0.44542	1.39	0.09310	N	1	B	0.15473	0.013	B	0.15484	0.013	T	0.29701	-1.0003	9	.	.	.	.	1.6065	0.02685	0.1433:0.3156:0.1252:0.4159	.	565	Q5JR59	MTUS2_HUMAN	V	575	ENSP00000392057:A575V	.	A	+	2	0	MTUS2	28498529	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.209000	0.17435	0.009000	0.14813	0.655000	0.94253	GCG		0.552	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270	
MTUS2	23281	broad.mit.edu	37	13	30071427	30071427	+	Missense_Mutation	SNP	G	G	A	rs370672492		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:30071427G>A	ENST00000380808.2	+	6	785	c.569G>A	c.(568-570)cGc>cAc	p.R190H	MTUS2_ENST00000542829.1_Missense_Mutation_p.R100H|MTUS2_ENST00000400542.3_3'UTR|MTUS2_ENST00000431530.3_Missense_Mutation_p.R1221H	NM_015233.5	NP_056048.1	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	1211						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.R190H(1)|p.R1221H(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						GACAGAGCCCGCCGCTTCGAA	0.612																																					p.R1221H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3662A	13						.	G	HIS/ARG,HIS/ARG	0,4218		0,0,2109	32.0	42.0	39.0		3662,569	1.2	0.0	13		39	1,8473		0,1,4236	no	missense,missense	MTUS2	NM_001033602.2,NM_015233.5	29,29	0,1,6345	AA,AG,GG		0.0118,0.0,0.0079	probably-damaging,probably-damaging	1221/1380,190/349	30071427	1,12691	2109	4237	6346	28969427	SO:0001583	missense	23281	exon11			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000380808.2:c.569G>A	13.37:g.30071427G>A	ENSP00000370186:p.Arg190His	Somatic		Capture	Illumina HiSeq	Phase_I	28969427	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000380808.2	37	CCDS41874.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.844409	0.51164	0.0	1.18E-4	ENSG00000132938	ENST00000431530;ENST00000380808;ENST00000542829;ENST00000417109	T;T;T	0.24151	2.67;2.17;1.87	5.17	1.19	0.21007	.	0.430109	0.26407	N	0.024559	T	0.29190	0.0726	L	0.43152	1.355	0.09310	N	1	P;D	0.63046	0.903;0.992	B;P	0.54706	0.343;0.759	T	0.07829	-1.0752	9	.	.	.	.	8.3755	0.32440	0.3903:0.0:0.6097:0.0	.	190;1211	Q5JR59-3;Q5JR59	.;MTUS2_HUMAN	H	1221;190;100;147	ENSP00000392057:R1221H;ENSP00000370186:R190H;ENSP00000445403:R100H	.	R	+	2	0	MTUS2	28969427	0.748000	0.28294	0.006000	0.13384	0.852000	0.48524	2.955000	0.49121	0.328000	0.23435	0.655000	0.94253	CGC		0.612	MTUS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044335.2	XM_166270	
MTUS2	23281	broad.mit.edu	37	13	30072638	30072638	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:30072638C>T	ENST00000380808.2	+	7	915	c.699C>T	c.(697-699)caC>caT	p.H233H	MTUS2_ENST00000542829.1_Silent_p.H143H|MTUS2_ENST00000400542.3_3'UTR|MTUS2_ENST00000431530.3_Silent_p.H1264H	NM_015233.5	NP_056048.1	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	1254						cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)	p.H233H(1)|p.H1264H(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						AGCAAATACACGAGCAAGAAA	0.448																																					p.H1264H												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C3792T	13						.						90.0	95.0	94.0					13																	30072638		1926	4127	6053	28970638	SO:0001819	synonymous_variant	23281	exon12			AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000380808.2:c.699C>T	13.37:g.30072638C>T		Somatic		Capture	Illumina HiSeq	Phase_I	28970638	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Silent	SNP	ENST00000380808.2	37	CCDS41874.1																																																																																				0.448	MTUS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044335.2	XM_166270	
SLC7A1	6541	broad.mit.edu	37	13	30091719	30091719	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:30091719T>C	ENST00000380752.5	-	10	1887	c.1501A>G	c.(1501-1503)Agc>Ggc	p.S501G	SLC7A1_ENST00000473577.1_5'UTR	NM_003045.4	NP_003036.1	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	501					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)	p.S501G(1)		endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|stomach(1)|urinary_tract(2)	24		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	CCTATGAGGCTGGTTGAAATG	0.488																																					p.S501G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1501G	13						.						149.0	147.0	147.0					13																	30091719		2203	4300	6503	28989719	SO:0001583	missense	6541	exon10			AF078107	CCDS9333.1	13q12.3	2013-05-22			ENSG00000139514	ENSG00000139514		"""Solute carriers"""	11057	protein-coding gene	gene with protein product	"""ecotropic retroviral receptor"", ""amino acid transporter, cationic 1"""	104615		ERR, ATRC1		1348489	Standard	NM_003045		Approved	CAT-1, HCAT1, REC1L	uc001uso.3	P30825	OTTHUMG00000016658	ENST00000380752.5:c.1501A>G	13.37:g.30091719T>C	ENSP00000370128:p.Ser501Gly	Somatic		Capture	Illumina HiSeq	Phase_I	28989719	NM_003045	Q5JR50	Missense_Mutation	SNP	ENST00000380752.5	37	CCDS9333.1	.	.	.	.	.	.	.	.	.	.	T	7.574	0.667384	0.14710	.	.	ENSG00000139514	ENST00000380752	D	0.85773	-2.03	5.24	1.56	0.23342	.	0.549745	0.21973	N	0.066432	T	0.67692	0.2920	N	0.17248	0.465	0.27113	N	0.962333	B	0.06786	0.001	B	0.08055	0.003	T	0.51841	-0.8654	10	0.25751	T	0.34	.	3.924	0.09256	0.1759:0.3575:0.0:0.4666	.	501	P30825	CTR1_HUMAN	G	501	ENSP00000370128:S501G	ENSP00000370128:S501G	S	-	1	0	SLC7A1	28989719	0.869000	0.29996	0.998000	0.56505	0.724000	0.41520	0.772000	0.26647	0.426000	0.26116	-0.256000	0.11100	AGC		0.488	SLC7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044337.2	NM_003045	
UBL3	5412	broad.mit.edu	37	13	30346296	30346296	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:30346296C>T	ENST00000380680.4	-	3	1321	c.176G>A	c.(175-177)cGa>cAa	p.R59Q		NM_007106.3	NP_009037.1	O95164	UBL3_HUMAN	ubiquitin-like 3	59	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.					extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)		p.R59Q(1)		large_intestine(3)|lung(1)	4		Lung SC(185;0.0281)		all cancers(112;0.0598)|GBM - Glioblastoma multiforme(144;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.147)		ATAAATAAGTCGTAGAATATT	0.373																																					p.R59Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G176A	13						.						147.0	135.0	139.0					13																	30346296		2203	4300	6503	29244296	SO:0001583	missense	5412	exon3			AF044221	CCDS9334.1	13q12-q13	2008-07-18			ENSG00000122042	ENSG00000122042			12504	protein-coding gene	gene with protein product		604711		PNSC1		10375635	Standard	NM_007106		Approved	HCG-1, DKFZP434K151, FLJ32018	uc001usp.3	O95164	OTTHUMG00000016661	ENST00000380680.4:c.176G>A	13.37:g.30346296C>T	ENSP00000370055:p.Arg59Gln	Somatic		Capture	Illumina HiSeq	Phase_I	29244296	NM_007106	B2R4J1|Q5RL72|Q5VZS0|Q6FIG8|Q96SG7	Missense_Mutation	SNP	ENST00000380680.4	37	CCDS9334.1	.	.	.	.	.	.	.	.	.	.	C	36	5.837919	0.97009	.	.	ENSG00000122042	ENST00000380680	.	.	.	6.07	6.07	0.98685	Ubiquitin supergroup (1);	0.000000	0.85682	D	0.000000	T	0.74846	0.3770	M	0.85197	2.74	0.80722	D	1	D	0.63046	0.992	P	0.48425	0.577	T	0.79184	-0.1908	9	0.72032	D	0.01	-10.6177	19.6407	0.95757	0.0:1.0:0.0:0.0	.	59	O95164	UBL3_HUMAN	Q	59	.	ENSP00000370055:R59Q	R	-	2	0	UBL3	29244296	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.224000	0.78042	2.890000	0.99128	0.585000	0.79938	CGA		0.373	UBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044342.1	NM_007106	
USPL1	10208	broad.mit.edu	37	13	31232713	31232713	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:31232713A>G	ENST00000255304.4	+	9	2841	c.2499A>G	c.(2497-2499)ccA>ccG	p.P833P		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	833					Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)	p.P833P(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		CAGGCCCTCCATCGTCTAATG	0.502																																					p.P833P	Ovarian(60;318 1180 1554 28110 31601)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2499G	13						.						75.0	74.0	74.0					13																	31232713		2203	4300	6503	30130713	SO:0001819	synonymous_variant	10208	exon9			X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 22"""	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.2499A>G	13.37:g.31232713A>G		Somatic		Capture	Illumina HiSeq	Phase_I	30130713	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Silent	SNP	ENST00000255304.4	37	CCDS9336.1																																																																																				0.502	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800	
FRY	10129	broad.mit.edu	37	13	32823675	32823675	+	Missense_Mutation	SNP	G	G	A	rs374001727		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:32823675G>A	ENST00000380250.3	+	49	7517	c.7021G>A	c.(7021-7023)Ggg>Agg	p.G2341R		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	2341						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G2341R(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)		TCCAATCATCGGGAGGCGGTA	0.512																																					p.G2341R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G7021A	13						.	G	ARG/GLY	0,3928		0,0,1964	55.0	56.0	55.0		7021	6.0	1.0	13		55	1,8307		0,1,4153	no	missense	FRY	NM_023037.2	125	0,1,6117	AA,AG,GG		0.012,0.0,0.0082	probably-damaging	2341/3014	32823675	1,12235	1964	4154	6118	31721675	SO:0001583	missense	10129	exon49			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.7021G>A	13.37:g.32823675G>A	ENSP00000369600:p.Gly2341Arg	Somatic		Capture	Illumina HiSeq	Phase_I	31721675	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	G	33	5.285720	0.95517	0.0	1.2E-4	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.29655	1.56	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.59972	0.2233	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60156	-0.7318	10	0.87932	D	0	.	20.4434	0.99119	0.0:0.0:1.0:0.0	.	2341	Q5TBA9	FRY_HUMAN	R	2341;1151	ENSP00000369600:G2341R	ENSP00000369600:G2341R	G	+	1	0	FRY	31721675	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	9.429000	0.97481	2.838000	0.97847	0.655000	0.94253	GGG		0.512	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
PDS5B	23047	broad.mit.edu	37	13	33258137	33258137	+	Nonsense_Mutation	SNP	A	A	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:33258137A>T	ENST00000315596.10	+	11	1366	c.1180A>T	c.(1180-1182)Aga>Tga	p.R394*		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	394				R -> G (in Ref. 2; AAD22134). {ECO:0000305}.	cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.R394*(2)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		TAATTTTGTGAGAGAGAGAAC	0.274																																					p.R394X												.	.	2	Substitution - Nonsense(2)	large_intestine(1)|endometrium(1)	c.A1180T	13						.						140.0	130.0	133.0					13																	33258137		1813	4068	5881	32156137	SO:0001587	stop_gained	23047	exon11			AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"""androgen-induced proliferation inhibitor"""	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.1180A>T	13.37:g.33258137A>T	ENSP00000313851:p.Arg394*	Somatic		Capture	Illumina HiSeq	Phase_I	32156137	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Nonsense_Mutation	SNP	ENST00000315596.10	37	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	A	36	5.852697	0.97030	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	.	.	.	5.11	5.11	0.69529	.	0.045487	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-3.1156	11.2434	0.48982	0.847:0.153:0.0:0.0	.	.	.	.	X	394	.	ENSP00000313851:R394X	R	+	1	2	PDS5B	32156137	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.075000	0.50073	2.064000	0.61679	0.482000	0.46254	AGA		0.274	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032	
PDS5B	23047	broad.mit.edu	37	13	33306326	33306326	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:33306326T>C	ENST00000315596.10	+	20	2398	c.2212T>C	c.(2212-2214)Tct>Cct	p.S738P		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	738					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.S738P(1)		NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		TGCGATATTTTCTAGTAAAGA	0.318																																					p.S738P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2212C	13						.						72.0	67.0	68.0					13																	33306326		1801	4064	5865	32204326	SO:0001583	missense	23047	exon20			AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"""androgen-induced proliferation inhibitor"""	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.2212T>C	13.37:g.33306326T>C	ENSP00000313851:p.Ser738Pro	Somatic		Capture	Illumina HiSeq	Phase_I	32204326	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	ENST00000315596.10	37	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	T	12.99	2.104359	0.37145	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	T	0.69806	-0.43	4.89	4.89	0.63831	Armadillo-like helical (1);Armadillo-type fold (1);	0.099483	0.64402	D	0.000001	T	0.38321	0.1036	N	0.01352	-0.895	0.54753	D	0.999986	B	0.11235	0.004	B	0.14023	0.01	T	0.29971	-0.9994	10	0.22706	T	0.39	-25.6723	14.7926	0.69854	0.0:0.0:0.0:1.0	.	738	Q9NTI5	PDS5B_HUMAN	P	738	ENSP00000313851:S738P	ENSP00000313851:S738P	S	+	1	0	PDS5B	32204326	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.158000	0.71851	1.956000	0.56807	0.397000	0.26171	TCT		0.318	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032	
STARD13	90627	broad.mit.edu	37	13	33681061	33681061	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:33681061T>C	ENST00000336934.5	-	13	3174	c.3058A>G	c.(3058-3060)Act>Gct	p.T1020A	STARD13_ENST00000255486.4_Missense_Mutation_p.T1012A|STARD13_ENST00000399365.3_Missense_Mutation_p.T902A	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	1020	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				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.T1020A(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)		GGCAAATCAGTTTTCCAGGTC	0.507																																					p.T1020A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3058G	13						.						100.0	101.0	101.0					13																	33681061		2203	4300	6503	32579061	SO:0001583	missense	90627	exon13			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.3058A>G	13.37:g.33681061T>C	ENSP00000338785:p.Thr1020Ala	Somatic		Capture	Illumina HiSeq	Phase_I	32579061	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	37	CCDS9348.1	.	.	.	.	.	.	.	.	.	.	T	18.63	3.664711	0.67700	.	.	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934	T;T;T	0.78364	-1.17;-1.17;-1.17	5.97	5.97	0.96955	Lipid-binding START (3);START-like domain (1);	0.000000	0.85682	D	0.000000	D	0.85093	0.5618	M	0.79805	2.47	0.80722	D	1	P;P;B	0.40553	0.721;0.572;0.086	P;P;B	0.49502	0.613;0.568;0.093	D	0.86089	0.1549	10	0.56958	D	0.05	.	16.4504	0.83984	0.0:0.0:0.0:1.0	.	985;1020;1012	Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;STA13_HUMAN;.	A	902;1012;1020	ENSP00000382300:T902A;ENSP00000255486:T1012A;ENSP00000338785:T1020A	ENSP00000255486:T1012A	T	-	1	0	STARD13	32579061	1.000000	0.71417	0.995000	0.50966	0.677000	0.39632	7.950000	0.87804	2.288000	0.76882	0.533000	0.62120	ACT		0.507	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
DCLK1	9201	broad.mit.edu	37	13	36700142	36700142	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:36700142G>A	ENST00000360631.3	-	2	344	c.133C>T	c.(133-135)Cgc>Tgc	p.R45C	DCLK1_ENST00000379892.4_Missense_Mutation_p.R45C|DCLK1_ENST00000255448.4_Missense_Mutation_p.R45C			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	45					axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.R45C(2)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		TGCAGCGTGCGGGTGCGGTAG	0.597																																					p.R45C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C133T	13						.						71.0	68.0	69.0					13																	36700142		2203	4300	6503	35598142	SO:0001583	missense	9201	exon2			AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"""doublecortin and CaM kinase-like 1"""	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.133C>T	13.37:g.36700142G>A	ENSP00000353846:p.Arg45Cys	Somatic		Capture	Illumina HiSeq	Phase_I	35598142	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	37		.	.	.	.	.	.	.	.	.	.	G	34	5.368740	0.95900	.	.	ENSG00000133083	ENST00000255448;ENST00000360631;ENST00000539451;ENST00000379892	T;T;T	0.71103	-0.54;-0.54;1.47	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.84183	0.5416	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	D	0.85163	0.0993	10	0.87932	D	0	.	19.7802	0.96413	0.0:0.0:1.0:0.0	.	45	O15075-2	.	C	45	ENSP00000255448:R45C;ENSP00000353846:R45C;ENSP00000369222:R45C	ENSP00000255448:R45C	R	-	1	0	DCLK1	35598142	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.472000	0.73567	2.675000	0.91044	0.655000	0.94253	CGC		0.597	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734	
SMAD9	4093	broad.mit.edu	37	13	37439876	37439876	+	Silent	SNP	G	G	A	rs191749029	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:37439876G>A	ENST00000399275.2	-	4	940	c.801C>T	c.(799-801)taC>taT	p.Y267Y	SMAD9_ENST00000379826.4_Silent_p.Y267Y|SMAD9_ENST00000350148.5_Silent_p.Y230Y			O15198	SMAD9_HUMAN	SMAD family member 9	267					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.Y230Y(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)		GGGGCTCCTCGTAACAAACTG	0.502													G|||	3	0.000599042	0.0008	0.0	5008	,	,		18114	0.002		0.0	False		,,,				2504	0.0				p.Y230Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C690T	13						.	G	,	1,4405	2.1+/-5.4	0,1,2202	54.0	50.0	51.0		801,690	-5.9	0.2	13		51	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SMAD9	NM_001127217.2,NM_005905.5	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	267/468,230/431	37439876	1,13005	2203	4300	6503	36337876	SO:0001819	synonymous_variant	4093	exon4				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.801C>T	13.37:g.37439876G>A		Somatic		Capture	Illumina HiSeq	Phase_I	36337876	NM_005905	A2A2Y6|O14989|Q5TBA1	Silent	SNP	ENST00000399275.2	37	CCDS45032.1																																																																																				0.502	SMAD9-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044525.2	NM_005905	
ALG5	29880	broad.mit.edu	37	13	37539850	37539850	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:37539850C>T	ENST00000239891.3	-	8	701	c.635G>A	c.(634-636)cGt>cAt	p.R212H	ALG5_ENST00000443765.1_Missense_Mutation_p.R182H|ALG5_ENST00000413537.2_3'UTR	NM_013338.4	NP_037470.1	Q9Y673	ALG5_HUMAN	ALG5, dolichyl-phosphate beta-glucosyltransferase	212					cellular protein metabolic process (GO:0044267)|determination of left/right symmetry (GO:0007368)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	dolichyl-phosphate beta-glucosyltransferase activity (GO:0004581)|oligosaccharyl transferase activity (GO:0004576)	p.R212H(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)		all cancers(112;5.79e-07)|Epithelial(112;1.81e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00785)|BRCA - Breast invasive adenocarcinoma(63;0.0127)|GBM - Glioblastoma multiforme(144;0.0472)		GAGAAGAGTACGGAAGTAAGA	0.393																																					p.R182H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G545A	13						.						89.0	88.0	88.0					13																	37539850		2203	4300	6503	36437850	SO:0001583	missense	29880	exon7			AF088028	CCDS9361.1, CCDS45033.1	13q13.1	2013-02-22	2013-02-21		ENSG00000120697	ENSG00000120697	2.4.1.117	"""Glycosyltransferase family 2 domain containing"""	20266	protein-coding gene	gene with protein product		604565	"""asparagine-linked glycosylation 5 homolog (yeast, dolichyl-phosphate beta-glucosyltransferase)"", ""asparagine-linked glycosylation 5, dolichyl-phosphate beta-glucosyltransferase homolog (S. cerevisiae)"""			10359825	Standard	NM_013338		Approved	bA421P11.2	uc001uvy.3	Q9Y673	OTTHUMG00000016741	ENST00000239891.3:c.635G>A	13.37:g.37539850C>T	ENSP00000239891:p.Arg212His	Somatic		Capture	Illumina HiSeq	Phase_I	36437850	NM_001142364	B4DR37|Q5TBA6	Missense_Mutation	SNP	ENST00000239891.3	37	CCDS9361.1	.	.	.	.	.	.	.	.	.	.	C	33	5.235437	0.95207	.	.	ENSG00000120697	ENST00000443765;ENST00000239891	T;T	0.61627	0.09;0.09	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.85788	0.5778	H	0.97659	4.05	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.90126	0.4203	10	0.87932	D	0	.	20.093	0.97828	0.0:1.0:0.0:0.0	.	182;212	Q9Y673-2;Q9Y673	.;ALG5_HUMAN	H	182;212	ENSP00000390533:R182H;ENSP00000239891:R212H	ENSP00000239891:R212H	R	-	2	0	ALG5	36437850	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.592000	0.82676	2.756000	0.94617	0.561000	0.74099	CGT		0.393	ALG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044528.2	NM_013338	
NAA16	79612	broad.mit.edu	37	13	41932462	41932462	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:41932462G>A	ENST00000379406.3	+	11	1434	c.1110G>A	c.(1108-1110)ccG>ccA	p.P370P	NAA16_ENST00000379367.3_Silent_p.P370P|NAA16_ENST00000403412.3_Silent_p.P370P	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	370					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)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)	p.P370P(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						AGGAACCCCCGACAACACTAC	0.348																																					p.P370P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1110A	13						.						82.0	80.0	81.0					13																	41932462		2203	4300	6503	40830462	SO:0001819	synonymous_variant	79612	exon11			AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"""N(alpha)-acetyltransferase subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	26164	protein-coding gene	gene with protein product			"""NMDA receptor regulated 1-like"""	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.1110G>A	13.37:g.41932462G>A		Somatic		Capture	Illumina HiSeq	Phase_I	40830462	NM_024561	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Silent	SNP	ENST00000379406.3	37	CCDS9379.1																																																																																				0.348	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527	
LACC1	144811	broad.mit.edu	37	13	44455171	44455171	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:44455171delA	ENST00000441843.1	+	2	535	c.50delA	c.(49-51)caafs	p.Q17fs	CCDC122_ENST00000444614.3_5'Flank|CCDC122_ENST00000476570.2_5'Flank|LACC1_ENST00000325686.6_Frame_Shift_Del_p.Q17fs	NM_001128303.1	NP_001121775.1	Q8IV20	LACC1_HUMAN	laccase (multicopper oxidoreductase) domain containing 1	17								p.N19fs*7(1)									TTGAACTCTCAAAAAAACTGC	0.358																																					p.Q17fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.50delA	13						.						72.0	74.0	73.0					13																	44455171		2203	4300	6503	43353171	SO:0001589	frameshift_variant	144811	exon2			AK096044	CCDS9391.1	13q14.11	2012-05-11	2011-08-09	2011-08-09	ENSG00000179630	ENSG00000179630			26789	protein-coding gene	gene with protein product		613409	"""chromosome 13 open reading frame 31"""	C13orf31		16740638, 22504414	Standard	NM_153218		Approved	FLJ38725	uc010acg.3	Q8IV20	OTTHUMG00000016826	ENST00000441843.1:c.50delA	13.37:g.44455171delA	ENSP00000391747:p.Gln17fs	Somatic		Capture	Illumina HiSeq	Phase_I	43353171	NM_001128303	A2A3Z6|Q8N8X5	Frame_Shift_Del	DEL	ENST00000441843.1	37	CCDS9391.1																																																																																				0.358	LACC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044726.3	NM_153218	
ZC3H13	23091	broad.mit.edu	37	13	46549464	46549464	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:46549464G>A	ENST00000242848.4	-	12	2770	c.2422C>T	c.(2422-2424)Cga>Tga	p.R808*	ZC3H13_ENST00000282007.3_Nonsense_Mutation_p.R808*			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	808	Arg/Glu-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R808*(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)		CTATCTTCTCGGATCTCTTCT	0.373																																					p.R808X	Esophageal Squamous(187;747 2077 11056 31291 44172)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2422T	13						.						361.0	324.0	337.0					13																	46549464		2203	4300	6503	45447465	SO:0001587	stop_gained	23091	exon12			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.2422C>T	13.37:g.46549464G>A	ENSP00000242848:p.Arg808*	Somatic		Capture	Illumina HiSeq	Phase_I	45447465	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Nonsense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	G	41	8.752862	0.98941	.	.	ENSG00000123200	ENST00000242848;ENST00000282007	.	.	.	5.51	3.66	0.41972	.	0.000000	0.46442	D	0.000283	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9281	0.63975	0.0:0.0:0.7237:0.2763	.	.	.	.	X	808	.	ENSP00000242848:R808X	R	-	1	2	ZC3H13	45447465	0.862000	0.29867	0.555000	0.28281	0.899000	0.52679	1.589000	0.36644	1.313000	0.45069	0.467000	0.42956	CGA		0.373	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070	
CPB2	1361	broad.mit.edu	37	13	46658368	46658368	+	Silent	SNP	G	G	A	rs201399827		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:46658368G>A	ENST00000181383.4	-	3	277	c.261C>T	c.(259-261)agC>agT	p.S87S	CPB2_ENST00000439329.3_Silent_p.S87S|CPB2-AS1_ENST00000415033.2_RNA|CPB2-AS1_ENST00000606243.1_RNA|CPB2-AS1_ENST00000606351.1_RNA|CPB2-AS1_ENST00000606991.1_RNA	NM_001872.3	NP_001863.3	Q96IY4	CBPB2_HUMAN	carboxypeptidase B2 (plasma)	87					blood coagulation (GO:0007596)|cellular response to glucose stimulus (GO:0071333)|fibrinolysis (GO:0042730)|liver regeneration (GO:0097421)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of plasminogen activation (GO:0010757)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to heat (GO:0009408)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.S87S(1)		NS(1)|cervix(1)|large_intestine(3)|liver(1)|lung(9)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)		ATGGAATTCCGCTCACATTTA	0.393																																					p.S87S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C261T	13						.						190.0	175.0	180.0					13																	46658368		2203	4300	6503	45556369	SO:0001819	synonymous_variant	1361	exon3			M75106	CCDS9401.1, CCDS73568.1	13q14.11	2012-02-10	2007-02-21		ENSG00000080618	ENSG00000080618			2300	protein-coding gene	gene with protein product	"""thrombin-activatable fibrinolysis inhibitor"", ""carboxypeptidase U"", ""plasma carboxypeptidase B"", ""carboxypeptidase R"""	603101	"""carboxypeptidase B2 (plasma, carboxypeptidase U)"""			1939207, 1427879	Standard	NM_001278541		Approved	CPU, PCPB, TAFI	uc001vaw.3	Q96IY4	OTTHUMG00000016867	ENST00000181383.4:c.261C>T	13.37:g.46658368G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45556369	NM_016413	A8K464|Q15114|Q5T9K1|Q5T9K2|Q9P2Y6	Silent	SNP	ENST00000181383.4	37	CCDS9401.1																																																																																				0.393	CPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044803.2	NM_001872	
KIAA0226L	80183	broad.mit.edu	37	13	46918923	46918923	+	Missense_Mutation	SNP	G	G	A	rs200512455	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:46918923G>A	ENST00000429979.1	-	14	2433	c.1829C>T	c.(1828-1830)aCg>aTg	p.T610M	KIAA0226L_ENST00000378787.3_Nonsense_Mutation_p.R559*|KIAA0226L_ENST00000534925.1_Missense_Mutation_p.T475M|KIAA0226L_ENST00000322896.6_Missense_Mutation_p.T453M|KIAA0226L_ENST00000378797.2_Nonsense_Mutation_p.R559*|KIAA0226L_ENST00000389908.3_Missense_Mutation_p.T610M|KIAA0226L_ENST00000378784.4_Missense_Mutation_p.T543M|KIAA0226L_ENST00000409879.2_Missense_Mutation_p.T453M|KIAA0226L_ENST00000378781.3_3'UTR	NM_025113.2	NP_079389.2	Q9H714	K226L_HUMAN	KIAA0226-like	610								p.T610M(1)		NS(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|pancreas(1)	26						GATGACAGTCGTATTCTGGCA	0.323													G|||	2	0.000399361	0.0	0.0	5008	,	,		20243	0.001		0.001	False		,,,				2504	0.0				p.T610M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1829T	13						.	G	MET/THR	0,4406		0,0,2203	91.0	80.0	84.0		1829	6.0	0.0	13		84	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KIAA0226L	NM_025113.2	81	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	610/663	46918923	3,13003	2203	4300	6503	45816924	SO:0001583	missense	80183	exon14			AK025215	CCDS31970.2, CCDS66543.1, CCDS66544.1, CCDS66545.1, CCDS73569.1	13q14.11	2011-08-09	2011-08-09	2011-08-09	ENSG00000102445	ENSG00000102445			20420	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 18"""	C13orf18			Standard	NM_001286766		Approved	FLJ21562	uc010acl.3	Q9H714	OTTHUMG00000016868	ENST00000429979.1:c.1829C>T	13.37:g.46918923G>A	ENSP00000396935:p.Thr610Met	Somatic		Capture	Illumina HiSeq	Phase_I	45816924	NM_025113	A8KAG9|A8XR19|B3KS87|Q5W051|Q5W053|Q6PJ74|Q6PK94|Q86XH7|Q8N5J6	Nonsense_Mutation	SNP	ENST00000429979.1	37	CCDS31970.2	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	1|1	0.0013192612137203166|0.0013192612137203166	G|G	41|41	9.096126|9.096126	0.99064|0.99064	0.0|0.0	3.49E-4|3.49E-4	ENSG00000102445|ENSG00000102445	ENST00000378797;ENST00000378787|ENST00000429979;ENST00000378784;ENST00000389908;ENST00000409879;ENST00000322896;ENST00000534925	.|T;T;T;T	.|0.44881	.|0.91;0.91;0.91;0.92	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	1.990470|.	0.02589|.	N|.	0.099721|.	.|T	.|0.63212	.|0.2492	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	.|D;D;D;P;P	.|0.69078	.|0.99;0.99;0.997;0.878;0.946	.|P;P;P;B;B	.|0.61658	.|0.892;0.892;0.892;0.441;0.403	.|T	.|0.60167	.|-0.7316	.|9	0.23302|0.46703	T|T	0.38|0.11	-1.5495|-1.5495	19.545|19.545	0.95291|0.95291	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|453;453;610;475;543	.|B7ZBN5;B7Z6E4;Q9H714;A8KAG9;Q9H714-3	.|.;.;K226L_HUMAN;.;.	X|M	559|610;543;610;453;453;475	.|ENSP00000396935:T610M;ENSP00000368061:T543M;ENSP00000374558:T610M;ENSP00000437501:T475M	ENSP00000368064:R559X|ENSP00000315633:T453M	R|T	-|-	1|2	2|0	KIAA0226L|KIAA0226L	45816924|45816924	0.051000|0.051000	0.20477|0.20477	0.024000|0.024000	0.17045|0.17045	0.663000|0.663000	0.39108|0.39108	2.429000|2.429000	0.44758|0.44758	2.861000|2.861000	0.98227|0.98227	0.655000|0.655000	0.94253|0.94253	CGA|ACG		0.323	KIAA0226L-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044809.2	NM_025113	
KPNA3	3839	broad.mit.edu	37	13	50279758	50279758	+	Splice_Site	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:50279758T>G	ENST00000261667.3	-	15	1785	c.1371A>C	c.(1369-1371)ggA>ggC	p.G457G		NM_002267.3	NP_002258.2	O00505	IMA4_HUMAN	karyopherin alpha 3 (importin alpha 4)	457					cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)|protein complex assembly (GO:0006461)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nuclear localization sequence binding (GO:0008139)|protein transporter activity (GO:0008565)	p.G457G(1)		cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(4)	21		Lung NSC(96;2.46e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.42e-09)		CACTCTTACCTCCACATTCCT	0.378																																					p.G457G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1371C	13						.						260.0	240.0	247.0					13																	50279758		2203	4300	6503	49177759	SO:0001630	splice_region_variant	3839	exon15			D89618	CCDS9421.1	13q14.3	2013-02-14			ENSG00000102753	ENSG00000102753		"""Importins"", ""Armadillo repeat containing"""	6396	protein-coding gene	gene with protein product		601892				9154134, 9435235	Standard	NM_002267		Approved	SRP1gamma, SRP4, hSRP1, IPOA4	uc001vdj.2	O00505	OTTHUMG00000016922	ENST00000261667.3:c.1372+1A>C	13.37:g.50279758T>G		Somatic		Capture	Illumina HiSeq	Phase_I	49177759	NM_002267	O00191|O43195|Q5JVM9|Q96AA7	Silent	SNP	ENST00000261667.3	37	CCDS9421.1	.	.	.	.	.	.	.	.	.	.	T	16.60	3.168533	0.57584	.	.	ENSG00000102753	ENST00000436760	.	.	.	5.86	5.86	0.93980	.	.	.	.	.	T	0.73273	0.3566	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72374	-0.4313	4	.	.	.	-12.3149	16.2669	0.82588	0.0:0.0:0.0:1.0	.	.	.	.	A	44	.	.	E	-	2	0	KPNA3	49177759	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.086000	0.64474	2.240000	0.73641	0.533000	0.62120	GAG		0.378	KPNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044939.2	NM_002267	Silent
THSD1	55901	broad.mit.edu	37	13	52952712	52952712	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:52952712C>T	ENST00000258613.4	-	5	1571	c.1393G>A	c.(1393-1395)Gag>Aag	p.E465K	THSD1_ENST00000349258.4_Missense_Mutation_p.E412K|THSD1_ENST00000544466.1_Missense_Mutation_p.E86K	NM_018676.3	NP_061146.1	Q9NS62	THSD1_HUMAN	thrombospondin, type I, domain containing 1	465					hematopoietic progenitor cell differentiation (GO:0002244)	cell periphery (GO:0071944)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)		p.E465K(1)		breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Breast(56;0.000207)|Lung NSC(96;0.00145)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.8e-08)		ATATTCTCCTCGTCCGAGTTC	0.642																																					p.E465K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1393A	13						.						46.0	52.0	50.0					13																	52952712		2203	4300	6503	51850713	SO:0001583	missense	55901	exon5			AK096289	CCDS9432.1, CCDS9433.1	13q14.13	2010-04-20	2004-03-11		ENSG00000136114	ENSG00000136114			17754	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain 1"""				Standard	NM_018676		Approved	TMTSP	uc001vgo.3	Q9NS62	OTTHUMG00000016963	ENST00000258613.4:c.1393G>A	13.37:g.52952712C>T	ENSP00000258613:p.Glu465Lys	Somatic		Capture	Illumina HiSeq	Phase_I	51850713	NM_018676	A2A3J3|B2RCF5|Q6P3U1|Q6UXZ2	Missense_Mutation	SNP	ENST00000258613.4	37	CCDS9432.1	.	.	.	.	.	.	.	.	.	.	c	20.8	4.058453	0.76074	.	.	ENSG00000136114	ENST00000349258;ENST00000544466;ENST00000258613	T;T;T	0.39787	1.75;1.06;2.07	6.06	5.21	0.72293	.	0.054513	0.64402	D	0.000001	T	0.62221	0.2410	M	0.71581	2.175	0.53005	D	0.999966	D;B	0.71674	0.998;0.236	P;B	0.62184	0.899;0.1	T	0.67562	-0.5639	10	0.87932	D	0	-29.8925	16.5116	0.84287	0.0:0.8692:0.1308:0.0	.	412;465	Q9NS62-2;Q9NS62	.;THSD1_HUMAN	K	412;86;465	ENSP00000340650:E412K;ENSP00000438512:E86K;ENSP00000258613:E465K	ENSP00000258613:E465K	E	-	1	0	THSD1	51850713	0.996000	0.38824	0.948000	0.38648	0.662000	0.39071	3.336000	0.52113	1.555000	0.49500	-0.182000	0.12963	GAG		0.642	THSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045058.3		
VPS36	51028	broad.mit.edu	37	13	53001152	53001152	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:53001152T>G	ENST00000378060.4	-	8	638	c.611A>C	c.(610-612)gAc>gCc	p.D204A		NM_001282168.1|NM_001282169.1|NM_016075.2	NP_001269097.1|NP_001269098.1|NP_057159.2	Q86VN1	VPS36_HUMAN	vacuolar protein sorting 36 homolog (S. cerevisiae)	204					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)	p.D204A(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	17		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)		ACCTTGTTTGTCTTTAATTTT	0.313																																					p.D204A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A611C	13						.						156.0	144.0	148.0					13																	53001152		2203	4298	6501	51899153	SO:0001583	missense	51028	exon8			AF151903	CCDS9434.1, CCDS73577.1	13q14.13	2008-02-05	2007-01-12	2005-08-02	ENSG00000136100	ENSG00000136100			20312	protein-coding gene	gene with protein product		610903	"""chromosome 13 open reading frame 9"", ""vacuolar protein sorting 36 homolog (yeast)"""	C13orf9		11278625, 15755741	Standard	NM_016075		Approved	CGI-145, Eap45	uc001vgs.3	Q86VN1	OTTHUMG00000016964	ENST00000378060.4:c.611A>C	13.37:g.53001152T>G	ENSP00000367299:p.Asp204Ala	Somatic		Capture	Illumina HiSeq	Phase_I	51899153	NM_016075	A8K125|Q3ZCV7|Q5H9S1|Q5VXB6|Q9H8Z5|Q9Y3E3	Missense_Mutation	SNP	ENST00000378060.4	37	CCDS9434.1	.	.	.	.	.	.	.	.	.	.	.	15.97	2.990957	0.54041	.	.	ENSG00000136100	ENST00000378060	.	.	.	6.16	6.16	0.99307	.	0.176914	0.64402	D	0.000013	T	0.37183	0.0994	N	0.05230	-0.09	0.80722	D	1	B	0.26845	0.161	B	0.29663	0.105	T	0.33752	-0.9856	9	0.11182	T	0.66	-16.1199	15.9872	0.80168	0.0:0.0:0.0:1.0	.	204	Q86VN1	VPS36_HUMAN	A	204	.	ENSP00000367299:D204A	D	-	2	0	VPS36	51899153	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.636000	0.83301	2.367000	0.80283	0.528000	0.53228	GAC		0.313	VPS36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045059.3		
PCDH8	5100	broad.mit.edu	37	13	53418891	53418891	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:53418891G>A	ENST00000377942.3	-	3	3220	c.3017C>T	c.(3016-3018)gCc>gTc	p.A1006V	PCDH8_ENST00000338862.4_Missense_Mutation_p.A909V	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	1006					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.A1006V(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)		GGGCAGCTGGGCCTGGTAGTA	0.582																																					p.A909V	GBM(36;25 841 9273 49207)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2726T	13						.						154.0	114.0	127.0					13																	53418891		2203	4300	6503	52316892	SO:0001583	missense	5100	exon3			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.3017C>T	13.37:g.53418891G>A	ENSP00000367177:p.Ala1006Val	Somatic		Capture	Illumina HiSeq	Phase_I	52316892	NM_032949	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Missense_Mutation	SNP	ENST00000377942.3	37	CCDS9438.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.467946	0.84533	.	.	ENSG00000136099	ENST00000377942;ENST00000338862;ENST00000418407;ENST00000448969	T;T	0.57273	0.58;0.41	5.95	5.95	0.96441	.	0.000000	0.43919	D	0.000516	T	0.64249	0.2581	L	0.36672	1.1	0.58432	D	0.99999	D;D	0.65815	0.995;0.991	P;P	0.61800	0.894;0.787	T	0.64470	-0.6400	10	0.72032	D	0.01	.	20.3747	0.98911	0.0:0.0:1.0:0.0	.	909;1006	O95206-2;O95206	.;PCDH8_HUMAN	V	1006;909;532;849	ENSP00000367177:A1006V;ENSP00000341350:A909V	ENSP00000341350:A909V	A	-	2	0	PCDH8	52316892	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.476000	0.97823	2.817000	0.96982	0.563000	0.77884	GCC		0.582	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590	
LMO7	4008	broad.mit.edu	37	13	76429401	76429401	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:76429401T>C	ENST00000321797.8	+	27	4689	c.3968T>C	c.(3967-3969)gTc>gCc	p.V1323A	LMO7_ENST00000465261.2_Intron|LMO7_ENST00000341547.4_Missense_Mutation_p.V1274A|LMO7_ENST00000526202.1_Missense_Mutation_p.V1200A|LMO7_ENST00000357063.3_Intron|LMO7_ENST00000377534.3_Intron			Q8WWI1	LMO7_HUMAN	LIM domain 7	1608					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.V1274A(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)		TCTAGGTCAGTCAGTGGGAAG	0.433																																					p.V1274A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3821C	13						.						123.0	106.0	112.0					13																	76429401		2203	4300	6503	75327402	SO:0001583	missense	4008	exon28			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.3968T>C	13.37:g.76429401T>C	ENSP00000317802:p.Val1323Ala	Somatic		Capture	Illumina HiSeq	Phase_I	75327402	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	37		.	.	.	.	.	.	.	.	.	.	T	19.96	3.923339	0.73213	.	.	ENSG00000136153	ENST00000341547;ENST00000321797;ENST00000526202	T;T;T	0.68765	0.18;-0.28;-0.35	5.87	5.87	0.94306	.	0.064020	0.64402	D	0.000009	D	0.82870	0.5131	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.991;0.996	D	0.85294	0.1069	10	0.87932	D	0	-16.3503	16.2813	0.82687	0.0:0.0:0.0:1.0	.	1200;1274	E9PMS6;Q8WWI1-3	.;.	A	1274;1323;1200	ENSP00000342112:V1274A;ENSP00000317802:V1323A;ENSP00000431129:V1200A	ENSP00000317802:V1323A	V	+	2	0	LMO7	75327402	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.244000	0.73946	0.533000	0.62120	GTC		0.433	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
EDNRB	1910	broad.mit.edu	37	13	78492461	78492461	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:78492461C>T	ENST00000334286.5	-	1	484	c.248G>A	c.(247-249)cGc>cAc	p.R83H	RNF219-AS1_ENST00000607862.1_RNA|EDNRB_ENST00000446573.1_Missense_Mutation_p.R83H|EDNRB_ENST00000377211.4_Missense_Mutation_p.R173H|EDNRB_ENST00000475537.1_5'Flank	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	83					aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)	p.R83H(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	GGAGATGGTGCGTGGCGGAGA	0.587																																					p.R83H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G248A	13						.						112.0	111.0	111.0					13																	78492461		2203	4300	6503	77390462	SO:0001583	missense	1910	exon1			L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"""GPCR / Class A : Endothelin receptors"""	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.248G>A	13.37:g.78492461C>T	ENSP00000335311:p.Arg83His	Somatic		Capture	Illumina HiSeq	Phase_I	77390462	NM_001122659	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Missense_Mutation	SNP	ENST00000334286.5	37	CCDS9461.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.976568	0.53720	.	.	ENSG00000136160	ENST00000377211;ENST00000446573;ENST00000334286	T;T;T	0.37584	1.19;1.19;1.19	4.75	2.98	0.34508	.	0.193847	0.29745	N	0.011315	T	0.33556	0.0867	M	0.68952	2.095	0.09310	N	0.999998	B;B;B	0.22003	0.028;0.063;0.005	B;B;B	0.20577	0.014;0.03;0.006	T	0.27640	-1.0068	10	0.48119	T	0.1	-6.7764	7.7707	0.29006	0.0:0.7423:0.0:0.2577	.	83;173;83	P24530-2;P24530-3;P24530	.;.;EDNRB_HUMAN	H	173;83;83	ENSP00000366416:R173H;ENSP00000403401:R83H;ENSP00000335311:R83H	ENSP00000335311:R83H	R	-	2	0	EDNRB	77390462	0.079000	0.21365	0.023000	0.16930	0.425000	0.31504	0.780000	0.26760	1.126000	0.42016	0.591000	0.81541	CGC		0.587	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1		
SLITRK1	114798	broad.mit.edu	37	13	84455488	84455488	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:84455488C>T	ENST00000377084.2	-	1	1040	c.155G>A	c.(154-156)cGt>cAt	p.R52H		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	52	LRRNT 1.				adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)		p.R52H(2)		NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		GGCAGTGAAACGCTGCAGACT	0.448																																					p.R52H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G155A	13						.						84.0	84.0	84.0					13																	84455488		2203	4300	6503	83353489	SO:0001583	missense	114798	exon1			AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"""leucine rich repeat containing 12"""	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.155G>A	13.37:g.84455488C>T	ENSP00000366288:p.Arg52His	Somatic		Capture	Illumina HiSeq	Phase_I	83353489	NM_052910	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	37	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	C	10.47	1.359937	0.24598	.	.	ENSG00000178235	ENST00000377084	T	0.58506	0.33	4.78	3.85	0.44370	.	0.054916	0.64402	D	0.000001	T	0.22859	0.0552	N	0.00926	-1.1	0.41002	D	0.984937	B	0.02656	0.0	B	0.01281	0.0	T	0.12837	-1.0532	10	0.39692	T	0.17	-5.765	4.7426	0.13022	0.0:0.7382:0.0:0.2618	.	52	Q96PX8	SLIK1_HUMAN	H	52	ENSP00000366288:R52H	ENSP00000366288:R52H	R	-	2	0	SLITRK1	83353489	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.917000	0.63369	2.475000	0.83589	0.561000	0.74099	CGT		0.448	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910	
SLITRK5	26050	broad.mit.edu	37	13	88327698	88327698	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:88327698C>T	ENST00000325089.6	+	2	274	c.55C>T	c.(55-57)Cat>Tat	p.H19Y	SLITRK5_ENST00000400028.3_Intron	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	19					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)		p.H19Y(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					CAGAAAAATGCATAGCTGGAT	0.438																																					p.H19Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C55T	13						.						115.0	104.0	108.0					13																	88327698		2203	4300	6503	87125699	SO:0001583	missense	26050	exon2			AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"""leucine rich repeat containing 11"""	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.55C>T	13.37:g.88327698C>T	ENSP00000366283:p.His19Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	87125699	NM_015567	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	37	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.118218	0.37339	.	.	ENSG00000165300	ENST00000325089	T	0.58358	0.34	5.77	5.77	0.91146	.	0.263887	0.37809	N	0.001927	T	0.41096	0.1144	L	0.39898	1.24	0.80722	D	1	P	0.40000	0.698	B	0.28709	0.093	T	0.31724	-0.9933	9	.	.	.	-0.9653	17.49	0.87701	0.0:1.0:0.0:0.0	.	19	O94991	SLIK5_HUMAN	Y	19	ENSP00000366283:H19Y	.	H	+	1	0	SLITRK5	87125699	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.459000	0.80802	2.744000	0.94065	0.561000	0.74099	CAT		0.438	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3		
SLITRK5	26050	broad.mit.edu	37	13	88329602	88329602	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:88329602C>T	ENST00000325089.6	+	2	2178	c.1959C>T	c.(1957-1959)ggC>ggT	p.G653G	SLITRK5_ENST00000400028.3_Silent_p.G412G	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	653					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)		p.G653G(2)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					CGAGCTTGGGCGCAGGCGGAG	0.652																																					p.G653G												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C1959T	13						.						69.0	75.0	73.0					13																	88329602		2203	4300	6503	87127603	SO:0001819	synonymous_variant	26050	exon2			AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"""leucine rich repeat containing 11"""	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.1959C>T	13.37:g.88329602C>T		Somatic		Capture	Illumina HiSeq	Phase_I	87127603	NM_015567	B3KNB8|B4DSH5|Q5VT81	Silent	SNP	ENST00000325089.6	37	CCDS9465.1																																																																																				0.652	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3		
STK24	8428	broad.mit.edu	37	13	99134530	99134530	+	Missense_Mutation	SNP	C	C	T	rs367740523		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:99134530C>T	ENST00000376547.3	-	3	500	c.355G>A	c.(355-357)Gca>Aca	p.A119T	STK24_ENST00000539966.1_Intron|STK24_ENST00000397517.2_Missense_Mutation_p.A107T	NM_003576.3	NP_003567.2	Q9Y6E0	STK24_HUMAN	serine/threonine kinase 24	119	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of cell migration (GO:0030336)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of axon regeneration (GO:0048679)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.A119T(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			AGATCTAGTGCGGAGCCTCCA	0.318																																					p.A119T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G355A	13						.	C	THR/ALA,THR/ALA	0,4406		0,0,2203	74.0	70.0	71.0		319,355	5.6	0.8	13		71	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	STK24	NM_001032296.2,NM_003576.3	58,58	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	107/432,119/444	99134530	1,13003	2203	4299	6502	97932531	SO:0001583	missense	8428	exon3			AF024636	CCDS9488.1, CCDS32001.1, CCDS66573.1	13q31.2-q32.3	2010-06-25	2010-06-25		ENSG00000102572	ENSG00000102572			11403	protein-coding gene	gene with protein product	"""STE20-like kinase 3"", ""sterile 20-like kinase 3"""	604984	"""serine/threonine kinase 24 (Ste20, yeast homolog)"""			9353338, 10644707	Standard	NM_003576		Approved	MST-3, MST3, MST3B, STK3, STE20	uc001vnn.1	Q9Y6E0	OTTHUMG00000017250	ENST00000376547.3:c.355G>A	13.37:g.99134530C>T	ENSP00000365730:p.Ala119Thr	Somatic		Capture	Illumina HiSeq	Phase_I	97932531	NM_003576	O14840|Q5JV92	Missense_Mutation	SNP	ENST00000376547.3	37	CCDS9488.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.369732|5.369732	0.95900|0.95900	0.0|0.0	1.16E-4|1.16E-4	ENSG00000102572|ENSG00000102572	ENST00000397517;ENST00000376547;ENST00000376533;ENST00000543110|ENST00000444574	T;T|.	0.24350|.	1.86;1.86|.	5.58|5.58	5.58|5.58	0.84498|0.84498	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|.	0.56097|.	U|.	0.000034|.	T|T	0.47525|0.47525	0.1450|0.1450	N|N	0.05510|0.05510	-0.035|-0.035	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.999|.	D;D|.	0.70935|.	0.971;0.971|.	T|T	0.42816|0.42816	-0.9429|-0.9429	10|5	0.72032|.	D|.	0.01|.	.|.	19.5791|19.5791	0.95458|0.95458	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	107;119|.	Q5U0E6;Q9Y6E0|.	.;STK24_HUMAN|.	T|H	107;119;95;107|24	ENSP00000380651:A107T;ENSP00000365730:A119T|.	ENSP00000365716:A95T|.	A|R	-|-	1|2	0|0	STK24|STK24	97932531|97932531	1.000000|1.000000	0.71417|0.71417	0.827000|0.827000	0.32855|0.32855	0.938000|0.938000	0.57974|0.57974	7.707000|7.707000	0.84623|0.84623	2.630000|2.630000	0.89119|0.89119	0.650000|0.650000	0.86243|0.86243	GCA|CGC		0.318	STK24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045549.2	NM_003576	
DOCK9	23348	broad.mit.edu	37	13	99549792	99549792	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:99549792G>A	ENST00000376460.1	-	15	1739	c.1659C>T	c.(1657-1659)agC>agT	p.S553S	DOCK9_ENST00000339416.2_Silent_p.S554S|DOCK9_ENST00000442173.1_Silent_p.S553S|DOCK9_ENST00000448493.2_Silent_p.S565S	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	554					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S554S(1)		breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					ATAGCTTATTGCTGTCTTGCC	0.388																																					p.S553S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1659T	13						.						244.0	238.0	240.0					13																	99549792		1884	4115	5999	98347793	SO:0001819	synonymous_variant	23348	exon15			AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"""Pleckstrin homology (PH) domain containing"""	14132	protein-coding gene	gene with protein product	"""zizimin1"""	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.1659C>T	13.37:g.99549792G>A		Somatic		Capture	Illumina HiSeq	Phase_I	98347793	NM_001130050	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Silent	SNP	ENST00000376460.1	37	CCDS45062.1																																																																																				0.388	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296	
PCID2	55795	broad.mit.edu	37	13	113834493	113834493	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr13:113834493G>A	ENST00000337344.4	-	11	915	c.839C>T	c.(838-840)gCg>gTg	p.A280V	PCID2_ENST00000246505.5_Missense_Mutation_p.A334V|PCID2_ENST00000375477.1_Missense_Mutation_p.A280V|PCID2_ENST00000375459.1_Missense_Mutation_p.A278V|PCID2_ENST00000375457.2_Missense_Mutation_p.A278V|PCID2_ENST00000375479.2_Missense_Mutation_p.A280V|PCID2_ENST00000493650.1_5'UTR	NM_001127202.2	NP_001120674.1	Q5JVF3	PCID2_HUMAN	PCI domain containing 2	280	PCI.				negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity (GO:2000117)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mRNA stability (GO:0043488)|spleen development (GO:0048536)			p.A334V(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)	20	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_lung(25;0.216)|all_epithelial(44;0.234)	all cancers(43;0.104)			GGTTACTTCCGCAAACTGCAT	0.433																																					p.A280V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C839T	13						.						136.0	130.0	132.0					13																	113834493		2203	4300	6503	112882494	SO:0001583	missense	55795	exon11			AK002167	CCDS9532.2, CCDS58301.1, CCDS58302.1	13q34	2006-03-31			ENSG00000126226	ENSG00000126226			25653	protein-coding gene	gene with protein product		613713				12477932	Standard	NM_001127203		Approved	FLJ11305	uc031qnm.1	Q5JVF3	OTTHUMG00000017385	ENST00000337344.4:c.839C>T	13.37:g.113834493G>A	ENSP00000337405:p.Ala280Val	Somatic		Capture	Illumina HiSeq	Phase_I	112882494	NM_018386	A6NK09|Q3ZCX1|Q5TC57|Q5TC58|Q9H7K1|Q9HBZ7|Q9NUK6|Q9NVY1|Q9NW44|Q9NWH3	Missense_Mutation	SNP	ENST00000337344.4	37	CCDS9532.2	.	.	.	.	.	.	.	.	.	.	G	13.35	2.210880	0.39102	.	.	ENSG00000126226	ENST00000337344;ENST00000375479;ENST00000375477;ENST00000246505;ENST00000375459;ENST00000375457;ENST00000375462;ENST00000246506;ENST00000351317	T;T;T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57;1.57;1.57	5.76	5.76	0.90799	PCI/PINT associated module (1);Proteasome component (PCI) domain (1);	0.252743	0.39083	N	0.001474	T	0.21674	0.0522	L	0.33485	1.01	0.80722	D	1	P;B	0.39131	0.661;0.092	B;B	0.25759	0.063;0.044	T	0.05419	-1.0886	10	0.15952	T	0.53	-4.5929	19.9732	0.97292	0.0:0.0:1.0:0.0	.	334;280	Q5JVF3-4;Q5JVF3	.;PCID2_HUMAN	V	280;280;280;334;278;278;257;280;257	ENSP00000337405:A280V;ENSP00000364628:A280V;ENSP00000364626:A280V;ENSP00000246505:A334V;ENSP00000364608:A278V;ENSP00000364606:A278V;ENSP00000327335:A257V	ENSP00000246505:A334V	A	-	2	0	PCID2	112882494	1.000000	0.71417	0.911000	0.35937	0.146000	0.21551	9.375000	0.97178	2.725000	0.93324	0.655000	0.94253	GCG		0.433	PCID2-002	KNOWN	alternative_3_UTR|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045897.1	NM_018386	
DLK1	8788	broad.mit.edu	37	14	101200929	101200929	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:101200929G>A	ENST00000341267.4	+	5	1090	c.848G>A	c.(847-849)cGc>cAc	p.R283H	DLK1_ENST00000331224.6_Intron|RP11-566J3.4_ENST00000608876.1_lincRNA	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	283					cell differentiation (GO:0030154)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|negative regulation of Notch signaling pathway (GO:0045746)|Notch signaling pathway (GO:0007219)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.R283H(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(16)|ovary(2)|prostate(1)|skin(1)	29		Melanoma(154;0.155)				CCGGAGCACCGCATCCTGAAG	0.657																																					p.R283H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G848A	14						.						58.0	63.0	61.0					14																	101200929		2203	4300	6503	100270682	SO:0001583	missense	8788	exon5			U15979	CCDS9963.1	14q32	2011-12-05	2001-12-03			ENSG00000185559			2907	protein-coding gene	gene with protein product		176290	"""delta-like homolog (Drosophila)"""			8095043, 7925474	Standard	NM_003836		Approved	FA1, pG2, Pref-1, ZOG, Delta1	uc001yhs.4	P80370		ENST00000341267.4:c.848G>A	14.37:g.101200929G>A	ENSP00000340292:p.Arg283His	Somatic		Capture	Illumina HiSeq	Phase_I	100270682	NM_003836	P15803|Q96DW5	Missense_Mutation	SNP	ENST00000341267.4	37	CCDS9963.1	.	.	.	.	.	.	.	.	.	.	G	0.784	-0.761152	0.02996	.	.	ENSG00000185559	ENST00000341267	D	0.87412	-2.25	4.46	0.431	0.16523	.	0.545556	0.18243	N	0.147163	T	0.69940	0.3167	N	0.11560	0.145	0.23555	N	0.997426	B	0.11235	0.004	B	0.09377	0.004	T	0.53795	-0.8388	9	.	.	.	.	7.6842	0.28530	0.5298:0.0:0.4702:0.0	.	283	P80370	DLK1_HUMAN	H	283	ENSP00000340292:R283H	.	R	+	2	0	DLK1	100270682	0.753000	0.28349	0.070000	0.20053	0.017000	0.09413	1.412000	0.34714	-0.232000	0.09811	-0.339000	0.08088	CGC		0.657	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1		
DIO3	1735	broad.mit.edu	37	14	102027943	102027943	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:102027943G>T	ENST00000510508.4	+	1	256	c.110G>T	c.(109-111)aGg>aTg	p.R37M	DIO3OS_ENST00000408206.1_lincRNA|DIO3_ENST00000359323.3_Missense_Mutation_p.R11M			P55073	IOD3_HUMAN	deiodinase, iodothyronine, type III	37					cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|positive regulation of multicellular organism growth (GO:0040018)|small molecule metabolic process (GO:0044281)|thyroid hormone catabolic process (GO:0042404)|thyroid hormone generation (GO:0006590)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thyroxine 5'-deiodinase activity (GO:0004800)|thyroxine 5-deiodinase activity (GO:0033798)	p.R11M(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(3)|skin(1)	22		all_neural(303;0.185)				CACTCCTTGAGGCTCTGCGCC	0.662																																					p.R37M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G110T	14						.						30.0	34.0	32.0					14																	102027943		2155	4249	6404	101097696	SO:0001583	missense	1735	exon1			S79854	CCDS41992.1, CCDS41992.2	14q32	2012-10-08			ENSG00000197406	ENSG00000197406			2885	protein-coding gene	gene with protein product		601038		TXDI3		9787088, 7593630	Standard	NM_001362		Approved		uc021sdx.1	P55073	OTTHUMG00000160681	ENST00000510508.4:c.110G>T	14.37:g.102027943G>T	ENSP00000427336:p.Arg37Met	Somatic		Capture	Illumina HiSeq	Phase_I	101097696	NM_001362	G3XAM0|Q8WVN5	Missense_Mutation	SNP	ENST00000510508.4	37	CCDS41992.2	.	.	.	.	.	.	.	.	.	.	g	9.129	1.010909	0.19277	.	.	ENSG00000197406;ENSG00000258865	ENST00000359323;ENST00000510508	T;T	0.34472	1.4;1.36	3.1	2.16	0.27623	.	0.266215	0.21912	U	0.067282	T	0.20333	0.0489	L	0.29908	0.895	0.09310	N	1	B	0.24483	0.104	B	0.13407	0.009	T	0.14364	-1.0475	10	0.49607	T	0.09	.	2.4403	0.04492	0.241:0.0:0.506:0.253	.	11	P55073	IOD3_HUMAN	M	11;37	ENSP00000352273:R11M;ENSP00000427336:R37M	ENSP00000352273:R37M	R	+	2	0	DIO3;AL049836.1	101097696	1.000000	0.71417	0.723000	0.30687	0.115000	0.19883	4.414000	0.59802	0.447000	0.26695	0.457000	0.33378	AGG		0.662	DIO3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000361712.4	NM_001362	
DIO3	1735	broad.mit.edu	37	14	102028653	102028653	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:102028653G>A	ENST00000510508.4	+	1	966	c.820G>A	c.(820-822)Ggc>Agc	p.G274S	DIO3OS_ENST00000408206.1_lincRNA|DIO3_ENST00000359323.3_Missense_Mutation_p.G248S			P55073	IOD3_HUMAN	deiodinase, iodothyronine, type III	274					cellular nitrogen compound metabolic process (GO:0034641)|hormone biosynthetic process (GO:0042446)|positive regulation of multicellular organism growth (GO:0040018)|small molecule metabolic process (GO:0044281)|thyroid hormone catabolic process (GO:0042404)|thyroid hormone generation (GO:0006590)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thyroxine 5'-deiodinase activity (GO:0004800)|thyroxine 5-deiodinase activity (GO:0033798)	p.G248S(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(3)|skin(1)	22		all_neural(303;0.185)				GTACCAGGGCGGCCGTGGCCC	0.607																																					p.G274S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G820A	14						.						55.0	63.0	60.0					14																	102028653		2079	4179	6258	101098406	SO:0001583	missense	1735	exon1			S79854	CCDS41992.1, CCDS41992.2	14q32	2012-10-08			ENSG00000197406	ENSG00000197406			2885	protein-coding gene	gene with protein product		601038		TXDI3		9787088, 7593630	Standard	NM_001362		Approved		uc021sdx.1	P55073	OTTHUMG00000160681	ENST00000510508.4:c.820G>A	14.37:g.102028653G>A	ENSP00000427336:p.Gly274Ser	Somatic		Capture	Illumina HiSeq	Phase_I	101098406	NM_001362	G3XAM0|Q8WVN5	Missense_Mutation	SNP	ENST00000510508.4	37	CCDS41992.2	.	.	.	.	.	.	.	.	.	.	G	20.8	4.047396	0.75846	.	.	ENSG00000197406;ENSG00000258865	ENST00000359323;ENST00000510508	T;T	0.35605	1.3;1.3	3.86	3.86	0.44501	.	0.000000	0.64402	U	0.000008	T	0.66636	0.2809	M	0.90977	3.165	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75019	-0.3465	10	0.51188	T	0.08	.	14.9928	0.71401	0.0:0.0:1.0:0.0	.	248	P55073	IOD3_HUMAN	S	248;274	ENSP00000352273:G248S;ENSP00000427336:G274S	ENSP00000352273:G274S	G	+	1	0	DIO3;AL049836.1	101098406	1.000000	0.71417	0.991000	0.47740	0.600000	0.36913	7.538000	0.82048	1.998000	0.58463	0.462000	0.41574	GGC		0.607	DIO3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000361712.4	NM_001362	
DYNC1H1	1778	broad.mit.edu	37	14	102461139	102461139	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:102461139G>A	ENST00000360184.4	+	13	3450	c.3286G>A	c.(3286-3288)Gca>Aca	p.A1096T		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1096	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.A1096T(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						CTTTGACAATGCAGAAACCAA	0.438																																					p.A1096T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3286A	14						.						78.0	75.0	76.0					14																	102461139		2203	4300	6503	101530892	SO:0001583	missense	1778	exon13			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.3286G>A	14.37:g.102461139G>A	ENSP00000348965:p.Ala1096Thr	Somatic		Capture	Illumina HiSeq	Phase_I	101530892	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.463096	0.63513	.	.	ENSG00000197102	ENST00000360184	T	0.75589	-0.95	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.57125	0.2032	N	0.05199	-0.095	0.80722	D	1	B	0.19706	0.038	B	0.14023	0.01	T	0.52465	-0.8572	10	0.20519	T	0.43	.	19.8991	0.96978	0.0:0.0:1.0:0.0	.	1096	Q14204	DYHC1_HUMAN	T	1096	ENSP00000348965:A1096T	ENSP00000348965:A1096T	A	+	1	0	DYNC1H1	101530892	1.000000	0.71417	0.616000	0.29078	0.959000	0.62525	9.826000	0.99387	2.706000	0.92434	0.557000	0.71058	GCA		0.438	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
MOK	5891	broad.mit.edu	37	14	102695660	102695660	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:102695660C>T	ENST00000361847.2	-	12	1457	c.1226G>A	c.(1225-1227)cGc>cAc	p.R409H	MOK_ENST00000520266.1_5'UTR|MOK_ENST00000193029.6_Intron|MOK_ENST00000522534.1_3'UTR|MOK_ENST00000524370.1_3'UTR|MOK_ENST00000522874.1_Missense_Mutation_p.R408H|MOK_ENST00000519058.1_3'UTR|MOK_ENST00000524214.1_Missense_Mutation_p.R379H|MOK_ENST00000523231.1_3'UTR|MOK_ENST00000561150.1_Intron|MOK_ENST00000517966.1_3'UTR|MOK_ENST00000522867.1_3'UTR	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	409					protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R409H(1)									GGTGGGCAGGCGACACTGCTG	0.582																																					p.R409H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1226A	14						.						63.0	62.0	62.0					14																	102695660		2203	4300	6503	101765413	SO:0001583	missense	5891	exon12			AB022694	CCDS9971.1, CCDS61552.1	14q32	2014-04-23	2011-09-06	2011-09-06	ENSG00000080823	ENSG00000080823			9833	protein-coding gene	gene with protein product		605762	"""renal tumor antigen"""	RAGE		8781117, 10421840	Standard	NM_014226		Approved	RAGE1, STK30	uc001ylm.4	Q9UQ07	OTTHUMG00000164896	ENST00000361847.2:c.1226G>A	14.37:g.102695660C>T	ENSP00000355304:p.Arg409His	Somatic		Capture	Illumina HiSeq	Phase_I	101765413	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Missense_Mutation	SNP	ENST00000361847.2	37	CCDS9971.1	.	.	.	.	.	.	.	.	.	.	C	4.720	0.133950	0.09032	.	.	ENSG00000080823	ENST00000522874;ENST00000361847;ENST00000524214	T;T;T	0.75589	-0.43;-0.49;-0.95	5.46	-0.693	0.11298	.	0.271371	0.34386	N	0.004016	T	0.50531	0.1621	N	0.17594	0.5	0.48087	D	0.999585	B;B	0.10296	0.003;0.002	B;B	0.04013	0.001;0.001	T	0.21143	-1.0254	10	0.13108	T	0.6	.	9.062	0.36440	0.0:0.4087:0.0:0.5913	.	379;409	E7ERR8;Q9UQ07	.;MOK_HUMAN	H	408;409;379	ENSP00000429469:R408H;ENSP00000355304:R409H;ENSP00000428942:R379H	ENSP00000355304:R409H	R	-	2	0	RAGE	101765413	0.620000	0.27068	0.480000	0.27341	0.124000	0.20399	0.202000	0.17295	0.021000	0.15133	0.561000	0.74099	CGC		0.582	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3		
TRAF3	7187	broad.mit.edu	37	14	103352552	103352552	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:103352552C>T	ENST00000560371.1	+	6	814	c.597C>T	c.(595-597)tgC>tgT	p.C199C	TRAF3_ENST00000539721.1_Intron|TRAF3_ENST00000347662.4_Silent_p.C199C|TRAF3_ENST00000392745.2_Silent_p.C199C|TRAF3_ENST00000351691.5_Silent_p.C199C	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	199					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.C199C(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)		ACTGTCCCTGCGTGGTGGTGT	0.592																																					p.C199C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C597T	14						.						76.0	60.0	66.0					14																	103352552		2203	4300	6503	102422305	SO:0001819	synonymous_variant	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.597C>T	14.37:g.103352552C>T		Somatic		Capture	Illumina HiSeq	Phase_I	102422305	NM_145725	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Silent	SNP	ENST00000560371.1	37	CCDS9975.1																																																																																				0.592	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725	
MARK3	4140	broad.mit.edu	37	14	103923549	103923549	+	Splice_Site	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:103923549G>T	ENST00000429436.2	+	6	993	c.483G>T	c.(481-483)caG>caT	p.Q161H	MARK3_ENST00000561071.1_Intron|MARK3_ENST00000216288.7_Splice_Site_p.Q161H|MARK3_ENST00000303622.9_Splice_Site_p.Q161H|MARK3_ENST00000440884.3_Splice_Site_p.Q161H|MARK3_ENST00000416682.2_Splice_Site_p.Q161H|MARK3_ENST00000553942.1_Splice_Site_p.Q161H|MARK3_ENST00000335102.5_Splice_Site_p.Q161H	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	161	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.Q161H(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			AATTTAGACAGGTATGAATTA	0.338																																					p.Q161H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G483T	14						.						127.0	126.0	126.0					14																	103923549		1849	4096	5945	102993302	SO:0001630	splice_region_variant	4140	exon6			M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.483+1G>T	14.37:g.103923549G>T		Somatic		Capture	Illumina HiSeq	Phase_I	102993302	NM_001128919	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	37	CCDS45165.1	.	.	.	.	.	.	.	.	.	.	G	16.93	3.259156	0.59321	.	.	ENSG00000075413	ENST00000335102;ENST00000440884;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942	T;T;T;T;T;T;T	0.76060	-0.99;2.66;-0.94;1.35;1.35;1.35;1.35	5.37	5.37	0.77165	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	0.84696	0.5529	M	0.71871	2.18	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	0.91635	0.997;0.994;0.999;0.996;0.994;0.998	D	0.85918	0.1444	10	0.87932	D	0	.	13.7496	0.62899	0.0739:0.0:0.9261:0.0	.	161;161;161;161;161;161	P27448-2;P27448-6;P27448;Q86TT8;P27448-4;P27448-3	.;.;MARK3_HUMAN;.;.;.	H	161	ENSP00000335347:Q161H;ENSP00000402104:Q161H;ENSP00000408092:Q161H;ENSP00000411397:Q161H;ENSP00000303698:Q161H;ENSP00000216288:Q161H;ENSP00000450772:Q161H	ENSP00000216288:Q161H	Q	+	3	2	MARK3	102993302	1.000000	0.71417	1.000000	0.80357	0.242000	0.25591	7.741000	0.84997	2.669000	0.90835	0.655000	0.94253	CAG		0.338	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918	Missense_Mutation
ZFYVE21	79038	broad.mit.edu	37	14	104194170	104194170	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:104194170G>A	ENST00000311141.2	+	3	311	c.277G>A	c.(277-279)Gtg>Atg	p.V93M	Y_RNA_ENST00000517287.1_RNA|ZFYVE21_ENST00000216602.6_Missense_Mutation_p.V93M	NM_024071.3	NP_076976.1	Q9BQ24	ZFY21_HUMAN	zinc finger, FYVE domain containing 21	93						cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)	metal ion binding (GO:0046872)	p.V93M(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(2)|skin(2)	8		Melanoma(154;0.226)		Epithelial(152;0.245)		TGTGGACCCCGTGCGGCAGTG	0.657																																					p.V93M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G277A	14						.						50.0	47.0	48.0					14																	104194170		2203	4300	6503	103263923	SO:0001583	missense	79038	exon3			AK057816	CCDS9985.1, CCDS55948.1	14q32.33	2011-09-07						"""Zinc fingers, FYVE domain containing"""	20760	protein-coding gene	gene with protein product		613504				21768110	Standard	NM_024071		Approved	MGC2550, ZF21	uc001yod.3	Q9BQ24		ENST00000311141.2:c.277G>A	14.37:g.104194170G>A	ENSP00000310543:p.Val93Met	Somatic		Capture	Illumina HiSeq	Phase_I	103263923	NM_024071	A8K3A4|Q86T05|Q96LT1	Missense_Mutation	SNP	ENST00000311141.2	37	CCDS9985.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.925498	0.92319	.	.	ENSG00000100711	ENST00000216602;ENST00000311141	T;T	0.49139	0.79;0.79	4.48	4.48	0.54585	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.70885	0.3275	M	0.82132	2.575	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.76735	-0.2850	10	0.87932	D	0	19.8964	17.3317	0.87267	0.0:0.0:1.0:0.0	.	93;93	Q9BQ24-2;Q9BQ24	.;ZFY21_HUMAN	M	93	ENSP00000216602:V93M;ENSP00000310543:V93M	ENSP00000216602:V93M	V	+	1	0	ZFYVE21	103263923	1.000000	0.71417	0.999000	0.59377	0.833000	0.47200	9.524000	0.98036	2.309000	0.77851	0.655000	0.94253	GTG		0.657	ZFYVE21-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000414616.1	NM_024071	
PPP1R13B	23368	broad.mit.edu	37	14	104209129	104209129	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:104209129C>A	ENST00000202556.9	-	10	1464	c.1182G>T	c.(1180-1182)caG>caT	p.Q394H	PPP1R13B_ENST00000555391.1_5'UTR|PPP1R13B_ENST00000423488.2_5'UTR	NM_015316.2	NP_056131.2	Q96KQ4	ASPP1_HUMAN	protein phosphatase 1, regulatory subunit 13B	394					intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.Q394H(1)		endometrium(6)|kidney(2)|large_intestine(7)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.173)|all_epithelial(191;0.131)|Melanoma(154;0.155)				AGCTAGAATTCTGTTTTAATG	0.473																																					p.Q394H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1182T	14						.						78.0	77.0	78.0					14																	104209129		1942	4143	6085	103278882	SO:0001583	missense	23368	exon10			AB018314	CCDS41997.1	14q32.33	2013-01-10	2011-10-04		ENSG00000088808	ENSG00000088808		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14950	protein-coding gene	gene with protein product		606455	"""protein phosphatase 1, regulatory (inhibitor) subunit 13B"""			9872452	Standard	NM_015316		Approved	p53BP2-like, KIAA0771, p85, ASPP1	uc001yof.1	Q96KQ4	OTTHUMG00000171647	ENST00000202556.9:c.1182G>T	14.37:g.104209129C>A	ENSP00000202556:p.Gln394His	Somatic		Capture	Illumina HiSeq	Phase_I	103278882	NM_015316	B2RMX5|O94870	Missense_Mutation	SNP	ENST00000202556.9	37	CCDS41997.1	.	.	.	.	.	.	.	.	.	.	C	16.41	3.116715	0.56505	.	.	ENSG00000088808	ENST00000202556;ENST00000380023	T	0.50813	0.73	5.93	-1.48	0.08745	.	0.558048	0.21695	N	0.070505	T	0.31136	0.0787	N	0.22421	0.69	0.80722	D	1	B	0.10296	0.003	B	0.10450	0.005	T	0.08806	-1.0704	10	0.32370	T	0.25	.	14.2304	0.65887	0.0:0.6881:0.0:0.3119	.	394	Q96KQ4	ASPP1_HUMAN	H	394;261	ENSP00000202556:Q394H	ENSP00000202556:Q394H	Q	-	3	2	PPP1R13B	103278882	0.953000	0.32496	0.132000	0.22025	0.998000	0.95712	0.067000	0.14510	-0.174000	0.10743	0.561000	0.74099	CAG		0.473	PPP1R13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414591.1	NM_015316	
CEP170B	283638	broad.mit.edu	37	14	105360153	105360153	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:105360153G>A	ENST00000414716.3	+	16	4466	c.4238G>A	c.(4237-4239)cGt>cAt	p.R1413H	CEP170B_ENST00000453495.1_Missense_Mutation_p.R1449H|CEP170B_ENST00000418279.1_Missense_Mutation_p.R1343H|CEP170B_ENST00000556508.1_Missense_Mutation_p.R1378H	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	1448						cytoplasm (GO:0005737)|microtubule (GO:0005874)		p.R1413H(1)									CAGGCCATCCGTGAGAACACA	0.622																																					p.R1343H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4028A	14						.						50.0	55.0	54.0					14																	105360153		2124	4229	6353	104431198	SO:0001583	missense	283638	exon15			AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"""Cep170-related"""		"""KIAA0284"""	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.4238G>A	14.37:g.105360153G>A	ENSP00000404151:p.Arg1413His	Somatic		Capture	Illumina HiSeq	Phase_I	104431198	NM_015005	Q2KHR7|Q86TI7	Missense_Mutation	SNP	ENST00000414716.3	37	CCDS45175.1	.	.	.	.	.	.	.	.	.	.	G	32	5.171169	0.94807	.	.	ENSG00000099814	ENST00000556508;ENST00000414716;ENST00000453495;ENST00000418279;ENST00000429757	T;T;T;T	0.58652	0.37;0.37;0.32;0.41	4.69	4.69	0.59074	.	0.066048	0.64402	D	0.000011	T	0.76033	0.3931	M	0.74258	2.255	0.46774	D	0.999193	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.987;0.991;0.973	T	0.80202	-0.1480	10	0.87932	D	0	-16.4935	17.1857	0.86866	0.0:0.0:1.0:0.0	.	1413;1448;1343	Q9Y4F5-2;Q9Y4F5;E9PFC1	.;K0284_HUMAN;.	H	1378;1413;1449;1343;81	ENSP00000451249:R1378H;ENSP00000404151:R1413H;ENSP00000407238:R1449H;ENSP00000415006:R1343H	ENSP00000251181:R65H	R	+	2	0	KIAA0284	104431198	1.000000	0.71417	0.964000	0.40570	0.951000	0.60555	9.546000	0.98097	2.150000	0.67090	0.436000	0.28706	CGT		0.622	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726	
OR4K2	390431	broad.mit.edu	37	14	20345146	20345146	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:20345146T>C	ENST00000298642.2	+	1	756	c.720T>C	c.(718-720)tgT>tgC	p.C240C		NM_001005501.1	NP_001005501.1	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K, member 2	240						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C240C(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(16)|ovary(2)|skin(9)|upper_aerodigestive_tract(2)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTTCTACTTGTACAGCTCATT	0.393																																					p.C240C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T720C	14						.						230.0	216.0	221.0					14																	20345146		2203	4299	6502	19414986	SO:0001819	synonymous_variant	390431	exon1				CCDS32023.1	14q11.2	2013-09-23			ENSG00000165762	ENSG00000165762		"""GPCR / Class A : Olfactory receptors"""	14728	protein-coding gene	gene with protein product							Standard	NM_001005501		Approved		uc001vwh.1	Q8NGD2	OTTHUMG00000170624	ENST00000298642.2:c.720T>C	14.37:g.20345146T>C		Somatic		Capture	Illumina HiSeq	Phase_I	19414986	NM_001005501	B2RNK8|Q6IFA5	Silent	SNP	ENST00000298642.2	37	CCDS32023.1																																																																																				0.393	OR4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409864.1		
OR4K5	79317	broad.mit.edu	37	14	20389032	20389032	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:20389032C>T	ENST00000315915.4	+	1	292	c.267C>T	c.(265-267)caC>caT	p.H89H		NM_001005483.1	NP_001005483.1	Q8NGD3	OR4K5_HUMAN	olfactory receptor, family 4, subfamily K, member 5	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H89H(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|liver(1)|lung(27)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TGAGTGCACACGAGACCATAT	0.428																																					p.H89H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C267T	14						.						279.0	297.0	291.0					14																	20389032		2203	4300	6503	19458872	SO:0001819	synonymous_variant	79317	exon1			BK004355	CCDS32024.1	14q11.22	2012-08-09				ENSG00000176281		"""GPCR / Class A : Olfactory receptors"""	14745	protein-coding gene	gene with protein product						14983052	Standard	NM_001005483		Approved		uc010tkw.2	Q8NGD3		ENST00000315915.4:c.267C>T	14.37:g.20389032C>T		Somatic		Capture	Illumina HiSeq	Phase_I	19458872	NM_001005483	Q6IFA7	Silent	SNP	ENST00000315915.4	37	CCDS32024.1																																																																																				0.428	OR4K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409867.1	NM_001005483	
TMEM55B	90809	broad.mit.edu	37	14	20927442	20927442	+	Missense_Mutation	SNP	G	G	A	rs146748243		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:20927442G>A	ENST00000250489.4	-	6	899	c.613C>T	c.(613-615)Cgc>Tgc	p.R205C	TMEM55B_ENST00000554028.1_Missense_Mutation_p.R38C|TMEM55B_ENST00000398020.4_Missense_Mutation_p.R212C			Q86T03	TM55B_HUMAN	transmembrane protein 55B	205						endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)	p.R205C(1)		endometrium(3)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	11	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0224)|READ - Rectum adenocarcinoma(17;0.193)		GGGTATCTGCGCCCAATAGAT	0.488													G|||	1	0.000199681	0.0	0.0	5008	,	,		20279	0.0		0.001	False		,,,				2504	0.0				p.R205C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C613T	14						.	G	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	170.0	164.0	166.0		634,613	3.1	1.0	14	dbSNP_134	166	10,8590	8.4+/-32.0	0,10,4290	yes	missense,missense	TMEM55B	NM_001100814.1,NM_144568.2	180,180	0,11,6492	AA,AG,GG		0.1163,0.0227,0.0846	probably-damaging,probably-damaging	212/285,205/278	20927442	11,12995	2203	4300	6503	19997282	SO:0001583	missense	90809	exon6			BC002867	CCDS9551.1, CCDS41911.1	14q11.1	2002-11-27	2005-07-18	2005-07-18	ENSG00000165782	ENSG00000165782			19299	protein-coding gene	gene with protein product		609865	"""chromosome 14 open reading frame 9"""	C14orf9			Standard	NM_144568		Approved	MGC26684	uc001vxk.2	Q86T03	OTTHUMG00000029545	ENST00000250489.4:c.613C>T	14.37:g.20927442G>A	ENSP00000250489:p.Arg205Cys	Somatic		Capture	Illumina HiSeq	Phase_I	19997282	NM_144568	B2RA35|Q86U09|Q8WUC0|Q9BU67|Q9NSU8	Missense_Mutation	SNP	ENST00000250489.4	37	CCDS9551.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	17.87|17.87	3.496123|3.496123	0.64186|0.64186	2.27E-4|2.27E-4	0.001163|0.001163	ENSG00000165782|ENSG00000165782	ENST00000553460|ENST00000250489;ENST00000398020;ENST00000554028	.|.	.|.	.|.	5.06|5.06	3.12|3.12	0.35913|0.35913	.|.	.|0.146689	.|0.44688	.|D	.|0.000421	T|T	0.52837|0.52837	0.1759|0.1759	L|L	0.34521|0.34521	1.04|1.04	0.42996|0.42996	D|D	0.994506|0.994506	.|D;D	.|0.76494	.|0.999;0.998	.|P;P	.|0.55055	.|0.767;0.738	T|T	0.56414|0.56414	-0.7983|-0.7983	5|9	.|0.56958	.|D	.|0.05	-9.2717|-9.2717	12.241|12.241	0.54541|0.54541	0.0:0.0:0.5632:0.4368|0.0:0.0:0.5632:0.4368	.|.	.|205;212	.|Q86T03;Q86T03-2	.|TM55B_HUMAN;.	V|C	44|205;212;38	.|.	.|ENSP00000250489:R205C	A|R	-|-	2|1	0|0	TMEM55B|TMEM55B	19997282|19997282	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	2.291000|2.291000	0.43540|0.43540	1.102000|1.102000	0.41551|0.41551	0.655000|0.655000	0.94253|0.94253	GCG|CGC		0.488	TMEM55B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000073643.3	NM_144568	
TMEM55B	90809	broad.mit.edu	37	14	20928428	20928428	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:20928428delT	ENST00000250489.4	-	3	649	c.363delA	c.(361-363)aaafs	p.K121fs	TMEM55B_ENST00000554028.1_5'UTR|TMEM55B_ENST00000398020.4_Frame_Shift_Del_p.K128fs			Q86T03	TM55B_HUMAN	transmembrane protein 55B	121						endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)	p.K121fs*15(1)		endometrium(3)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	11	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0224)|READ - Rectum adenocarcinoma(17;0.193)		ATCGAACATATTTTTTCCCTG	0.488																																					p.K121fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.363delA	14						.						100.0	99.0	99.0					14																	20928428		2203	4300	6503	19998268	SO:0001589	frameshift_variant	90809	exon3			BC002867	CCDS9551.1, CCDS41911.1	14q11.1	2002-11-27	2005-07-18	2005-07-18	ENSG00000165782	ENSG00000165782			19299	protein-coding gene	gene with protein product		609865	"""chromosome 14 open reading frame 9"""	C14orf9			Standard	NM_144568		Approved	MGC26684	uc001vxk.2	Q86T03	OTTHUMG00000029545	ENST00000250489.4:c.363delA	14.37:g.20928428delT	ENSP00000250489:p.Lys121fs	Somatic		Capture	Illumina HiSeq	Phase_I	19998268	NM_144568	B2RA35|Q86U09|Q8WUC0|Q9BU67|Q9NSU8	Frame_Shift_Del	DEL	ENST00000250489.4	37	CCDS9551.1																																																																																				0.488	TMEM55B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000073643.3	NM_144568	
TPPP2	122664	broad.mit.edu	37	14	21499195	21499195	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:21499195G>A	ENST00000321760.6	+	3	346	c.198G>A	c.(196-198)acG>acA	p.T66T	TPPP2_ENST00000460647.2_Silent_p.T66T|NDRG2_ENST00000403829.3_Intron|AL161668.5_ENST00000533984.1_lincRNA|TPPP2_ENST00000530140.2_Silent_p.T66T|RP11-998D10.1_ENST00000531638.1_5'Flank	NM_173846.4	NP_776245.2	P59282	TPPP2_HUMAN	tubulin polymerization-promoting protein family member 2	66						cytoplasm (GO:0005737)		p.T66T(1)		endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		GAACCATCACGTTTCAACAGT	0.488																																					p.T66T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G198A	14						.						89.0	83.0	85.0					14																	21499195		2203	4300	6503	20569035	SO:0001819	synonymous_variant	122664	exon3			AY072034	CCDS9566.1	14q11.2	2014-01-21	2007-05-02	2007-05-02	ENSG00000179636	ENSG00000179636			19293	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 8"""	C14orf8		15590652, 17105200	Standard	NM_173846		Approved	p25beta, p18, CT152	uc001vzh.3	P59282	OTTHUMG00000029642	ENST00000321760.6:c.198G>A	14.37:g.21499195G>A		Somatic		Capture	Illumina HiSeq	Phase_I	20569035	NM_173846	Q2VYF3	Silent	SNP	ENST00000321760.6	37	CCDS9566.1	.	.	.	.	.	.	.	.	.	.	G	4.826	0.153609	0.09185	.	.	ENSG00000179636	ENST00000555751	.	.	.	4.84	-8.33	0.00992	.	.	.	.	.	T	0.33381	0.0861	.	.	.	0.46631	D	0.999133	.	.	.	.	.	.	T	0.44329	-0.9335	4	.	.	.	-3.5712	1.7747	0.03019	0.1754:0.3905:0.2298:0.2043	.	.	.	.	H	5	.	.	R	+	2	0	TPPP2	20569035	0.262000	0.24073	0.113000	0.21522	0.605000	0.37080	-0.286000	0.08399	-0.948000	0.03668	-1.202000	0.01658	CGT		0.488	TPPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073914.3	NM_173846	
OR5AU1	390445	broad.mit.edu	37	14	21623810	21623810	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:21623810G>T	ENST00000304418.3	-	1	412	c.375C>A	c.(373-375)tcC>tcA	p.S125S		NM_001004731.1	NP_001004731.1	Q8NGC0	O5AU1_HUMAN	olfactory receptor, family 5, subfamily AU, member 1	125						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S125S(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(12)|pancreas(1)	21	all_cancers(95;0.00238)		Epithelial(56;6.88e-07)|all cancers(55;6.02e-06)	GBM - Glioblastoma multiforme(265;0.0192)		CAACCGTGGAGGAGTAGCAGA	0.517																																					p.S125S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C375A	14						.						93.0	79.0	83.0					14																	21623810		2203	4300	6503	20693650	SO:0001819	synonymous_variant	390445	exon1			AL157687	CCDS32042.1	14q11.2	2013-09-23			ENSG00000169327	ENSG00000169327		"""GPCR / Class A : Olfactory receptors"""	15362	protein-coding gene	gene with protein product							Standard	NM_001004731		Approved		uc010tlp.2	Q8NGC0	OTTHUMG00000170753	ENST00000304418.3:c.375C>A	14.37:g.21623810G>T		Somatic		Capture	Illumina HiSeq	Phase_I	20693650	NM_001004731	B2RP78|Q6IEU2|Q96R10	Silent	SNP	ENST00000304418.3	37	CCDS32042.1																																																																																				0.517	OR5AU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410213.1		
SUPT16H	11198	broad.mit.edu	37	14	21834673	21834673	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:21834673T>C	ENST00000216297.2	-	8	1309	c.971A>G	c.(970-972)gAc>gGc	p.D324G		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	324					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.D324G(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)		GTTATACACGTCACATATCTT	0.343																																					p.D324G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A971G	14						.						202.0	187.0	192.0					14																	21834673		2203	4300	6503	20904513	SO:0001583	missense	11198	exon8			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.971A>G	14.37:g.21834673T>C	ENSP00000216297:p.Asp324Gly	Somatic		Capture	Illumina HiSeq	Phase_I	20904513	NM_007192	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Missense_Mutation	SNP	ENST00000216297.2	37	CCDS9569.1	.	.	.	.	.	.	.	.	.	.	T	16.89	3.246506	0.59103	.	.	ENSG00000092201	ENST00000216297;ENST00000538230	T	0.80738	-1.41	5.44	5.44	0.79542	Peptidase M24, structural domain (3);	0.104914	0.64402	D	0.000007	D	0.86230	0.5883	M	0.80982	2.52	0.80722	D	1	B	0.33841	0.428	P	0.45660	0.489	D	0.86680	0.1916	10	0.54805	T	0.06	-26.4236	14.4863	0.67619	0.0:0.0:0.0:1.0	.	324	Q9Y5B9	SP16H_HUMAN	G	324	ENSP00000216297:D324G	ENSP00000216297:D324G	D	-	2	0	SUPT16H	20904513	1.000000	0.71417	0.995000	0.50966	0.471000	0.32888	7.322000	0.79097	2.053000	0.61076	0.533000	0.62120	GAC		0.343	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2		
METTL3	56339	broad.mit.edu	37	14	21968698	21968698	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:21968698G>A	ENST00000298717.4	-	6	1394	c.1243C>T	c.(1243-1245)Cgc>Tgc	p.R415C		NM_019852.3	NP_062826.2	Q86U44	MTA70_HUMAN	methyltransferase like 3	415					circadian rhythm (GO:0007623)|gene expression (GO:0010467)|mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|RNA methylation (GO:0001510)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)	p.R415C(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(95;0.000628)		Epithelial(56;6.61e-06)	GBM - Glioblastoma multiforme(265;0.0146)		TTGAGCCTGCGCATCTCATCA	0.498																																					p.R415C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1243T	14						.						163.0	130.0	141.0					14																	21968698		2203	4300	6503	21038538	SO:0001583	missense	56339	exon6			AF014837	CCDS32044.1	14q11.1	2012-06-12			ENSG00000165819	ENSG00000165819	2.1.1.62		17563	protein-coding gene	gene with protein product	"""N6-adenosine-methyltransferase 70 kDa subunit"""	612472					Standard	XM_006720206		Approved	Spo8, M6A, MT-A70	uc001wbc.3	Q86U44	OTTHUMG00000168825	ENST00000298717.4:c.1243C>T	14.37:g.21968698G>A	ENSP00000298717:p.Arg415Cys	Somatic		Capture	Illumina HiSeq	Phase_I	21038538	NM_019852	O14736|Q86V05|Q9HB32	Missense_Mutation	SNP	ENST00000298717.4	37	CCDS32044.1	.	.	.	.	.	.	.	.	.	.	G	19.14	3.769820	0.69992	.	.	ENSG00000165819	ENST00000298717	T	0.42900	0.96	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.52273	0.1724	L	0.38838	1.175	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.52726	-0.8537	10	0.87932	D	0	-10.9755	11.2102	0.48793	0.0:0.0:0.7156:0.2844	.	415	Q86U44	MTA70_HUMAN	C	415	ENSP00000298717:R415C	ENSP00000298717:R415C	R	-	1	0	METTL3	21038538	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.420000	0.52735	2.738000	0.93877	0.591000	0.81541	CGC		0.498	METTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401227.1	NM_019852	
SALL2	6297	broad.mit.edu	37	14	21991028	21991028	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:21991028C>T	ENST00000327430.3	-	2	3128	c.2834G>A	c.(2833-2835)tGc>tAc	p.C945Y	SALL2_ENST00000317492.5_Intron|SALL2_ENST00000538754.1_Intron|SALL2_ENST00000450879.2_Missense_Mutation_p.C808Y|AE000658.22_ENST00000535893.1_RNA	NM_005407.1	NP_005398.1	Q9Y467	SALL2_HUMAN	spalt-like transcription factor 2	945					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.C945Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2)	43	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		GCCCTGCCTGCAGAAAACACA	0.597																																					p.C945Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2834A	14						.						50.0	52.0	51.0					14																	21991028		2203	4300	6503	21060868	SO:0001583	missense	6297	exon2			AB002358	CCDS32045.1	14q11.1-q12.1	2013-10-17	2013-10-17		ENSG00000165821	ENSG00000165821		"""Zinc fingers, C2H2-type"""	10526	protein-coding gene	gene with protein product		602219	"""sal (Drosophila)-like 2"", ""sal-like 2 (Drosophila)"""			8975705	Standard	XM_005267983		Approved	KIAA0360, Hsal2, ZNF795	uc001wbe.3	Q9Y467	OTTHUMG00000168826	ENST00000327430.3:c.2834G>A	14.37:g.21991028C>T	ENSP00000333537:p.Cys945Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	21060868	NM_005407	B2RMX6|B9EGK8|Q8N656|Q9Y4G1	Missense_Mutation	SNP	ENST00000327430.3	37	CCDS32045.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.82|18.82	3.705465|3.705465	0.68615|0.68615	.|.	.|.	ENSG00000165821|ENSG00000165821	ENST00000546363|ENST00000327430;ENST00000450879	.|D;D	.|0.85861	.|-2.04;-2.04	4.79|4.79	4.79|4.79	0.61399|0.61399	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|0.000000	.|0.42821	.|D	.|0.000651	D|D	0.95611|0.95611	0.8573|0.8573	H|H	0.98996|0.98996	4.395|4.395	0.54753|0.54753	D|D	0.999982|0.999982	.|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	D|D	0.97276|0.97276	0.9914|0.9914	5|10	.|0.87932	.|D	.|0	-9.4383|-9.4383	15.3617|15.3617	0.74483|0.74483	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|808;808;706;945	.|B4DK65;E7EW59;B4DFD9;Q9Y467	.|.;.;.;SALL2_HUMAN	T|Y	804|945;808	.|ENSP00000333537:C945Y;ENSP00000396773:C808Y	.|ENSP00000333537:C945Y	A|C	-|-	1|2	0|0	SALL2|SALL2	21060868|21060868	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	6.724000|6.724000	0.74747|0.74747	2.480000|2.480000	0.83734|0.83734	0.563000|0.563000	0.77884|0.77884	GCA|TGC		0.597	SALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401242.1	NM_005407	
LRP10	26020	broad.mit.edu	37	14	23345070	23345070	+	Missense_Mutation	SNP	C	C	T	rs373629359		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:23345070C>T	ENST00000359591.4	+	5	1604	c.913C>T	c.(913-915)Cgg>Tgg	p.R305W	LRP10_ENST00000546834.1_Missense_Mutation_p.R305W	NM_014045.3	NP_054764.2	Q7Z4F1	LRP10_HUMAN	low density lipoprotein receptor-related protein 10	305	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				endocytosis (GO:0006897)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.R305W(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(2)	32	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.00549)		CTACCATGTGCGGGGCTATTG	0.597																																					p.R305W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C913T	14						.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	89.0	78.0	82.0		913	3.9	1.0	14		82	0,8600		0,0,4300	no	missense	LRP10	NM_014045.3	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	305/714	23345070	1,13005	2203	4300	6503	22414910	SO:0001583	missense	26020	exon5			AF131760	CCDS9578.1	14q11.2	2013-05-29			ENSG00000197324	ENSG00000197324		"""Low density lipoprotein receptors"""	14553	protein-coding gene	gene with protein product		609921				11123907	Standard	XM_005267510		Approved	DKFZP564C1940, MGC8675, LRP9, MST087, MSTP087	uc001whd.3	Q7Z4F1	OTTHUMG00000028705	ENST00000359591.4:c.913C>T	14.37:g.23345070C>T	ENSP00000352601:p.Arg305Trp	Somatic		Capture	Illumina HiSeq	Phase_I	22414910	NM_014045	A8K4R5|D3DS31|O95882|Q14CK7|Q86T02|Q8NCZ4|Q9HC42|Q9UG33	Missense_Mutation	SNP	ENST00000359591.4	37	CCDS9578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.68|12.68	2.009917|2.009917	0.35415|0.35415	2.27E-4|2.27E-4	0.0|0.0	ENSG00000197324|ENSG00000197324	ENST00000551466|ENST00000359591;ENST00000546834	.|D;D	.|0.94000	.|-3.12;-3.33	5.97|5.97	3.92|3.92	0.45320|0.45320	.|CUB (4);	.|0.332734	.|0.33235	.|N	.|0.005131	D|D	0.90293|0.90293	0.6964|0.6964	L|L	0.43152|0.43152	1.355|1.355	0.30079|0.30079	N|N	0.809382|0.809382	.|B	.|0.14438	.|0.01	.|B	.|0.04013	.|0.001	D|D	0.87118|0.87118	0.2189|0.2189	5|10	.|0.72032	.|D	.|0.01	-10.9614|-10.9614	15.648|15.648	0.77070|0.77070	0.2594:0.7405:0.0:0.0|0.2594:0.7405:0.0:0.0	.|.	.|305	.|Q7Z4F1	.|LRP10_HUMAN	V|W	206|305	.|ENSP00000352601:R305W;ENSP00000447559:R305W	.|ENSP00000352601:R305W	A|R	+|+	2|1	0|2	LRP10|LRP10	22414910|22414910	0.073000|0.073000	0.21202|0.21202	0.999000|0.999000	0.59377|0.59377	0.962000|0.962000	0.63368|0.63368	0.172000|0.172000	0.16704|0.16704	1.472000|1.472000	0.48140|0.48140	0.655000|0.655000	0.94253|0.94253	GCG|CGG		0.597	LRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071663.3		
PRMT5	10419	broad.mit.edu	37	14	23392349	23392349	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:23392349C>T	ENST00000324366.8	-	13	1619	c.1396G>A	c.(1396-1398)Ggg>Agg	p.G466R	PRMT5_ENST00000553897.1_Missense_Mutation_p.G422R|PRMT5-AS1_ENST00000457443.2_RNA|PRMT5_ENST00000397440.4_Missense_Mutation_p.G295R|PRMT5_ENST00000553641.1_5'Flank|PRMT5-AS1_ENST00000424245.2_RNA|PRMT5-AS1_ENST00000609885.1_RNA|PRMT5_ENST00000397441.2_Missense_Mutation_p.G449R|PRMT5_ENST00000538452.1_Missense_Mutation_p.G360R|PRMT5-AS1_ENST00000599580.2_RNA|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000216350.8_Missense_Mutation_p.G405R|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5-AS1_ENST00000587245.2_RNA	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	466	Beta barrel. {ECO:0000269|PubMed:23071334}.|SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)	p.G466R(1)|p.G449R(1)		endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		GTGTACTCCCCGGGGATGCTC	0.507																																					p.G466R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1396A	14						.						62.0	55.0	57.0					14																	23392349		2203	4300	6503	22462189	SO:0001583	missense	10419	exon13			AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"""Protein arginine methyltransferases"""	10894	protein-coding gene	gene with protein product		604045	"""skb1 (S. pombe) homolog"", ""SKB1 homolog (S. pombe)"""	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.1396G>A	14.37:g.23392349C>T	ENSP00000319169:p.Gly466Arg	Somatic		Capture	Illumina HiSeq	Phase_I	22462189	NM_006109	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Missense_Mutation	SNP	ENST00000324366.8	37	CCDS9579.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.722|7.722	0.697382|0.697382	0.15106|0.15106	.|.	.|.	ENSG00000100462|ENSG00000100462	ENST00000324366;ENST00000397441;ENST00000397440;ENST00000216350;ENST00000555454;ENST00000538452;ENST00000553897|ENST00000454731	T;T;T;T;T;T;T|.	0.21932|.	1.98;1.98;1.98;1.98;1.98;1.98;1.98|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.140114|.	0.64402|.	D|.	0.000004|.	T|T	0.22282|0.22282	0.0537|0.0537	N|N	0.02247|0.02247	-0.625|-0.625	0.39954|0.39954	D|D	0.97457|0.97457	B;B;B;B;B|.	0.18310|.	0.002;0.002;0.008;0.027;0.001|.	B;B;B;B;B|.	0.14023|.	0.005;0.004;0.01;0.007;0.001|.	T|T	0.22277|0.22277	-1.0221|-1.0221	10|5	0.13853|.	T|.	0.58|.	-17.2863|-17.2863	7.8464|7.8464	0.29428|0.29428	0.162:0.7571:0.0:0.0808|0.162:0.7571:0.0:0.0808	.|.	422;405;295;466;449|.	G3V5W5;B4DX49;A8MTP3;O14744;A8MZ91|.	.;.;.;ANM5_HUMAN;.|.	R|Q	466;449;295;405;65;360;422|8	ENSP00000319169:G466R;ENSP00000380583:G449R;ENSP00000380582:G295R;ENSP00000216350:G405R;ENSP00000451245:G65R;ENSP00000444915:G360R;ENSP00000452555:G422R|.	ENSP00000216350:G405R|.	G|R	-|-	1|2	0|0	PRMT5|PRMT5	22462189|22462189	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.076000|0.076000	0.17211|0.17211	2.908000|2.908000	0.48750|0.48750	2.826000|2.826000	0.97356|0.97356	0.561000|0.561000	0.74099|0.74099	GGG|CGG		0.507	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3		
C14orf93	60686	broad.mit.edu	37	14	23467870	23467870	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:23467870A>G	ENST00000299088.6	-	2	792	c.363T>C	c.(361-363)ccT>ccC	p.P121P	C14orf93_ENST00000397377.1_5'UTR|RP11-298I3.4_ENST00000555294.1_RNA|C14orf93_ENST00000406429.2_Silent_p.P121P|RP11-298I3.4_ENST00000556503.1_RNA|C14orf93_ENST00000397379.3_Silent_p.P121P|C14orf93_ENST00000557513.1_5'Flank|C14orf93_ENST00000341470.4_Silent_p.P121P|C14orf93_ENST00000397382.4_Silent_p.P121P	NM_001130708.1|NM_021944.2	NP_001124180.1|NP_068763.2	Q9H972	CN093_HUMAN	chromosome 14 open reading frame 93	121						extracellular region (GO:0005576)	poly(A) RNA binding (GO:0044822)	p.P121P(1)		kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	17	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0127)		CAGGCTCCTCAGGTGGGGAAC	0.587																																					p.P121P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T363C	14						.						58.0	60.0	60.0					14																	23467870		2203	4300	6503	22537710	SO:0001819	synonymous_variant	60686	exon2			AK023026	CCDS9583.1, CCDS61399.1, CCDS61400.1	14q11.1	2012-09-25			ENSG00000100802	ENSG00000100802			20162	protein-coding gene	gene with protein product							Standard	XM_005267971		Approved	FLJ12154	uc001wih.3	Q9H972	OTTHUMG00000028712	ENST00000299088.6:c.363T>C	14.37:g.23467870A>G		Somatic		Capture	Illumina HiSeq	Phase_I	22537710	NM_001130708	B7WP03|D3DS38|D3DS39|Q86SE6|Q96CF7|Q9HA68	Silent	SNP	ENST00000299088.6	37	CCDS9583.1																																																																																				0.587	C14orf93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071688.5	NM_021944	
ACIN1	22985	broad.mit.edu	37	14	23549214	23549214	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:23549214G>A	ENST00000262710.1	-	6	1831	c.1504C>T	c.(1504-1506)Cct>Tct	p.P502S	ACIN1_ENST00000457657.1_Missense_Mutation_p.P462S|ACIN1_ENST00000555053.1_Missense_Mutation_p.P502S|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000605057.1_Missense_Mutation_p.P444S	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	502					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.P502S(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)		TGAACCAGAGGCAGGACACTC	0.512																																					p.P502S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1504T	14						.						99.0	104.0	103.0					14																	23549214		2203	4300	6503	22619054	SO:0001583	missense	22985	exon6			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.1504C>T	14.37:g.23549214G>A	ENSP00000262710:p.Pro502Ser	Somatic		Capture	Illumina HiSeq	Phase_I	22619054	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	37	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.521118	0.44866	.	.	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.34072	1.38;1.38;1.38	5.42	4.5	0.54988	.	0.000000	0.40640	N	0.001049	T	0.23688	0.0573	N	0.24115	0.695	0.28923	N	0.89202	P;P;D	0.55385	0.867;0.791;0.971	B;B;B	0.41510	0.359;0.196;0.3	T	0.08848	-1.0702	10	0.32370	T	0.25	-9.6911	11.517	0.50526	0.0:0.0:0.8222:0.1778	.	502;502;462	G3V3M7;Q9UKV3;E7EQT4	.;ACINU_HUMAN;.	S	502;462;502	ENSP00000262710:P502S;ENSP00000405677:P462S;ENSP00000451328:P502S	ENSP00000262710:P502S	P	-	1	0	ACIN1	22619054	0.997000	0.39634	0.998000	0.56505	0.948000	0.59901	0.834000	0.27518	2.821000	0.97095	0.650000	0.86243	CCT		0.512	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
HOMEZ	57594	broad.mit.edu	37	14	23746003	23746003	+	Missense_Mutation	SNP	G	G	A	rs111256939		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:23746003G>A	ENST00000357460.5	-	2	598	c.434C>T	c.(433-435)gCg>gTg	p.A145V	HOMEZ_ENST00000431326.2_Missense_Mutation_p.A147V|HOMEZ_ENST00000561013.1_Missense_Mutation_p.A147V	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	145					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A145V(1)		endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		GGGCCGTCCCGCATGATGAGT	0.527																																					p.A145V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C434T	14						.						128.0	129.0	129.0					14																	23746003		1889	4113	6002	22815843	SO:0001583	missense	57594	exon2			AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.434C>T	14.37:g.23746003G>A	ENSP00000350049:p.Ala145Val	Somatic		Capture	Illumina HiSeq	Phase_I	22815843	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Missense_Mutation	SNP	ENST00000357460.5	37	CCDS45085.1	.	.	.	.	.	.	.	.	.	.	G	14.10	2.435715	0.43224	.	.	ENSG00000215271	ENST00000357460;ENST00000431326	T;T	0.26223	1.75;1.75	6.17	5.28	0.74379	.	0.226735	0.36555	N	0.002536	T	0.17746	0.0426	L	0.27053	0.805	0.26871	N	0.967747	B;B	0.25667	0.131;0.08	B;B	0.16722	0.016;0.007	T	0.12528	-1.0544	10	0.35671	T	0.21	-4.8495	11.2724	0.49147	0.0827:0.0:0.9173:0.0	.	147;145	F8WCA3;Q8IX15	.;HOMEZ_HUMAN	V	145;147	ENSP00000350049:A145V;ENSP00000406579:A147V	ENSP00000350049:A145V	A	-	2	0	HOMEZ	22815843	0.741000	0.28217	0.993000	0.49108	0.962000	0.63368	1.219000	0.32479	1.620000	0.50308	0.655000	0.94253	GCG		0.527	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
SLC22A17	51310	broad.mit.edu	37	14	23821265	23821265	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:23821265G>T	ENST00000206544.8	-	1	495	c.159C>A	c.(157-159)acC>acA	p.T53T	SLC22A17_ENST00000474057.1_5'UTR|SLC22A17_ENST00000397260.3_5'UTR|SLC22A17_ENST00000354772.3_Silent_p.T53T|SLC22A17_ENST00000397267.1_Silent_p.T53T	NM_020372.2	NP_065105.2	Q8WUG5	S22AH_HUMAN	solute carrier family 22, member 17	53					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|siderophore transport (GO:0015891)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|vacuole (GO:0005773)	transmembrane signaling receptor activity (GO:0004888)|transmembrane transporter activity (GO:0022857)	p.T53T(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15	all_cancers(95;7.12e-06)			GBM - Glioblastoma multiforme(265;0.00643)		GGTCGGTACTGGTGGCGACAC	0.662																																					p.T53T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C159A	14						.						25.0	21.0	22.0					14																	23821265		2200	4296	6496	22891105	SO:0001819	synonymous_variant	51310	exon1			AJ243653	CCDS9593.1, CCDS9594.2	14q11.2	2013-05-22	2008-01-11		ENSG00000092096	ENSG00000092096		"""Solute carriers"""	23095	protein-coding gene	gene with protein product	"""neutrophil gelatinase-associated lipocalin receptor"""	611461				16377569	Standard	NM_016609		Approved	BOCT, BOIT, NGALR	uc001wjl.3	Q8WUG5	OTTHUMG00000028740	ENST00000206544.8:c.159C>A	14.37:g.23821265G>T		Somatic		Capture	Illumina HiSeq	Phase_I	22891105	NM_020372	A4UA13|A8MUT0|Q2TAB0|Q5BKY8|Q86U04|Q9H1D3|Q9NQD5	Silent	SNP	ENST00000206544.8	37	CCDS9593.1																																																																																				0.662	SLC22A17-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157223.3	NM_020372	
MYH7	4625	broad.mit.edu	37	14	23884930	23884930	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:23884930G>A	ENST00000355349.3	-	35	5227	c.5065C>T	c.(5065-5067)Cgt>Tgt	p.R1689C	CTD-2201G16.1_ENST00000557368.1_RNA|MIR208B_ENST00000401172.1_RNA	NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	1689					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|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)	p.R1689C(2)		NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		ACCACGGCACGCAACTCCTCC	0.627																																					p.R1689C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C5065T	14						.						75.0	66.0	69.0					14																	23884930		2203	4300	6503	22954770	SO:0001583	missense	4625	exon35			M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"""Myosins / Myosin superfamily : Class II"""	7577	protein-coding gene	gene with protein product		160760	"""myopathy, distal 1"", ""myosin, heavy polypeptide 7, cardiac muscle, beta"""	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.5065C>T	14.37:g.23884930G>A	ENSP00000347507:p.Arg1689Cys	Somatic		Capture	Illumina HiSeq	Phase_I	22954770	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Missense_Mutation	SNP	ENST00000355349.3	37	CCDS9601.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.909553	0.72868	.	.	ENSG00000092054	ENST00000355349;ENST00000544444	D	0.83250	-1.7	5.31	4.4	0.53042	Myosin tail (1);	.	.	.	.	D	0.94019	0.8084	H	0.97186	3.955	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95988	0.8983	9	0.87932	D	0	.	15.3427	0.74311	0.0:0.0:0.8594:0.1406	.	1689	P12883	MYH7_HUMAN	C	1689;1694	ENSP00000347507:R1689C	ENSP00000347507:R1689C	R	-	1	0	MYH7	22954770	0.998000	0.40836	0.998000	0.56505	0.992000	0.81027	2.975000	0.49281	1.435000	0.47434	0.561000	0.74099	CGT		0.627	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	
LRRC16B	90668	broad.mit.edu	37	14	24522950	24522950	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:24522950G>A	ENST00000342740.5	+	2	227	c.73G>A	c.(73-75)Gtg>Atg	p.V25M	LRRC16B_ENST00000334420.7_5'UTR|RP11-468E2.9_ENST00000558293.1_RNA	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	25						cytoplasm (GO:0005737)		p.V25M(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)		CCAAGGGGCCGTGCTCCAACA	0.622																																					p.V25M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G73A	14						.						51.0	42.0	45.0					14																	24522950		2203	4300	6503	23592790	SO:0001583	missense	90668	exon2			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.73G>A	14.37:g.24522950G>A	ENSP00000340467:p.Val25Met	Somatic		Capture	Illumina HiSeq	Phase_I	23592790	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	.	.	.	.	.	.	.	.	.	.	G	14.13	2.444369	0.43429	.	.	ENSG00000186648	ENST00000342740	T	0.16073	2.37	5.08	4.12	0.48240	.	0.104216	0.39146	N	0.001458	T	0.23806	0.0576	L	0.38175	1.15	0.80722	D	1	D	0.71674	0.998	P	0.58520	0.84	T	0.00307	-1.1830	10	0.42905	T	0.14	-16.0757	10.2938	0.43612	0.0:0.0:0.8033:0.1967	.	25	Q8ND23	LR16B_HUMAN	M	25	ENSP00000340467:V25M	ENSP00000340467:V25M	V	+	1	0	LRRC16B	23592790	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.725000	0.47294	2.517000	0.84864	0.462000	0.41574	GTG		0.622	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
CPNE6	9362	broad.mit.edu	37	14	24542860	24542860	+	Silent	SNP	C	C	T	rs560953312		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:24542860C>T	ENST00000397016.2	+	4	632	c.321C>T	c.(319-321)ctC>ctT	p.L107L	CPNE6_ENST00000216775.2_Silent_p.L107L|CPNE6_ENST00000560092.1_3'UTR|CPNE6_ENST00000537691.1_Silent_p.L162L	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	107	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)	p.L107L(1)		endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		ATACCTTCCTCGGCTCTACGG	0.587													C|||	1	0.000199681	0.0	0.0	5008	,	,		18103	0.001		0.0	False		,,,				2504	0.0				p.L107L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C321T	14						.						73.0	63.0	66.0					14																	24542860		2203	4300	6503	23612700	SO:0001819	synonymous_variant	9362	exon3			AB009288	CCDS9607.1, CCDS61413.1	14q11.2	2008-07-09			ENSG00000100884	ENSG00000100884			2319	protein-coding gene	gene with protein product		605688				9645480	Standard	NM_001280558		Approved		uc001wll.3	O95741	OTTHUMG00000028781	ENST00000397016.2:c.321C>T	14.37:g.24542860C>T		Somatic		Capture	Illumina HiSeq	Phase_I	23612700	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Silent	SNP	ENST00000397016.2	37	CCDS9607.1																																																																																				0.587	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5		
FITM1	161247	broad.mit.edu	37	14	24600787	24600787	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:24600787G>A	ENST00000267426.5	+	1	304	c.15G>A	c.(13-15)ccG>ccA	p.P5P	RP11-468E2.6_ENST00000558325.1_Missense_Mutation_p.G193S|FITM1_ENST00000559294.1_5'Flank	NM_203402.2	NP_981947.1	A5D6W6	FITM1_HUMAN	fat storage-inducing transmembrane protein 1	5					lipid particle organization (GO:0034389)|positive regulation of sequestering of triglyceride (GO:0010890)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)		p.P5P(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						agcgggggccggtggtggggg	0.672																																					p.P5P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G15A	14						.						5.0	7.0	6.0					14																	24600787		2008	4096	6104	23670627	SO:0001819	synonymous_variant	161247	exon1				CCDS9611.1	14q12	2009-07-09			ENSG00000139914	ENSG00000139914			33714	protein-coding gene	gene with protein product	"""fat-inducing transcript 1"""	612028				18160536	Standard	NM_203402		Approved	FIT1	uc001wmf.2	A5D6W6	OTTHUMG00000133476	ENST00000267426.5:c.15G>A	14.37:g.24600787G>A		Somatic		Capture	Illumina HiSeq	Phase_I	23670627	NM_203402	Q8IUQ7	Silent	SNP	ENST00000267426.5	37	CCDS9611.1																																																																																				0.672	FITM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257366.1	NM_203402	
IPO4	79711	broad.mit.edu	37	14	24653066	24653066	+	Silent	SNP	G	G	A	rs184433827	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:24653066G>A	ENST00000354464.6	-	19	2084	c.1908C>T	c.(1906-1908)gaC>gaT	p.D636D	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	636					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)		p.D636D(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CACTCTCATCGTCAAACAGAA	0.552													G|||	8	0.00159744	0.0045	0.0	5008	,	,		16204	0.0		0.0	False		,,,				2504	0.002				p.D636D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1908T	14						.	G		11,4077		0,11,2033	104.0	107.0	106.0		1908	-7.5	1.0	14		106	0,8414		0,0,4207	no	coding-synonymous	IPO4	NM_024658.3		0,11,6240	AA,AG,GG		0.0,0.2691,0.088		636/1082	24653066	11,12491	2044	4207	6251	23722906	SO:0001819	synonymous_variant	79711	exon19			AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1908C>T	14.37:g.24653066G>A		Somatic		Capture	Illumina HiSeq	Phase_I	23722906	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Silent	SNP	ENST00000354464.6	37	CCDS9616.1																																																																																				0.552	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
TM9SF1	10548	broad.mit.edu	37	14	24662277	24662277	+	Missense_Mutation	SNP	G	G	A	rs138817054	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:24662277G>A	ENST00000261789.4	-	3	902	c.544C>T	c.(544-546)Cgg>Tgg	p.R182W	TM9SF1_ENST00000528669.1_Missense_Mutation_p.R182W|TM9SF1_ENST00000556387.1_Missense_Mutation_p.R391W|TM9SF1_ENST00000524835.1_Missense_Mutation_p.R95W|TM9SF1_ENST00000530611.1_Missense_Mutation_p.R391W|TM9SF1_ENST00000396854.4_Missense_Mutation_p.R182W|RP11-468E2.2_ENST00000561419.1_5'Flank	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	182					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)		p.R182W(1)		NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		TTGACGTCCCGCACTGAAACA	0.522																																					p.R182W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C544T	14						.	G	TRP/ARG,TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	106.0	99.0	101.0		544,544	2.3	1.0	14	dbSNP_134	101	0,8600		0,0,4300	yes	missense,missense	TM9SF1	NM_001014842.1,NM_006405.5	101,101	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging,probably-damaging	182/490,182/607	24662277	2,13004	2203	4300	6503	23732117	SO:0001583	missense	10548	exon3			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.544C>T	14.37:g.24662277G>A	ENSP00000261789:p.Arg182Trp	Somatic		Capture	Illumina HiSeq	Phase_I	23732117	NM_001014842	D3DS65|Q86SZ6|Q96FI8	Missense_Mutation	SNP	ENST00000261789.4	37	CCDS9617.1	.	.	.	.	.	.	.	.	.	.	G	18.41	3.616897	0.66672	4.54E-4	0.0	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000396854;ENST00000528895;ENST00000530563;ENST00000530468;ENST00000525592;ENST00000528010;ENST00000530611	T;T;T;T;T;T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83;0.83	5.1	2.26	0.28386	.	0.065735	0.64402	D	0.000016	T	0.57417	0.2052	L	0.57536	1.79	0.45097	D	0.998112	D;D;D	0.76494	0.999;0.999;0.994	D;P;P	0.65443	0.935;0.892;0.862	T	0.55121	-0.8190	10	0.66056	D	0.02	-13.0069	7.4193	0.27063	0.0797:0.0:0.6244:0.2958	.	182;182;182	E9PJM1;Q86SZ6;O15321	.;.;TM9S1_HUMAN	W	182;182;391;95;182;182;95;182;182;182;391	ENSP00000261789:R182W;ENSP00000432997:R182W;ENSP00000451949:R391W;ENSP00000434387:R95W;ENSP00000380063:R182W;ENSP00000431447:R182W;ENSP00000437127:R95W;ENSP00000435857:R182W;ENSP00000432435:R182W;ENSP00000433792:R182W;ENSP00000433967:R391W	ENSP00000433967:R391W	R	-	1	2	TM9SF1;RP11-468E2.1	23732117	0.998000	0.40836	0.996000	0.52242	0.995000	0.86356	2.322000	0.43814	0.305000	0.22832	0.655000	0.94253	CGG		0.522	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405	
TM9SF1	10548	broad.mit.edu	37	14	24664008	24664008	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:24664008C>T	ENST00000261789.4	-	2	576	c.218G>A	c.(217-219)cGt>cAt	p.R73H	TM9SF1_ENST00000528669.1_Missense_Mutation_p.R73H|TM9SF1_ENST00000556387.1_Missense_Mutation_p.R282H|TM9SF1_ENST00000524835.1_5'UTR|TM9SF1_ENST00000530611.1_Missense_Mutation_p.R282H|TM9SF1_ENST00000396854.4_Missense_Mutation_p.R73H	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	73					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)		p.R73H(1)		NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		GCTTTTGTGACGTATCTTCTC	0.488																																					p.R73H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G218A	14						.						399.0	397.0	398.0					14																	24664008		2203	4300	6503	23733848	SO:0001583	missense	10548	exon2			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.218G>A	14.37:g.24664008C>T	ENSP00000261789:p.Arg73His	Somatic		Capture	Illumina HiSeq	Phase_I	23733848	NM_001014842	D3DS65|Q86SZ6|Q96FI8	Missense_Mutation	SNP	ENST00000261789.4	37	CCDS9617.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.092797	0.56075	.	.	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000396854;ENST00000528895;ENST00000530468;ENST00000525592;ENST00000528010;ENST00000530611	T;T;T;T;T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94	5.17	5.17	0.71159	.	0.064498	0.64402	D	0.000007	T	0.31327	0.0793	N	0.20807	0.61	0.39004	D	0.959407	B;B	0.22080	0.064;0.003	B;B	0.18561	0.022;0.002	T	0.13764	-1.0497	10	0.52906	T	0.07	-7.2686	16.2171	0.82237	0.0:1.0:0.0:0.0	.	73;73	Q86SZ6;O15321	.;TM9S1_HUMAN	H	73;73;282;73;73;73;73;73;282	ENSP00000261789:R73H;ENSP00000432997:R73H;ENSP00000451949:R282H;ENSP00000380063:R73H;ENSP00000431447:R73H;ENSP00000435857:R73H;ENSP00000432435:R73H;ENSP00000433792:R73H;ENSP00000433967:R282H	ENSP00000433967:R282H	R	-	2	0	TM9SF1;RP11-468E2.1	23733848	0.993000	0.37304	0.171000	0.22900	0.995000	0.86356	2.996000	0.49449	2.700000	0.92200	0.563000	0.77884	CGT		0.488	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405	
NOP9	161424	broad.mit.edu	37	14	24774228	24774228	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:24774228G>A	ENST00000267425.3	+	10	1931	c.1838G>A	c.(1837-1839)cGa>cAa	p.R613Q	NOP9_ENST00000396802.3_3'UTR	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	613							poly(A) RNA binding (GO:0044822)	p.R613Q(1)									CTAAAGCGGCGAGAGGCTTGG	0.572																																					p.R613Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1838A	14						.						49.0	45.0	47.0					14																	24774228		2203	4300	6503	23844068	SO:0001583	missense	161424	exon10				CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 21"", ""NOP9 nucleolar protein homolog (yeast)"""	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.1838G>A	14.37:g.24774228G>A	ENSP00000267425:p.Arg613Gln	Somatic		Capture	Illumina HiSeq	Phase_I	23844068	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Missense_Mutation	SNP	ENST00000267425.3	37	CCDS9624.1	.	.	.	.	.	.	.	.	.	.	G	34	5.382864	0.95967	.	.	ENSG00000196943	ENST00000267425;ENST00000544934	T	0.35421	1.31	5.75	5.75	0.90469	.	0.062520	0.64402	D	0.000010	T	0.47875	0.1469	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.35919	-0.9769	10	0.40728	T	0.16	-7.0522	16.8541	0.86001	0.0:0.0:1.0:0.0	.	613	Q86U38	CN021_HUMAN	Q	613;164	ENSP00000267425:R613Q	ENSP00000267425:R613Q	R	+	2	0	C14orf21	23844068	1.000000	0.71417	0.990000	0.47175	0.857000	0.48899	2.820000	0.48057	2.711000	0.92665	0.655000	0.94253	CGA		0.572	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
ADCY4	196883	broad.mit.edu	37	14	24793571	24793571	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:24793571C>T	ENST00000310677.4	-	16	1963	c.1850G>A	c.(1849-1851)aGc>aAc	p.S617N	ADCY4_ENST00000554068.2_Missense_Mutation_p.S617N|ADCY4_ENST00000418030.2_Missense_Mutation_p.S617N|ADCY4_ENST00000396747.3_Missense_Mutation_p.S310N	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	617					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)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|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)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.S617N(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		GAAGGTGATGCTATACGTGAT	0.572																																					p.S617N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1850A	14						.						79.0	74.0	76.0					14																	24793571		2203	4300	6503	23863411	SO:0001583	missense	196883	exon16			AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"""Adenylate cyclases"""	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.1850G>A	14.37:g.24793571C>T	ENSP00000312126:p.Ser617Asn	Somatic		Capture	Illumina HiSeq	Phase_I	23863411	NM_001198592	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Missense_Mutation	SNP	ENST00000310677.4	37	CCDS9627.1	.	.	.	.	.	.	.	.	.	.	C	19.82	3.897860	0.72639	.	.	ENSG00000129467	ENST00000310677;ENST00000554068;ENST00000418030;ENST00000396747	T;T;T;T	0.79247	-1.05;-1.05;-1.05;-1.25	5.58	5.58	0.84498	.	0.512393	0.18174	N	0.149341	T	0.66761	0.2822	N	0.22421	0.69	0.36585	D	0.87379	B	0.12013	0.005	B	0.17098	0.017	T	0.64939	-0.6289	10	0.27785	T	0.31	.	15.0747	0.72069	0.0:1.0:0.0:0.0	.	617	Q8NFM4	ADCY4_HUMAN	N	617;617;617;310	ENSP00000312126:S617N;ENSP00000452250:S617N;ENSP00000393177:S617N;ENSP00000379971:S310N	ENSP00000312126:S617N	S	-	2	0	ADCY4	23863411	1.000000	0.71417	0.993000	0.49108	0.939000	0.58152	4.894000	0.63206	2.638000	0.89438	0.655000	0.94253	AGC		0.572	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4		
RIPK3	11035	broad.mit.edu	37	14	24806110	24806110	+	Silent	SNP	C	C	T	rs200066851		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:24806110C>T	ENST00000216274.5	-	9	1535	c.1317G>A	c.(1315-1317)ccG>ccA	p.P439P	ADCY4_ENST00000554068.2_5'Flank|RP11-934B9.3_ENST00000555591.1_Silent_p.P113P|ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000418030.2_5'Flank|ADCY4_ENST00000396747.3_5'Flank|RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000558563.1_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	439	Pro-rich.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)	p.P439P(1)		NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		GATTTGGCTCCGGGGTCCTGC	0.542													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18213	0.0		0.0	False		,,,				2504	0.0				p.P439P	Pancreas(58;918 1191 4668 13304 15331)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1317A	14						.						119.0	114.0	116.0					14																	24806110		2203	4300	6503	23875950	SO:0001819	synonymous_variant	11035	exon9			AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.1317G>A	14.37:g.24806110C>T		Somatic		Capture	Illumina HiSeq	Phase_I	23875950	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Silent	SNP	ENST00000216274.5	37	CCDS9628.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	2.905	-0.226700	0.06022	.	.	ENSG00000129465	ENST00000554569	.	.	.	4.17	-6.3	0.02007	.	.	.	.	.	T	0.15132	0.0365	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24119	-1.0169	4	.	.	.	0.1652	0.3745	0.00385	0.2556:0.2602:0.2602:0.224	.	.	.	.	Q	120	.	.	R	-	2	0	RIPK3	23875950	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.516000	0.06282	-1.311000	0.02309	-0.894000	0.02916	CGG		0.542	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871	
NYNRIN	57523	broad.mit.edu	37	14	24877505	24877505	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:24877505G>A	ENST00000382554.3	+	3	947	c.629G>A	c.(628-630)gGc>gAc	p.G210D		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	210					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)	p.G210D(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						AGCCGCTTCGGCATCTCTGAC	0.642																																					p.G210D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G629A	14						.						35.0	42.0	40.0					14																	24877505		2085	4219	6304	23947345	SO:0001583	missense	57523	exon3			AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"""Cousin of GIN1"""		"""KIAA1305"""	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.629G>A	14.37:g.24877505G>A	ENSP00000371994:p.Gly210Asp	Somatic		Capture	Illumina HiSeq	Phase_I	23947345	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	37	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.096611	0.56075	.	.	ENSG00000205978	ENST00000382554	T	0.13196	2.61	5.06	4.15	0.48705	.	0.462149	0.16728	N	0.201970	T	0.09905	0.0243	L	0.27053	0.805	0.32577	N	0.529022	B	0.32031	0.352	B	0.29440	0.102	T	0.05022	-1.0911	10	0.72032	D	0.01	.	9.6607	0.39954	0.0971:0.0:0.9029:0.0	.	210	Q9P2P1	NYNRI_HUMAN	D	210	ENSP00000371994:G210D	ENSP00000371994:G210D	G	+	2	0	NYNRIN	23947345	0.992000	0.36948	0.999000	0.59377	0.459000	0.32528	4.153000	0.58118	2.619000	0.88677	0.655000	0.94253	GGC		0.642	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1		
FOXG1	2290	broad.mit.edu	37	14	29237769	29237769	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:29237769G>A	ENST00000313071.4	+	1	1483	c.1284G>A	c.(1282-1284)tcG>tcA	p.S428S	FOXG1_ENST00000382535.3_Silent_p.S428S	NM_005249.4	NP_005240.3	P55316	FOXG1_HUMAN	forkhead box G1	428					aging (GO:0007568)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|dorsal/ventral pattern formation (GO:0009953)|inner ear morphogenesis (GO:0042472)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron fate determination (GO:0048664)|positive regulation of cell cycle (GO:0045787)|positive regulation of neuroblast proliferation (GO:0002052)|pyramidal neuron migration (GO:0021852)|regulation of mitotic cell cycle (GO:0007346)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S428S(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(2)	43			LUAD - Lung adenocarcinoma(48;0.011)|Lung(238;0.0575)	GBM - Glioblastoma multiforme(265;0.00413)		CAATGACTTCGCAGAGCAGCA	0.642																																					p.S428S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1284A	14						.						57.0	52.0	53.0					14																	29237769		2203	4300	6503	28307520	SO:0001819	synonymous_variant	2290	exon1				CCDS9636.1	14q11-q13	2007-10-05	2007-05-16	2007-05-16	ENSG00000176165	ENSG00000176165		"""Forkhead boxes"""	3811	protein-coding gene	gene with protein product		164874	"""forkhead box G1B"", ""forkhead box G1C"", ""forkhead box G1A"""	FKHL2, FOXG1B, FKHL4, FKH2, FKHL1, FOXG1C, FKHL3, FOXG1A		7959731, 17260156	Standard	NM_005249		Approved	HFK2, QIN, BF1, HFK1, HFK3, HBF-3	uc001wqe.4	P55316	OTTHUMG00000140187	ENST00000313071.4:c.1284G>A	14.37:g.29237769G>A		Somatic		Capture	Illumina HiSeq	Phase_I	28307520	NM_005249	A6NFY2|P55315|Q14488|Q86XT7	Silent	SNP	ENST00000313071.4	37	CCDS9636.1																																																																																				0.642	FOXG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276559.3		
PRKD1	5587	broad.mit.edu	37	14	30105513	30105513	+	Silent	SNP	G	G	A	rs543331086		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:30105513G>A	ENST00000331968.5	-	7	1402	c.1173C>T	c.(1171-1173)gaC>gaT	p.D391D	PRKD1_ENST00000415220.2_Silent_p.D399D|PRKD1_ENST00000551644.1_5'Flank	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	391					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|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 histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.D391D(2)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		TTCTGTTGGCGTCCTCGTGGT	0.498													G|||	1	0.000199681	0.0	0.0	5008	,	,		16844	0.001		0.0	False		,,,				2504	0.0				p.D391D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1173T	14						.						314.0	249.0	271.0					14																	30105513		2203	4300	6503	29175264	SO:0001819	synonymous_variant	5587	exon7				CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	9407	protein-coding gene	gene with protein product		605435	"""protein kinase C, mu"""	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.1173C>T	14.37:g.30105513G>A		Somatic		Capture	Illumina HiSeq	Phase_I	29175264	NM_002742	A6NL64|B2RAF6	Silent	SNP	ENST00000331968.5	37	CCDS9637.1																																																																																				0.498	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742	
HECTD1	25831	broad.mit.edu	37	14	31642954	31642954	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:31642954C>T	ENST00000399332.1	-	5	1150	c.662G>A	c.(661-663)gGt>gAt	p.G221D	HECTD1_ENST00000553700.1_Missense_Mutation_p.G221D	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	221					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)	p.G221D(1)		breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TGGGTCAACACCACGACGGGT	0.483																																					p.G221D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G662A	14						.						50.0	49.0	50.0					14																	31642954		1990	4181	6171	30712705	SO:0001583	missense	25831	exon5			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.662G>A	14.37:g.31642954C>T	ENSP00000382269:p.Gly221Asp	Somatic		Capture	Illumina HiSeq	Phase_I	30712705	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.162944	0.78226	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000556224	T;T;T	0.30714	1.52;1.52;1.52	5.78	4.88	0.63580	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.48978	0.1530	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.38067	-0.9678	10	0.18710	T	0.47	-20.4671	16.3447	0.83118	0.1332:0.8668:0.0:0.0	.	221	Q9ULT8	HECD1_HUMAN	D	221	ENSP00000450697:G221D;ENSP00000382269:G221D;ENSP00000452015:G221D	ENSP00000261312:G221D	G	-	2	0	HECTD1	30712705	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.374000	0.79633	1.543000	0.49345	0.591000	0.81541	GGT		0.483	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
BAZ1A	11177	broad.mit.edu	37	14	35228014	35228014	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:35228014G>A	ENST00000382422.2	-	24	4609	c.4282C>T	c.(4282-4284)Cga>Tga	p.R1428*	BAZ1A_ENST00000360310.1_Nonsense_Mutation_p.R1428*|BAZ1A_ENST00000358716.4_Nonsense_Mutation_p.R1396*			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1428					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)	p.R1428*(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		CCTCCCTGTCGGCCAGAACTC	0.408																																					p.R1428X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C4282T	14						.						99.0	90.0	93.0					14																	35228014		2203	4300	6503	34297765	SO:0001587	stop_gained	11177	exon25			AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"""Zinc fingers, PHD-type"""	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.4282C>T	14.37:g.35228014G>A	ENSP00000371859:p.Arg1428*	Somatic		Capture	Illumina HiSeq	Phase_I	34297765	NM_013448	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Nonsense_Mutation	SNP	ENST00000382422.2	37	CCDS9651.1	.	.	.	.	.	.	.	.	.	.	.	47	13.033414	0.99715	.	.	ENSG00000198604	ENST00000358716;ENST00000382422;ENST00000360310;ENST00000543083	.	.	.	5.46	0.789	0.18607	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.2846	0.82712	0.0:0.0:0.4527:0.5473	.	.	.	.	X	1396;1428;1428;1080	.	ENSP00000351555:R1396X	R	-	1	2	BAZ1A	34297765	0.997000	0.39634	0.977000	0.42913	0.992000	0.81027	2.416000	0.44644	0.220000	0.20860	0.655000	0.94253	CGA		0.408	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1		
NKX2-1	7080	broad.mit.edu	37	14	36986894	36986894	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:36986894G>A	ENST00000518149.1	-	3	1310	c.705C>T	c.(703-705)ggC>ggT	p.G235G	NKX2-1_ENST00000354822.5_Silent_p.G265G|NKX2-1_ENST00000522719.2_Silent_p.G235G|NKX2-1-AS1_ENST00000521292.2_RNA|RP11-896J10.3_ENST00000521945.1_RNA|NKX2-1_ENST00000498187.2_Silent_p.G235G			P43699	NKX21_HUMAN	NK2 homeobox 1	235	Poly-Gly.				anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|brain development (GO:0007420)|cerebral cortex cell migration (GO:0021795)|cerebral cortex GABAergic interneuron differentiation (GO:0021892)|Clara cell differentiation (GO:0060486)|developmental induction (GO:0031128)|endoderm development (GO:0007492)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|forebrain development (GO:0030900)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain neuron fate commitment (GO:0021877)|globus pallidus development (GO:0021759)|hippocampus development (GO:0021766)|Leydig cell differentiation (GO:0033327)|locomotory behavior (GO:0007626)|lung development (GO:0030324)|lung saccule development (GO:0060430)|menarche (GO:0042696)|negative regulation of cell migration (GO:0030336)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron migration (GO:0001764)|oligodendrocyte differentiation (GO:0048709)|phospholipid metabolic process (GO:0006644)|pituitary gland development (GO:0021983)|positive regulation of circadian rhythm (GO:0042753)|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)|response to hormone (GO:0009725)|rhythmic process (GO:0048511)|thyroid gland development (GO:0030878)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|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)	p.G235G(1)		large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(2)	7	all_cancers(3;4.47e-51)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.165)		Lung(8;1.8e-08)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.014)|all cancers(34;0.0366)|LUSC - Lung squamous cell carcinoma(13;0.132)	GBM - Glioblastoma multiforme(112;0.0171)		cgcccccgccgccgccgctgt	0.687			A		NSCLC																																p.G235G			Dom	yes		14	14q13	7080	NK2 homeobox 1		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C705T	14						.						7.0	7.0	7.0					14																	36986894		2155	4207	6362	36056645	SO:0001819	synonymous_variant	7080	exon2				CCDS9659.1, CCDS41945.1	14q13.3	2012-03-09	2007-07-26	2007-07-26	ENSG00000136352	ENSG00000136352		"""Homeoboxes / ANTP class : NKL subclass"""	11825	protein-coding gene	gene with protein product		600635	"""benign chorea"", ""thyroid transcription factor 1"""	NKX2A, BCH, TITF1		1976511	Standard	NM_001079668		Approved	TTF-1, TTF1	uc001wtu.3	P43699	OTTHUMG00000140225	ENST00000518149.1:c.705C>T	14.37:g.36986894G>A		Somatic		Capture	Illumina HiSeq	Phase_I	36056645	NM_003317	D3DSA3|O14954|O14955|Q7KZF6|Q9BRJ8	Silent	SNP	ENST00000518149.1	37	CCDS9659.1																																																																																				0.687	NKX2-1-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376225.2	NM_003317	
SSTR1	6751	broad.mit.edu	37	14	38678895	38678895	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:38678895G>A	ENST00000267377.2	+	3	918	c.301G>A	c.(301-303)Gcc>Acc	p.A101T		NM_001049.2	NP_001040.1	P30872	SSR1_HUMAN	somatostatin receptor 1	101					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glutamate receptor signaling pathway (GO:0007215)|negative regulation of cell proliferation (GO:0008285)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)	p.A101T(1)		breast(1)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00444)	Octreotide(DB00104)|Pasireotide(DB06663)	CCTAAATCTGGCCATTGCTGA	0.582																																					p.A101T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G301A	14						.						191.0	175.0	180.0					14																	38678895		2203	4300	6503	37748646	SO:0001583	missense	6751	exon3				CCDS9666.1	14q13	2012-08-08			ENSG00000139874	ENSG00000139874		"""GPCR / Class A : Somatostatin receptors"""	11330	protein-coding gene	gene with protein product		182451				8449518	Standard	NM_001049		Approved		uc001wul.1	P30872	OTTHUMG00000140249	ENST00000267377.2:c.301G>A	14.37:g.38678895G>A	ENSP00000267377:p.Ala101Thr	Somatic		Capture	Illumina HiSeq	Phase_I	37748646	NM_001049		Missense_Mutation	SNP	ENST00000267377.2	37	CCDS9666.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.103362	0.56291	.	.	ENSG00000139874	ENST00000267377	T	0.56103	0.48	4.8	3.9	0.45041	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000016	T	0.75525	0.3861	M	0.88775	2.98	0.58432	D	0.999992	D	0.89917	1.0	D	0.91635	0.999	T	0.80991	-0.1135	10	0.87932	D	0	.	13.5256	0.61593	0.0:0.0:0.8429:0.1571	.	101	P30872	SSR1_HUMAN	T	101	ENSP00000267377:A101T	ENSP00000267377:A101T	A	+	1	0	SSTR1	37748646	1.000000	0.71417	1.000000	0.80357	0.200000	0.23975	9.623000	0.98386	1.237000	0.43756	-0.181000	0.13052	GCC		0.582	SSTR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409930.2		
MIS18BP1	55320	broad.mit.edu	37	14	45711241	45711241	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:45711241delT	ENST00000310806.4	-	4	1597	c.1139delA	c.(1138-1140)aatfs	p.N380fs	MIS18BP1_ENST00000492652.1_5'UTR	NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	380					CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.N380fs*3(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						TCCCACCTGATTTTTTTTAAG	0.308																																					p.N380fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1139delA	14						.						56.0	65.0	62.0					14																	45711241		2202	4295	6497	44780991	SO:0001589	frameshift_variant	55320	exon4			AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"""kinetochore null 2 homolog (C. elegans)"""		"""chromosome 14 open reading frame 106"""	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.1139delA	14.37:g.45711241delT	ENSP00000309790:p.Asn380fs	Somatic		Capture	Illumina HiSeq	Phase_I	44780991	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Frame_Shift_Del	DEL	ENST00000310806.4	37	CCDS9684.1																																																																																				0.308	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2		
C14orf182	283551	broad.mit.edu	37	14	50472378	50472378	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:50472378A>T	ENST00000399206.1	-	1	1860	c.140T>A	c.(139-141)gTt>gAt	p.V47D	C14orf182_ENST00000529902.1_5'UTR	NM_001012706.1	NP_001012724.1	A1A4T8	CN182_HUMAN	chromosome 14 open reading frame 182	47								p.V47D(1)		large_intestine(2)|urinary_tract(1)	3						GTGTCGTAGAACTGTGTGTGA	0.532																																					p.V47D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T140A	14						.						238.0	258.0	252.0					14																	50472378		2054	4193	6247	49542128	SO:0001583	missense	283551	exon1			AK090420	CCDS41949.1	14q22.1	2009-02-24			ENSG00000214900	ENSG00000214900			27503	protein-coding gene	gene with protein product							Standard	NM_001012706		Approved		uc001wxi.1	A1A4T8		ENST00000399206.1:c.140T>A	14.37:g.50472378A>T	ENSP00000382157:p.Val47Asp	Somatic		Capture	Illumina HiSeq	Phase_I	49542128	NM_001012706	A8MYX4	Missense_Mutation	SNP	ENST00000399206.1	37	CCDS41949.1	.	.	.	.	.	.	.	.	.	.	A	10.31	1.314796	0.23908	.	.	ENSG00000214900	ENST00000399206	T	0.59224	0.28	3.06	-4.58	0.03410	.	.	.	.	.	T	0.42585	0.1209	.	.	.	0.09310	N	1	P	0.45827	0.867	B	0.41271	0.352	T	0.37934	-0.9684	8	0.66056	D	0.02	.	4.7632	0.13118	0.4668:0.3094:0.2238:0.0	.	47	A1A4T8-2	.	D	47	ENSP00000382157:V47D	ENSP00000382157:V47D	V	-	2	0	C14orf182	49542128	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.853000	0.04303	-1.116000	0.02969	-0.375000	0.07067	GTT		0.532	C14orf182-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395717.1	NM_001012706	
SOS2	6655	broad.mit.edu	37	14	50641224	50641224	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:50641224C>T	ENST00000216373.5	-	8	1290	c.1016G>A	c.(1015-1017)cGt>cAt	p.R339H	SOS2_ENST00000555794.1_5'UTR|SOS2_ENST00000543680.1_Intron	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	339	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R339H(2)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					CAGCATAAGACGTGGAAGGAC	0.378																																					p.R339H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1016A	14						.						111.0	82.0	92.0					14																	50641224		2203	4300	6503	49710974	SO:0001583	missense	6655	exon8			L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11188	protein-coding gene	gene with protein product		601247	"""son of sevenless (Drosophilia) homolog 2"""			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.1016G>A	14.37:g.50641224C>T	ENSP00000216373:p.Arg339His	Somatic		Capture	Illumina HiSeq	Phase_I	49710974	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	37	CCDS9697.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.347167	0.82022	.	.	ENSG00000100485	ENST00000216373	D	0.92348	-3.02	5.6	4.72	0.59763	Dbl homology (DH) domain (5);	0.051123	0.85682	D	0.000000	D	0.94159	0.8126	L	0.60455	1.87	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.61275	0.886;0.886	D	0.94482	0.7694	10	0.72032	D	0.01	.	14.443	0.67330	0.0:0.9292:0.0:0.0707	.	369;339	Q59G32;Q07890	.;SOS2_HUMAN	H	339	ENSP00000216373:R339H	ENSP00000216373:R339H	R	-	2	0	SOS2	49710974	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.403000	0.66338	1.368000	0.46115	0.591000	0.81541	CGT		0.378	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
MAP4K5	11183	broad.mit.edu	37	14	50889858	50889858	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:50889858G>A	ENST00000013125.4	-	31	2752	c.2434C>T	c.(2434-2436)Cgc>Tgc	p.R812C		NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	812	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.R812C(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					CCTAATAAGCGGAAAACTCTT	0.318																																					p.R812C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2434T	14						.						52.0	50.0	51.0					14																	50889858		1810	4063	5873	49959608	SO:0001583	missense	11183	exon31			U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6867	protein-coding gene	gene with protein product	"""germinal center kinase-related"""	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.2434C>T	14.37:g.50889858G>A	ENSP00000013125:p.Arg812Cys	Somatic		Capture	Illumina HiSeq	Phase_I	49959608	NM_006575	Q8IYF6	Missense_Mutation	SNP	ENST00000013125.4	37		.	.	.	.	.	.	.	.	.	.	G	22.5	4.298522	0.81025	.	.	ENSG00000012983	ENST00000013125	T	0.05447	3.44	5.64	5.64	0.86602	Citron-like (3);	0.049620	0.85682	D	0.000000	T	0.31702	0.0805	M	0.85373	2.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.91	T	0.05338	-1.0891	10	0.87932	D	0	.	19.7167	0.96124	0.0:0.0:1.0:0.0	.	812;812	B2R928;Q9Y4K4	.;M4K5_HUMAN	C	812	ENSP00000013125:R812C	ENSP00000013125:R812C	R	-	1	0	MAP4K5	49959608	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.366000	0.79548	2.673000	0.90976	0.650000	0.86243	CGC		0.318	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575	
TRIM9	114088	broad.mit.edu	37	14	51561330	51561330	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:51561330C>T	ENST00000298355.3	-	1	1449	c.328G>A	c.(328-330)Gcc>Acc	p.A110T	TRIM9_ENST00000360392.4_Missense_Mutation_p.A110T|TRIM9_ENST00000338969.5_Missense_Mutation_p.A110T	NM_015163.5	NP_055978.4	Q9C026	TRIM9_HUMAN	tripartite motif containing 9	110					negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of SNARE complex assembly (GO:0035544)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|synaptic vesicle (GO:0008021)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A110T(2)		breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_epithelial(31;0.00418)|Breast(41;0.148)					AAGTGGGTGGCCGGTGGCGGC	0.711																																					p.A110T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G328A	14						.																																			50631080	SO:0001583	missense	114088	exon1			AF220036	CCDS9703.1, CCDS45105.1	14q21.3	2013-02-11	2011-01-25		ENSG00000100505	ENSG00000100505		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16288	protein-coding gene	gene with protein product		606555	"""tripartite motif-containing 9"""			11331580, 11524423	Standard	NM_015163		Approved	SPRING, RNF91	uc001wyx.4	Q9C026	OTTHUMG00000140291	ENST00000298355.3:c.328G>A	14.37:g.51561330C>T	ENSP00000298355:p.Ala110Thr	Somatic		Capture	Illumina HiSeq	Phase_I	50631080	NM_052978	D3DSB7|D3DSB8|Q92557|Q96D24|Q96NI4|Q9C025|Q9C027	Missense_Mutation	SNP	ENST00000298355.3	37	CCDS9703.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.129249	0.37533	.	.	ENSG00000100505	ENST00000298355;ENST00000338969;ENST00000360392	T;T;T	0.29397	1.57;1.57;1.57	5.24	2.33	0.28932	Zinc finger, RING-type (1);	0.443643	0.24375	N	0.039068	T	0.12603	0.0306	N	0.02539	-0.55	0.23981	N	0.996275	B;B;B	0.24368	0.014;0.017;0.102	B;B;B	0.23574	0.009;0.04;0.047	T	0.24905	-1.0147	10	0.13108	T	0.6	.	14.6346	0.68680	0.0:0.4887:0.5113:0.0	.	110;110;110	Q9C026-5;Q9C026-4;Q9C026	.;.;TRIM9_HUMAN	T	110	ENSP00000298355:A110T;ENSP00000342970:A110T;ENSP00000353561:A110T	ENSP00000298355:A110T	A	-	1	0	TRIM9	50631080	0.990000	0.36364	0.996000	0.52242	0.981000	0.71138	1.236000	0.32683	0.184000	0.20083	0.561000	0.74099	GCC		0.711	TRIM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276874.1	NM_015163	
NID2	22795	broad.mit.edu	37	14	52473368	52473368	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:52473368delT	ENST00000216286.5	-	20	3890	c.3891delA	c.(3889-3891)aaafs	p.K1297fs	NID2_ENST00000541773.1_Frame_Shift_Del_p.K1196fs	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	1297					basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)	p.K1297fs*26(1)		NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					TACACTCCAGTTTTTTGGTTC	0.433																																					p.K1297fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3891delA	14						.						194.0	177.0	183.0					14																	52473368		2203	4300	6503	51543118	SO:0001589	frameshift_variant	22795	exon20			AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.3891delA	14.37:g.52473368delT	ENSP00000216286:p.Lys1297fs	Somatic		Capture	Illumina HiSeq	Phase_I	51543118	NM_007361	A8K6I7|B4DU19|O43710	Frame_Shift_Del	DEL	ENST00000216286.5	37	CCDS9706.1																																																																																				0.433	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
MAPK1IP1L	93487	broad.mit.edu	37	14	55529755	55529755	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:55529755A>G	ENST00000395468.4	+	3	615	c.438A>G	c.(436-438)ggA>ggG	p.G146G		NM_144578.3	NP_653179.1	Q8NDC0	MISSL_HUMAN	mitogen-activated protein kinase 1 interacting protein 1-like	146	Pro-rich.							p.G146G(1)		endometrium(2)|large_intestine(1)|lung(3)	6						GTCCATGGGGATCCATGTCTT	0.557																																					p.G146G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A438G	14						.						62.0	50.0	54.0					14																	55529755		2203	4300	6503	54599508	SO:0001819	synonymous_variant	93487	exon3			AK025580	CCDS32085.1	14q22.1	2008-01-30	2008-01-30	2008-01-16		ENSG00000168175			19840	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 32"", ""mitogen activated protein kinase 1 interacting protein 1-like"""	C14orf32		12011110	Standard	NM_144578		Approved		uc001xbq.1	Q8NDC0		ENST00000395468.4:c.438A>G	14.37:g.55529755A>G		Somatic		Capture	Illumina HiSeq	Phase_I	54599508	NM_144578	B2RDD8|Q96BG5	Silent	SNP	ENST00000395468.4	37	CCDS32085.1																																																																																				0.557	MAPK1IP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411302.2	NM_144578	
KIAA0586	9786	broad.mit.edu	37	14	58949326	58949326	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:58949326G>A	ENST00000556134.1	+	22	3269	c.2995G>A	c.(2995-2997)Gct>Act	p.A999T	KIAA0586_ENST00000261244.5_Missense_Mutation_p.A938T|KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000354386.6_Missense_Mutation_p.A1067T|KIAA0586_ENST00000423743.3_Missense_Mutation_p.A970T	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	999					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)		p.A938T(1)		endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CGAAGCTCTTGCTGAGACCAT	0.438																																					p.A938T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2812A	14						.						101.0	100.0	100.0					14																	58949326		1876	4130	6006	58019079	SO:0001583	missense	9786	exon20			AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.2995G>A	14.37:g.58949326G>A	ENSP00000452351:p.Ala999Thr	Somatic		Capture	Illumina HiSeq	Phase_I	58019079	NM_014749	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Missense_Mutation	SNP	ENST00000556134.1	37	CCDS58321.1	.	.	.	.	.	.	.	.	.	.	G	15.80	2.938866	0.52972	.	.	ENSG00000100578	ENST00000354386;ENST00000556134;ENST00000423743;ENST00000261244;ENST00000546216	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	5.9	4.01	0.46588	.	0.449872	0.21847	N	0.068229	T	0.50343	0.1610	L	0.41710	1.295	0.23089	N	0.998313	B;P;D;B;P;B	0.65815	0.275;0.707;0.995;0.319;0.707;0.275	B;B;P;B;B;B	0.61940	0.096;0.22;0.896;0.069;0.22;0.096	T	0.35549	-0.9784	10	0.16896	T	0.51	.	8.5141	0.33235	0.1367:0.0:0.7364:0.1269	.	874;874;1067;938;999;970	F5GWA3;B7Z7W7;E7EWM8;E9PGW8;Q9BVV6;Q6UV20	.;.;.;.;K0586_HUMAN;.	T	1067;999;970;938;874	ENSP00000346359:A1067T;ENSP00000452351:A999T;ENSP00000399427:A970T;ENSP00000261244:A938T	ENSP00000261244:A938T	A	+	1	0	KIAA0586	58019079	1.000000	0.71417	0.996000	0.52242	0.640000	0.38277	1.958000	0.40402	0.762000	0.33152	0.650000	0.86243	GCT		0.438	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749	
DACT1	51339	broad.mit.edu	37	14	59113387	59113387	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:59113387G>A	ENST00000335867.4	+	4	2070	c.2046G>A	c.(2044-2046)tcG>tcA	p.S682S	DACT1_ENST00000541264.2_Silent_p.S401S|DACT1_ENST00000556859.1_Silent_p.S401S|DACT1_ENST00000395153.3_Silent_p.S645S			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	682			S -> L (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)	p.S682S(1)		endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						GGAAGTCCTCGGCCGAGATTT	0.701																																					p.S645S												DACT1,large_intestine,rectum,Substitution - Missense,+1 	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1935A	14						.						12.0	13.0	13.0					14																	59113387		2169	4263	6432	58183140	SO:0001819	synonymous_variant	51339	exon4			AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"""dapper homolog 1, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"""			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.2046G>A	14.37:g.59113387G>A		Somatic		Capture	Illumina HiSeq	Phase_I	58183140	NM_001079520	A8MYJ2|Q86TY0	Silent	SNP	ENST00000335867.4	37	CCDS9736.1																																																																																				0.701	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651	
PPM1A	5494	broad.mit.edu	37	14	60749519	60749519	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:60749519G>A	ENST00000395076.4	+	2	528	c.98G>A	c.(97-99)cGt>cAt	p.R33H	PPM1A_ENST00000325642.3_Missense_Mutation_p.R106H|PPM1A_ENST00000325658.3_Missense_Mutation_p.R33H|PPM1A_ENST00000529574.1_Missense_Mutation_p.R33H	NM_021003.4	NP_066283.1	P35813	PPM1A_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1A	33					cell cycle arrest (GO:0007050)|dephosphorylation (GO:0016311)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|N-terminal protein myristoylation (GO:0006499)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|protein dephosphorylation (GO:0006470)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|voltage-gated calcium channel complex (GO:0005891)	calmodulin-dependent protein phosphatase activity (GO:0033192)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)|R-SMAD binding (GO:0070412)|signal transducer activity (GO:0004871)	p.R33H(1)		cervix(1)|endometrium(1)|large_intestine(8)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.046)		CAAGGCTGGCGTGTTGAAATG	0.488																																					p.R33H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G98A	14						.						411.0	367.0	382.0					14																	60749519		2203	4300	6503	59819272	SO:0001583	missense	5494	exon2			S87759	CCDS9744.1, CCDS9745.1, CCDS45120.1	14q23.1	2013-01-24	2010-03-05		ENSG00000100614	ENSG00000100614	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9275	protein-coding gene	gene with protein product	"""phosphatase 2C alpha"", ""protein phosphatase 2C, alpha isoform"""	606108	"""protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform"""			1311954	Standard	NM_177952		Approved	MGC9201, PP2Calpha, PP2CA	uc001xew.4	P35813	OTTHUMG00000140333	ENST00000395076.4:c.98G>A	14.37:g.60749519G>A	ENSP00000378514:p.Arg33His	Somatic		Capture	Illumina HiSeq	Phase_I	59819272	NM_021003	B5BU11|J3KNM0|O75551	Missense_Mutation	SNP	ENST00000395076.4	37	CCDS9744.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.913490	0.92178	.	.	ENSG00000100614	ENST00000325642;ENST00000529574;ENST00000395076;ENST00000325658;ENST00000528241;ENST00000525399;ENST00000531937	T;T;T;T;T;T;T	0.17370	2.28;2.28;2.28;2.28;2.28;2.28;2.28	5.75	5.75	0.90469	Protein phosphatase 2C-like (4);	0.000000	0.85682	D	0.000000	T	0.61085	0.2319	H	0.97682	4.055	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	0.75628	-0.3252	10	0.87932	D	0	-3.536	19.9233	0.97095	0.0:0.0:1.0:0.0	.	33;33;33	P35813;P35813-2;B2R8E4	PPM1A_HUMAN;.;.	H	106;33;33;33;33;33;33	ENSP00000327255:R106H;ENSP00000432966:R33H;ENSP00000378514:R33H;ENSP00000314850:R33H;ENSP00000431453:R33H;ENSP00000435398:R33H;ENSP00000435575:R33H	ENSP00000327255:R106H	R	+	2	0	PPM1A	59819272	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.869000	0.99810	2.704000	0.92352	0.591000	0.81541	CGT		0.488	PPM1A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276949.2	NM_021003	
SIX4	51804	broad.mit.edu	37	14	61180203	61180203	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:61180203A>G	ENST00000216513.4	-	3	2327	c.2268T>C	c.(2266-2268)tgT>tgC	p.C756C		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	756					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.C756C(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)		CCAGGTCTTCACAGACAGTAT	0.403																																					p.C756C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2268C	14						.						117.0	109.0	112.0					14																	61180203		2203	4300	6503	60249956	SO:0001819	synonymous_variant	51804	exon3			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.2268T>C	14.37:g.61180203A>G		Somatic		Capture	Illumina HiSeq	Phase_I	60249956	NM_017420	Q4QQH5|Q4V764	Silent	SNP	ENST00000216513.4	37	CCDS9749.2																																																																																				0.403	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2		
SIX4	51804	broad.mit.edu	37	14	61180612	61180612	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:61180612A>G	ENST00000216513.4	-	3	1918	c.1859T>C	c.(1858-1860)tTt>tCt	p.F620S		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	620					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.F620S(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)		ACTGAGAGAAAAATTGTGAGT	0.468																																					p.F620S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1859C	14						.						80.0	74.0	76.0					14																	61180612		2203	4300	6503	60250365	SO:0001583	missense	51804	exon3			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.1859T>C	14.37:g.61180612A>G	ENSP00000216513:p.Phe620Ser	Somatic		Capture	Illumina HiSeq	Phase_I	60250365	NM_017420	Q4QQH5|Q4V764	Missense_Mutation	SNP	ENST00000216513.4	37	CCDS9749.2	.	.	.	.	.	.	.	.	.	.	A	17.92	3.506381	0.64410	.	.	ENSG00000100625	ENST00000216513;ENST00000554079	D;T	0.94376	-3.41;0.23	5.71	5.71	0.89125	.	0.189181	0.47852	D	0.000201	D	0.92951	0.7757	N	0.19112	0.55	0.80722	D	1	D	0.69078	0.997	P	0.60789	0.879	D	0.94353	0.7581	10	0.87932	D	0	.	15.988	0.80176	1.0:0.0:0.0:0.0	.	620	Q9UIU6	SIX4_HUMAN	S	620;293	ENSP00000216513:F620S;ENSP00000451537:F293S	ENSP00000216513:F620S	F	-	2	0	SIX4	60250365	1.000000	0.71417	0.993000	0.49108	0.882000	0.50991	6.414000	0.73318	2.188000	0.69820	0.533000	0.62120	TTT		0.468	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2		
SNAPC1	6617	broad.mit.edu	37	14	62261672	62261672	+	Missense_Mutation	SNP	A	A	T	rs368193722		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:62261672A>T	ENST00000216294.4	+	10	1182	c.1078A>T	c.(1078-1080)Act>Tct	p.T360S		NM_003082.3	NP_003073.1	Q16533	SNPC1_HUMAN	small nuclear RNA activating complex, polypeptide 1, 43kDa	360					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)	p.T360S(1)		endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)	13				OV - Ovarian serous cystadenocarcinoma(108;0.0639)|BRCA - Breast invasive adenocarcinoma(234;0.186)		TTTAGAGTTCACTGCATCCAA	0.294																																					p.T360S	NSCLC(27;223 907 37180 39193 46568)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1078T	14						.						97.0	114.0	109.0					14																	62261672		2203	4299	6502	61331425	SO:0001583	missense	6617	exon10			Z47542	CCDS9755.1	14q22	2008-08-11	2002-08-29		ENSG00000023608	ENSG00000023608			11134	protein-coding gene	gene with protein product		600591	"""small nuclear RNA activating complex, polypeptide 1, 43kD"""			9644240	Standard	NM_003082		Approved	SNAP43, PTFgamma	uc001xft.3	Q16533	OTTHUMG00000140343	ENST00000216294.4:c.1078A>T	14.37:g.62261672A>T	ENSP00000216294:p.Thr360Ser	Somatic		Capture	Illumina HiSeq	Phase_I	61331425	NM_003082		Missense_Mutation	SNP	ENST00000216294.4	37	CCDS9755.1	.	.	.	.	.	.	.	.	.	.	A	6.193	0.403695	0.11754	.	.	ENSG00000023608	ENST00000216294	.	.	.	4.15	0.0749	0.14397	.	0.552786	0.16438	N	0.214415	T	0.30293	0.0760	L	0.51422	1.61	0.19775	N	0.999954	B	0.31318	0.319	B	0.20955	0.032	T	0.11867	-1.0570	9	0.26408	T	0.33	-2.4887	10.303	0.43663	0.4322:0.5678:0.0:0.0	.	360	Q16533	SNPC1_HUMAN	S	360	.	ENSP00000216294:T360S	T	+	1	0	SNAPC1	61331425	0.018000	0.18449	0.315000	0.25238	0.187000	0.23431	0.054000	0.14205	0.005000	0.14708	0.460000	0.39030	ACT		0.294	SNAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276976.2	NM_003082	
KCNH5	27133	broad.mit.edu	37	14	63174810	63174810	+	Missense_Mutation	SNP	G	G	A	rs376570579		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:63174810G>A	ENST00000322893.7	-	11	2651	c.2383C>T	c.(2383-2385)Ctc>Ttc	p.L795F	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	795					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.L795F(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)		TTGACTTTGAGACATTTTTGG	0.468																																					p.L795F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2383T	14						.						108.0	108.0	108.0					14																	63174810		2203	4300	6503	62244563	SO:0001583	missense	27133	exon11			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.2383C>T	14.37:g.63174810G>A	ENSP00000321427:p.Leu795Phe	Somatic		Capture	Illumina HiSeq	Phase_I	62244563	NM_139318	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.216796	0.39201	.	.	ENSG00000140015	ENST00000322893	D	0.99051	-5.37	5.83	5.83	0.93111	.	0.076132	0.56097	D	0.000038	D	0.97586	0.9209	L	0.50333	1.59	0.80722	D	1	P	0.47350	0.894	B	0.38562	0.276	D	0.97346	0.9960	10	0.33141	T	0.24	.	20.1374	0.98035	0.0:0.0:1.0:0.0	.	795	Q8NCM2	KCNH5_HUMAN	F	795	ENSP00000321427:L795F	ENSP00000321427:L795F	L	-	1	0	KCNH5	62244563	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	4.517000	0.60503	2.763000	0.94921	0.563000	0.77884	CTC		0.468	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
SYNE2	23224	broad.mit.edu	37	14	64522760	64522760	+	Silent	SNP	C	C	A	rs373355920		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:64522760C>A	ENST00000344113.4	+	49	10055	c.9843C>A	c.(9841-9843)ccC>ccA	p.P3281P	SYNE2_ENST00000358025.3_Silent_p.P3281P|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Silent_p.P3314P	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3281					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.P3281P(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TCATTATACCCTACAGAGTAG	0.433																																					p.P3281P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9843A	14						.	C	,	2,3882		0,2,1940	78.0	72.0	74.0		9843,9843	-0.8	0.0	14		74	0,8272		0,0,4136	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	0,2,6076	AA,AC,CC		0.0,0.0515,0.0165	,	3281/6886,3281/6908	64522760	2,12154	1942	4136	6078	63592513	SO:0001819	synonymous_variant	23224	exon49			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.9843C>A	14.37:g.64522760C>A		Somatic		Capture	Illumina HiSeq	Phase_I	63592513	NM_015180	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																				0.433	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
SYNE2	23224	broad.mit.edu	37	14	64537473	64537473	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:64537473A>G	ENST00000344113.4	+	52	10754	c.10542A>G	c.(10540-10542)ttA>ttG	p.L3514L	SYNE2_ENST00000358025.3_Silent_p.L3514L|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000555002.1_Silent_p.L148L|SYNE2_ENST00000554584.1_Silent_p.L3547L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3514					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.L3514L(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TAGACTGTTTATGCCAATATG	0.443																																					p.L3514L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A10542G	14						.						82.0	78.0	79.0					14																	64537473		1877	4116	5993	63607226	SO:0001819	synonymous_variant	23224	exon52			AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.10542A>G	14.37:g.64537473A>G		Somatic		Capture	Illumina HiSeq	Phase_I	63607226	NM_015180	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																				0.443	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
MTHFD1	4522	broad.mit.edu	37	14	64908171	64908171	+	Splice_Site	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:64908171G>T	ENST00000545908.1	+	19	2281	c.2052G>T	c.(2050-2052)gaG>gaT	p.E684D	CTD-2555O16.2_ENST00000556640.1_RNA|CTD-2555O16.4_ENST00000609125.1_RNA|MTHFD1_ENST00000216605.8_Splice_Site_p.E628D			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	628	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.E628D(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)	AGACACTGGAGGTGAGCAGAG	0.502																																					p.E628D	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1884T	14						.						167.0	132.0	144.0					14																	64908171		2203	4300	6503	63977924	SO:0001630	splice_region_variant	4522	exon19			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.2052+1G>T	14.37:g.64908171G>T		Somatic		Capture	Illumina HiSeq	Phase_I	63977924	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	37		.	.	.	.	.	.	.	.	.	.	G	35	5.481463	0.96307	.	.	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605	T;T;T	0.29655	1.56;1.56;1.56	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.69993	0.3173	H	0.95365	3.66	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.79108	0.992;0.977	T	0.78638	-0.2126	10	0.87932	D	0	-31.965	20.2699	0.98469	0.0:0.0:1.0:0.0	.	684;628	F5H2F4;G3V2B8	.;.	D	684;628;684	ENSP00000438588:E684D;ENSP00000450560:E628D;ENSP00000216605:E684D	ENSP00000216605:E628D	E	+	3	2	MTHFD1	63977924	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.662000	0.83803	2.854000	0.98071	0.655000	0.94253	GAG		0.502	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1		Missense_Mutation
HSPA2	3306	broad.mit.edu	37	14	65008470	65008470	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:65008470G>A	ENST00000394709.1	+	2	979	c.903G>A	c.(901-903)acG>acA	p.T301T	RP11-973N13.4_ENST00000554918.1_RNA|HSPA2_ENST00000247207.6_Silent_p.T301T			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	301					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)	p.T301T(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		CGTCCATCACGCGCGCCCGCT	0.667																																					p.T301T	Pancreas(136;1211 1835 24894 31984 38227)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G903A	14						.						20.0	21.0	20.0					14																	65008470		2202	4300	6502	64078223	SO:0001819	synonymous_variant	3306	exon1			L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"""Heat shock proteins / HSP70"""	5235	protein-coding gene	gene with protein product		140560	"""heat shock 70kD protein 2"""				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311	ENST00000394709.1:c.903G>A	14.37:g.65008470G>A		Somatic		Capture	Illumina HiSeq	Phase_I	64078223	NM_021979	Q15508|Q53XM3|Q9UE78	Silent	SNP	ENST00000394709.1	37	CCDS9766.1																																																																																				0.667	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1		
SPTB	6710	broad.mit.edu	37	14	65237692	65237692	+	Silent	SNP	C	C	T	rs199823808		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:65237692C>T	ENST00000389721.5	-	26	5741	c.5709G>A	c.(5707-5709)gcG>gcA	p.A1903A	SPTB_ENST00000389720.3_Silent_p.A1903A|SPTB_ENST00000542895.1_Silent_p.A1903A|SPTB_ENST00000389722.3_Silent_p.A1903A|SPTB_ENST00000556626.1_Silent_p.A1903A	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1903					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)	p.A1903A(1)		breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GGAATTTATCCGCCGTGTCCA	0.642													C|||	1	0.000199681	0.0	0.0	5008	,	,		20824	0.0		0.001	False		,,,				2504	0.0				p.A1903A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G5709A	14						.						56.0	58.0	57.0					14																	65237692		2203	4300	6503	64307445	SO:0001819	synonymous_variant	6710	exon26				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.5709G>A	14.37:g.65237692C>T		Somatic		Capture	Illumina HiSeq	Phase_I	64307445	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																				0.642	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
SPTB	6710	broad.mit.edu	37	14	65271701	65271701	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:65271701G>A	ENST00000389721.5	-	2	288	c.256C>T	c.(256-258)Cgc>Tgc	p.R86C	SPTB_ENST00000389720.3_Missense_Mutation_p.R86C|SPTB_ENST00000542895.1_Missense_Mutation_p.R86C|SPTB_ENST00000389722.3_Missense_Mutation_p.R86C|SPTB_ENST00000556626.1_Missense_Mutation_p.R86C	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	86	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)	p.R86C(2)		breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		ATGAGCATGCGCCCATCCCGC	0.582																																					p.R86C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C256T	14						.						89.0	86.0	87.0					14																	65271701		2203	4300	6503	64341454	SO:0001583	missense	6710	exon2				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.256C>T	14.37:g.65271701G>A	ENSP00000374371:p.Arg86Cys	Somatic		Capture	Illumina HiSeq	Phase_I	64341454	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	G	18.73	3.686497	0.68157	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.59502	0.26;0.26;0.26;0.26;0.26	4.67	1.58	0.23477	Calponin homology domain (5);	0.063724	0.64402	D	0.000018	T	0.66416	0.2787	L	0.45352	1.415	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.985	T	0.68911	-0.5284	10	0.87932	D	0	.	12.8185	0.57679	0.0:0.0:0.4898:0.5102	.	86;90	P11277;Q59FP5	SPTB1_HUMAN;.	C	90;86;86;86;86;86	ENSP00000374372:R86C;ENSP00000451752:R86C;ENSP00000374371:R86C;ENSP00000443882:R86C;ENSP00000374370:R86C	ENSP00000374370:R86C	R	-	1	0	SPTB	64341454	0.997000	0.39634	0.865000	0.33974	0.990000	0.78478	2.391000	0.44424	0.682000	0.31407	0.650000	0.86243	CGC		0.582	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
GPHN	10243	broad.mit.edu	37	14	67578599	67578599	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:67578599C>T	ENST00000315266.5	+	14	2457	c.1336C>T	c.(1336-1338)Cga>Tga	p.R446*	GPHN_ENST00000478722.1_Nonsense_Mutation_p.R479*|GPHN_ENST00000544752.2_3'UTR|GPHN_ENST00000543237.1_Nonsense_Mutation_p.R492*|GPHN_ENST00000305960.9_Nonsense_Mutation_p.R415*	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	446	MPT adenylyltransferase.				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.R479*(3)		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)		ACTTGAAGTGCGAATTCTGGT	0.383			T	MLL	AL																																p.R446X			Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	.	3	Substitution - Nonsense(3)	large_intestine(2)|endometrium(1)	c.C1336T	14						.						80.0	84.0	83.0					14																	67578599		2203	4300	6503	66648352	SO:0001587	stop_gained	10243	exon14			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.1336C>T	14.37:g.67578599C>T	ENSP00000312771:p.Arg446*	Somatic		Capture	Illumina HiSeq	Phase_I	66648352	NM_001024218	Q9H4E9|Q9P2G2	Nonsense_Mutation	SNP	ENST00000315266.5	37	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	C	39	7.860533	0.98531	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000543237;ENST00000305960	.	.	.	5.07	4.17	0.49024	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.3156	14.435	0.67274	0.1489:0.8511:0.0:0.0	.	.	.	.	X	446;479;492;415	.	ENSP00000303019:R415X	R	+	1	2	GPHN	66648352	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	6.070000	0.71220	1.089000	0.41292	0.655000	0.94253	CGA		0.383	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806	
ZFYVE26	23503	broad.mit.edu	37	14	68244376	68244376	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:68244376G>A	ENST00000347230.4	-	25	5012	c.4874C>T	c.(4873-4875)gCc>gTc	p.A1625V	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.A1625V	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1625					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)	p.A1625V(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		GTGAGAAGTGGCCAAGCTAGT	0.537																																					p.A1625V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4874T	14						.						238.0	203.0	215.0					14																	68244376		2203	4300	6503	67314129	SO:0001583	missense	23503	exon25			AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"""Zinc fingers, FYVE domain containing"""	20761	protein-coding gene	gene with protein product	"""spastizin"", ""FYVE-CENT"""	612012	"""spastic paraplegia 15 (complicated, autosomal recessive)"""	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.4874C>T	14.37:g.68244376G>A	ENSP00000251119:p.Ala1625Val	Somatic		Capture	Illumina HiSeq	Phase_I	67314129	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.254063	0.80135	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.30448	1.68;1.53	5.5	5.5	0.81552	.	0.187536	0.45361	D	0.000361	T	0.38506	0.1043	M	0.69823	2.125	0.48511	D	0.99966	P;P	0.42692	0.787;0.732	B;B	0.40199	0.23;0.322	T	0.39035	-0.9633	10	0.62326	D	0.03	-14.434	17.5731	0.87940	0.0:0.0:1.0:0.0	.	1625;1625	G3V2D8;Q68DK2	.;ZFY26_HUMAN	V	1625;1604;1625	ENSP00000251119:A1625V;ENSP00000450603:A1625V	ENSP00000251119:A1625V	A	-	2	0	ZFYVE26	67314129	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.438000	0.66550	2.587000	0.87381	0.563000	0.77884	GCC		0.537	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
ACTN1	87	broad.mit.edu	37	14	69341707	69341707	+	Missense_Mutation	SNP	G	G	A	rs148344567		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:69341707G>A	ENST00000193403.6	-	21	2931	c.2548C>T	c.(2548-2550)Cgc>Tgc	p.R850C	ACTN1_ENST00000538545.2_Missense_Mutation_p.R888C|ACTN1_ENST00000376839.3_Missense_Mutation_p.R780C|ACTN1_ENST00000438964.2_Missense_Mutation_p.R845C|ACTN1_ENST00000394419.4_Missense_Mutation_p.R872C	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	850					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.R850C(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)		GGCAGCTCGCGGCGCAGCTCG	0.652																																					p.R845C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2533T	14						.	G	CYS/ARG,CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	34.0	35.0	35.0		2548,2614,2533	3.8	0.9	14	dbSNP_134	35	2,8596	2.2+/-6.3	0,2,4297	no	missense,missense,missense	ACTN1	NM_001102.3,NM_001130004.1,NM_001130005.1	180,180,180	0,3,6499	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging,probably-damaging,probably-damaging	850/893,872/915,845/888	69341707	3,13001	2203	4299	6502	68411460	SO:0001583	missense	87	exon21			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.2548C>T	14.37:g.69341707G>A	ENSP00000193403:p.Arg850Cys	Somatic		Capture	Illumina HiSeq	Phase_I	68411460	NM_001130005	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.623869	0.46840	2.27E-4	2.33E-4	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	4.68	3.78	0.43462	EF-hand, Ca insensitive (1);EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.67933	0.2946	M	0.86864	2.845	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.76071	0.96;0.987;0.96;0.985	T	0.75836	-0.3177	10	0.87932	D	0	.	14.5736	0.68229	0.0:0.0:0.8528:0.1472	.	845;872;850;492	P12814-2;Q1HE25;P12814;B4DFY0	.;.;ACTN1_HUMAN;.	C	850;872;845;780;888	ENSP00000193403:R850C;ENSP00000377941:R872C;ENSP00000414272:R845C;ENSP00000366035:R780C;ENSP00000439828:R888C	ENSP00000193403:R850C	R	-	1	0	ACTN1	68411460	1.000000	0.71417	0.878000	0.34440	0.069000	0.16628	3.163000	0.50763	1.311000	0.45024	0.650000	0.86243	CGC		0.652	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102	
GALNT16	57452	broad.mit.edu	37	14	69814645	69814645	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:69814645G>A	ENST00000337827.4	+	14	1792	c.1465G>A	c.(1465-1467)Gcc>Acc	p.A489T	GALNT16_ENST00000448469.3_Missense_Mutation_p.A489T|GALNT16_ENST00000553669.1_Missense_Mutation_p.A489T	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	Q8N428	GLT16_HUMAN	polypeptide N-acetylgalactosaminyltransferase 16	489	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.A489T(1)									GTGCCTGGCTGCCACCTCCAC	0.572																																					p.A489T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1465A	14						.						148.0	116.0	127.0					14																	69814645		2203	4300	6503	68884398	SO:0001583	missense	57452	exon14			AB032956	CCDS32107.1	14q24.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000100626	ENSG00000100626	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	23233	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 16"""	615132	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16"""	GALNTL1		10574461, 22186971	Standard	NM_020692		Approved	KIAA1130, GalNAc-T16	uc010aqu.2	Q8N428	OTTHUMG00000171231	ENST00000337827.4:c.1465G>A	14.37:g.69814645G>A	ENSP00000336729:p.Ala489Thr	Somatic		Capture	Illumina HiSeq	Phase_I	68884398	NM_020692	Q4KMG3|Q58A55|Q9ULT9	Missense_Mutation	SNP	ENST00000337827.4	37	CCDS32107.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.411759	0.62399	.	.	ENSG00000100626	ENST00000337827;ENST00000536652;ENST00000448469;ENST00000553669	T;T;T	0.28454	1.61;1.61;1.61	5.76	2.53	0.30540	Ricin B-related lectin (1);Ricin B lectin (3);	0.185583	0.56097	N	0.000028	T	0.25269	0.0614	M	0.64997	1.995	0.29715	N	0.839136	B;P	0.47484	0.017;0.896	B;B	0.40825	0.025;0.341	T	0.34800	-0.9814	10	0.72032	D	0.01	.	2.3779	0.04346	0.2879:0.0:0.4725:0.2397	.	489;489	Q8N428;Q58A55	GLTL1_HUMAN;.	T	489;115;489;489	ENSP00000336729:A489T;ENSP00000402970:A489T;ENSP00000451200:A489T	ENSP00000336729:A489T	A	+	1	0	GALNTL1	68884398	0.993000	0.37304	0.985000	0.45067	0.992000	0.81027	2.198000	0.42705	0.770000	0.33336	0.655000	0.94253	GCC		0.572	GALNT16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412434.1	NM_001168368	
SLC8A3	6547	broad.mit.edu	37	14	70633480	70633480	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:70633480G>A	ENST00000381269.2	-	2	2413	c.1660C>T	c.(1660-1662)Cgg>Tgg	p.R554W	SLC8A3_ENST00000356921.2_Missense_Mutation_p.R554W|SLC8A3_ENST00000534137.1_Missense_Mutation_p.R554W|SLC8A3_ENST00000357887.3_Missense_Mutation_p.R554W|SLC8A3_ENST00000528359.1_Missense_Mutation_p.R554W	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	554	Calx-beta 2.				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.R554W(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)		CCTGATGTCCGCAGAACCTTG	0.488																																					p.R554W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1660T	14						.						92.0	90.0	91.0					14																	70633480		2203	4300	6503	69703233	SO:0001583	missense	6547	exon2			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.1660C>T	14.37:g.70633480G>A	ENSP00000370669:p.Arg554Trp	Somatic		Capture	Illumina HiSeq	Phase_I	69703233	NM_033262	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Missense_Mutation	SNP	ENST00000381269.2	37	CCDS35498.1	.	.	.	.	.	.	.	.	.	.	G	14.03	2.415223	0.42817	.	.	ENSG00000100678	ENST00000356921;ENST00000381269;ENST00000357887;ENST00000534137;ENST00000528359	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94	5.69	3.79	0.43588	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.77928	0.4204	H	0.98883	4.36	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.998;0.999	D	0.85695	0.1309	10	0.87932	D	0	.	13.8157	0.63290	0.0:0.0:0.4088:0.5912	.	554;554;554;554	P57103-2;P57103;Q96QG2;Q96QG1	.;NAC3_HUMAN;.;.	W	554	ENSP00000349392:R554W;ENSP00000370669:R554W;ENSP00000350560:R554W;ENSP00000436688:R554W;ENSP00000433531:R554W	ENSP00000349392:R554W	R	-	1	2	SLC8A3	69703233	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.178000	0.42519	0.677000	0.31305	0.650000	0.86243	CGG		0.488	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1		
PCNX	22990	broad.mit.edu	37	14	71575419	71575419	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:71575419C>T	ENST00000304743.2	+	34	6846	c.6400C>T	c.(6400-6402)Cgg>Tgg	p.R2134W	PCNX_ENST00000439984.3_Missense_Mutation_p.R2023W|PCNX_ENST00000556272.1_3'UTR|PCNX_ENST00000238570.5_Missense_Mutation_p.R2062W	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	2134	Ser-rich.					integral component of membrane (GO:0016021)		p.R2134W(1)		NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		CTATAGCAGCCGGCATTCATC	0.567																																					p.R2134W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6400T	14						.						65.0	62.0	63.0					14																	71575419		2203	4300	6503	70645172	SO:0001583	missense	22990	exon34			AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.6400C>T	14.37:g.71575419C>T	ENSP00000304192:p.Arg2134Trp	Somatic		Capture	Illumina HiSeq	Phase_I	70645172	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.001808	0.74932	.	.	ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984	T;T;T	0.11495	3.19;3.23;2.77	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.35335	0.0928	M	0.66939	2.045	0.49687	D	0.999818	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.993;0.993	T	0.00857	-1.1538	10	0.66056	D	0.02	.	20.3593	0.98849	0.0:1.0:0.0:0.0	.	2062;2023;2134	Q96RV3-3;B2RTR6;Q96RV3	.;.;PCX1_HUMAN	W	2134;2062;2023	ENSP00000304192:R2134W;ENSP00000238570:R2062W;ENSP00000396617:R2023W	ENSP00000238570:R2062W	R	+	1	2	PCNX	70645172	1.000000	0.71417	1.000000	0.80357	0.259000	0.26198	5.634000	0.67833	2.822000	0.97130	0.557000	0.71058	CGG		0.567	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
DPF3	8110	broad.mit.edu	37	14	73140967	73140967	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:73140967G>A	ENST00000556509.1	-	8	851	c.852C>T	c.(850-852)tgC>tgT	p.C284C	DPF3_ENST00000541685.1_Silent_p.C284C|DPF3_ENST00000546183.1_Silent_p.C294C|DPF3_ENST00000557704.1_5'UTR	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	284					chromatin modification (GO:0016568)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)	p.C284C(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)	22				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		CACAGTCTGCGCAGGACACCA	0.572																																					p.C284C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C852T	14						.						50.0	57.0	55.0					14																	73140967		2111	4243	6354	72210720	SO:0001819	synonymous_variant	8110	exon8			U43919	CCDS45133.1, CCDS61495.1, CCDS61496.1, CCDS61497.1	14q24.2	2014-05-13			ENSG00000205683	ENSG00000205683		"""Zinc fingers, PHD-type"""	17427	protein-coding gene	gene with protein product		601672				11845289, 8812431	Standard	NM_012074		Approved	cer-d4, Cerd4, FLJ14079, BAF45c	uc010ari.1	Q92784		ENST00000556509.1:c.852C>T	14.37:g.73140967G>A		Somatic		Capture	Illumina HiSeq	Phase_I	72210720	NM_012074	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Silent	SNP	ENST00000556509.1	37																																																																																					0.572	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2		
ZFYVE1	53349	broad.mit.edu	37	14	73441529	73441529	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:73441529G>A	ENST00000556143.1	-	10	2665	c.1945C>T	c.(1945-1947)Cgg>Tgg	p.R649W	ZFYVE1_ENST00000553891.1_Missense_Mutation_p.R649W|ZFYVE1_ENST00000394207.2_Missense_Mutation_p.R234W|ZFYVE1_ENST00000318876.5_Missense_Mutation_p.R635W|ZFYVE1_ENST00000554145.1_5'Flank|ZFYVE1_ENST00000555072.1_Missense_Mutation_p.R234W	NM_001281735.1|NM_021260.2	NP_001268664.1|NP_067083.1	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1	649					negative regulation of phosphatase activity (GO:0010923)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|ER-mitochondrion membrane contact site (GO:0044233)|Golgi stack (GO:0005795)|perinuclear region of cytoplasm (GO:0048471)|pre-autophagosomal structure (GO:0000407)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|zinc ion binding (GO:0008270)	p.R649W(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(17)|ovary(1)|prostate(2)|skin(1)	35		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		TCACAGACCCGCACTGGCGCA	0.627																																					p.R234W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C700T	14						.						88.0	85.0	86.0					14																	73441529		2203	4300	6503	72511282	SO:0001583	missense	53349	exon7			AF251025	CCDS9811.1, CCDS41969.1, CCDS61498.1	14q24.2	2014-06-13	2003-02-28	2003-03-07		ENSG00000165861		"""Zinc fingers, FYVE domain containing"""	13180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 172"""	605471	"""zinc finger protein, subfamily 2A (FYVE domain containing), 1"""	ZNFN2A1		11024279, 11256955	Standard	NM_021260		Approved	DFCP1, KIAA1589, TAFF1, PPP1R172	uc001xnm.3	Q9HBF4		ENST00000556143.1:c.1945C>T	14.37:g.73441529G>A	ENSP00000450742:p.Arg649Trp	Somatic		Capture	Illumina HiSeq	Phase_I	72511282	NM_178441	J3KNL9|Q8WYX7|Q96K57|Q9BXP9|Q9HCI3	Missense_Mutation	SNP	ENST00000556143.1	37	CCDS9811.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.768501	0.90020	.	.	ENSG00000165861	ENST00000553891;ENST00000318876;ENST00000556143;ENST00000394207;ENST00000555072	D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53	6.06	4.21	0.49690	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	0.110994	0.64402	D	0.000011	D	0.94801	0.8321	H	0.99777	4.77	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.96781	0.9575	10	0.87932	D	0	-22.2587	15.6634	0.77206	0.0:0.0:0.749:0.251	.	649;649	G3V5N8;Q9HBF4	.;ZFYV1_HUMAN	W	649;635;649;234;234	ENSP00000452442:R649W;ENSP00000326921:R635W;ENSP00000450742:R649W;ENSP00000377757:R234W;ENSP00000452232:R234W	ENSP00000326921:R649W	R	-	1	2	ZFYVE1	72511282	1.000000	0.71417	0.995000	0.50966	0.967000	0.64934	1.588000	0.36633	0.863000	0.35553	0.650000	0.86243	CGG		0.627	ZFYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413172.1	NM_021260	
ZFYVE1	53349	broad.mit.edu	37	14	73460009	73460009	+	Missense_Mutation	SNP	G	G	T	rs142964507		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:73460009G>T	ENST00000556143.1	-	4	1765	c.1045C>A	c.(1045-1047)Cgt>Agt	p.R349S	ZFYVE1_ENST00000553891.1_Missense_Mutation_p.R349S|ZFYVE1_ENST00000318876.5_Missense_Mutation_p.R349S	NM_001281735.1|NM_021260.2	NP_001268664.1|NP_067083.1	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1	349					negative regulation of phosphatase activity (GO:0010923)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|ER-mitochondrion membrane contact site (GO:0044233)|Golgi stack (GO:0005795)|perinuclear region of cytoplasm (GO:0048471)|pre-autophagosomal structure (GO:0000407)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|zinc ion binding (GO:0008270)	p.R349S(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(17)|ovary(1)|prostate(2)|skin(1)	35		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		TCAGGGAAACGGCCCAGCTTC	0.527																																					p.R349S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1045A	14						.						77.0	76.0	76.0					14																	73460009		2203	4300	6503	72529762	SO:0001583	missense	53349	exon4			AF251025	CCDS9811.1, CCDS41969.1, CCDS61498.1	14q24.2	2014-06-13	2003-02-28	2003-03-07		ENSG00000165861		"""Zinc fingers, FYVE domain containing"""	13180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 172"""	605471	"""zinc finger protein, subfamily 2A (FYVE domain containing), 1"""	ZNFN2A1		11024279, 11256955	Standard	NM_021260		Approved	DFCP1, KIAA1589, TAFF1, PPP1R172	uc001xnm.3	Q9HBF4		ENST00000556143.1:c.1045C>A	14.37:g.73460009G>T	ENSP00000450742:p.Arg349Ser	Somatic		Capture	Illumina HiSeq	Phase_I	72529762	NM_021260	J3KNL9|Q8WYX7|Q96K57|Q9BXP9|Q9HCI3	Missense_Mutation	SNP	ENST00000556143.1	37	CCDS9811.1	.	.	.	.	.	.	.	.	.	.	G	12.35	1.912819	0.33721	.	.	ENSG00000165861	ENST00000553891;ENST00000318876;ENST00000556143	T;T;T	0.63744	-0.06;-0.06;-0.05	5.47	4.58	0.56647	.	0.132210	0.49916	D	0.000137	T	0.47303	0.1438	L	0.47716	1.5	0.80722	D	1	B;B	0.33777	0.425;0.094	B;B	0.28011	0.085;0.018	T	0.38693	-0.9649	10	0.22706	T	0.39	-24.2404	6.326	0.21244	0.1627:0.0:0.6885:0.1488	.	349;349	G3V5N8;Q9HBF4	.;ZFYV1_HUMAN	S	349	ENSP00000452442:R349S;ENSP00000326921:R349S;ENSP00000450742:R349S	ENSP00000326921:R349S	R	-	1	0	ZFYVE1	72529762	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.418000	0.59828	1.324000	0.45282	0.555000	0.69702	CGT		0.527	ZFYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413172.1	NM_021260	
ZFYVE1	53349	broad.mit.edu	37	14	73464734	73464734	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:73464734G>A	ENST00000556143.1	-	3	1493	c.773C>T	c.(772-774)gCc>gTc	p.A258V	ZFYVE1_ENST00000553891.1_Missense_Mutation_p.A258V|ZFYVE1_ENST00000318876.5_Missense_Mutation_p.A258V	NM_001281735.1|NM_021260.2	NP_001268664.1|NP_067083.1	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1	258					negative regulation of phosphatase activity (GO:0010923)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|ER-mitochondrion membrane contact site (GO:0044233)|Golgi stack (GO:0005795)|perinuclear region of cytoplasm (GO:0048471)|pre-autophagosomal structure (GO:0000407)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|zinc ion binding (GO:0008270)	p.A258V(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(17)|ovary(1)|prostate(2)|skin(1)	35		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		GTCTGAGATGGCCAGGACCTT	0.522																																					p.A258V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C773T	14						.						133.0	111.0	119.0					14																	73464734		2203	4300	6503	72534487	SO:0001583	missense	53349	exon3			AF251025	CCDS9811.1, CCDS41969.1, CCDS61498.1	14q24.2	2014-06-13	2003-02-28	2003-03-07		ENSG00000165861		"""Zinc fingers, FYVE domain containing"""	13180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 172"""	605471	"""zinc finger protein, subfamily 2A (FYVE domain containing), 1"""	ZNFN2A1		11024279, 11256955	Standard	NM_021260		Approved	DFCP1, KIAA1589, TAFF1, PPP1R172	uc001xnm.3	Q9HBF4		ENST00000556143.1:c.773C>T	14.37:g.73464734G>A	ENSP00000450742:p.Ala258Val	Somatic		Capture	Illumina HiSeq	Phase_I	72534487	NM_021260	J3KNL9|Q8WYX7|Q96K57|Q9BXP9|Q9HCI3	Missense_Mutation	SNP	ENST00000556143.1	37	CCDS9811.1	.	.	.	.	.	.	.	.	.	.	G	35	5.582343	0.96578	.	.	ENSG00000165861	ENST00000553891;ENST00000318876;ENST00000556143	T;T;T	0.62232	0.04;0.04;0.04	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.82706	0.5095	M	0.86268	2.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.84414	0.0567	10	0.87932	D	0	-23.5545	20.089	0.97809	0.0:0.0:1.0:0.0	.	258;258	G3V5N8;Q9HBF4	.;ZFYV1_HUMAN	V	258	ENSP00000452442:A258V;ENSP00000326921:A258V;ENSP00000450742:A258V	ENSP00000326921:A258V	A	-	2	0	ZFYVE1	72534487	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.869000	0.99810	2.765000	0.95021	0.591000	0.81541	GCC		0.522	ZFYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413172.1	NM_021260	
PAPLN	89932	broad.mit.edu	37	14	73733456	73733456	+	Silent	SNP	C	C	T	rs147741444		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:73733456C>T	ENST00000554301.1	+	24	3580	c.3417C>T	c.(3415-3417)ccC>ccT	p.P1139P	PAPLN_ENST00000340738.5_Silent_p.P1112P|PAPLN_ENST00000555445.1_Silent_p.P1123P|PAPLN_ENST00000381166.3_Intron|PAPLN_ENST00000427855.1_Silent_p.P1139P			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	1139	Ig-like C2-type 3.					basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)	p.P1112P(1)		NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		CAGGACTGCCCCCTACTGTGA	0.542																																					p.P1112P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3336T	14						.	G		1,4405		0,1,2202	166.0	129.0	142.0		3336	-3.0	0.0	14	dbSNP_134	142	0,8600		0,0,4300	no	coding-synonymous	PAPLN	NM_173462.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		1112/1252	73733456	1,13005	2203	4300	6503	72803209	SO:0001819	synonymous_variant	89932	exon24			BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.3417C>T	14.37:g.73733456C>T		Somatic		Capture	Illumina HiSeq	Phase_I	72803209	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Silent	SNP	ENST00000554301.1	37																																																																																					0.542	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
NUMB	8650	broad.mit.edu	37	14	73759459	73759459	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:73759459T>C	ENST00000355058.3	-	8	711	c.433A>G	c.(433-435)Atg>Gtg	p.M145V	NUMB_ENST00000560335.1_Missense_Mutation_p.M145V|NUMB_ENST00000454166.4_Missense_Mutation_p.M145V|NUMB_ENST00000544991.3_Missense_Mutation_p.M145V|NUMB_ENST00000554521.2_Missense_Mutation_p.M134V|NUMB_ENST00000356296.4_Missense_Mutation_p.M145V|NUMB_ENST00000557597.1_Missense_Mutation_p.M134V|NUMB_ENST00000554546.1_Missense_Mutation_p.M134V|NUMB_ENST00000559312.1_Missense_Mutation_p.M145V|NUMB_ENST00000555738.2_Missense_Mutation_p.M134V|NUMB_ENST00000555394.1_Missense_Mutation_p.M145V|NUMB_ENST00000556772.1_Start_Codon_SNP_p.M1V|NUMB_ENST00000535282.1_Missense_Mutation_p.M134V|NUMB_ENST00000555238.1_Missense_Mutation_p.M145V|NUMB_ENST00000359560.3_Missense_Mutation_p.M134V			P49757	NUMB_HUMAN	numb homolog (Drosophila)	145	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|lateral ventricle development (GO:0021670)|lung epithelial cell differentiation (GO:0060487)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of protein localization to plasma membrane (GO:1903077)|neuroblast division in subventricular zone (GO:0021849)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration (GO:0030335)|positive regulation of neurogenesis (GO:0050769)|positive regulation of polarized epithelial cell differentiation (GO:0030862)	apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.M145V(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00471)|OV - Ovarian serous cystadenocarcinoma(108;0.161)		TTGACAGCCATGAAGCAGTGA	0.468																																					p.M145V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A433G	14						.						83.0	79.0	80.0					14																	73759459		2203	4300	6503	72829212	SO:0001583	missense	8650	exon8			L40393	CCDS9814.1, CCDS32115.1, CCDS32116.1, CCDS55927.1	14q24.3	2011-11-25	2001-11-28			ENSG00000133961			8060	protein-coding gene	gene with protein product		603728	"""numb (Drosophila) homolog"", ""chromosome 14 open reading frame 41"""	C14orf41			Standard	NM_003744		Approved		uc001xny.1	P49757		ENST00000355058.3:c.433A>G	14.37:g.73759459T>C	ENSP00000347169:p.Met145Val	Somatic		Capture	Illumina HiSeq	Phase_I	72829212	NM_001005744	B1P2N5|B1P2N6|B1P2N7|B1P2N8|B1P2N9|B4E2B1|Q6NUQ7|Q86SY1|Q8WW73|Q9UBG1|Q9UEQ4|Q9UKE8|Q9UKE9|Q9UKF0|Q9UQJ4	Missense_Mutation	SNP	ENST00000355058.3	37	CCDS32116.1	.	.	.	.	.	.	.	.	.	.	T	27.3	4.822079	0.90873	.	.	ENSG00000133961	ENST00000554546;ENST00000356296;ENST00000557597;ENST00000555238;ENST00000556772;ENST00000355058;ENST00000359560;ENST00000555394;ENST00000544991;ENST00000454166;ENST00000555738;ENST00000554521;ENST00000535282;ENST00000326018;ENST00000555859;ENST00000555307;ENST00000554394	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.36157	2.25;2.25;2.25;2.25;1.27;2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25	5.5	5.5	0.81552	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.38401	0.1039	N	0.04090	-0.28	0.80722	D	1	B;D;B;B;B;B;P;P;D;P;P	0.56035	0.021;0.958;0.021;0.139;0.008;0.004;0.633;0.889;0.974;0.709;0.746	B;D;B;B;B;B;P;D;P;P;P	0.74348	0.031;0.983;0.166;0.072;0.035;0.006;0.647;0.913;0.792;0.651;0.748	T	0.51052	-0.8754	10	0.44086	T	0.13	-13.0888	15.9025	0.79392	0.0:0.0:0.0:1.0	.	134;145;134;145;145;134;134;134;145;134;145	B1P2N6;B1P2N5;B1P2N8;B1P2N7;G3V3R1;Q86SW5;B2RCI6;P49757-4;P49757-2;P49757-3;P49757	.;.;.;.;.;.;.;.;.;.;NUMB_HUMAN	V	134;145;134;145;1;145;134;145;145;145;134;134;134;109;109;145;145	ENSP00000452416:M134V;ENSP00000348644:M145V;ENSP00000451117:M134V;ENSP00000451300:M145V;ENSP00000451513:M1V;ENSP00000347169:M145V;ENSP00000352563:M134V;ENSP00000451625:M145V;ENSP00000446001:M145V;ENSP00000394025:M145V;ENSP00000452069:M134V;ENSP00000450817:M134V;ENSP00000441258:M134V;ENSP00000451326:M109V;ENSP00000452357:M145V;ENSP00000451374:M145V	ENSP00000315193:M109V	M	-	1	0	NUMB	72829212	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.182000	0.71995	2.226000	0.72624	0.459000	0.35465	ATG		0.468	NUMB-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414416.1		
ELMSAN1	91748	broad.mit.edu	37	14	74203901	74203901	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:74203901G>A	ENST00000286523.5	-	3	2331	c.1549C>T	c.(1549-1551)Cga>Tga	p.R517*	ELMSAN1_ENST00000394071.2_Nonsense_Mutation_p.R517*|ELMSAN1_ENST00000486739.1_5'Flank	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	517					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R517*(1)									CTGTCTTCTCGTGCTCGCTTG	0.552																																					p.R517X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1549T	14						.						111.0	97.0	102.0					14																	74203901		2203	4300	6503	73273654	SO:0001587	stop_gained	91748	exon3			BF971739	CCDS9819.1	14q24.3	2012-09-25	2012-09-25	2012-09-25	ENSG00000156030	ENSG00000156030			19853	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 117"", ""chromosome 14 open reading frame 43"""	C14orf117, C14orf43			Standard	NM_194278		Approved	LSR68	uc001xou.3	Q6PJG2	OTTHUMG00000150359	ENST00000286523.5:c.1549C>T	14.37:g.74203901G>A	ENSP00000286523:p.Arg517*	Somatic		Capture	Illumina HiSeq	Phase_I	73273654	NM_001043318	Q6PK13|Q6PK59|Q6ZS23	Nonsense_Mutation	SNP	ENST00000286523.5	37	CCDS9819.1	.	.	.	.	.	.	.	.	.	.	G	46	12.666165	0.99687	.	.	ENSG00000156030	ENST00000394071;ENST00000286523;ENST00000423556;ENST00000435371	.	.	.	5.24	4.3	0.51218	.	0.000000	0.56097	D	0.000021	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.4359	13.718	0.62710	0.0:0.0:0.8469:0.1531	.	.	.	.	X	517	.	ENSP00000286523:R517X	R	-	1	2	C14orf43	73273654	1.000000	0.71417	0.994000	0.49952	0.983000	0.72400	4.455000	0.60075	2.732000	0.93576	0.655000	0.94253	CGA		0.552	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278	
ABCD4	5826	broad.mit.edu	37	14	74761871	74761871	+	Silent	SNP	C	C	T	rs139683556		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:74761871C>T	ENST00000356924.4	-	7	842	c.699G>A	c.(697-699)gcG>gcA	p.A233A	AC005519.4_ENST00000554532.2_RNA|ABCD4_ENST00000298816.7_Intron|ABCD4_ENST00000557554.1_Intron|ABCD4_ENST00000557588.1_Silent_p.A191A	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	233	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cobalamin metabolic process (GO:0009235)|transmembrane transport (GO:0055085)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.A233A(1)|p.R2Q(1)		cervix(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00153)		CAGCAGGCTCCGCATTCACCC	0.542													C|||	1	0.000199681	0.0	0.0	5008	,	,		21838	0.001		0.0	False		,,,				2504	0.0				p.A233A												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	c.G699A	14						.	C		2,4404	4.2+/-10.8	0,2,2201	153.0	119.0	131.0		699	-9.8	0.2	14	dbSNP_134	131	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ABCD4	NM_005050.3		0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231		233/607	74761871	3,13003	2203	4300	6503	73831624	SO:0001819	synonymous_variant	5826	exon7			AF009746	CCDS9828.1	14q24	2012-03-14			ENSG00000119688	ENSG00000119688		"""ATP binding cassette transporters / subfamily D"""	68	protein-coding gene	gene with protein product		603214		PXMP1L		9266848, 9302272	Standard	NR_003256		Approved	PMP69, P70R, EST352188	uc001xpr.2	O14678	OTTHUMG00000171207	ENST00000356924.4:c.699G>A	14.37:g.74761871C>T		Somatic		Capture	Illumina HiSeq	Phase_I	73831624	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Missense_Mutation	SNP	ENST00000356924.4	37	CCDS9828.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	4.137	0.023669	0.08006	4.54E-4	1.16E-4	ENSG00000119688	ENST00000537629;ENST00000556971	.	.	.	4.88	-9.76	0.00503	.	.	.	.	.	T	0.42017	0.1184	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52902	-0.8513	5	0.32370	T	0.25	.	2.8504	0.05555	0.1999:0.078:0.2892:0.4329	.	.	.	.	Q	2;193	.	ENSP00000443843:R2Q	R	-	2	0	ABCD4	73831624	0.007000	0.16637	0.154000	0.22540	0.535000	0.34838	-1.067000	0.03451	-3.392000	0.00172	-2.197000	0.00309	CGG		0.542	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
ABCD4	5826	broad.mit.edu	37	14	74764652	74764652	+	Missense_Mutation	SNP	G	G	A	rs145141432	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:74764652G>A	ENST00000356924.4	-	4	549	c.406C>T	c.(406-408)Cgg>Tgg	p.R136W	ABCD4_ENST00000298816.7_Missense_Mutation_p.R49W|ABCD4_ENST00000557554.1_Intron|ABCD4_ENST00000557588.1_Missense_Mutation_p.R136W	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	136	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cobalamin metabolic process (GO:0009235)|transmembrane transport (GO:0055085)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.R136W(1)		cervix(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00153)		ATGTCATCCCGCAGCACGTTG	0.587													G|||	7	0.00139776	0.0053	0.0	5008	,	,		19057	0.0		0.0	False		,,,				2504	0.0				p.R136W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C406T	14						.	G	TRP/ARG	5,4401	9.9+/-24.2	0,5,2198	110.0	92.0	98.0		406	5.2	1.0	14	dbSNP_134	98	0,8600		0,0,4300	yes	missense	ABCD4	NM_005050.3	101	0,5,6498	AA,AG,GG		0.0,0.1135,0.0384	probably-damaging	136/607	74764652	5,13001	2203	4300	6503	73834405	SO:0001583	missense	5826	exon4			AF009746	CCDS9828.1	14q24	2012-03-14			ENSG00000119688	ENSG00000119688		"""ATP binding cassette transporters / subfamily D"""	68	protein-coding gene	gene with protein product		603214		PXMP1L		9266848, 9302272	Standard	NR_003256		Approved	PMP69, P70R, EST352188	uc001xpr.2	O14678	OTTHUMG00000171207	ENST00000356924.4:c.406C>T	14.37:g.74764652G>A	ENSP00000349396:p.Arg136Trp	Somatic		Capture	Illumina HiSeq	Phase_I	73834405	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Missense_Mutation	SNP	ENST00000356924.4	37	CCDS9828.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	20.6	4.013952	0.75161	0.001135	0.0	ENSG00000119688	ENST00000356924;ENST00000298816;ENST00000557588	D;D;D	0.99656	-6.31;-6.31;-6.31	5.23	5.23	0.72850	ABC transporter, N-terminal (1);ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	0.175528	0.50627	D	0.000118	D	0.99248	0.9738	M	0.63428	1.95	0.45227	D	0.998232	D;D	0.71674	0.998;0.995	P;D	0.66979	0.888;0.948	D	0.95927	0.8935	10	0.72032	D	0.01	.	18.8069	0.92041	0.0:0.0:1.0:0.0	.	49;136	F8W7M4;O14678	.;ABCD4_HUMAN	W	136;49;136	ENSP00000349396:R136W;ENSP00000298816:R49W;ENSP00000451993:R136W	ENSP00000298816:R49W	R	-	1	2	ABCD4	73834405	1.000000	0.71417	0.999000	0.59377	0.953000	0.61014	5.244000	0.65400	2.422000	0.82143	0.561000	0.74099	CGG		0.587	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
VRTN	55237	broad.mit.edu	37	14	74824008	74824008	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:74824008G>A	ENST00000256362.4	+	2	763	c.522G>A	c.(520-522)tgG>tgA	p.W174*		NM_018228.2	NP_060698.2	Q9H8Y1	VRTN_HUMAN	vertebrae development associated	174					transposition, DNA-mediated (GO:0006313)		sequence-specific DNA binding (GO:0043565)|transposase activity (GO:0004803)	p.W174*(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(15)|ovary(5)|prostate(2)|skin(1)|urinary_tract(1)	41						CCAACGTGTGGCACTTGTATG	0.602																																					p.W174X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G522A	14						.						120.0	113.0	116.0					14																	74824008		2203	4300	6503	73893761	SO:0001587	stop_gained	55237	exon2			AK001673	CCDS9830.1	14q24.2	2012-12-07	2012-12-07	2010-10-20	ENSG00000133980	ENSG00000133980			20223	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 115"", ""vertebrae development homolog (pig)"""	C14orf115		21232157	Standard	NM_018228		Approved	FLJ10811, vertnin	uc001xpw.4	Q9H8Y1	OTTHUMG00000171208	ENST00000256362.4:c.522G>A	14.37:g.74824008G>A	ENSP00000256362:p.Trp174*	Somatic		Capture	Illumina HiSeq	Phase_I	73893761	NM_018228	Q9NVC7	Nonsense_Mutation	SNP	ENST00000256362.4	37	CCDS9830.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.448082	0.84101	.	.	ENSG00000133980	ENST00000256362	.	.	.	5.05	5.05	0.67936	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	1.8595	16.7434	0.85465	0.0:0.0:1.0:0.0	.	.	.	.	X	174	.	ENSP00000256362:W174X	W	+	3	0	VRTN	73893761	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	8.796000	0.91877	2.628000	0.89032	0.561000	0.74099	TGG		0.602	VRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412339.1	NM_018228	
DLST	1743	broad.mit.edu	37	14	75348660	75348660	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:75348660C>T	ENST00000334220.4	+	1	65	c.4C>T	c.(4-6)Ctg>Ttg	p.L2L	DLST_ENST00000555190.1_3'UTR|DLST_ENST00000334212.6_5'UTR	NM_001933.4	NP_001924.2	P36957	ODO2_HUMAN	dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex)	2					cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|generation of precursor metabolites and energy (GO:0006091)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|oxoglutarate dehydrogenase complex (GO:0045252)	dihydrolipoyllysine-residue succinyltransferase activity (GO:0004149)	p.L2L(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(234;0.00698)		CGCCGTGATGCTGTCCCGATC	0.716																																					p.L2L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4T	14						.						18.0	14.0	15.0					14																	75348660		2190	4282	6472	74418413	SO:0001819	synonymous_variant	1743	exon1				CCDS9833.1	14q23.1	2008-08-11			ENSG00000119689	ENSG00000119689	2.3.1.61		2911	protein-coding gene	gene with protein product		126063		DLTS		8009371	Standard	NM_001933		Approved		uc001xqv.2	P36957		ENST00000334220.4:c.4C>T	14.37:g.75348660C>T		Somatic		Capture	Illumina HiSeq	Phase_I	74418413	NM_001933	B7Z5W8|E7ESY5|Q7LDY7|Q9BQ32	Silent	SNP	ENST00000334220.4	37	CCDS9833.1	.	.	.	.	.	.	.	.	.	.	C	17.03	3.284444	0.59867	.	.	ENSG00000119689	ENST00000554806	T	0.10192	2.9	4.46	3.58	0.41010	.	.	.	.	.	T	0.17450	0.0419	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01027	-1.1476	6	0.56958	D	0.05	-47.2056	6.7056	0.23248	0.0:0.791:0.0:0.209	.	.	.	.	V	1	ENSP00000451957:A1V	ENSP00000238671:A1V	A	+	2	0	DLST	74418413	1.000000	0.71417	1.000000	0.80357	0.505000	0.33919	1.355000	0.34068	1.090000	0.41315	0.591000	0.81541	GCT		0.716	DLST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413637.1		
MLH3	27030	broad.mit.edu	37	14	75516252	75516252	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:75516252G>T	ENST00000556740.1	-	1	142	c.107C>A	c.(106-108)gCt>gAt	p.A36D	MLH3_ENST00000555671.1_5'Flank|MLH3_ENST00000238662.7_Missense_Mutation_p.A36D|MLH3_ENST00000556257.1_Missense_Mutation_p.A36D|MLH3_ENST00000355774.2_Missense_Mutation_p.A36D|MLH3_ENST00000380968.2_De_novo_Start_OutOfFrame|MLH3_ENST00000544985.1_5'Flank			Q9UHC1	MLH3_HUMAN	mutL homolog 3	36					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)	p.A36D(1)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		TTTTGCTTCAGCATCAATACT	0.448								Mismatch excision repair (MMR)																													p.A36D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C107A	14						.						109.0	100.0	103.0					14																	75516252		2203	4300	6503	74586005	SO:0001583	missense	27030	exon2			AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"""mutL (E. coli) homolog 3"", ""mutL homolog 3 (E. coli)"""			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.107C>A	14.37:g.75516252G>T	ENSP00000452316:p.Ala36Asp	Somatic		Capture	Illumina HiSeq	Phase_I	74586005	NM_001040108	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	37	CCDS32123.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.526892	0.85706	.	.	ENSG00000119684	ENST00000355774;ENST00000238662;ENST00000556257;ENST00000556740;ENST00000553263;ENST00000557648	D;D;D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11;-3.11;-3.11	5.22	5.22	0.72569	ATPase-like, ATP-binding domain (4);	0.000000	0.85682	D	0.000000	D	0.98090	0.9370	H	0.99261	4.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99663	1.0994	10	0.87932	D	0	-14.487	19.1636	0.93544	0.0:0.0:1.0:0.0	.	36;36	Q9UHC1-2;Q9UHC1	.;MLH3_HUMAN	D	36	ENSP00000348020:A36D;ENSP00000238662:A36D;ENSP00000451540:A36D;ENSP00000452316:A36D;ENSP00000451192:A36D;ENSP00000451095:A36D	ENSP00000238662:A36D	A	-	2	0	MLH3	74586005	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.809000	0.99208	2.590000	0.87494	0.655000	0.94253	GCT		0.448	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381	
TTLL5	23093	broad.mit.edu	37	14	76147918	76147918	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:76147918G>A	ENST00000298832.9	+	4	417	c.212G>A	c.(211-213)cGa>cAa	p.R71Q	TTLL5_ENST00000556977.1_Missense_Mutation_p.R71Q|TTLL5_ENST00000286650.5_Missense_Mutation_p.R71Q|TTLL5_ENST00000557636.1_Missense_Mutation_p.R71Q	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	71	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)	p.R71Q(1)		NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		AAGATTGTACGAACGGACAGT	0.338																																					p.R71Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G212A	14						.						156.0	144.0	148.0					14																	76147918		2203	4300	6503	75217671	SO:0001583	missense	23093	exon4			AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"""Tubulin tyrosine ligase-like family"""	19963	protein-coding gene	gene with protein product		612268	"""KIAA0998"""	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.212G>A	14.37:g.76147918G>A	ENSP00000298832:p.Arg71Gln	Somatic		Capture	Illumina HiSeq	Phase_I	75217671	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Missense_Mutation	SNP	ENST00000298832.9	37	CCDS32124.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.777498	0.90195	.	.	ENSG00000119685	ENST00000557003;ENST00000556977;ENST00000557636;ENST00000286650;ENST00000298832	T;T;T	0.06849	3.84;3.25;3.91	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.07863	0.0197	L	0.28274	0.84	0.80722	D	1	P;P;P	0.45212	0.853;0.802;0.74	B;B;B	0.40444	0.329;0.177;0.129	T	0.44667	-0.9313	10	0.16420	T	0.52	.	18.3166	0.90223	0.0:0.0:1.0:0.0	.	71;71;71	G3V2J9;Q6EMB2;Q6EMB2-3	.;TTLL5_HUMAN;.	Q	71	ENSP00000450713:R71Q;ENSP00000286650:R71Q;ENSP00000298832:R71Q	ENSP00000286650:R71Q	R	+	2	0	TTLL5	75217671	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.138000	0.71717	2.629000	0.89072	0.655000	0.94253	CGA		0.338	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072	
NRXN3	9369	broad.mit.edu	37	14	80164036	80164036	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:80164036G>A	ENST00000557594.1	+	4	1618	c.665G>A	c.(664-666)cGc>cAc	p.R222H	NRXN3_ENST00000281127.7_Missense_Mutation_p.R222H|NRXN3_ENST00000554719.1_Missense_Mutation_p.R854H|NRXN3_ENST00000556003.1_Intron|RP11-242P2.1_ENST00000553322.1_RNA|NRXN3_ENST00000335750.5_Missense_Mutation_p.R854H|NRXN3_ENST00000428277.2_Missense_Mutation_p.R252H	NM_001272020.1	NP_001258949.1	Q9HDB5	NRX3B_HUMAN	neurexin 3	222	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)	p.R252H(1)|p.R854H(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		GACAAAGGACGCCTCTTCCAA	0.453																																					p.R222H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G665A	14						.						81.0	78.0	79.0					14																	80164036		2203	4300	6503	79233789	SO:0001583	missense	9369	exon4			AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"""chromosome 14 open reading frame 60"""	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000557594.1:c.665G>A	14.37:g.80164036G>A	ENSP00000451672:p.Arg222His	Somatic		Capture	Illumina HiSeq	Phase_I	79233789	NM_138970	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000557594.1	37		.	.	.	.	.	.	.	.	.	.	G	21.8	4.205086	0.79127	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750;ENST00000557594;ENST00000281127;ENST00000428277	T;T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17;-1.17	5.76	5.76	0.90799	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.89842	0.6832	M	0.84846	2.72	0.54753	D	0.999986	D;D;P;B	0.89917	1.0;0.999;0.733;0.276	D;D;B;B	0.83275	0.996;0.97;0.32;0.055	D	0.89731	0.3926	9	.	.	.	.	19.9514	0.97200	0.0:0.0:1.0:0.0	.	252;222;222;854	Q9HDB5-4;Q9HDB5-2;Q9HDB5;Q9Y4C0-3	.;.;NRX3B_HUMAN;.	H	1227;1246;854;854;222;222;252	ENSP00000451648:R854H;ENSP00000338349:R854H;ENSP00000451672:R222H;ENSP00000281127:R222H;ENSP00000394426:R252H	.	R	+	2	0	NRXN3	79233789	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	6.828000	0.75308	2.718000	0.92993	0.557000	0.71058	CGC		0.453	NRXN3-004	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000413790.1	NM_001105250	
SPATA7	55812	broad.mit.edu	37	14	88892589	88892589	+	Missense_Mutation	SNP	C	C	T	rs374126653		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:88892589C>T	ENST00000393545.4	+	6	675	c.386C>T	c.(385-387)cCg>cTg	p.P129L	SPATA7_ENST00000356583.5_Missense_Mutation_p.P97L|SPATA7_ENST00000556553.1_Missense_Mutation_p.P97L|SPATA7_ENST00000045347.7_Missense_Mutation_p.P129L	NM_018418.4	NP_060888.2	Q9P0W8	SPAT7_HUMAN	spermatogenesis associated 7	129					response to stimulus (GO:0050896)|visual perception (GO:0007601)			p.P129L(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	18						TCAGGCGAACCGCAAATTGAG	0.368													C|||	1	0.000199681	0.0	0.0	5008	,	,		18651	0.0		0.0	False		,,,				2504	0.001				p.P97L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C290T	14						.	C	LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	44.0	42.0	43.0		290,386	3.5	0.8	14		43	0,8600		0,0,4300	no	missense,missense	SPATA7	NM_001040428.3,NM_018418.4	98,98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	97/568,129/600	88892589	1,13005	2203	4300	6503	87962342	SO:0001583	missense	55812	exon5			AF144487	CCDS9883.1, CCDS32132.1	14q31.3	2011-02-17				ENSG00000042317			20423	protein-coding gene	gene with protein product		609868	"""Leber congenital amaurosis 3"""	LCA3		9799089, 19268277	Standard	NM_018418		Approved	HSD3	uc001xwq.3	Q9P0W8		ENST00000393545.4:c.386C>T	14.37:g.88892589C>T	ENSP00000377176:p.Pro129Leu	Somatic		Capture	Illumina HiSeq	Phase_I	87962342	NM_001040428	Q5BKY5|Q8WX30|Q96HF3|Q9H0X0|Q9P0W7	Missense_Mutation	SNP	ENST00000393545.4	37	CCDS9883.1	.	.	.	.	.	.	.	.	.	.	C	12.51	1.958932	0.34565	2.27E-4	0.0	ENSG00000042317	ENST00000556553;ENST00000393545;ENST00000356583;ENST00000555401;ENST00000553885;ENST00000045347	T;T;T;T;T;T	0.18960	2.18;2.18;2.18;2.18;2.18;2.18	5.38	3.47	0.39725	.	0.699813	0.14078	N	0.342911	T	0.17280	0.0415	L	0.55481	1.735	0.38892	D	0.957145	P;P;P	0.50819	0.897;0.845;0.939	B;B;B	0.39935	0.292;0.18;0.314	T	0.08411	-1.0723	10	0.29301	T	0.29	-7.4034	6.0761	0.19915	0.0:0.6669:0.1708:0.1623	.	97;97;129	A8K3L6;Q9P0W8-2;Q9P0W8	.;.;SPAT7_HUMAN	L	97;129;97;72;115;129	ENSP00000451128:P97L;ENSP00000377176:P129L;ENSP00000348991:P97L;ENSP00000452435:P72L;ENSP00000450606:P115L;ENSP00000045347:P129L	ENSP00000045347:P129L	P	+	2	0	SPATA7	87962342	0.482000	0.25948	0.818000	0.32626	0.029000	0.11900	0.652000	0.24888	1.344000	0.45657	0.650000	0.86243	CCG		0.368	SPATA7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410172.1		
PTPN21	11099	broad.mit.edu	37	14	88935347	88935347	+	Silent	SNP	C	C	T	rs150207988		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:88935347C>T	ENST00000556564.1	-	18	3593	c.3309G>A	c.(3307-3309)ccG>ccA	p.P1103P	PTPN21_ENST00000328736.3_Silent_p.P1103P	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	1103	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein tyrosine phosphatase activity (GO:0004725)	p.P1103P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|liver(1)|lung(7)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						GGACCAACAACGGAGGGTTGG	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		19382	0.001		0.0	False		,,,				2504	0.0				p.P1103P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3309A	14						.	C		0,4406		0,0,2203	119.0	94.0	102.0		3309	-11.8	0.0	14	dbSNP_134	102	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PTPN21	NM_007039.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1103/1175	88935347	1,13005	2203	4300	6503	88005100	SO:0001819	synonymous_variant	11099	exon18			X79510	CCDS9884.1	14q31	2011-06-09				ENSG00000070778		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9651	protein-coding gene	gene with protein product		603271				7519780	Standard	NM_007039		Approved	PTPD1, PTPRL10	uc001xwv.4	Q16825		ENST00000556564.1:c.3309G>A	14.37:g.88935347C>T		Somatic		Capture	Illumina HiSeq	Phase_I	88005100	NM_007039		Silent	SNP	ENST00000556564.1	37	CCDS9884.1																																																																																				0.493	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1		
FOXN3	1112	broad.mit.edu	37	14	89878505	89878505	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:89878505C>T	ENST00000345097.4	-	2	432	c.316G>A	c.(316-318)Gat>Aat	p.D106N	RP11-33N16.3_ENST00000555070.1_RNA|FOXN3_ENST00000261302.5_Missense_Mutation_p.D106N|RP11-33N16.2_ENST00000556383.1_RNA|FOXN3_ENST00000555353.1_Missense_Mutation_p.D106N|FOXN3_ENST00000557258.1_Missense_Mutation_p.D106N	NM_001085471.1	NP_001078940.1	O00409	FOXN3_HUMAN	forkhead box N3	106					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D106N(1)		endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TGCCTGGCATCGTAGGGCATG	0.602																																					p.D106N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G316A	14						.						61.0	62.0	61.0					14																	89878505		2203	4300	6503	88948258	SO:0001583	missense	1112	exon2				CCDS32138.1, CCDS41977.1	14q32.11	2012-04-17	2007-05-02	2007-05-02	ENSG00000053254	ENSG00000053254		"""Forkhead boxes"""	1928	protein-coding gene	gene with protein product		602628	"""chromosome 14 open reading frame 116"", ""checkpoint suppressor 1"""	C14orf116, CHES1		9154802	Standard	NM_005197		Approved		uc001xxo.4	O00409	OTTHUMG00000170898	ENST00000345097.4:c.316G>A	14.37:g.89878505C>T	ENSP00000343288:p.Asp106Asn	Somatic		Capture	Illumina HiSeq	Phase_I	88948258	NM_001085471	Q96II7|Q9UIE7	Missense_Mutation	SNP	ENST00000345097.4	37	CCDS41977.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.966764	0.53507	.	.	ENSG00000053254	ENST00000345097;ENST00000261302;ENST00000557258;ENST00000555353;ENST00000555855	D;D;D;D;D	0.95412	-3.61;-3.61;-3.42;-3.42;-3.7	5.15	5.15	0.70609	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.190971	0.43579	D	0.000559	D	0.93517	0.7931	L	0.53729	1.69	0.80722	D	1	P;D	0.56746	0.949;0.977	B;B	0.39876	0.312;0.214	D	0.93857	0.7150	10	0.49607	T	0.09	.	18.6345	0.91372	0.0:1.0:0.0:0.0	.	106;106	O00409;O00409-2	FOXN3_HUMAN;.	N	106	ENSP00000343288:D106N;ENSP00000261302:D106N;ENSP00000452005:D106N;ENSP00000452227:D106N;ENSP00000451135:D106N	ENSP00000261302:D106N	D	-	1	0	FOXN3	88948258	1.000000	0.71417	0.997000	0.53966	0.761000	0.43186	7.818000	0.86416	2.416000	0.81992	0.555000	0.69702	GAT		0.602	FOXN3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410902.2	NM_005197	
TTC7B	145567	broad.mit.edu	37	14	91007829	91007829	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:91007829G>A	ENST00000328459.6	-	20	2536	c.2415C>T	c.(2413-2415)ggC>ggT	p.G805G	TTC7B_ENST00000357056.2_Silent_p.G822G|TTC7B_ENST00000554654.1_5'UTR	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	805								p.G805G(1)		NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				GGAGGACCTCGCCCAGCCCGT	0.652																																					p.G805G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2415T	14						.						49.0	41.0	44.0					14																	91007829		2203	4300	6503	90077582	SO:0001819	synonymous_variant	145567	exon20			BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"""Tetratricopeptide (TTC) repeat domain containing"""	19858	protein-coding gene	gene with protein product			"""tetratricopeptide repeat domain 7 like 1"""	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.2415C>T	14.37:g.91007829G>A		Somatic		Capture	Illumina HiSeq	Phase_I	90077582	NM_001010854	Q86U24|Q86VT3	Silent	SNP	ENST00000328459.6	37	CCDS32140.1	.	.	.	.	.	.	.	.	.	.	G	13.02	2.113848	0.37339	.	.	ENSG00000165914	ENST00000555894;ENST00000557292	.	.	.	5.61	-5.34	0.02705	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-21.3707	2.1506	0.03798	0.4384:0.2224:0.1837:0.1555	.	.	.	.	X	147;233	.	.	R	-	1	2	TTC7B	90077582	0.004000	0.15560	0.813000	0.32504	0.979000	0.70002	-1.342000	0.02645	-1.204000	0.02648	-0.448000	0.05591	CGA		0.652	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2		
CCDC88C	440193	broad.mit.edu	37	14	91780098	91780098	+	Missense_Mutation	SNP	C	C	T	rs375082540		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:91780098C>T	ENST00000389857.6	-	15	2148	c.2062G>A	c.(2062-2064)Gtg>Atg	p.V688M		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	688					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.V688M(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)				TGCAGGGACACGTTCTGCAAG	0.622																																					p.V688M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2062A	14						.	C	MET/VAL	1,4237		0,1,2118	32.0	33.0	33.0		2062	3.2	0.8	14		33	1,8457		0,1,4228	no	missense	CCDC88C	NM_001080414.3	21	0,2,6346	TT,TC,CC		0.0118,0.0236,0.0158	probably-damaging	688/2029	91780098	2,12694	2119	4229	6348	90849851	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.2062G>A	14.37:g.91780098C>T	ENSP00000374507:p.Val688Met	Somatic		Capture	Illumina HiSeq	Phase_I	90849851	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	.	.	.	.	.	.	.	.	.	.	C	10.84	1.463226	0.26248	2.36E-4	1.18E-4	ENSG00000015133	ENST00000389857	T	0.34859	1.34	5.0	3.17	0.36434	.	0.155118	0.29335	U	0.012457	T	0.35008	0.0917	M	0.75447	2.3	0.44275	D	0.997134	B	0.33238	0.403	B	0.23574	0.047	T	0.22382	-1.0218	10	0.72032	D	0.01	-18.8596	10.5668	0.45177	0.0:0.7819:0.0:0.2181	.	688	Q9P219	DAPLE_HUMAN	M	688	ENSP00000374507:V688M	ENSP00000374507:V688M	V	-	1	0	CCDC88C	90849851	0.004000	0.15560	0.825000	0.32803	0.673000	0.39480	1.013000	0.29937	0.509000	0.28195	0.561000	0.74099	GTG		0.622	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
LGMN	5641	broad.mit.edu	37	14	93172963	93172963	+	Silent	SNP	G	G	A	rs141204016		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:93172963G>A	ENST00000393218.2	-	13	1393	c.1056C>T	c.(1054-1056)atC>atT	p.I352I	LGMN_ENST00000555699.1_Intron|LGMN_ENST00000557434.1_Intron|LGMN_ENST00000334869.4_Silent_p.I352I	NM_001008530.2	NP_001008530.1	Q99538	LGMN_HUMAN	legumain	352					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|innate immune response (GO:0045087)|negative regulation of ERBB signaling pathway (GO:1901185)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of neuron apoptotic process (GO:0043524)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|receptor catabolic process (GO:0032801)|renal system process (GO:0003014)|response to acidic pH (GO:0010447)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|toll-like receptor signaling pathway (GO:0002224)|vitamin D metabolic process (GO:0042359)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)	p.I352I(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|skin(2)	18		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		GCAAGGAGACGATCTTACGCA	0.637																																					p.I352I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1056T	14						.	G	,	1,4405	2.1+/-5.4	0,1,2202	57.0	52.0	54.0		1056,1056	-6.4	0.1	14	dbSNP_134	54	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	LGMN	NM_001008530.2,NM_005606.6	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	352/434,352/434	93172963	1,13005	2203	4300	6503	92242716	SO:0001819	synonymous_variant	5641	exon13			D55696	CCDS9904.1	14q32.12	2011-04-08		2002-01-18	ENSG00000100600	ENSG00000100600			9472	protein-coding gene	gene with protein product		602620	"""protease, cysteine, 1 (legumain)"""	PRSC1		8893817, 9065484	Standard	NM_001008530		Approved	LGMN1	uc001yaw.3	Q99538		ENST00000393218.2:c.1056C>T	14.37:g.93172963G>A		Somatic		Capture	Illumina HiSeq	Phase_I	92242716	NM_001008530	O00123|Q86TV2|Q86TV3|Q9BTY1	Silent	SNP	ENST00000393218.2	37	CCDS9904.1																																																																																				0.637	LGMN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412288.1	NM_005606	
UNC79	57578	broad.mit.edu	37	14	94008900	94008900	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:94008900C>T	ENST00000393151.2	+	14	1613	c.1613C>T	c.(1612-1614)gCg>gTg	p.A538V	UNC79_ENST00000555664.1_Missense_Mutation_p.A538V|UNC79_ENST00000256339.4_Missense_Mutation_p.A361V|UNC79_ENST00000553484.1_Missense_Mutation_p.A538V			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	538					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A361V(1)		breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						CACTCCACTGCGTATATGATG	0.512																																					p.A361V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1082T	14						.						195.0	150.0	165.0					14																	94008900		2203	4300	6503	93078653	SO:0001583	missense	57578	exon14			AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.1613C>T	14.37:g.94008900C>T	ENSP00000376858:p.Ala538Val	Somatic		Capture	Illumina HiSeq	Phase_I	93078653	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		.	.	.	.	.	.	.	.	.	.	C	35	5.534497	0.96460	.	.	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.55305	0.1912	L	0.58810	1.83	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.54296	-0.8315	10	0.87932	D	0	-15.6674	20.0618	0.97678	0.0:1.0:0.0:0.0	.	538	C9JQL1	.	V	361;538;538;538;538	ENSP00000256339:A361V;ENSP00000450868:A538V;ENSP00000451360:A538V;ENSP00000376858:A538V	ENSP00000256339:A361V	A	+	2	0	KIAA1409	93078653	1.000000	0.71417	0.926000	0.36857	0.981000	0.71138	7.779000	0.85648	2.730000	0.93505	0.650000	0.86243	GCG		0.512	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
UNC79	57578	broad.mit.edu	37	14	94088466	94088466	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:94088466C>T	ENST00000393151.2	+	30	4887	c.4887C>T	c.(4885-4887)agC>agT	p.S1629S	UNC79_ENST00000555664.1_Silent_p.S1629S|UNC79_ENST00000256339.4_Silent_p.S1452S|UNC79_ENST00000553484.1_Silent_p.S1651S			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1629					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S1452S(1)		breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						CCTCCGACAGCGACTCTCTTG	0.493																																					p.S1452S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4356T	14						.						88.0	90.0	89.0					14																	94088466		2203	4300	6503	93158219	SO:0001819	synonymous_variant	57578	exon30			AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.4887C>T	14.37:g.94088466C>T		Somatic		Capture	Illumina HiSeq	Phase_I	93158219	NM_020818	B5MDL6|Q6ZUT7	Silent	SNP	ENST00000393151.2	37																																																																																					0.493	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
SERPINA3	12	broad.mit.edu	37	14	95081024	95081024	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:95081024C>T	ENST00000467132.1	+	2	1394	c.246C>T	c.(244-246)acC>acT	p.T82T	SERPINA3_ENST00000393080.4_Silent_p.T82T|SERPINA3_ENST00000393078.3_Silent_p.T82T|RP11-986E7.7_ENST00000553947.1_3'UTR|SERPINA3_ENST00000482740.1_5'Flank			P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3	82					acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of endopeptidase activity (GO:0010951)|regulation of lipid metabolic process (GO:0019216)|regulation of proteolysis (GO:0030162)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	DNA binding (GO:0003677)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.T82T(2)		NS(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(17)|ovary(2)|pancreas(1)|skin(3)|stomach(1)	40		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		GCATCTCCACCGCCTTGGCCT	0.532																																					p.T82T												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C246T	14						.						101.0	98.0	99.0					14																	95081024		2203	4300	6503	94150777	SO:0001819	synonymous_variant	12	exon2			K01500	CCDS32150.1	14q32.1	2014-06-03	2005-08-18		ENSG00000196136	ENSG00000196136		"""Serine (or cysteine) peptidase inhibitors"""	16	protein-coding gene	gene with protein product		107280	"""alpha-1-antichymotrypsin"", ""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3"""	AACT		3260956, 24172014	Standard	NM_001085		Approved	ACT, alpha-1-antichymotrypsin	uc001ydp.3	P01011	OTTHUMG00000029851	ENST00000467132.1:c.246C>T	14.37:g.95081024C>T		Somatic		Capture	Illumina HiSeq	Phase_I	94150777	NM_001085	B3KVQ7|Q13703|Q2TU87|Q2TU88|Q59GP9|Q6LBY8|Q6LDT7|Q6NSC9|Q8N177|Q96DW8|Q9UC47|Q9UNU9	Silent	SNP	ENST00000467132.1	37	CCDS32150.1																																																																																				0.532	SERPINA3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268080.3	NM_001085	
SYNE3	161176	broad.mit.edu	37	14	95916404	95916404	+	Missense_Mutation	SNP	G	G	A	rs376830751	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:95916404G>A	ENST00000334258.5	-	7	1327	c.1313C>T	c.(1312-1314)gCg>gTg	p.A438V	SYNE3_ENST00000554873.1_Missense_Mutation_p.A195V|SYNE3_ENST00000553340.1_Missense_Mutation_p.A438V|SYNE3_ENST00000557275.1_Missense_Mutation_p.A438V	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	438					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)	p.A438V(1)		breast(1)|endometrium(2)|lung(25)	28						CAGCTCCACCGCCGCGGCATT	0.642													g|||	3	0.000599042	0.0	0.0	5008	,	,		16552	0.003		0.0	False		,,,				2504	0.0				p.A438V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1313T	14						.						14.0	15.0	15.0					14																	95916404		2195	4293	6488	94986157	SO:0001583	missense	161176	exon7			AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.1313C>T	14.37:g.95916404G>A	ENSP00000334308:p.Ala438Val	Somatic		Capture	Illumina HiSeq	Phase_I	94986157	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	g	12.27	1.886224	0.33348	.	.	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275;ENST00000553340	T;T;T;T	0.14516	3.53;2.5;3.53;2.94	5.16	1.13	0.20643	.	0.568727	0.14526	N	0.314200	T	0.07638	0.0192	L	0.36672	1.1	0.09310	N	1	P;P;P	0.44816	0.844;0.844;0.758	B;B;B	0.28465	0.058;0.09;0.026	T	0.24799	-1.0150	10	0.44086	T	0.13	-7.2393	7.5774	0.27944	0.0:0.3898:0.432:0.1782	.	438;438;438	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	V	438;195;438;438	ENSP00000334308:A438V;ENSP00000452154:A195V;ENSP00000450562:A438V;ENSP00000450774:A438V	ENSP00000334308:A438V	A	-	2	0	C14orf49	94986157	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.138000	0.10374	-0.308000	0.08792	-1.641000	0.00772	GCG		0.642	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
SYNE3	161176	broad.mit.edu	37	14	95934195	95934195	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:95934195G>A	ENST00000334258.5	-	2	268	c.254C>T	c.(253-255)gCc>gTc	p.A85V	SYNE3_ENST00000553340.1_Missense_Mutation_p.A85V|SYNE3_ENST00000557275.1_Missense_Mutation_p.A85V	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	85					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)	p.A85V(1)		breast(1)|endometrium(2)|lung(25)	28						CTTCAGCCGGGCCAGGATCCC	0.622																																					p.A85V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C254T	14						.						75.0	59.0	64.0					14																	95934195		2203	4300	6503	95003948	SO:0001583	missense	161176	exon2			AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.254C>T	14.37:g.95934195G>A	ENSP00000334308:p.Ala85Val	Somatic		Capture	Illumina HiSeq	Phase_I	95003948	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	G	7.837	0.721138	0.15372	.	.	ENSG00000176438	ENST00000334258;ENST00000557275;ENST00000553340	T;T;T	0.35789	1.29;1.29;1.29	4.43	3.4	0.38934	.	0.201034	0.24576	N	0.037352	T	0.32315	0.0825	M	0.62723	1.935	0.09310	N	0.999993	B;B;B	0.15930	0.015;0.015;0.009	B;B;B	0.13407	0.009;0.009;0.004	T	0.20773	-1.0265	10	0.32370	T	0.25	-1.7109	7.9539	0.30031	0.2764:0.0:0.7236:0.0	.	85;85;85	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	V	85	ENSP00000334308:A85V;ENSP00000450562:A85V;ENSP00000450774:A85V	ENSP00000334308:A85V	A	-	2	0	C14orf49	95003948	0.726000	0.28059	0.971000	0.41717	0.621000	0.37620	0.978000	0.29488	0.809000	0.34255	0.561000	0.74099	GCC		0.622	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
BDKRB2	624	broad.mit.edu	37	14	96706989	96706989	+	Silent	SNP	C	C	T	rs201395940		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:96706989C>T	ENST00000306005.3	+	3	520	c.324C>T	c.(322-324)tgC>tgT	p.C108C	BDKRB2_ENST00000554311.1_Silent_p.C108C|BDKRB2_ENST00000542454.2_Silent_p.C81C|BDKRB2_ENST00000539359.1_Silent_p.C81C|RP11-404P21.8_ENST00000553811.1_Intron	NM_000623.3	NP_000614.1	P30411	BKRB2_HUMAN	bradykinin receptor B2	108					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.C108C(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)	TCCTGGCCTGCGGGCTGCCCT	0.587																																					p.C108C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C324T	14						.	C		3,4403	6.2+/-15.9	0,3,2200	108.0	109.0	109.0		324	0.7	0.9	14		109	0,8600		0,0,4300	no	coding-synonymous	BDKRB2	NM_000623.3		0,3,6500	TT,TC,CC		0.0,0.0681,0.0231		108/392	96706989	3,13003	2203	4300	6503	95776742	SO:0001819	synonymous_variant	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.324C>T	14.37:g.96706989C>T		Somatic		Capture	Illumina HiSeq	Phase_I	95776742	NM_000623		Silent	SNP	ENST00000306005.3	37	CCDS9942.1																																																																																				0.587	BDKRB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413294.1		
VRK1	7443	broad.mit.edu	37	14	97299905	97299905	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:97299905G>A	ENST00000216639.3	+	2	246	c.97G>A	c.(97-99)Gca>Aca	p.A33T		NM_003384.2	NP_003375.1	Q99986	VRK1_HUMAN	vaccinia related kinase 1	33					Golgi disassembly (GO:0090166)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-T3 phosphorylation (GO:0072355)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi stack (GO:0005795)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H3-S10 specific) (GO:0035175)|histone kinase activity (H3-T3 specific) (GO:0072354)|nucleosomal histone binding (GO:0031493)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.A33T(1)		NS(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(1)|stomach(1)	12		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)		AACTGACATGGCAAAAAAGGA	0.418																																					p.A33T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G97A	14						.						145.0	136.0	139.0					14																	97299905		2203	4300	6503	96369658	SO:0001583	missense	7443	exon2			AB000449	CCDS9947.1	14q32.2	2012-07-05			ENSG00000100749	ENSG00000100749			12718	protein-coding gene	gene with protein product		602168				9344656	Standard	XM_006720247		Approved		uc001yft.3	Q99986	OTTHUMG00000171459	ENST00000216639.3:c.97G>A	14.37:g.97299905G>A	ENSP00000216639:p.Ala33Thr	Somatic		Capture	Illumina HiSeq	Phase_I	96369658	NM_003384	Q3SYL2	Missense_Mutation	SNP	ENST00000216639.3	37	CCDS9947.1	.	.	.	.	.	.	.	.	.	.	G	6.358	0.434206	0.12045	.	.	ENSG00000100749	ENST00000216639	T	0.42131	0.98	6.05	-5.79	0.02354	Protein kinase-like domain (1);	0.971136	0.08517	N	0.934055	T	0.16085	0.0387	N	0.05383	-0.06	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22208	-1.0223	10	0.17369	T	0.5	0.4377	4.6303	0.12498	0.114:0.0801:0.379:0.4269	.	33	Q99986	VRK1_HUMAN	T	33	ENSP00000216639:A33T	ENSP00000216639:A33T	A	+	1	0	VRK1	96369658	0.000000	0.05858	0.000000	0.03702	0.424000	0.31475	-0.965000	0.03829	-1.407000	0.02043	0.655000	0.94253	GCA		0.418	VRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413520.1	NM_003384	
WARS	7453	broad.mit.edu	37	14	100828197	100828197	+	Missense_Mutation	SNP	G	G	A	rs2234522		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:100828197G>A	ENST00000355338.2	-	3	779	c.161C>T	c.(160-162)gCg>gTg	p.A54V	WARS_ENST00000554084.1_5'UTR|WARS_ENST00000392882.2_Missense_Mutation_p.A54V|WARS_ENST00000344102.5_Missense_Mutation_p.A13V|WARS_ENST00000557135.1_Missense_Mutation_p.A54V|WARS_ENST00000358655.4_Missense_Mutation_p.A13V|WARS_ENST00000556645.1_Missense_Mutation_p.A13V	NM_173701.1	NP_776049.1	P23381	SYWC_HUMAN	tryptophanyl-tRNA synthetase	54	WHEP-TRS. {ECO:0000255|PROSITE- ProRule:PRU00531}.		A -> S (in dbSNP:rs2234521).		angiogenesis (GO:0001525)|gene expression (GO:0010467)|negative regulation of cell proliferation (GO:0008285)|regulation of angiogenesis (GO:0045765)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)	p.A54V(1)		breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	20		all_cancers(154;0.00223)|all_lung(585;2.48e-06)|all_epithelial(191;0.000564)|Melanoma(154;0.152)			L-Tryptophan(DB00150)	ATCCTCCCCCGCGGCAGCTTT	0.463													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18636	0.0		0.0	False		,,,				2504	0.0				p.A54V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C161T	14						.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	119.0	121.0	120.0		161,161,38,38	-2.2	0.0	14	dbSNP_98	120	0,8600		0,0,4300	no	missense,missense,missense,missense	WARS	NM_004184.3,NM_173701.1,NM_213645.1,NM_213646.1	64,64,64,64	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign	54/472,54/472,13/431,13/431	100828197	1,13005	2203	4300	6503	99897950	SO:0001583	missense	7453	exon3			M61715	CCDS9960.1, CCDS9961.1	14q32.2	2014-03-19			ENSG00000140105	ENSG00000140105	6.1.1.2	"""Aminoacyl tRNA synthetases / Class I"""	12729	protein-coding gene	gene with protein product	"""tryptophan tRNA ligase 1, cytoplasmic"""	191050		IFI53		1537332, 1763065	Standard	NM_004184		Approved	IFP53	uc001yhl.1	P23381	OTTHUMG00000171572	ENST00000355338.2:c.161C>T	14.37:g.100828197G>A	ENSP00000347495:p.Ala54Val	Somatic		Capture	Illumina HiSeq	Phase_I	99897950	NM_173701	A6NGN1|A6NID3|P78535|Q502Y0|Q53XB6|Q9UDI5|Q9UDL3	Missense_Mutation	SNP	ENST00000355338.2	37	CCDS9960.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	8.576	0.881279	0.17467	2.27E-4	0.0	ENSG00000140105	ENST00000392882;ENST00000358655;ENST00000355338;ENST00000344102;ENST00000557135;ENST00000556645;ENST00000553395;ENST00000556504;ENST00000557722;ENST00000557297;ENST00000556435;ENST00000556338;ENST00000556698;ENST00000553524;ENST00000555410;ENST00000554772;ENST00000556660;ENST00000553413;ENST00000553769;ENST00000553545;ENST00000554820;ENST00000554509;ENST00000556209;ENST00000554605;ENST00000555813;ENST00000556695;ENST00000556295;ENST00000555031	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.41758	1.54;0.99;1.54;0.99;1.54;0.99;0.99;0.99;1.54;0.99;0.99;0.99;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54	5.91	-2.24	0.06909	WHEP-TRS (2);S15/NS1, RNA-binding (2);	0.532701	0.21996	N	0.066061	T	0.26231	0.0640	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17228	-1.0376	10	0.35671	T	0.21	-3.9234	14.1551	0.65413	0.2385:0.0:0.7615:0.0	rs2234522;rs2234522	54	P23381	SYWC_HUMAN	V	54;13;54;13;54;13;13;13;54;13;13;13;54;54;88;54;54;54;54;54;54;88;54;54;54;54;54;54	ENSP00000376620:A54V;ENSP00000351481:A13V;ENSP00000347495:A54V;ENSP00000339485:A13V;ENSP00000451460:A54V;ENSP00000451887:A13V;ENSP00000451490:A13V;ENSP00000451251:A13V;ENSP00000450500:A54V;ENSP00000451599:A13V;ENSP00000452519:A13V;ENSP00000451544:A13V;ENSP00000450427:A54V;ENSP00000451349:A54V;ENSP00000450934:A88V;ENSP00000451469:A54V;ENSP00000451402:A54V;ENSP00000452550:A54V;ENSP00000451906:A54V;ENSP00000451716:A54V;ENSP00000450563:A54V;ENSP00000451894:A88V;ENSP00000451027:A54V;ENSP00000450978:A54V;ENSP00000451953:A54V;ENSP00000451777:A54V;ENSP00000451377:A54V;ENSP00000450623:A54V	ENSP00000339485:A13V	A	-	2	0	WARS	99897950	0.133000	0.22466	0.001000	0.08648	0.002000	0.02628	1.806000	0.38892	-0.318000	0.08665	-1.063000	0.02288	GCG		0.463	WARS-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414236.1	NM_004184	
AHNAK2	113146	broad.mit.edu	37	14	105408519	105408519	+	Silent	SNP	G	G	A	rs202130765		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr14:105408519G>A	ENST00000333244.5	-	7	13388	c.13269C>T	c.(13267-13269)gaC>gaT	p.D4423D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4423						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.D4423D(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GCAGAGACACGTCCAGGTTGG	0.612																																					p.D4423D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C13269T	14						.						97.0	103.0	101.0					14																	105408519		1999	4164	6163	104479564	SO:0001819	synonymous_variant	113146	exon7			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.13269C>T	14.37:g.105408519G>A		Somatic		Capture	Illumina HiSeq	Phase_I	104479564	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																				0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
OR4M2	390538	broad.mit.edu	37	15	22368759	22368759	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:22368759C>A	ENST00000332663.2	+	1	282	c.184C>A	c.(184-186)Ctg>Atg	p.L62M	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L62M(2)		NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		TATGTATTTCCTGTTGGCTAA	0.388																																					p.L62M												.	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.C184A	15						.						494.0	428.0	450.0					15																	22368759		2203	4300	6503	19870123	SO:0001583	missense	390538	exon1			AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"""GPCR / Class A : Olfactory receptors"""	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.184C>A	15.37:g.22368759C>A	ENSP00000329467:p.Leu62Met	Somatic		Capture	Illumina HiSeq	Phase_I	19870123	NM_001004719	B9EH16|Q6IEY2	Missense_Mutation	SNP	ENST00000332663.2	37	CCDS32172.1	.	.	.	.	.	.	.	.	.	.	.	14.73	2.622476	0.46840	.	.	ENSG00000182974	ENST00000332663	T	0.03152	4.03	2.5	2.5	0.30297	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36740	N	0.002434	T	0.12817	0.0311	M	0.86028	2.79	0.26793	N	0.969362	D	0.65815	0.995	P	0.59703	0.862	T	0.02484	-1.1152	10	0.72032	D	0.01	-6.7748	5.3487	0.16024	0.0:0.8342:0.0:0.1658	.	62	Q8NGB6	OR4M2_HUMAN	M	62	ENSP00000329467:L62M	ENSP00000329467:L62M	L	+	1	2	OR4M2	19870123	0.001000	0.12720	1.000000	0.80357	0.984000	0.73092	-0.131000	0.10482	1.422000	0.47177	0.448000	0.29417	CTG		0.388	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1		
TUBGCP5	114791	broad.mit.edu	37	15	22864335	22864335	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:22864335G>A	ENST00000283645.4	+	16	2423	c.2293G>A	c.(2293-2295)Gca>Aca	p.A765T	TUBGCP5_ENST00000453949.2_Missense_Mutation_p.A765T	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	765					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)	p.A765T(1)		breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		ACTCCAAGAAGCAGTAGGACA	0.363																																					p.A765T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2293A	15						.						86.0	84.0	85.0					15																	22864335		2203	4300	6503	20415776	SO:0001583	missense	114791	exon16			AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"""gamma-tubulin complex component GCP5"""	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.2293G>A	15.37:g.22864335G>A	ENSP00000283645:p.Ala765Thr	Somatic		Capture	Illumina HiSeq	Phase_I	20415776	NM_052903	E9PB12|Q6IQ52|Q96PY8	Missense_Mutation	SNP	ENST00000283645.4	37	CCDS10008.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.293688	0.60086	.	.	ENSG00000153575	ENST00000283645;ENST00000453949	T;T	0.09073	3.02;3.02	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.13200	0.0320	L	0.48642	1.525	0.58432	D	0.99999	P;P	0.39696	0.683;0.683	B;B	0.42798	0.398;0.398	T	0.00920	-1.1514	10	0.66056	D	0.02	-19.7044	16.9999	0.86378	0.0:0.0:1.0:0.0	.	765;765	Q96RT8;E9PB12	GCP5_HUMAN;.	T	765	ENSP00000283645:A765T;ENSP00000409217:A765T	ENSP00000283645:A765T	A	+	1	0	TUBGCP5	20415776	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.100000	0.76989	2.761000	0.94854	0.591000	0.81541	GCA		0.363	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903	
CYFIP1	23191	broad.mit.edu	37	15	22993152	22993152	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:22993152C>T	ENST00000313077.7	+	26	3164	c.3039C>T	c.(3037-3039)agC>agT	p.S1013S	CYFIP1_ENST00000435939.2_Silent_p.S582S|CYFIP1_ENST00000560848.1_Silent_p.S1013S	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1									p.S1013S(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		TCGAGCAGAGCCTGGTGAGTG	0.662																																					p.S1013S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3039T	15						.						52.0	51.0	51.0					15																	22993152		2203	4300	6503	20544593	SO:0001819	synonymous_variant	23191	exon26			D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.3039C>T	15.37:g.22993152C>T		Somatic		Capture	Illumina HiSeq	Phase_I	20544593	NM_014608		Silent	SNP	ENST00000313077.7	37	CCDS10009.1																																																																																				0.662	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608	
CYFIP1	23191	broad.mit.edu	37	15	22999456	22999456	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:22999456C>T	ENST00000313077.7	+	29	3453	c.3328C>T	c.(3328-3330)Cgc>Tgc	p.R1110C	CYFIP1_ENST00000435939.2_Missense_Mutation_p.R679C|CYFIP1_ENST00000560848.1_Missense_Mutation_p.R1110C	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1									p.R1110C(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		CCCCATCTGGCGCGGGCCTCT	0.592																																					p.R1110C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3328T	15						.						59.0	59.0	59.0					15																	22999456		2203	4300	6503	20550897	SO:0001583	missense	23191	exon29			D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.3328C>T	15.37:g.22999456C>T	ENSP00000324549:p.Arg1110Cys	Somatic		Capture	Illumina HiSeq	Phase_I	20550897	NM_014608		Missense_Mutation	SNP	ENST00000313077.7	37	CCDS10009.1	.	.	.	.	.	.	.	.	.	.	C	31	5.063093	0.93898	.	.	ENSG00000068793	ENST00000313077;ENST00000412127;ENST00000435939	T;T	0.23754	1.89;1.89	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000002	T	0.31513	0.0799	N	0.17082	0.46	0.80722	D	1	B;D	0.63046	0.129;0.992	B;P	0.56088	0.022;0.791	T	0.05402	-1.0887	10	0.42905	T	0.14	-15.0561	19.4921	0.95054	0.0:1.0:0.0:0.0	.	679;1110	Q7L576-2;Q7L576	.;CYFP1_HUMAN	C	1110;1112;679	ENSP00000324549:R1110C;ENSP00000405956:R679C	ENSP00000324549:R1110C	R	+	1	0	CYFIP1	20550897	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.977000	0.70492	2.624000	0.88883	0.561000	0.74099	CGC		0.592	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608	
MAGEL2	54551	broad.mit.edu	37	15	23889460	23889460	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:23889460G>A	ENST00000532292.1	-	1	1715	c.1621C>T	c.(1621-1623)Cgg>Tgg	p.R541W		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	424					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)	p.V572V(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		TTTGTCTCCCGGACATCCAAC	0.463																																					p.R1144W												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3430T	15						.						49.0	49.0	49.0					15																	23889460		1877	4106	5983	21440553	SO:0001583	missense	54551	exon1			AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.1621C>T	15.37:g.23889460G>A	ENSP00000433433:p.Arg541Trp	Somatic		Capture	Illumina HiSeq	Phase_I	21440553	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	37																																																																																					0.463	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066	
NPAP1	23742	broad.mit.edu	37	15	24921797	24921797	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:24921797G>A	ENST00000329468.2	+	1	1257	c.783G>A	c.(781-783)gcG>gcA	p.A261A		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	261					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.A261A(1)									ATGCAACAGCGCCCCCTGAGC	0.642																																					p.A261A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G783A	15						.						31.0	34.0	33.0					15																	24921797		2202	4300	6502	22472890	SO:0001819	synonymous_variant	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.783G>A	15.37:g.24921797G>A		Somatic		Capture	Illumina HiSeq	Phase_I	22472890	NM_018958		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																				0.642	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
GABRG3	2567	broad.mit.edu	37	15	27772649	27772649	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:27772649C>T	ENST00000333743.6	+	8	1190	c.936C>T	c.(934-936)taC>taT	p.Y312Y	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	312					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.Y312Y(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GCGTGTCCTACGTGACCGCCA	0.552																																					p.Y312Y	NSCLC(114;800 1656 7410 37729 45293)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C936T	15						.						129.0	124.0	126.0					15																	27772649		2191	4290	6481	25446244	SO:0001819	synonymous_variant	2567	exon8				CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4088	protein-coding gene	gene with protein product	"""GABA(G) receptor, gamma 3"""	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.936C>T	15.37:g.27772649C>T		Somatic		Capture	Illumina HiSeq	Phase_I	25446244	NM_033223	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	C	7.669	0.686660	0.14973	.	.	ENSG00000182256	ENST00000451330	.	.	.	5.48	-6.45	0.01914	.	.	.	.	.	T	0.63283	0.2498	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66164	-0.5992	4	.	.	.	.	15.9473	0.79803	0.0:0.3173:0.0:0.6827	.	.	.	.	M	75	.	.	T	+	2	0	GABRG3	25446244	0.030000	0.19436	0.799000	0.32177	0.823000	0.46562	-0.902000	0.04088	-1.235000	0.02545	-0.253000	0.11424	ACG		0.552	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
HERC2	8924	broad.mit.edu	37	15	28465671	28465671	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:28465671G>A	ENST00000261609.7	-	37	5880	c.5772C>T	c.(5770-5772)taC>taT	p.Y1924Y		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.Y1924Y(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)		GCTTGAGGTCGTATTTTCCTT	0.567																																					p.Y1924Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5772T	15						.						111.0	104.0	106.0					15																	28465671		2203	4297	6500	26139266	SO:0001819	synonymous_variant	8924	exon37			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.5772C>T	15.37:g.28465671G>A		Somatic		Capture	Illumina HiSeq	Phase_I	26139266	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																				0.567	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
NDNL2	56160	broad.mit.edu	37	15	29561692	29561692	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:29561692G>C	ENST00000332303.4	-	1	341	c.218C>G	c.(217-219)gCc>gGc	p.A73G	FAM189A1_ENST00000261275.4_Intron	NM_138704.3	NP_619649.1	Q96MG7	MAGG1_HUMAN	necdin-like 2	73					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)		p.A73G(1)		breast(3)|large_intestine(2)|lung(3)	8		all_lung(180;4.69e-11)|Breast(32;0.0013)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00736)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		ggcgggggcggcctgggcccg	0.701											OREG0032044	type=REGULATORY REGION|TFbs=RELA|Dataset=RELA (p65) ChIP-PET Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with paired-end diTag sequencing (ChIP-PET)																									p.A73G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C218G	15						.						20.0	22.0	21.0					15																	29561692		2199	4292	6491	27348984	SO:0001583	missense	56160	exon1			AF490510	CCDS10023.1	15q13.1	2008-02-01			ENSG00000185115	ENSG00000185115			7677	protein-coding gene	gene with protein product		608243				18086888	Standard	NM_138704		Approved	HCA4, MAGEG1, MAGEL3, NSE3, NSMCE3	uc001zco.3	Q96MG7	OTTHUMG00000129261	ENST00000332303.4:c.218C>G	15.37:g.29561692G>C	ENSP00000330694:p.Ala73Gly	Somatic	810	Capture	Illumina HiSeq	Phase_I	27348984	NM_138704	Q8IW16|Q8TEI6|Q9H214	Missense_Mutation	SNP	ENST00000332303.4	37	CCDS10023.1	.	.	.	.	.	.	.	.	.	.	G	11.98	1.801208	0.31869	.	.	ENSG00000185115	ENST00000332303	T	0.03413	3.94	3.41	2.45	0.29901	.	.	.	.	.	T	0.03053	0.0090	L	0.27053	0.805	0.09310	N	1	P	0.42908	0.793	B	0.38842	0.283	T	0.47837	-0.9086	9	0.31617	T	0.26	.	8.55	0.33447	0.0:0.238:0.762:0.0	.	73	Q96MG7	MAGG1_HUMAN	G	73	ENSP00000330694:A73G	ENSP00000330694:A73G	A	-	2	0	NDNL2	27348984	0.658000	0.27402	0.002000	0.10522	0.019000	0.09904	2.296000	0.43584	0.959000	0.37980	0.563000	0.77884	GCC		0.701	NDNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251370.1	NM_138704	
TJP1	7082	broad.mit.edu	37	15	30053873	30053873	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:30053873G>A	ENST00000346128.6	-	7	1267	c.793C>T	c.(793-795)Cgg>Tgg	p.R265W	TJP1_ENST00000495972.2_Missense_Mutation_p.R265W|TJP1_ENST00000400011.2_Missense_Mutation_p.R269W|TJP1_ENST00000356107.6_Missense_Mutation_p.R265W|TJP1_ENST00000545208.2_Missense_Mutation_p.R265W	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	265					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.R265W(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)		AGCGTAGCCCGTTCATCTCTT	0.408																																					p.R265W	Melanoma(77;681 1843 6309 6570)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C793T	15						.						120.0	116.0	117.0					15																	30053873		1907	4119	6026	27841165	SO:0001583	missense	7082	exon7				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.793C>T	15.37:g.30053873G>A	ENSP00000281537:p.Arg265Trp	Somatic		Capture	Illumina HiSeq	Phase_I	27841165	NM_175610	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.148434	0.78001	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	5.81	5.81	0.92471	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.66934	0.2840	M	0.76002	2.32	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.983;0.995;0.993;0.992	T	0.65047	-0.6263	9	.	.	.	.	20.0688	0.97709	0.0:0.0:1.0:0.0	.	258;265;265;269	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	W	265;269;265;265;265	ENSP00000281537:R265W;ENSP00000382890:R269W;ENSP00000441202:R265W;ENSP00000348416:R265W	.	R	-	1	2	TJP1	27841165	1.000000	0.71417	0.993000	0.49108	0.552000	0.35366	3.456000	0.53000	2.751000	0.94390	0.555000	0.69702	CGG		0.408	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257	
FMN1	342184	broad.mit.edu	37	15	33091138	33091138	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:33091138G>A	ENST00000559047.1	-	16	3996	c.3997C>T	c.(3997-3999)Cga>Tga	p.R1333*	FMN1_ENST00000561249.1_Nonsense_Mutation_p.R1235*|FMN1_ENST00000334528.9_Nonsense_Mutation_p.R1110*			Q68DA7	FMN1_HUMAN	formin 1	1333	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R1110*(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		CCAAAATATCGTACTGTTGTT	0.453																																					p.R1110X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C3328T	15						.						71.0	63.0	65.0					15																	33091138		1874	4120	5994	30878430	SO:0001587	stop_gained	342184	exon15			AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.3997C>T	15.37:g.33091138G>A	ENSP00000454047:p.Arg1333*	Somatic		Capture	Illumina HiSeq	Phase_I	30878430	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Nonsense_Mutation	SNP	ENST00000559047.1	37		.	.	.	.	.	.	.	.	.	.	C	45	11.407197	0.99557	.	.	ENSG00000248905	ENST00000334528	.	.	.	5.86	4.95	0.65309	.	0.550760	0.21334	N	0.076259	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	11.5959	0.50972	0.0:0.8077:0.1258:0.0665	.	.	.	.	X	1110	.	ENSP00000333950:R1110X	R	-	1	2	FMN1	30878430	0.301000	0.24444	0.795000	0.32087	0.987000	0.75469	2.379000	0.44318	0.837000	0.34925	-0.120000	0.15030	CGA		0.453	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
RYR3	6263	broad.mit.edu	37	15	34032157	34032157	+	Missense_Mutation	SNP	C	C	T	rs201466342		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:34032157C>T	ENST00000389232.4	+	51	7851	c.7781C>T	c.(7780-7782)gCg>gTg	p.A2594V	RYR3_ENST00000415757.3_Missense_Mutation_p.A2594V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2594	4 X approximate repeats.				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.A2594V(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)		TCAGTGGATGCGGATGGCAAC	0.463																																					p.A2594V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C7781T	15						.	C	VAL/ALA	3,3929		0,3,1963	95.0	90.0	92.0		7781	5.6	1.0	15		92	0,8286		0,0,4143	yes	missense	RYR3	NM_001036.3	64	0,3,6106	TT,TC,CC		0.0,0.0763,0.0246	benign	2594/4871	34032157	3,12215	1966	4143	6109	31819449	SO:0001583	missense	6263	exon51				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.7781C>T	15.37:g.34032157C>T	ENSP00000373884:p.Ala2594Val	Somatic		Capture	Illumina HiSeq	Phase_I	31819449	NM_001036	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.005800	0.74932	7.63E-4	0.0	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.96802	-4.13;-4.13	5.55	5.55	0.83447	.	0.136757	0.47852	D	0.000216	D	0.92548	0.7633	L	0.41027	1.25	0.58432	D	0.999998	P;P	0.44429	0.542;0.835	B;B	0.29440	0.031;0.102	D	0.92078	0.5670	10	0.35671	T	0.21	.	19.6941	0.96016	0.0:1.0:0.0:0.0	.	2594;2594	Q15413-2;Q15413	.;RYR3_HUMAN	V	2594	ENSP00000373884:A2594V;ENSP00000399610:A2594V	ENSP00000354735:A2594V	A	+	2	0	RYR3	31819449	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	7.320000	0.79064	2.885000	0.99019	0.655000	0.94253	GCG		0.463	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
THBS1	7057	broad.mit.edu	37	15	39877702	39877702	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:39877702G>A	ENST00000260356.5	+	7	1223	c.1058G>A	c.(1057-1059)tGc>tAc	p.C353Y		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	353	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)	p.C353Y(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		AAGGTGTCCTGCCCCATCATG	0.498																																					p.C353Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1058A	15						.						254.0	166.0	196.0					15																	39877702		2200	4297	6497	37664994	SO:0001583	missense	7057	exon7				CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1058G>A	15.37:g.39877702G>A	ENSP00000260356:p.Cys353Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	37664994	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	G	32	5.159567	0.94686	.	.	ENSG00000137801	ENST00000260356	D	0.99474	-5.97	5.86	5.86	0.93980	von Willebrand factor, type C (4);	0.000000	0.36338	N	0.002654	D	0.99785	0.9910	H	0.98664	4.295	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.97219	0.9876	10	0.62326	D	0.03	-24.7531	19.1667	0.93560	0.0:0.0:1.0:0.0	.	353	P07996	TSP1_HUMAN	Y	353	ENSP00000260356:C353Y	ENSP00000260356:C353Y	C	+	2	0	THBS1	37664994	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.869000	0.99810	2.773000	0.95371	0.655000	0.94253	TGC		0.498	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
EIF2AK4	440275	broad.mit.edu	37	15	40231721	40231721	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:40231721G>A	ENST00000263791.5	+	2	203	c.160G>A	c.(160-162)Gaa>Aaa	p.E54K	EIF2AK4_ENST00000559624.1_Missense_Mutation_p.E54K|EIF2AK4_ENST00000382727.2_Missense_Mutation_p.E54K|EIF2AK4_ENST00000560648.1_Missense_Mutation_p.E54K	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	54	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)	p.E54K(2)		NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		AGAGCCCCCTGAAATCAATTT	0.343																																					p.E54K												.	.	2	Substitution - Missense(2)	large_intestine(1)|NS(1)	c.G160A	15						.						94.0	86.0	88.0					15																	40231721		1796	4065	5861	38019013	SO:0001583	missense	440275	exon2			AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.160G>A	15.37:g.40231721G>A	ENSP00000263791:p.Glu54Lys	Somatic		Capture	Illumina HiSeq	Phase_I	38019013	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	37	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	G	31	5.085238	0.94100	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.42900	0.96;0.96	5.7	5.7	0.88788	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.000000	0.85682	D	0.000000	T	0.60612	0.2282	M	0.63843	1.955	0.58432	D	0.999995	D;D	0.69078	0.997;0.996	D;D	0.81914	0.995;0.977	T	0.51865	-0.8651	10	0.12766	T	0.61	-21.6972	18.5987	0.91239	0.0:0.0:1.0:0.0	.	54;54	Q9P2K8;Q9P2K8-3	E2AK4_HUMAN;.	K	54	ENSP00000263791:E54K;ENSP00000372174:E54K	ENSP00000263791:E54K	E	+	1	0	EIF2AK4	38019013	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.169000	0.89672	2.665000	0.90641	0.655000	0.94253	GAA		0.343	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1		
EIF2AK4	440275	broad.mit.edu	37	15	40259936	40259936	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:40259936C>T	ENST00000263791.5	+	9	1452	c.1409C>T	c.(1408-1410)gCt>gTt	p.A470V	EIF2AK4_ENST00000382727.2_Missense_Mutation_p.A470V|EIF2AK4_ENST00000559624.1_Missense_Mutation_p.A470V	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	470	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)	p.A470V(1)		NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		AGTGACAATGCTCTGCCTTAT	0.502																																					p.A470V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1409T	15						.						135.0	128.0	130.0					15																	40259936		1981	4166	6147	38047228	SO:0001583	missense	440275	exon9			AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.1409C>T	15.37:g.40259936C>T	ENSP00000263791:p.Ala470Val	Somatic		Capture	Illumina HiSeq	Phase_I	38047228	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	37	CCDS42016.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.824954	0.90955	.	.	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.60040	0.22;0.22	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.179734	0.48767	D	0.000166	T	0.58366	0.2117	N	0.25060	0.705	0.47094	D	0.999319	P;P	0.52061	0.916;0.95	P;P	0.56434	0.798;0.72	T	0.52162	-0.8612	10	0.25751	T	0.34	-17.7614	16.9776	0.86317	0.0:0.8728:0.1272:0.0	.	470;470	Q9P2K8;Q9P2K8-3	E2AK4_HUMAN;.	V	470	ENSP00000263791:A470V;ENSP00000372174:A470V	ENSP00000263791:A470V	A	+	2	0	EIF2AK4	38047228	0.999000	0.42202	0.979000	0.43373	0.972000	0.66771	4.124000	0.57924	2.803000	0.96430	0.650000	0.86243	GCT		0.502	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1		
PLCB2	5330	broad.mit.edu	37	15	40590556	40590556	+	Silent	SNP	C	C	T	rs577175439		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:40590556C>T	ENST00000260402.3	-	11	1272	c.1023G>A	c.(1021-1023)tcG>tcA	p.S341S	PLCB2_ENST00000456256.2_Silent_p.S341S|PLCB2-AS1_ENST00000559520.1_RNA|PLCB2_ENST00000557821.1_Silent_p.S341S	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	341	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.S341S(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		ACATCTCAGCCGAGGAGAGGC	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		20651	0.001		0.0	False		,,,				2504	0.0				p.S341S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1023A	15						.						34.0	37.0	36.0					15																	40590556		2083	4242	6325	38377848	SO:0001819	synonymous_variant	5330	exon11				CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.1023G>A	15.37:g.40590556C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38377848	NM_004573	A8K6J2|B9EGH5	Silent	SNP	ENST00000260402.3	37	CCDS42020.1																																																																																				0.632	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1		
ZFYVE19	84936	broad.mit.edu	37	15	41105093	41105093	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:41105093C>T	ENST00000355341.4	+	7	1524	c.1023C>T	c.(1021-1023)ccC>ccT	p.P341P	ZFYVE19_ENST00000570108.1_Silent_p.P318P|ZFYVE19_ENST00000336455.5_Silent_p.P331P|ZFYVE19_ENST00000299173.10_Intron|ZFYVE19_ENST00000564258.1_Silent_p.P166P	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19	341					abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis checkpoint (GO:0031565)|negative regulation of cytokinesis (GO:0032466)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|midbody (GO:0030496)	phosphatidylinositol-3-phosphate binding (GO:0032266)|zinc ion binding (GO:0008270)	p.P341P(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9		all_cancers(109;3.31e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		GACAGGACCCCGAGAGAGGTG	0.637																																					p.P341P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1023T	15						.						42.0	50.0	47.0					15																	41105093		2028	4181	6209	38892385	SO:0001819	synonymous_variant	84936	exon7			AK027746	CCDS42025.1, CCDS58353.1, CCDS58354.1, CCDS58355.1	15q14	2008-05-02				ENSG00000166140		"""Zinc fingers, FYVE domain containing"""	20758	protein-coding gene	gene with protein product							Standard	NM_001077268		Approved	FLJ14840	uc031qrk.1	Q96K21		ENST00000355341.4:c.1023C>T	15.37:g.41105093C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38892385	NM_001077268	B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Silent	SNP	ENST00000355341.4	37	CCDS42025.1																																																																																				0.637	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1	NM_032850	
VPS18	57617	broad.mit.edu	37	15	41195112	41195112	+	Missense_Mutation	SNP	G	G	A	rs373196086		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:41195112G>A	ENST00000220509.5	+	5	2834	c.2495G>A	c.(2494-2496)cGc>cAc	p.R832H		NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	832					endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|vesicle-mediated transport (GO:0016192)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)	p.R832H(1)		autonomic_ganglia(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	28		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		AGTGCCCAGCGCATCCGGCGA	0.627																																					p.R832H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2495A	15						.	G	HIS/ARG	0,4406		0,0,2203	67.0	70.0	69.0		2495	5.8	1.0	15		69	1,8599	1.2+/-3.3	0,1,4299	no	missense	VPS18	NM_020857.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	832/974	41195112	1,13005	2203	4300	6503	38982404	SO:0001583	missense	57617	exon5			AF308802	CCDS10069.1	15q14-q15	2006-12-19	2006-12-19		ENSG00000104142	ENSG00000104142			15972	protein-coding gene	gene with protein product		608551	"""vacuolar protein sorting protein 18"""			11250079, 16203730	Standard	NM_020857		Approved	KIAA1475, PEP3	uc001zne.3	Q9P253	OTTHUMG00000130135	ENST00000220509.5:c.2495G>A	15.37:g.41195112G>A	ENSP00000220509:p.Arg832His	Somatic		Capture	Illumina HiSeq	Phase_I	38982404	NM_020857	Q8TCG0|Q96DI3|Q9H268	Missense_Mutation	SNP	ENST00000220509.5	37	CCDS10069.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.824497	0.90955	0.0	1.16E-4	ENSG00000104142	ENST00000220509	T	0.44083	0.93	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.55657	0.1934	L	0.45581	1.43	0.80722	D	1	D	0.71674	0.998	P	0.58210	0.835	T	0.50964	-0.8765	10	0.46703	T	0.11	-31.6896	19.9616	0.97254	0.0:0.0:1.0:0.0	.	832	Q9P253	VPS18_HUMAN	H	832	ENSP00000220509:R832H	ENSP00000220509:R832H	R	+	2	0	VPS18	38982404	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.869000	0.99810	2.724000	0.93272	0.561000	0.74099	CGC		0.627	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2		
MAPKBP1	23005	broad.mit.edu	37	15	42103106	42103106	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:42103106C>T	ENST00000456763.2	+	4	428	c.232C>T	c.(232-234)Cgg>Tgg	p.R78W	MAPKBP1_ENST00000514566.1_Missense_Mutation_p.R78W|MAPKBP1_ENST00000457542.2_Missense_Mutation_p.R78W|MAPKBP1_ENST00000260357.7_5'UTR|MAPKBP1_ENST00000221214.6_Missense_Mutation_p.R78W|MAPKBP1_ENST00000507762.1_3'UTR	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	78								p.R78W(1)|p.R78G(1)		breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		GTTCAATCCCCGGAAACACAA	0.557																																					p.R78W												.	.	2	Substitution - Missense(2)	large_intestine(1)|skin(1)	c.C232T	15						.						169.0	153.0	159.0					15																	42103106		2203	4300	6503	39890398	SO:0001583	missense	23005	exon4			AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"""WD repeat domain containing"""	29536	protein-coding gene	gene with protein product			"""mitogen activated protein kinase binding protein 1"""			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.232C>T	15.37:g.42103106C>T	ENSP00000393099:p.Arg78Trp	Somatic		Capture	Illumina HiSeq	Phase_I	39890398	NM_014994	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	37	CCDS45239.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	20.2|20.2	3.957411|3.957411	0.73902|0.73902	.|.	.|.	ENSG00000137802|ENSG00000137802	ENST00000507762|ENST00000457542;ENST00000221214;ENST00000456763;ENST00000514566;ENST00000510535	.|T;T;T;T;T	.|0.58210	.|4.95;0.35;4.95;4.95;2.26	5.03|5.03	3.07|3.07	0.35406|0.35406	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.|0.221418	.|0.41294	.|D	.|0.000906	T|T	0.62392|0.62392	0.2424|0.2424	L|L	0.47190|0.47190	1.495|1.495	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.999;0.999;0.998	.|P;D;D	.|0.64042	.|0.899;0.915;0.921	T|T	0.64786|0.64786	-0.6325|-0.6325	6|10	0.87932|0.87932	D|D	0|0	-19.5738|-19.5738	13.2219|13.2219	0.59892|0.59892	0.4842:0.5158:0.0:0.0|0.4842:0.5158:0.0:0.0	.|.	.|78;78;78	.|O60336-2;O60336;O60336-6	.|.;MABP1_HUMAN;.	L|W	58|78	.|ENSP00000397570:R78W;ENSP00000221214:R78W;ENSP00000393099:R78W;ENSP00000426154:R78W;ENSP00000422132:R78W	ENSP00000421891:P47L|ENSP00000221214:R78W	P|R	+|+	2|1	0|2	MAPKBP1|MAPKBP1	39890398|39890398	0.977000|0.977000	0.34250|0.34250	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	0.390000|0.390000	0.20768|0.20768	0.645000|0.645000	0.30675|0.30675	0.655000|0.655000	0.94253|0.94253	CCG|CGG		0.557	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994	
SPTBN5	51332	broad.mit.edu	37	15	42147062	42147062	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:42147062C>T	ENST00000320955.6	-	56	9763	c.9536G>A	c.(9535-9537)cGc>cAc	p.R3179H	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3179					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)	p.R3179H(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		GTGGGGATAGCGCCTGGGTGC	0.592																																					p.R3144H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G9431A	15						.						58.0	61.0	60.0					15																	42147062		1935	4136	6071	39934354	SO:0001583	missense	51332	exon56			AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.9536G>A	15.37:g.42147062C>T	ENSP00000317790:p.Arg3179His	Somatic		Capture	Illumina HiSeq	Phase_I	39934354	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	1.469	-0.560262	0.03939	.	.	ENSG00000137877	ENST00000320955	T	0.34275	1.37	5.2	-5.5	0.02576	.	1.645850	0.03129	N	0.164983	T	0.14227	0.0344	N	0.08118	0	0.09310	N	1	B	0.33103	0.397	B	0.33392	0.163	T	0.08126	-1.0737	10	0.13853	T	0.58	.	1.4043	0.02277	0.1999:0.3694:0.1003:0.3304	.	3179	Q9NRC6	SPTN5_HUMAN	H	3179	ENSP00000317790:R3179H	ENSP00000317790:R3179H	R	-	2	0	SPTBN5	39934354	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.938000	0.03938	-1.680000	0.01450	-1.545000	0.00906	CGC		0.592	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
SPTBN5	51332	broad.mit.edu	37	15	42164500	42164500	+	Splice_Site	SNP	C	C	T	rs554140412	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:42164500C>T	ENST00000320955.6	-	27	5392	c.5165G>A	c.(5164-5166)cGg>cAg	p.R1722Q		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1722					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)	p.R1722Q(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		GTGTCCTCACCGTGTGGCCGC	0.627													C|||	2	0.000399361	0.0	0.0	5008	,	,		18561	0.0		0.0	False		,,,				2504	0.002				p.R1687Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5060A	15						.						34.0	39.0	37.0					15																	42164500		2160	4261	6421	39951792	SO:0001630	splice_region_variant	51332	exon27			AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.5165+1G>A	15.37:g.42164500C>T		Somatic		Capture	Illumina HiSeq	Phase_I	39951792	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		.	.	.	.	.	.	.	.	.	.	.	17.55	3.416626	0.62511	.	.	ENSG00000137877	ENST00000320955	T	0.61040	0.14	4.55	4.55	0.56014	.	0.000000	0.64402	D	0.000002	T	0.79678	0.4487	M	0.90870	3.155	0.35322	D	0.784881	D	0.89917	1.0	D	0.91635	0.999	D	0.87919	0.2702	9	.	.	.	.	12.8232	0.57704	0.0:1.0:0.0:0.0	.	1722	Q9NRC6	SPTN5_HUMAN	Q	1722	ENSP00000317790:R1722Q	.	R	-	2	0	SPTBN5	39951792	0.990000	0.36364	0.991000	0.47740	0.096000	0.18686	2.234000	0.43035	2.087000	0.62958	0.561000	0.74099	CGG		0.627	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	Missense_Mutation
PLA2G4D	283748	broad.mit.edu	37	15	42364008	42364008	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:42364008T>C	ENST00000290472.3	-	15	1631	c.1537A>G	c.(1537-1539)Agg>Ggg	p.R513G		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	513	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)	p.R513G(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		GGGATCCTCCTCATCAGCCGT	0.617																																					p.R513G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1537G	15						.						49.0	53.0	52.0					15																	42364008		2203	4299	6502	40151300	SO:0001583	missense	283748	exon15			AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1537A>G	15.37:g.42364008T>C	ENSP00000290472:p.Arg513Gly	Somatic		Capture	Illumina HiSeq	Phase_I	40151300	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	.	.	.	.	.	.	.	.	.	.	T	16.91	3.252913	0.59212	.	.	ENSG00000159337	ENST00000290472	T	0.04194	3.68	4.79	4.79	0.61399	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.374808	0.23768	N	0.044741	T	0.07188	0.0182	L	0.34521	1.04	0.36349	D	0.859993	P	0.47484	0.896	P	0.46172	0.506	T	0.31641	-0.9936	10	0.59425	D	0.04	-7.4413	14.0078	0.64475	0.0:0.0:0.0:1.0	.	513	Q86XP0	PA24D_HUMAN	G	513	ENSP00000290472:R513G	ENSP00000290472:R513G	R	-	1	2	PLA2G4D	40151300	1.000000	0.71417	0.950000	0.38849	0.231000	0.25187	2.538000	0.45710	1.798000	0.52647	0.459000	0.35465	AGG		0.617	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
GANC	2595	broad.mit.edu	37	15	42614213	42614213	+	Missense_Mutation	SNP	C	C	T	rs368575859		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:42614213C>T	ENST00000318010.8	+	11	1528	c.1288C>T	c.(1288-1290)Cgt>Tgt	p.R430C		NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	430					carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)	p.R430C(1)		breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	GAGCAAAAAGCGTAAGGTAAA	0.428																																					p.R430C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1288T	15						.	C	CYS/ARG	0,4406		0,0,2203	52.0	46.0	48.0		1288	5.4	1.0	15		48	1,8597	1.2+/-3.3	0,1,4298	no	missense	GANC	NM_198141.2	180	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	430/915	42614213	1,13003	2203	4299	6502	40401505	SO:0001583	missense	2595	exon11			AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	3.2.1.20		4139	protein-coding gene	gene with protein product		104180				6995030, 12370436	Standard	NM_198141		Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000318010.8:c.1288C>T	15.37:g.42614213C>T	ENSP00000326227:p.Arg430Cys	Somatic		Capture	Illumina HiSeq	Phase_I	40401505	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Missense_Mutation	SNP	ENST00000318010.8	37	CCDS10084.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.042404	0.75732	0.0	1.16E-4	ENSG00000214013	ENST00000318010	D	0.92911	-3.13	5.4	5.4	0.78164	Glycoside hydrolase, superfamily (1);	0.051919	0.64402	D	0.000001	D	0.97176	0.9077	M	0.92691	3.335	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97924	1.0316	10	0.87932	D	0	-10.4203	19.18	0.93619	0.0:1.0:0.0:0.0	.	430	Q8TET4	GANC_HUMAN	C	430	ENSP00000326227:R430C	ENSP00000326227:R430C	R	+	1	0	GANC	40401505	1.000000	0.71417	0.992000	0.48379	0.831000	0.47069	3.750000	0.55157	2.532000	0.85374	0.561000	0.74099	CGT		0.428	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141	
ZNF106	64397	broad.mit.edu	37	15	42740764	42740764	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:42740764G>A	ENST00000263805.4	-	3	2898	c.2572C>T	c.(2572-2574)Cga>Tga	p.R858*	ZNF106_ENST00000565380.1_Nonsense_Mutation_p.R86*|ZNF106_ENST00000565611.1_Nonsense_Mutation_p.R43*	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	858					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R858*(1)									GAAAGGCTTCGCTTTCTTGCC	0.498																																					p.R858X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2572T	15						.						66.0	61.0	63.0					15																	42740764		2203	4299	6502	40528056	SO:0001587	stop_gained	64397	exon3			AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"""Zinc fingers, C2H2-type"""	12886	protein-coding gene	gene with protein product	"""SH3-domain binding protein 3"""		"""zinc finger protein 106 homolog (mouse)"""	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.2572C>T	15.37:g.42740764G>A	ENSP00000263805:p.Arg858*	Somatic		Capture	Illumina HiSeq	Phase_I	40528056	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Nonsense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	G	44	10.672520	0.99447	.	.	ENSG00000103994	ENST00000263805;ENST00000434903	.	.	.	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7285	18.7539	0.91825	0.0:0.0:1.0:0.0	.	.	.	.	X	858;86	.	ENSP00000263805:R858X	R	-	1	2	ZFP106	40528056	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.938000	0.87678	2.652000	0.90054	0.655000	0.94253	CGA		0.498	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
TMEM62	80021	broad.mit.edu	37	15	43476512	43476512	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:43476512C>T	ENST00000260403.2	+	14	1939	c.1660C>T	c.(1660-1662)Cgg>Tgg	p.R554W	CCNDBP1_ENST00000356633.5_5'Flank|CCNDBP1_ENST00000300213.4_5'Flank|RP11-473C18.3_ENST00000565685.1_RNA|EPB42_ENST00000563128.1_Intron|TMEM62_ENST00000569369.1_3'UTR	NM_024956.3	NP_079232.3	Q0P6H9	TMM62_HUMAN	transmembrane protein 62	554						integral component of membrane (GO:0016021)		p.R554W(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		all_cancers(109;1.16e-10)|all_epithelial(112;2.01e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;4.23e-07)		CTTGCTGCAGCGGTGCTTTGG	0.448																																					p.R554W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1660T	15						.						176.0	167.0	170.0					15																	43476512		2203	4299	6502	41263804	SO:0001583	missense	80021	exon14			BC009981	CCDS32210.1	15q15.2	2014-09-11			ENSG00000137842	ENSG00000137842			26269	protein-coding gene	gene with protein product							Standard	NM_024956		Approved	FLJ23375	uc001zqr.3	Q0P6H9	OTTHUMG00000176485	ENST00000260403.2:c.1660C>T	15.37:g.43476512C>T	ENSP00000260403:p.Arg554Trp	Somatic		Capture	Illumina HiSeq	Phase_I	41263804	NM_024956	Q6I9Y5|Q9H5J6	Missense_Mutation	SNP	ENST00000260403.2	37	CCDS32210.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.969191	0.74246	.	.	ENSG00000137842	ENST00000260403	.	.	.	5.13	2.16	0.27623	.	0.000000	0.85682	D	0.000000	T	0.77678	0.4166	M	0.77103	2.36	0.58432	D	0.999999	D	0.89917	1.0	D	0.79108	0.992	T	0.79662	-0.1710	9	0.72032	D	0.01	-10.4301	14.2245	0.65850	0.3913:0.6087:0.0:0.0	.	554	Q0P6H9	TMM62_HUMAN	W	554	.	ENSP00000260403:R554W	R	+	1	2	TMEM62	41263804	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	2.454000	0.44979	0.298000	0.22638	0.561000	0.74099	CGG		0.448	TMEM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432227.1	NM_024956	
EPB42	2038	broad.mit.edu	37	15	43501560	43501560	+	Silent	SNP	G	G	A	rs138033246	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:43501560G>A	ENST00000441366.2	-	6	969	c.744C>T	c.(742-744)agC>agT	p.S248S	EPB42_ENST00000563128.1_5'Flank|EPB42_ENST00000540029.1_Silent_p.S170S|EPB42_ENST00000300215.3_Silent_p.S278S	NM_000119.2|NM_001114134.1	NP_000110.2|NP_001107606.1	P16452	EPB42_HUMAN	erythrocyte membrane protein band 4.2	248					cell morphogenesis (GO:0000902)|erythrocyte maturation (GO:0043249)|hemoglobin metabolic process (GO:0020027)|iron ion homeostasis (GO:0055072)|peptide cross-linking (GO:0018149)|regulation of cell shape (GO:0008360)|spleen development (GO:0048536)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|structural constituent of cytoskeleton (GO:0005200)	p.S278S(1)		endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.7e-07)		GGATGGGCACGCTGCCCCGGC	0.652													G|||	3	0.000599042	0.0	0.0043	5008	,	,		17478	0.0		0.0	False		,,,				2504	0.0				p.S248S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C744T	15						.	G	,	1,4405	2.1+/-5.4	0,1,2202	47.0	47.0	47.0		834,744	-1.9	1.0	15	dbSNP_134	47	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous	EPB42	NM_000119.2,NM_001114134.1	,	0,1,6500	AA,AG,GG		0.0,0.0227,0.0077	,	278/722,248/692	43501560	1,13001	2203	4298	6501	41288852	SO:0001819	synonymous_variant	2038	exon6			M60298	CCDS10093.1, CCDS45249.1	15q15-q21	2013-05-02			ENSG00000166947	ENSG00000166947		"""Transglutaminases"""	3381	protein-coding gene	gene with protein product	"""Erythrocyte surface protein band 4.2"""	177070				1284644	Standard	NM_000119		Approved	PA, MGC116735, MGC116737	uc001zrb.4	P16452	OTTHUMG00000130701	ENST00000441366.2:c.744C>T	15.37:g.43501560G>A		Somatic		Capture	Illumina HiSeq	Phase_I	41288852	NM_001114134	Q4KKX0|Q4VB97	Silent	SNP	ENST00000441366.2	37	CCDS45249.1																																																																																				0.652	EPB42-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432219.1	NM_000119	
TGM5	9333	broad.mit.edu	37	15	43544971	43544971	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:43544971G>A	ENST00000220420.5	-	6	855	c.848C>T	c.(847-849)gCc>gTc	p.A283V	TGM5_ENST00000349114.4_Missense_Mutation_p.A201V	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	283					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.A283V(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	GCACATGACGGCAGCAAAGAC	0.592																																					p.A201V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C602T	15						.						73.0	72.0	72.0					15																	43544971		2202	4299	6501	41332263	SO:0001583	missense	9333	exon5			AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"""Transglutaminases"""	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.848C>T	15.37:g.43544971G>A	ENSP00000220420:p.Ala283Val	Somatic		Capture	Illumina HiSeq	Phase_I	41332263	NM_004245	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.590703	0.86851	.	.	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	D;D	0.88277	-2.36;-2.36	4.88	4.88	0.63580	Transglutaminase, conserved site (1);Transglutaminase-like (2);	0.000000	0.85682	D	0.000000	D	0.94725	0.8298	M	0.84773	2.715	0.46279	D	0.998966	D;D	0.89917	1.0;0.999	D;D	0.77557	0.987;0.99	D	0.95459	0.8541	10	0.87932	D	0	-14.1091	15.8779	0.79180	0.0:0.0:1.0:0.0	.	201;283	O43548-2;O43548	.;TGM5_HUMAN	V	283;201;282	ENSP00000220420:A283V;ENSP00000220419:A201V	ENSP00000220420:A283V	A	-	2	0	TGM5	41332263	0.949000	0.32298	0.710000	0.30468	0.958000	0.62258	1.875000	0.39578	2.408000	0.81797	0.655000	0.94253	GCC		0.592	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245	
TUBGCP4	27229	broad.mit.edu	37	15	43690283	43690283	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:43690283C>T	ENST00000260383.7	+	13	1581	c.1327C>T	c.(1327-1329)Cgg>Tgg	p.R443W	TUBGCP4_ENST00000564079.1_Missense_Mutation_p.R442W|TUBGCP4_ENST00000399460.3_Missense_Mutation_p.R307W			Q9UGJ1	GCP4_HUMAN	tubulin, gamma complex associated protein 4	443					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)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|spindle pole (GO:0000922)	structural constituent of cytoskeleton (GO:0005200)	p.R442W(1)		breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(4)|prostate(2)|upper_aerodigestive_tract(2)	21		all_cancers(109;1.27e-10)|all_epithelial(112;4.82e-09)|Lung NSC(122;1.72e-06)|all_lung(180;1.59e-05)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;3.53e-07)		AACTTCTCCCCGGGAAGCCCC	0.468																																					p.R442W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1324T	15						.						127.0	124.0	125.0					15																	43690283		1815	4070	5885	41477575	SO:0001583	missense	27229	exon13			AJ249677	CCDS42030.1, CCDS66745.1	15q15.3	2014-08-12			ENSG00000137822	ENSG00000137822			16691	protein-coding gene	gene with protein product		609610				10562286	Standard	NM_001286414		Approved	76P, FLJ14797	uc001zrn.3	Q9UGJ1	OTTHUMG00000176647	ENST00000260383.7:c.1327C>T	15.37:g.43690283C>T	ENSP00000260383:p.Arg443Trp	Somatic		Capture	Illumina HiSeq	Phase_I	41477575	NM_014444	B3KNK6|Q969X3|Q9NVF0	Missense_Mutation	SNP	ENST00000260383.7	37		.	.	.	.	.	.	.	.	.	.	C	24.1	4.490965	0.84962	.	.	ENSG00000137822	ENST00000260383;ENST00000399460	T	0.08807	3.05	5.77	4.86	0.63082	.	0.047574	0.85682	N	0.000000	T	0.16727	0.0402	L	0.46157	1.445	0.58432	D	0.999999	D;D	0.65815	0.995;0.994	P;P	0.58970	0.849;0.764	T	0.00611	-1.1645	10	0.59425	D	0.04	-18.7968	9.4358	0.38637	0.1412:0.7867:0.0:0.0721	.	443;442	Q9UGJ1;Q9UGJ1-2	GCP4_HUMAN;.	W	442;307	ENSP00000382387:R307W	ENSP00000260383:R442W	R	+	1	2	TUBGCP4	41477575	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.641000	0.54360	1.578000	0.49821	0.655000	0.94253	CGG		0.468	TUBGCP4-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000432970.1	NM_014444	
PPIP5K1	9677	broad.mit.edu	37	15	43873473	43873473	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:43873473C>T	ENST00000396923.3	-	8	1012	c.891G>A	c.(889-891)ctG>ctA	p.L297L	PPIP5K1_ENST00000420765.1_Silent_p.L297L|PPIP5K1_ENST00000334933.4_Silent_p.L297L|PPIP5K1_ENST00000381885.1_Silent_p.L297L|PPIP5K1_ENST00000432870.3_5'UTR|PPIP5K1_ENST00000360301.4_Silent_p.L297L|PPIP5K1_ENST00000348806.6_Silent_p.L297L|PPIP5K1_ENST00000381879.4_Silent_p.L297L|PPIP5K1_ENST00000360135.4_Silent_p.L297L			Q6PFW1	VIP1_HUMAN	diphosphoinositol pentakisphosphate kinase 1	297					inositol metabolic process (GO:0006020)|inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	acid phosphatase activity (GO:0003993)|ATP binding (GO:0005524)|diphosphoinositol-pentakisphosphate kinase activity (GO:0033857)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol-1,3,4,5,6-pentakisphosphate kinase activity (GO:0000827)	p.L297L(1)		large_intestine(1)	1						CCATGGCAGTCAGCATGACTG	0.507																																					p.L297L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G891A	15						.						156.0	138.0	144.0					15																	43873473		2198	4296	6494	41660765	SO:0001819	synonymous_variant	9677	exon8			AF502586	CCDS32215.1, CCDS45252.1, CCDS53937.1	15q15.3	2010-01-27	2010-01-26	2010-01-26	ENSG00000168781	ENSG00000168781	2.7.4.24		29023	protein-coding gene	gene with protein product		610979	"""histidine acid phosphatase domain containing 2A"""	HISPPD2A		17412958, 17690096, 18981179	Standard	NM_001190214		Approved	KIAA0377, IPS1, VIP1	uc001zrw.3	Q6PFW1	OTTHUMG00000059758	ENST00000396923.3:c.891G>A	15.37:g.43873473C>T		Somatic		Capture	Illumina HiSeq	Phase_I	41660765	NM_001130859	O15082|Q5HYF8|Q7Z3A7|Q86TE7|Q86UV3|Q86UV4|Q86XW8|Q8IZN0	Silent	SNP	ENST00000396923.3	37	CCDS45252.1																																																																																				0.507	PPIP5K1-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132907.1	NM_014659	
CKMT1B	1159	broad.mit.edu	37	15	43891392	43891392	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:43891392A>G	ENST00000441322.1	+	9	1535	c.1175A>G	c.(1174-1176)tAt>tGt	p.Y392C	CKMT1B_ENST00000300283.6_Missense_Mutation_p.Y392C			P12532	KCRU_HUMAN	creatine kinase, mitochondrial 1B	392	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)	p.Y392C(1)		large_intestine(1)|lung(3)|skin(1)	5		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;3.56e-07)	Creatine(DB00148)	GGAGTAAACTATTTGATTGAT	0.483																																					p.Y392C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1175G	15						.						196.0	174.0	181.0					15																	43891392		2200	4297	6497	41678684	SO:0001583	missense	1159	exon10			AK094322, J04469	CCDS10097.1	15q15	2005-04-15		2005-04-15	ENSG00000237289	ENSG00000237289	2.7.3.2		1995	protein-coding gene	gene with protein product		123290	"""creatine kinase, mitochondrial 1 (ubiquitous)"""	CKMT, CKMT1			Standard	XM_005254150		Approved	UMTCK	uc001zsc.3	P12532	OTTHUMG00000059900	ENST00000441322.1:c.1175A>G	15.37:g.43891392A>G	ENSP00000413255:p.Tyr392Cys	Somatic		Capture	Illumina HiSeq	Phase_I	41678684	NM_020990	B4DIT8|B7ZA09|Q0VAM3|Q32NF6|Q53FC4	Missense_Mutation	SNP	ENST00000441322.1	37	CCDS10097.1	.	.	.	.	.	.	.	.	.	.	A	14.27	2.486322	0.44147	.	.	ENSG00000237289	ENST00000300283;ENST00000441322	T;T	0.11277	2.79;2.79	4.03	2.87	0.33458	ATP:guanido phosphotransferase, catalytic domain (2);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.059264	0.64402	D	0.000001	T	0.10294	0.0252	L	0.46157	1.445	0.80722	D	1	B;B	0.14438	0.003;0.01	B;B	0.15052	0.001;0.012	T	0.08554	-1.0716	10	0.46703	T	0.11	0.7739	9.2445	0.37518	0.8382:0.0:0.0:0.1618	.	423;392	P12532-2;P12532	.;KCRU_HUMAN	C	392	ENSP00000300283:Y392C;ENSP00000413255:Y392C	ENSP00000300283:Y392C	Y	+	2	0	CKMT1B	41678684	1.000000	0.71417	0.998000	0.56505	0.730000	0.41778	6.097000	0.71452	0.688000	0.31529	0.260000	0.18958	TAT		0.483	CKMT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133147.2	NM_020990	
ELL3	80237	broad.mit.edu	37	15	44068278	44068278	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:44068278G>A	ENST00000319359.3	-	3	881	c.240C>T	c.(238-240)ggC>ggT	p.G80G	RP11-296A16.1_ENST00000417761.2_3'UTR|SERF2_ENST00000381359.1_5'Flank|ELL3_ENST00000497465.1_5'Flank	NM_025165.2	NP_079441.1	Q9HB65	ELL3_HUMAN	elongation factor RNA polymerase II-like 3	80					DNA-templated transcription, elongation (GO:0006354)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epithelial to mesenchymal transition (GO:0010717)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	enhancer binding (GO:0035326)	p.G80G(1)		cervix(1)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)	13		all_cancers(109;7.57e-15)|all_epithelial(112;3.51e-12)|Lung NSC(122;4.72e-08)|all_lung(180;4.9e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;7.81e-07)		TACCACCAGCGCCCTCCTGAC	0.582																																					p.G80G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C240T	15						.						103.0	91.0	95.0					15																	44068278		2198	4298	6496	41855570	SO:0001819	synonymous_variant	80237	exon3			AF276512	CCDS10102.1	15q15.1	2008-02-05			ENSG00000128886	ENSG00000128886			23113	protein-coding gene	gene with protein product		609885				10882741	Standard	NM_025165		Approved	FLJ22637	uc001zsw.1	Q9HB65	OTTHUMG00000059936	ENST00000319359.3:c.240C>T	15.37:g.44068278G>A		Somatic		Capture	Illumina HiSeq	Phase_I	41855570	NM_025165	B3KQ66|B3KX08|Q6I9Z7|Q9H634	Silent	SNP	ENST00000319359.3	37	CCDS10102.1																																																																																				0.582	ELL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133236.2	NM_025165	
DUOXA1	90527	broad.mit.edu	37	15	45412393	45412393	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:45412393G>A	ENST00000560572.1	-	5	685	c.680C>T	c.(679-681)gCc>gTc	p.A227V	DUOXA1_ENST00000559014.1_Missense_Mutation_p.A227V|DUOXA1_ENST00000430224.2_Missense_Mutation_p.A182V|DUOXA1_ENST00000267803.4_Missense_Mutation_p.A227V|DUOXA1_ENST00000558996.1_Missense_Mutation_p.A182V|DUOXA1_ENST00000558422.1_Missense_Mutation_p.A182V	NM_001276266.1	NP_001263195.1	Q1HG43	DOXA1_HUMAN	dual oxidase maturation factor 1	227					hydrogen peroxide metabolic process (GO:0042743)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein transport (GO:0015031)|regulation of inflammatory response (GO:0050727)|regulation of thyroid hormone generation (GO:2000609)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A227V(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(109;6.02e-08)|all_epithelial(112;1.83e-06)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.82e-18)|GBM - Glioblastoma multiforme(94;4.39e-07)|COAD - Colon adenocarcinoma(120;0.0676)|Colorectal(133;0.0686)		GAGTGATGTGGCCATGGAGAA	0.562																																					p.A227V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C680T	15						.						190.0	173.0	178.0					15																	45412393		2198	4298	6496	43199685	SO:0001583	missense	90527	exon8			BC029819	CCDS10119.1, CCDS61619.1, CCDS61620.1, CCDS61621.1	15q21.1	2006-11-29	2006-01-23	2006-07-25	ENSG00000140254	ENSG00000140254			26507	protein-coding gene	gene with protein product		612771				16651268	Standard	NM_144565		Approved	FLJ32334, NUMBIP, NIP, mol	uc010bec.4	Q1HG43	OTTHUMG00000131352	ENST00000560572.1:c.680C>T	15.37:g.45412393G>A	ENSP00000454084:p.Ala227Val	Somatic		Capture	Illumina HiSeq	Phase_I	43199685	NM_144565	Q8N6K9|Q96MI4	Missense_Mutation	SNP	ENST00000560572.1	37		.	.	.	.	.	.	.	.	.	.	G	12.34	1.907222	0.33628	.	.	ENSG00000140254	ENST00000267803;ENST00000430224	T;T	0.49720	0.77;0.77	5.12	2.18	0.27775	.	0.465542	0.23608	N	0.046371	T	0.18173	0.0436	N	0.03281	-0.365	0.29028	N	0.885885	B;B;B;B	0.18610	0.029;0.001;0.001;0.015	B;B;B;B	0.28991	0.097;0.007;0.007;0.03	T	0.33803	-0.9854	10	0.02654	T	1	-2.1538	4.251	0.10695	0.3435:0.1797:0.4768:0.0	.	182;182;227;227	B5M0C0;B5M0B8;Q1HG43;A8K9Q6	.;.;DOXA1_HUMAN;.	V	227;182	ENSP00000267803:A227V;ENSP00000415512:A182V	ENSP00000267803:A227V	A	-	2	0	DUOXA1	43199685	0.000000	0.05858	0.415000	0.26534	0.905000	0.53344	-0.228000	0.09114	0.306000	0.22856	-0.321000	0.08615	GCC		0.562	DUOXA1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000416242.1	NM_144565	
DUOX1	53905	broad.mit.edu	37	15	45437127	45437127	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:45437127C>T	ENST00000321429.4	+	19	2578	c.2171C>T	c.(2170-2172)gCg>gTg	p.A724V	DUOX1_ENST00000389037.3_Missense_Mutation_p.A724V|DUOX1_ENST00000561166.1_Missense_Mutation_p.A370V	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	724					cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)	p.A724V(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		GAGCGGCAGGCGCTGGTGGAA	0.582																																					p.A724V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2171T	15						.						83.0	97.0	93.0					15																	45437127		2198	4298	6496	43224419	SO:0001583	missense	53905	exon19			AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"""EF-hand domain containing"""	3062	protein-coding gene	gene with protein product	"""NADPH thyroid oxidase 1"", ""flavoprotein NADPH oxidase"", ""nicotinamide adenine dinucleotide phosphate oxidase"""	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.2171C>T	15.37:g.45437127C>T	ENSP00000317997:p.Ala724Val	Somatic		Capture	Illumina HiSeq	Phase_I	43224419	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation	SNP	ENST00000321429.4	37	CCDS32221.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.668657	0.29604	.	.	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	D;D	0.86030	-2.06;-2.06	4.81	1.6	0.23607	.	0.754367	0.13329	N	0.396042	T	0.73024	0.3534	L	0.32530	0.975	0.38535	D	0.949074	B	0.06786	0.001	B	0.04013	0.001	T	0.61178	-0.7115	10	0.29301	T	0.29	-6.5763	3.7204	0.08454	0.1858:0.6012:0.0:0.213	.	724	Q9NRD9	DUOX1_HUMAN	V	724	ENSP00000317997:A724V;ENSP00000373689:A724V	ENSP00000317997:A724V	A	+	2	0	DUOX1	43224419	0.000000	0.05858	0.973000	0.42090	0.710000	0.40934	-0.145000	0.10265	0.226000	0.20979	0.655000	0.94253	GCG		0.582	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
FBN1	2200	broad.mit.edu	37	15	48744764	48744764	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:48744764C>T	ENST00000316623.5	-	45	5995	c.5540G>A	c.(5539-5541)tGc>tAc	p.C1847Y		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1847	EGF-like 30; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.C1847Y(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CATACCATTGCACTGTCCTGT	0.517																																					p.C1847Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5540A	15						.						127.0	107.0	114.0					15																	48744764		2198	4296	6494	46532056	SO:0001583	missense	2200	exon45			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.5540G>A	15.37:g.48744764C>T	ENSP00000325527:p.Cys1847Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	46532056	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.792380	0.90453	.	.	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.87571	-2.27	5.22	5.22	0.72569	EGF-like region, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.94879	0.8345	M	0.90198	3.095	0.80722	D	1	D	0.69078	0.997	D	0.83275	0.996	D	0.95614	0.8675	10	0.87932	D	0	.	18.7385	0.91765	0.0:1.0:0.0:0.0	.	1847	P35555	FBN1_HUMAN	Y	1847;415;737	ENSP00000325527:C1847Y	ENSP00000325527:C1847Y	C	-	2	0	FBN1	46532056	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.629000	0.83207	2.592000	0.87571	0.555000	0.69702	TGC		0.517	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		
FBN1	2200	broad.mit.edu	37	15	48776095	48776095	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:48776095T>A	ENST00000316623.5	-	31	4213	c.3758A>T	c.(3757-3759)cAg>cTg	p.Q1253L		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1253	EGF-like 20; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.Q1253L(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		ATTTGTGCACTGACCACCATC	0.413																																					p.Q1253L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3758T	15						.						157.0	122.0	134.0					15																	48776095		2198	4296	6494	46563387	SO:0001583	missense	2200	exon31			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.3758A>T	15.37:g.48776095T>A	ENSP00000325527:p.Gln1253Leu	Somatic		Capture	Illumina HiSeq	Phase_I	46563387	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.037272	0.93630	.	.	ENSG00000166147	ENST00000316623	D	0.87029	-2.2	6.17	6.17	0.99709	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.87204	0.6119	N	0.12182	0.205	0.80722	D	1	D	0.60160	0.987	D	0.67725	0.953	D	0.88781	0.3271	10	0.48119	T	0.1	.	16.4837	0.84171	0.0:0.0:0.0:1.0	.	1253	P35555	FBN1_HUMAN	L	1253	ENSP00000325527:Q1253L	ENSP00000325527:Q1253L	Q	-	2	0	FBN1	46563387	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	CAG		0.413	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		
FBN1	2200	broad.mit.edu	37	15	48796125	48796125	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:48796125G>A	ENST00000316623.5	-	17	2427	c.1972C>T	c.(1972-1974)Cgg>Tgg	p.R658W		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	658					extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.R658W(1)		NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CATGTGCTCCGCATGTGTGTG	0.458																																					p.R658W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1972T	15	GRCh37	CI075630	FBN1	I		.						122.0	109.0	114.0					15																	48796125		2197	4296	6493	46583417	SO:0001583	missense	2200	exon17			X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.1972C>T	15.37:g.48796125G>A	ENSP00000325527:p.Arg658Trp	Somatic		Capture	Illumina HiSeq	Phase_I	46583417	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.568641	0.86439	.	.	ENSG00000166147	ENST00000316623	D	0.92911	-3.13	5.53	5.53	0.82687	Matrix fibril-associated (2);	0.000000	0.85682	D	0.000000	D	0.93772	0.8009	L	0.43152	1.355	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.93487	0.6832	10	0.66056	D	0.02	.	13.1788	0.59642	0.0:0.0:0.8406:0.1594	.	658	P35555	FBN1_HUMAN	W	658	ENSP00000325527:R658W	ENSP00000325527:R658W	R	-	1	2	FBN1	46583417	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.373000	0.73128	2.882000	0.98803	0.655000	0.94253	CGG		0.458	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		
COPS2	9318	broad.mit.edu	37	15	49420279	49420279	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:49420279G>A	ENST00000388901.5	-	13	1273	c.1200C>T	c.(1198-1200)ggC>ggT	p.G400G	COPS2_ENST00000299259.6_Silent_p.G407G|COPS2_ENST00000542928.1_Silent_p.G336G	NM_001143887.1|NM_004236.3	NP_001137359.1|NP_004227.1	P61201	CSN2_HUMAN	COP9 signalosome subunit 2	400	PCI.				cell proliferation (GO:0008283)|cullin deneddylation (GO:0010388)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)	p.G400G(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(2)	18		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		GATCAATTCGGCCATGAATAG	0.368																																					p.G400G	NSCLC(36;322 1063 10349 30082 48062)|Esophageal Squamous(122;685 1633 15569 21293 52803)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1200T	15						.						120.0	114.0	116.0					15																	49420279		2196	4295	6491	47207571	SO:0001819	synonymous_variant	9318	exon13			AF212227	CCDS32235.1, CCDS45257.1	15q21.2	2013-03-14	2013-03-14						30747	protein-coding gene	gene with protein product		604508	"""COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis)"""			7776974, 9535219	Standard	NM_004236		Approved	TRIP15, ALIEN, CSN2	uc001zxh.3	P61201		ENST00000388901.5:c.1200C>T	15.37:g.49420279G>A		Somatic		Capture	Illumina HiSeq	Phase_I	47207571	NM_004236	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Silent	SNP	ENST00000388901.5	37	CCDS32235.1																																																																																				0.368	COPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417840.1	NM_004236	
ATP8B4	79895	broad.mit.edu	37	15	50212513	50212513	+	Missense_Mutation	SNP	G	G	A	rs200106056		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:50212513G>A	ENST00000284509.6	-	18	1994	c.1853C>T	c.(1852-1854)gCg>gTg	p.A618V	ATP8B4_ENST00000559829.1_Missense_Mutation_p.A618V	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	618						Golgi apparatus (GO:0005794)|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.A618V(1)		breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		GGCAGCATTCGCATCTTCAAG	0.448																																					p.A618V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1853T	15						.						165.0	151.0	156.0					15																	50212513		2196	4295	6491	47999805	SO:0001583	missense	79895	exon18			AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"""ATPases / P-type"""	13536	protein-coding gene	gene with protein product		609123	"""ATPase, Class I, type 8B, member 4"""			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.1853C>T	15.37:g.50212513G>A	ENSP00000284509:p.Ala618Val	Somatic		Capture	Illumina HiSeq	Phase_I	47999805	NM_024837	Q9H727	Missense_Mutation	SNP	ENST00000284509.6	37	CCDS32238.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.945262	0.73672	.	.	ENSG00000104043	ENST00000284509	T	0.67698	-0.28	5.64	5.64	0.86602	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.057062	0.64402	D	0.000002	D	0.82852	0.5127	M	0.91717	3.235	0.46954	D	0.99926	D	0.54047	0.964	P	0.55391	0.775	D	0.86556	0.1838	10	0.72032	D	0.01	.	17.1963	0.86893	0.0:0.0:1.0:0.0	.	618	Q8TF62	AT8B4_HUMAN	V	618	ENSP00000284509:A618V	ENSP00000284509:A618V	A	-	2	0	ATP8B4	47999805	1.000000	0.71417	0.979000	0.43373	0.956000	0.61745	7.193000	0.77780	2.664000	0.90586	0.561000	0.74099	GCG		0.448	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837	
DMXL2	23312	broad.mit.edu	37	15	51829785	51829785	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:51829785G>T	ENST00000251076.5	-	11	1804	c.1517C>A	c.(1516-1518)cCt>cAt	p.P506H	DMXL2_ENST00000543779.2_Missense_Mutation_p.P506H|DMXL2_ENST00000449909.3_Missense_Mutation_p.P506H	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	506						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.P506H(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)		AAGCATATCAGGATTCTTATT	0.398																																					p.P506H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1517A	15						.						167.0	152.0	157.0					15																	51829785		2195	4293	6488	49617077	SO:0001583	missense	23312	exon11			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.1517C>A	15.37:g.51829785G>T	ENSP00000251076:p.Pro506His	Somatic		Capture	Illumina HiSeq	Phase_I	49617077	NM_015263	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	G	18.00	3.525330	0.64747	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	T;T;T	0.11604	2.76;2.76;2.76	4.88	4.88	0.63580	.	0.051982	0.85682	D	0.000000	T	0.33847	0.0877	M	0.75615	2.305	0.38124	D	0.93796	D;D;D	0.76494	0.999;0.996;0.999	D;P;D	0.66716	0.946;0.819;0.91	T	0.33471	-0.9867	10	0.87932	D	0	.	18.0229	0.89260	0.0:0.0:1.0:0.0	.	506;506;506	F5GWF1;B2RTR3;Q8TDJ6	.;.;DMXL2_HUMAN	H	506	ENSP00000251076:P506H;ENSP00000441858:P506H;ENSP00000400855:P506H	ENSP00000251076:P506H	P	-	2	0	DMXL2	49617077	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.410000	0.97335	2.255000	0.74692	0.650000	0.86243	CCT		0.398	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
LEO1	123169	broad.mit.edu	37	15	52244057	52244057	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:52244057C>T	ENST00000299601.5	-	9	1655	c.1595G>A	c.(1594-1596)cGc>cAc	p.R532H	LEO1_ENST00000315141.5_Missense_Mutation_p.R472H	NM_138792.2	NP_620147.1	Q8WVC0	LEO1_HUMAN	Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	532					endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|mRNA polyadenylation (GO:0006378)|negative regulation of myeloid cell differentiation (GO:0045638)|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)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)		p.R532H(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|skin(1)	14				all cancers(107;0.00264)		CATTTCTGTGCGTTGGCATTC	0.418																																					p.R532H	Esophageal Squamous(40;229 896 18505 32465 43844)|Ovarian(53;886 1123 14462 18432 23189)											.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1595A	15						.						194.0	160.0	171.0					15																	52244057		2195	4293	6488	50031349	SO:0001583	missense	123169	exon9			AY302186	CCDS10146.1, CCDS66767.1	15q21.2	2008-02-05			ENSG00000166477	ENSG00000166477			30401	protein-coding gene	gene with protein product		610507				15632063	Standard	NM_001286430		Approved		uc002abo.3	Q8WVC0	OTTHUMG00000131843	ENST00000299601.5:c.1595G>A	15.37:g.52244057C>T	ENSP00000299601:p.Arg532His	Somatic		Capture	Illumina HiSeq	Phase_I	50031349	NM_138792	Q96N99	Missense_Mutation	SNP	ENST00000299601.5	37	CCDS10146.1	.	.	.	.	.	.	.	.	.	.	.	33	5.266653	0.95399	.	.	ENSG00000166477	ENST00000299601;ENST00000538386;ENST00000315141	.	.	.	5.63	5.63	0.86233	.	0.047340	0.85682	N	0.000000	T	0.73377	0.3579	L	0.37800	1.135	0.80722	D	1	D;B	0.76494	0.999;0.009	D;B	0.79108	0.992;0.008	T	0.74825	-0.3533	9	0.66056	D	0.02	.	19.6961	0.96026	0.0:1.0:0.0:0.0	.	472;532	Q8WVC0-2;Q8WVC0	.;LEO1_HUMAN	H	532;510;472	.	ENSP00000299601:R532H	R	-	2	0	LEO1	50031349	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.629000	0.83207	2.654000	0.90174	0.650000	0.86243	CGC		0.418	LEO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254791.2	NM_138792	
MYO5C	55930	broad.mit.edu	37	15	52532030	52532030	+	Missense_Mutation	SNP	G	G	A	rs375271766		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:52532030G>A	ENST00000261839.7	-	21	2764	c.2603C>T	c.(2602-2604)gCg>gTg	p.A868V	MYO5C_ENST00000443683.2_Intron	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	868	IQ 5. {ECO:0000255|PROSITE- ProRule:PRU00116}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A868V(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)		GGCCAGCCACGCCCGTGCGTA	0.453																																					p.A868V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2603T	15						.	G	VAL/ALA	0,3940		0,0,1970	64.0	63.0	63.0		2603	5.4	0.9	15		63	1,8321		0,1,4160	no	missense	MYO5C	NM_018728.3	64	0,1,6130	AA,AG,GG		0.012,0.0,0.0082	possibly-damaging	868/1743	52532030	1,12261	1970	4161	6131	50319322	SO:0001583	missense	55930	exon21			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.2603C>T	15.37:g.52532030G>A	ENSP00000261839:p.Ala868Val	Somatic		Capture	Illumina HiSeq	Phase_I	50319322	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	G	34	5.374454	0.95923	0.0	1.2E-4	ENSG00000128833	ENST00000261839	T	0.28255	1.62	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.37517	0.1006	M	0.66378	2.025	0.80722	D	1	P	0.47253	0.892	B	0.41571	0.36	T	0.25152	-1.0140	10	0.40728	T	0.16	.	18.8578	0.92260	0.0:0.0:1.0:0.0	.	868	Q9NQX4	MYO5C_HUMAN	V	868	ENSP00000261839:A868V	ENSP00000261839:A868V	A	-	2	0	MYO5C	50319322	1.000000	0.71417	0.877000	0.34402	0.929000	0.56500	7.512000	0.81728	2.544000	0.85801	0.650000	0.86243	GCG		0.453	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728	
WDR72	256764	broad.mit.edu	37	15	54015068	54015068	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:54015068G>A	ENST00000396328.1	-	3	430	c.191C>T	c.(190-192)tCg>tTg	p.S64L	WDR72_ENST00000360509.5_Missense_Mutation_p.S64L|WDR72_ENST00000557913.1_Missense_Mutation_p.S64L|WDR72_ENST00000559418.1_Missense_Mutation_p.S64L	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	64								p.S64L(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		ACATGTTACCGAAGCTGAATG	0.378																																					p.S64L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C191T	15						.						129.0	120.0	123.0					15																	54015068		2194	4293	6487	51802360	SO:0001583	missense	256764	exon3			BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"""WD repeat domain containing"""	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.191C>T	15.37:g.54015068G>A	ENSP00000379619:p.Ser64Leu	Somatic		Capture	Illumina HiSeq	Phase_I	51802360	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.216901	0.79352	.	.	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.61510	0.1;0.1	5.79	5.79	0.91817	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.388659	0.24715	N	0.036190	T	0.60130	0.2245	L	0.58810	1.83	0.34707	D	0.727374	D	0.55385	0.971	B	0.43838	0.433	T	0.72050	-0.4407	10	0.54805	T	0.06	.	19.0242	0.92926	0.0:0.0:1.0:0.0	.	64	Q3MJ13	WDR72_HUMAN	L	64	ENSP00000379619:S64L;ENSP00000353699:S64L	ENSP00000353699:S64L	S	-	2	0	WDR72	51802360	1.000000	0.71417	0.280000	0.24747	0.859000	0.49053	7.154000	0.77437	2.740000	0.93945	0.563000	0.77884	TCG		0.378	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
RAB27A	5873	broad.mit.edu	37	15	55522650	55522650	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:55522650C>T	ENST00000396307.2	-	3	439	c.188G>A	c.(187-189)gGc>gAc	p.G63D	RAB27A_ENST00000564609.1_Missense_Mutation_p.G63D|RAB27A_ENST00000336787.1_Missense_Mutation_p.G63D|RAB27A_ENST00000569493.1_Missense_Mutation_p.G63D	NM_004580.4	NP_004571.2	P51159	RB27A_HUMAN	RAB27A, member RAS oncogene family	63					antigen processing and presentation (GO:0019882)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cytotoxic T cell degranulation (GO:0043316)|exocytosis (GO:0006887)|exosomal secretion (GO:1990182)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|multivesicular body organization (GO:0036257)|multivesicular body sorting pathway (GO:0071985)|natural killer cell degranulation (GO:0043320)|positive regulation of exocytosis (GO:0045921)|positive regulation of gene expression (GO:0010628)|protein targeting (GO:0006605)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle transport (GO:0048489)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|photoreceptor outer segment (GO:0001750)|secretory granule membrane (GO:0030667)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.G63D(1)		endometrium(1)|large_intestine(2)|liver(1)|lung(3)|ovary(1)|skin(1)	9				all cancers(107;0.0273)|GBM - Glioblastoma multiforme(80;0.0993)		CTGGCCTCTGCCAGTGGCTCC	0.478																																					p.G63D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G188A	15						.						86.0	84.0	85.0					15																	55522650		2193	4292	6485	53309942	SO:0001583	missense	5873	exon3			U38654	CCDS10153.1	15q15-q21.1	2014-09-17			ENSG00000069974	ENSG00000069974		"""RAB, member RAS oncogene"""	9766	protein-coding gene	gene with protein product		603868				7592656	Standard	NM_183235		Approved	RAB27, RAM, GS2, HsT18676	uc002acq.3	P51159	OTTHUMG00000131959	ENST00000396307.2:c.188G>A	15.37:g.55522650C>T	ENSP00000379601:p.Gly63Asp	Somatic		Capture	Illumina HiSeq	Phase_I	53309942	NM_004580	O00195|Q6FI40|Q9UIR9|Q9Y5U3	Missense_Mutation	SNP	ENST00000396307.2	37	CCDS10153.1	.	.	.	.	.	.	.	.	.	.	C	19.54	3.847707	0.71603	.	.	ENSG00000069974	ENST00000396307;ENST00000396304;ENST00000336787	T;T	0.73897	-0.79;-0.79	5.75	5.75	0.90469	Small GTP-binding protein domain (1);	0.101029	0.64402	D	0.000001	T	0.60983	0.2311	N	0.08118	0	0.80722	D	1	B	0.19200	0.034	B	0.22152	0.038	T	0.58797	-0.7573	10	0.66056	D	0.02	-10.4633	18.9315	0.92568	0.0:1.0:0.0:0.0	.	63	P51159	RB27A_HUMAN	D	63	ENSP00000379601:G63D;ENSP00000337761:G63D	ENSP00000337761:G63D	G	-	2	0	RAB27A	53309942	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.893000	0.69798	2.716000	0.92895	0.655000	0.94253	GGC		0.478	RAB27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254918.1	NM_004580, NM_183236	
NEDD4	4734	broad.mit.edu	37	15	56208895	56208895	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:56208895G>A	ENST00000508342.1	-	1	434	c.135C>T	c.(133-135)aaC>aaT	p.N45N	NEDD4_ENST00000506154.1_Silent_p.N45N|NEDD4_ENST00000435532.3_Intron|NEDD4_ENST00000338963.2_Silent_p.N45N	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	45					adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)	p.N45N(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		TTTGAACAACGTTAGACGTTG	0.428																																					p.N45N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C135T	15						.						188.0	168.0	175.0					15																	56208895		2193	4291	6484	53996187	SO:0001819	synonymous_variant	4734	exon1			D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"""receptor-potentiating factor 1"""	602278	"""neural precursor cell expressed, developmentally down-regulated 4"""			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.135C>T	15.37:g.56208895G>A		Somatic		Capture	Illumina HiSeq	Phase_I	53996187	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Silent	SNP	ENST00000508342.1	37																																																																																					0.428	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400	
MYZAP	100820829	broad.mit.edu	37	15	57929907	57929907	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:57929907G>A	ENST00000267853.5	+	9	1042	c.948G>A	c.(946-948)ctG>ctA	p.L316L	GCOM1_ENST00000380561.2_Silent_p.L285L|GCOM1_ENST00000574161.1_Silent_p.L316L|GCOM1_ENST00000587652.1_Silent_p.L316L|GCOM1_ENST00000572390.1_Silent_p.L316L|GCOM1_ENST00000380568.3_Silent_p.L316L|POLR2M_ENST00000380563.2_5'UTR|GCOM1_ENST00000380560.2_Silent_p.L247L|GCOM1_ENST00000380569.2_Silent_p.L316L|GCOM1_ENST00000396180.1_Silent_p.L285L|MYZAP_ENST00000380565.4_Silent_p.L316L			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	316					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)		p.L316L(1)									GTCATCAACTGCAACTTCAAC	0.373																																					p.L316L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G948A	15						.						101.0	89.0	93.0					15																	57929907		2192	4292	6484	55717199	SO:0001819	synonymous_variant	145781	exon9			FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"""myocardium-enriched zonula adherens protein"""	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.948G>A	15.37:g.57929907G>A		Somatic		Capture	Illumina HiSeq	Phase_I	55717199	NM_152451	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Silent	SNP	ENST00000267853.5	37	CCDS10162.1																																																																																				0.373	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100	
ALDH1A2	8854	broad.mit.edu	37	15	58254280	58254280	+	Missense_Mutation	SNP	C	C	T	rs376965202		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:58254280C>T	ENST00000249750.4	-	10	1948	c.1181G>A	c.(1180-1182)cGa>cAa	p.R394Q	ALDH1A2_ENST00000559517.1_Missense_Mutation_p.R298Q|ALDH1A2_ENST00000347587.3_Missense_Mutation_p.R356Q|ALDH1A2_ENST00000558231.1_Missense_Mutation_p.R365Q|ALDH1A2_ENST00000537372.1_Missense_Mutation_p.R373Q	NM_003888.3	NP_003879.2	O94788	AL1A2_HUMAN	aldehyde dehydrogenase 1 family, member A2	394					9-cis-retinoic acid biosynthetic process (GO:0042904)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|cardiac muscle tissue development (GO:0048738)|cellular response to retinoic acid (GO:0071300)|determination of bilateral symmetry (GO:0009855)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract development (GO:0048566)|embryonic forelimb morphogenesis (GO:0035115)|face development (GO:0060324)|heart morphogenesis (GO:0003007)|hindbrain development (GO:0030902)|kidney development (GO:0001822)|liver development (GO:0001889)|lung development (GO:0030324)|midgut development (GO:0007494)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of cell proliferation (GO:0008285)|neural crest cell development (GO:0014032)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|proximal/distal pattern formation (GO:0009954)|regulation of endothelial cell proliferation (GO:0001936)|response to cytokine (GO:0034097)|response to estradiol (GO:0032355)|response to vitamin A (GO:0033189)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)|retinoic acid receptor signaling pathway (GO:0048384)|retinol metabolic process (GO:0042572)|ureter maturation (GO:0035799)|vitamin A metabolic process (GO:0006776)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|retinal binding (GO:0016918)|retinal dehydrogenase activity (GO:0001758)	p.R394Q(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(80;0.152)|all cancers(107;0.18)	Tretinoin(DB00755)|Vitamin A(DB00162)	AAACCCCTTTCGGCCCAGTCC	0.478																																					p.R298Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G893A	15						.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4384		0,0,2192	107.0	103.0	105.0		1118,1181,1067,893	4.6	0.9	15		105	1,8583	1.2+/-3.3	0,1,4291	no	missense,missense,missense,missense	ALDH1A2	NM_001206897.1,NM_003888.3,NM_170696.2,NM_170697.2	43,43,43,43	0,1,6483	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign	373/498,394/519,356/481,298/423	58254280	1,12967	2192	4292	6484	56041572	SO:0001583	missense	8854	exon8			AB015228	CCDS10163.1, CCDS10164.1, CCDS45266.1, CCDS55968.1	15q21.2	2011-02-18			ENSG00000128918	ENSG00000128918		"""Aldehyde dehydrogenases"""	15472	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 2"""	603687				9819382	Standard	NM_003888		Approved	RALDH2	uc002aex.3	O94788	OTTHUMG00000132624	ENST00000249750.4:c.1181G>A	15.37:g.58254280C>T	ENSP00000249750:p.Arg394Gln	Somatic		Capture	Illumina HiSeq	Phase_I	56041572	NM_170697	B3KY52|B4DZR2|F5H2Y9|H0YM00|Q2PJS6|Q8NHQ4|Q9UBR8|Q9UFY0	Missense_Mutation	SNP	ENST00000249750.4	37	CCDS10163.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.031835	0.54790	0.0	1.16E-4	ENSG00000128918	ENST00000249750;ENST00000430119;ENST00000543386;ENST00000347587;ENST00000537372	T;T;T	0.15952	2.38;2.38;2.38	5.72	4.59	0.56863	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.659654	0.15137	N	0.278493	T	0.15478	0.0373	L	0.35341	1.055	0.20926	N	0.999827	B;B;B;B	0.17465	0.003;0.002;0.022;0.006	B;B;B;B	0.16722	0.0;0.0;0.016;0.004	T	0.08371	-1.0725	10	0.59425	D	0.04	.	13.3969	0.60858	0.0:0.8939:0.0:0.1061	.	365;373;356;394	B4DH89;F5H2Y9;O94788-2;O94788	.;.;.;AL1A2_HUMAN	Q	394;298;365;356;373	ENSP00000249750:R394Q;ENSP00000309623:R356Q;ENSP00000438296:R373Q	ENSP00000249750:R394Q	R	-	2	0	ALDH1A2	56041572	0.121000	0.22262	0.940000	0.37924	0.989000	0.77384	1.682000	0.37628	2.865000	0.98341	0.655000	0.94253	CGA		0.478	ALDH1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255869.1		
VPS13C	54832	broad.mit.edu	37	15	62217710	62217710	+	Missense_Mutation	SNP	G	G	A	rs146858303		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:62217710G>A	ENST00000261517.5	-	53	6627	c.6554C>T	c.(6553-6555)aCg>aTg	p.T2185M	VPS13C_ENST00000395898.3_Missense_Mutation_p.T2142M|VPS13C_ENST00000249837.3_Missense_Mutation_p.T2142M|VPS13C_ENST00000395896.4_Missense_Mutation_p.T2185M	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.T2185M(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						TGAAGCCCACGTACATTTTTC	0.279													G|||	1	0.000199681	0.0	0.0	5008	,	,		16184	0.0		0.001	False		,,,				2504	0.0				p.T2142M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6425T	15						.						31.0	33.0	32.0					15																	62217710		2197	4285	6482	60005002	SO:0001583	missense	54832	exon51			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.6554C>T	15.37:g.62217710G>A	ENSP00000261517:p.Thr2185Met	Somatic		Capture	Illumina HiSeq	Phase_I	60005002	NM_017684		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.366	0.435662	0.12104	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.42900	0.96;0.96;0.96	4.9	-0.584	0.11702	.	0.887861	0.09911	N	0.739837	T	0.18087	0.0434	N	0.11201	0.11	0.09310	N	1	B;B;B;B	0.20459	0.045;0.005;0.045;0.003	B;B;B;B	0.19946	0.027;0.01;0.027;0.004	T	0.22556	-1.0213	10	0.23891	T	0.37	.	1.368	0.02205	0.4283:0.143:0.2823:0.1464	.	2142;2185;2142;2185	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	M	2142;2185;2185;2185	ENSP00000249837:T2142M;ENSP00000261517:T2185M;ENSP00000379233:T2185M	ENSP00000249837:T2142M	T	-	2	0	VPS13C	60005002	0.002000	0.14202	0.117000	0.21633	0.841000	0.47740	0.347000	0.20014	0.231000	0.21079	-1.047000	0.02352	ACG		0.279	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
TLN2	83660	broad.mit.edu	37	15	63008651	63008651	+	Missense_Mutation	SNP	G	G	A	rs375098264		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:63008651G>A	ENST00000561311.1	+	22	2986	c.2756G>A	c.(2755-2757)cGa>cAa	p.R919Q	TLN2_ENST00000306829.6_Missense_Mutation_p.R919Q			Q9Y4G6	TLN2_HUMAN	talin 2	919	Ala-rich.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.R919Q(1)		NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						ATTGTCAACCGACTGGAGGTA	0.438																																					p.R919Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2756A	15						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	47.0	48.0	48.0		2756	5.8	1.0	15		48	0,8600		0,0,4300	no	missense	TLN2	NM_015059.2	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	919/2543	63008651	1,13005	2203	4300	6503	60795943	SO:0001583	missense	83660	exon20			AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.2756G>A	15.37:g.63008651G>A	ENSP00000453508:p.Arg919Gln	Somatic		Capture	Illumina HiSeq	Phase_I	60795943	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	G	36	5.609820	0.96637	2.27E-4	0.0	ENSG00000171914	ENST00000306829	T	0.69306	-0.39	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.72334	0.3447	M	0.77103	2.36	0.80722	D	1	P	0.52061	0.95	P	0.44422	0.449	T	0.72388	-0.4309	10	0.33940	T	0.23	-14.8184	20.0129	0.97467	0.0:0.0:1.0:0.0	.	919	Q9Y4G6	TLN2_HUMAN	Q	919	ENSP00000303476:R919Q	ENSP00000303476:R919Q	R	+	2	0	TLN2	60795943	1.000000	0.71417	0.967000	0.41034	0.957000	0.61999	4.125000	0.57931	2.902000	0.99343	0.650000	0.86243	CGA		0.438	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
DAPK2	23604	broad.mit.edu	37	15	64275875	64275875	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:64275875C>T	ENST00000457488.1	-	3	201	c.171G>A	c.(169-171)cgG>cgA	p.R57R	DAPK2_ENST00000261891.3_Silent_p.R57R|DAPK2_ENST00000558069.1_Silent_p.R57R|DAPK2_ENST00000558482.1_5'UTR	NM_014326.3	NP_055141.2	Q9UIK4	DAPK2_HUMAN	death-associated protein kinase 2	57	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anoikis (GO:0043276)|apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein serine/threonine kinase activity (GO:0004674)	p.R57R(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|skin(1)|stomach(1)	11				LUAD - Lung adenocarcinoma(2;0.215)		CCCGGCTCTGCCGCTTCTTGA	0.627																																					p.R57R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G171A	15						.						37.0	36.0	36.0					15																	64275875		2203	4300	6503	62062928	SO:0001819	synonymous_variant	23604	exon3			AB018001	CCDS10188.1	15q22.1	2008-07-18			ENSG00000035664	ENSG00000035664			2675	protein-coding gene	gene with protein product						10376525	Standard	XM_005254265		Approved	DRP-1, MGC119312	uc002amr.3	Q9UIK4	OTTHUMG00000132947	ENST00000457488.1:c.171G>A	15.37:g.64275875C>T		Somatic		Capture	Illumina HiSeq	Phase_I	62062928	NM_014326	E9JGM7|O75892|Q24JS1	Silent	SNP	ENST00000457488.1	37	CCDS10188.1																																																																																				0.627	DAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256479.1	NM_014326	
TRIP4	9325	broad.mit.edu	37	15	64698592	64698592	+	Missense_Mutation	SNP	G	G	A	rs143968963		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:64698592G>A	ENST00000261884.3	+	6	821	c.761G>A	c.(760-762)cGa>cAa	p.R254Q	TRIP4_ENST00000559565.1_Intron	NM_016213.4	NP_057297.2	Q15650	TRIP4_HUMAN	thyroid hormone receptor interactor 4	254					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.R254Q(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21						CAAGAATTGCGAATTAAGTCT	0.398													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21627	0.0		0.0	False		,,,				2504	0.0				p.R254Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G761A	15						.	G	GLN/ARG	3,4403	6.2+/-15.9	0,3,2200	107.0	104.0	105.0		761	3.9	0.6	15	dbSNP_134	105	0,8600		0,0,4300	no	missense	TRIP4	NM_016213.4	43	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	probably-damaging	254/582	64698592	3,13003	2203	4300	6503	62485645	SO:0001583	missense	9325	exon6			L40371	CCDS10194.1	15q22.1	2014-02-17			ENSG00000103671	ENSG00000103671		"""-"""	12310	protein-coding gene	gene with protein product	"""zinc finger, C2HC5-type"""	604501				7776974	Standard	NM_016213		Approved	HsT17391, ZC2HC5	uc002anm.3	Q15650	OTTHUMG00000133033	ENST00000261884.3:c.761G>A	15.37:g.64698592G>A	ENSP00000261884:p.Arg254Gln	Somatic		Capture	Illumina HiSeq	Phase_I	62485645	NM_016213	B2RAS0|Q96ED7|Q9UKH0	Missense_Mutation	SNP	ENST00000261884.3	37	CCDS10194.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.153541	0.57259	6.81E-4	0.0	ENSG00000103671	ENST00000261884	.	.	.	5.73	3.86	0.44501	.	0.376341	0.28760	N	0.014230	T	0.31638	0.0803	L	0.43152	1.355	0.36124	D	0.845654	D	0.54964	0.969	B	0.37304	0.246	T	0.33369	-0.9871	9	0.13108	T	0.6	-15.6333	9.4714	0.38844	0.2135:0.0:0.7865:0.0	.	254	Q15650	TRIP4_HUMAN	Q	254	.	ENSP00000261884:R254Q	R	+	2	0	TRIP4	62485645	0.952000	0.32445	0.595000	0.28798	0.996000	0.88848	1.401000	0.34589	0.889000	0.36185	0.557000	0.71058	CGA		0.398	TRIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256635.2	NM_016213	
ANKDD1A	348094	broad.mit.edu	37	15	65214132	65214132	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:65214132G>A	ENST00000380230.3	+	4	309	c.280G>A	c.(280-282)Gcg>Acg	p.A94T	ANKDD1A_ENST00000496660.1_Missense_Mutation_p.A3T|AC069368.3_ENST00000437723.1_Missense_Mutation_p.A166T|ANKDD1A_ENST00000395720.1_Missense_Mutation_p.A94T|ANKDD1A_ENST00000357698.3_Missense_Mutation_p.A94T|ANKDD1A_ENST00000319580.8_Missense_Mutation_p.C16Y|ANKDD1A_ENST00000395723.1_Missense_Mutation_p.A3T|ANKDD1A_ENST00000491145.1_3'UTR	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	94					signal transduction (GO:0007165)			p.A94T(1)		NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						TGGGATGAATGCGCTTCTCCT	0.542																																					p.A94T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G280A	15						.						149.0	112.0	125.0					15																	65214132		2202	4299	6501	63001185	SO:0001583	missense	348094	exon4				CCDS10197.2	15q22.31	2013-01-10	2006-02-16		ENSG00000166839	ENSG00000166839		"""Ankyrin repeat domain containing"""	28002	protein-coding gene	gene with protein product						12477932	Standard	NM_182703		Approved	FLJ25870	uc002aoa.3	Q495B1	OTTHUMG00000133051	ENST00000380230.3:c.280G>A	15.37:g.65214132G>A	ENSP00000369579:p.Ala94Thr	Somatic		Capture	Illumina HiSeq	Phase_I	63001185	NM_182703	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Missense_Mutation	SNP	ENST00000380230.3	37	CCDS10197.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.47|12.47	1.947621|1.947621	0.34377|0.34377	.|.	.|.	ENSG00000249240;ENSG00000166839;ENSG00000166839;ENSG00000166839;ENSG00000166839;ENSG00000166839|ENSG00000166839	ENST00000437723;ENST00000380230;ENST00000357698;ENST00000395720;ENST00000496660;ENST00000395723|ENST00000319580	T;T;T;T;T;T|.	0.69685|.	-0.42;-0.42;-0.42;-0.42;-0.42;-0.42|.	4.63|4.63	2.71|2.71	0.32032|0.32032	Ankyrin repeat-containing domain (4);|.	0.189542|.	0.32028|.	N|.	0.006700|.	T|T	0.58566|0.58566	0.2131|0.2131	M|M	0.78801|0.78801	2.425|2.425	0.09310|0.09310	N|N	1|1	P;P;B|.	0.36909|.	0.474;0.573;0.419|.	B;B;B|.	0.33846|.	0.171;0.139;0.106|.	T|T	0.52162|0.52162	-0.8612|-0.8612	10|6	0.33141|0.87932	T|D	0.24|0	-7.9538|-7.9538	9.9065|9.9065	0.41379|0.41379	0.0:0.0:0.6327:0.3673|0.0:0.0:0.6327:0.3673	.|.	94;94;94|.	Q495B1;Q495B1-2;Q495B1-1|.	AKD1A_HUMAN;.;.|.	T|Y	166;94;94;94;3;3|16	ENSP00000397942:A166T;ENSP00000369579:A94T;ENSP00000350329:A94T;ENSP00000379070:A94T;ENSP00000420999:A3T;ENSP00000379073:A3T|.	ENSP00000397942:A166T|ENSP00000325895:C16Y	A|C	+|+	1|2	0|0	AC069368.3;ANKDD1A|ANKDD1A	63001185|63001185	0.892000|0.892000	0.30473|0.30473	0.006000|0.006000	0.13384|0.13384	0.741000|0.741000	0.42261|0.42261	3.302000|3.302000	0.51849|0.51849	0.555000|0.555000	0.29079|0.29079	0.655000|0.655000	0.94253|0.94253	GCG|TGC		0.542	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703	
DPP8	54878	broad.mit.edu	37	15	65793045	65793045	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:65793045C>T	ENST00000341861.5	-	4	2073	c.493G>A	c.(493-495)Gga>Aga	p.G165R	DPP8_ENST00000300141.6_Missense_Mutation_p.G149R|DPP8_ENST00000358939.4_Missense_Mutation_p.G149R|DPP8_ENST00000321147.6_Missense_Mutation_p.G165R|Y_RNA_ENST00000516408.1_RNA|DPP8_ENST00000321118.7_Missense_Mutation_p.G165R|DPP8_ENST00000559233.1_Missense_Mutation_p.G165R|DPP8_ENST00000339244.5_Missense_Mutation_p.G165R	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	165					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)	p.G149R(3)|p.G149*(1)		NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						GAAGCAATTCCGACTGTTCCA	0.403																																					p.G149R												.	.	4	Substitution - Missense(3)|Substitution - Nonsense(1)	large_intestine(2)|lung(1)|endometrium(1)	c.G445A	15						.						210.0	199.0	203.0					15																	65793045		2201	4299	6500	63580098	SO:0001583	missense	54878	exon4			AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"""dipeptidyl peptidase VIII"", ""dipeptidyl peptidase IV-related protein-1"", ""prolyl dipeptidase DPP8"""	606819	"""dipeptidylpeptidase 8"""			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.493G>A	15.37:g.65793045C>T	ENSP00000339208:p.Gly165Arg	Somatic		Capture	Illumina HiSeq	Phase_I	63580098	NM_017743	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Missense_Mutation	SNP	ENST00000341861.5	37	CCDS10207.1	.	.	.	.	.	.	.	.	.	.	C	19.62	3.862324	0.71949	.	.	ENSG00000074603	ENST00000341861;ENST00000358939;ENST00000300141;ENST00000321147;ENST00000321118;ENST00000339244;ENST00000395652	T;T;T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53;1.53;1.53	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.47820	0.1466	M	0.72479	2.2	0.33684	D	0.612533	P;B;P;P	0.46457	0.878;0.35;0.878;0.807	P;B;P;B	0.48815	0.591;0.089;0.591;0.387	T	0.60556	-0.7240	10	0.87932	D	0	-5.4525	20.2885	0.98538	0.0:1.0:0.0:0.0	.	149;149;165;165	Q6V1X1-3;Q6V1X1-4;Q6V1X1-2;Q6V1X1	.;.;.;DPP8_HUMAN	R	165;149;149;165;165;165;165	ENSP00000339208:G165R;ENSP00000351817:G149R;ENSP00000300141:G149R;ENSP00000318111:G165R;ENSP00000316373:G165R;ENSP00000341230:G165R;ENSP00000379013:G165R	ENSP00000300141:G149R	G	-	1	0	DPP8	63580098	1.000000	0.71417	0.995000	0.50966	0.917000	0.54804	6.262000	0.72514	2.791000	0.96007	0.650000	0.86243	GGA		0.403	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743	
SLC24A1	9187	broad.mit.edu	37	15	65917837	65917837	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:65917837C>T	ENST00000261892.6	+	2	1706	c.1419C>T	c.(1417-1419)tgC>tgT	p.C473C	SLC24A1_ENST00000544319.2_Silent_p.C473C|SLC24A1_ENST00000339868.6_Silent_p.C473C|SLC24A1_ENST00000399033.4_Silent_p.C473C|SLC24A1_ENST00000537259.1_Silent_p.C473C|SLC24A1_ENST00000546330.1_Silent_p.C473C	NM_001254740.1|NM_004727.2	NP_001241669.1|NP_004718.1	O60721	NCKX1_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	473					calcium ion transport (GO:0006816)|ion transport (GO:0006811)|phototransduction, visible light (GO:0007603)|response to light intensity (GO:0009642)|rhodopsin mediated signaling pathway (GO:0016056)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)	p.C473C(1)		breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						CCATTGTTTGCGACGAGTACT	0.582																																					p.R474X												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1420T	15						.						181.0	181.0	181.0					15																	65917837		2113	4245	6358	63704891	SO:0001819	synonymous_variant	9187	exon2			AF062922	CCDS45284.1, CCDS73742.1, CCDS73743.1, CCDS73744.1	15q22.31	2014-01-28			ENSG00000074621	ENSG00000074621		"""Solute carriers"""	10975	protein-coding gene	gene with protein product		603617				9856482	Standard	NM_004727		Approved	NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D	uc010ujf.2	O60721	OTTHUMG00000167960	ENST00000261892.6:c.1419C>T	15.37:g.65917837C>T		Somatic		Capture	Illumina HiSeq	Phase_I	63704891	NM_004727	O43485|O75184|Q17RM9	Silent	SNP	ENST00000261892.6	37	CCDS45284.1																																																																																				0.582	SLC24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397304.1	NM_004727	
DENND4A	10260	broad.mit.edu	37	15	65983195	65983195	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:65983195C>T	ENST00000431932.2	-	22	3813	c.3605G>A	c.(3604-3606)cGt>cAt	p.R1202H	DENND4A_ENST00000443035.3_Missense_Mutation_p.R1245H|DENND4A_ENST00000567323.1_5'Flank	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1202					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R1204H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						AGCTAAATCACGCCTAGCAGA	0.413																																					p.R1245H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3734A	15						.						78.0	77.0	77.0					15																	65983195		1971	4152	6123	63770249	SO:0001583	missense	10260	exon23			AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"""DENN/MADD domain containing"""	24321	protein-coding gene	gene with protein product		600382	"""c-myc promoter binding protein"""	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.3605G>A	15.37:g.65983195C>T	ENSP00000396830:p.Arg1202His	Somatic		Capture	Illumina HiSeq	Phase_I	63770249	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	37	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872696	0.91587	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.16196	2.46;2.36	5.37	5.37	0.77165	.	0.509864	0.17197	N	0.183278	T	0.43389	0.1245	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.996	T	0.23013	-1.0200	10	0.87932	D	0	.	19.4761	0.94989	0.0:1.0:0.0:0.0	.	1245;1202	E7EPL3;Q7Z401	.;MYCPP_HUMAN	H	1245;1202	ENSP00000391167:R1245H;ENSP00000396830:R1202H	ENSP00000396830:R1202H	R	-	2	0	DENND4A	63770249	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	7.000000	0.76290	2.687000	0.91594	0.655000	0.94253	CGT		0.413	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848	
SMAD3	4088	broad.mit.edu	37	15	67358559	67358559	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:67358559C>T	ENST00000327367.4	+	1	377	c.67C>T	c.(67-69)Cag>Tag	p.Q23*		NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	23	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|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 factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q23*(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		GAAGGGCGAGCAGAACGGGCA	0.647																																					p.Q23X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C67T	15						.						81.0	78.0	79.0					15																	67358559		2201	4299	6500	65145613	SO:0001587	stop_gained	4088	exon1			BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"""SMADs"""	6769	protein-coding gene	gene with protein product		603109	"""MAD, mothers against decapentaplegic homolog 3 (Drosophila)"", ""SMAD, mothers against DPP homolog 3 (Drosophila)"""	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.67C>T	15.37:g.67358559C>T	ENSP00000332973:p.Gln23*	Somatic		Capture	Illumina HiSeq	Phase_I	65145613	NM_005902	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Nonsense_Mutation	SNP	ENST00000327367.4	37	CCDS10222.1	.	.	.	.	.	.	.	.	.	.	C	40	8.398993	0.98794	.	.	ENSG00000166949	ENST00000327367;ENST00000535241	.	.	.	4.55	4.55	0.56014	.	0.070992	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	16.6536	0.85223	0.0:1.0:0.0:0.0	.	.	.	.	X	23	.	ENSP00000332973:Q23X	Q	+	1	0	SMAD3	65145613	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.470000	0.80973	2.210000	0.71456	0.555000	0.69702	CAG		0.647	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902	
CORO2B	10391	broad.mit.edu	37	15	68937536	68937536	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:68937536G>A	ENST00000566799.1	+	2	82	c.53G>A	c.(52-54)cGg>cAg	p.R18Q	CORO2B_ENST00000540068.1_Missense_Mutation_p.R13Q|CORO2B_ENST00000543950.1_Missense_Mutation_p.R13Q|CORO2B_ENST00000261861.5_Missense_Mutation_p.R13Q			Q9UQ03	COR2B_HUMAN	coronin, actin binding protein, 2B	18					actin cytoskeleton organization (GO:0030036)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|membrane (GO:0016020)	actin binding (GO:0003779)|actin filament binding (GO:0051015)	p.R18Q(1)		kidney(3)|large_intestine(13)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						TCCAAGTTCCGGAATGTCTAC	0.612																																					p.R18Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G53A	15						.						87.0	73.0	77.0					15																	68937536		2200	4298	6498	66724590	SO:0001583	missense	10391	exon2			AB010098	CCDS53952.1, CCDS10229.2	15q22.31	2013-01-10	2001-11-28		ENSG00000103647	ENSG00000103647		"""Coronins"", ""WD repeat domain containing"""	2256	protein-coding gene	gene with protein product	"""clipin C"", ""coronin, actin-binding, 2B"""	605002	"""coronin, actin-binding protein, 2B"""			10224093, 10231032	Standard	NM_001190456		Approved	ClipinC, KIAA0925	uc021spj.1	Q9UQ03	OTTHUMG00000133288	ENST00000566799.1:c.53G>A	15.37:g.68937536G>A	ENSP00000454783:p.Arg18Gln	Somatic		Capture	Illumina HiSeq	Phase_I	66724590	NM_006091	A8K0W3|O94767|Q8TAN1	Missense_Mutation	SNP	ENST00000566799.1	37	CCDS10229.2	.	.	.	.	.	.	.	.	.	.	G	34	5.338139	0.95758	.	.	ENSG00000103647	ENST00000261861;ENST00000540068;ENST00000543950	T;T	0.71817	-0.6;-0.6	4.38	4.38	0.52667	Domain of unknown function DUF1899 (1);	0.000000	0.85682	D	0.000000	D	0.88078	0.6340	M	0.94142	3.5	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.91793	0.5445	10	0.87932	D	0	-17.718	15.8812	0.79207	0.0:0.0:1.0:0.0	.	18	Q9UQ03	COR2B_HUMAN	Q	18;13;13	ENSP00000446250:R13Q;ENSP00000443819:R13Q	ENSP00000261861:R18Q	R	+	2	0	CORO2B	66724590	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.540000	0.98080	2.142000	0.66516	0.563000	0.77884	CGG		0.612	CORO2B-203	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_006091	
ANP32A	8125	broad.mit.edu	37	15	69079768	69079768	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:69079768C>T	ENST00000465139.2	-	3	454	c.311G>A	c.(310-312)aGc>aAc	p.S104N	ANP32A_ENST00000560303.1_Missense_Mutation_p.S104N|ANP32A_ENST00000483551.2_5'UTR	NM_006305.3	NP_006296.1	P39687	AN32A_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	104					gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA metabolic process (GO:0016071)|nucleocytoplasmic transport (GO:0006913)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)	p.S104N(1)		endometrium(1)|large_intestine(1)|lung(2)	4						CTCTATTGTGCTGAGGTCTTT	0.483																																					p.S104N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G311A	15						.						100.0	111.0	108.0					15																	69079768		2200	4298	6498	66866822	SO:0001583	missense	8125	exon3			AF025684	CCDS45292.1	15q23	2008-05-14			ENSG00000140350	ENSG00000140350		"""ANP32 acidic nuclear phosphoproteins"""	13233	protein-coding gene	gene with protein product		600832		C15orf1		8970164, 9144194	Standard	NM_006305		Approved	LANP, PP32, I1PP2A, PHAPI, MAPM, mapmodulin	uc002arl.3	P39687	OTTHUMG00000154502	ENST00000465139.2:c.311G>A	15.37:g.69079768C>T	ENSP00000417864:p.Ser104Asn	Somatic		Capture	Illumina HiSeq	Phase_I	66866822	NM_006305	B2R6T4|Q53FK4|Q5J8L8|Q7M4N6	Missense_Mutation	SNP	ENST00000465139.2	37	CCDS45292.1	.	.	.	.	.	.	.	.	.	.	C	18.86	3.713351	0.68730	.	.	ENSG00000140350	ENST00000358235;ENST00000465139	T	0.55052	0.54	5.6	5.6	0.85130	.	0.035154	0.85682	D	0.000000	T	0.48554	0.1506	L	0.39467	1.215	0.80722	D	1	B	0.13594	0.008	B	0.17433	0.018	T	0.37009	-0.9724	10	0.46703	T	0.11	.	18.6073	0.91271	0.0:1.0:0.0:0.0	.	104	P39687	AN32A_HUMAN	N	104	ENSP00000417864:S104N	ENSP00000350970:S104N	S	-	2	0	ANP32A	66866822	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.619000	0.83057	2.640000	0.89533	0.655000	0.94253	AGC		0.483	ANP32A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335525.2		
TLE3	7090	broad.mit.edu	37	15	70347546	70347546	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:70347546C>T	ENST00000558939.1	-	15	2806	c.1429G>A	c.(1429-1431)Gcc>Acc	p.A477T	TLE3_ENST00000559929.1_Missense_Mutation_p.A487T|TLE3_ENST00000559191.1_Missense_Mutation_p.A58T|TLE3_ENST00000557997.1_Missense_Mutation_p.A469T|TLE3_ENST00000560939.1_Missense_Mutation_p.A479T|TLE3_ENST00000559048.1_Missense_Mutation_p.A477T|TLE3_ENST00000539550.1_Missense_Mutation_p.A404T|TLE3_ENST00000558201.1_Missense_Mutation_p.A483T|TLE3_ENST00000558379.1_Missense_Mutation_p.A472T|TLE3_ENST00000442299.2_Missense_Mutation_p.A469T|TLE3_ENST00000560589.1_Missense_Mutation_p.A421T|TLE3_ENST00000317509.8_Missense_Mutation_p.A465T|TLE3_ENST00000440567.3_Missense_Mutation_p.A467T|TLE3_ENST00000557907.1_Missense_Mutation_p.A469T|TLE3_ENST00000451782.2_Missense_Mutation_p.A474T	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	477					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.A477T(2)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ATCTGCCGGGCGTGCCTCGGG	0.642																																					p.A465T												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G1393A	15						.						59.0	66.0	64.0					15																	70347546		2199	4298	6497	68134600	SO:0001583	missense	7090	exon15			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.1429G>A	15.37:g.70347546C>T	ENSP00000452871:p.Ala477Thr	Somatic		Capture	Illumina HiSeq	Phase_I	68134600	NM_020908	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	37	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	C	35	5.475341	0.96291	.	.	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550;ENST00000542329	T;T;T;T	0.11495	2.77;2.77;2.77;2.77	4.54	4.54	0.55810	WD40 repeat-like-containing domain (1);	0.179933	0.48286	D	0.000195	T	0.37652	0.1011	M	0.87682	2.9	0.80722	D	1	D;D;D;D;D;D;D;D	0.76494	0.997;0.997;0.999;0.997;0.997;0.993;0.999;0.993	P;P;D;P;D;P;D;P	0.68621	0.889;0.778;0.959;0.778;0.916;0.684;0.955;0.771	T	0.42103	-0.9471	10	0.62326	D	0.03	-19.861	16.2284	0.82315	0.0:1.0:0.0:0.0	.	467;474;469;472;465;477;477;404	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	T	469;474;477;467;404;144	ENSP00000390007:A469T;ENSP00000394717:A474T;ENSP00000415057:A467T;ENSP00000442594:A404T	ENSP00000319233:A477T	A	-	1	0	TLE3	68134600	1.000000	0.71417	0.970000	0.41538	0.965000	0.64279	7.553000	0.82203	2.352000	0.79861	0.462000	0.41574	GCC		0.642	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
NR2E3	10002	broad.mit.edu	37	15	72105839	72105839	+	RNA	SNP	C	C	A	rs566024312		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:72105839C>A	ENST00000398840.2	+	0	1048							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.A286A(1)		breast(1)|endometrium(1)|lung(1)	3						CCTCTGCTGCCGGTGGTGCCC	0.662																																					p.A286A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C858A	15						.						30.0	33.0	32.0					15																	72105839		1956	4136	6092	69892893			10002	exon6				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.72105839C>A		Somatic		Capture	Illumina HiSeq	Phase_I	69892893	NM_014249	B6ZGU0|Q9UHM4	Silent	SNP	ENST00000398840.2	37																																																																																					0.662	NR2E3-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014249	
ARIH1	25820	broad.mit.edu	37	15	72873198	72873198	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:72873198C>T	ENST00000379887.4	+	12	1656	c.1342C>T	c.(1342-1344)Cac>Tac	p.H448Y	ARIH1_ENST00000562891.1_3'UTR	NM_005744.3	NP_005735.2	Q9Y4X5	ARI1_HUMAN	ariadne RBR E3 ubiquitin protein ligase 1	448					cytokine-mediated signaling pathway (GO:0019221)|protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ubiquitin ligase complex (GO:0000151)	small conjugating protein ligase activity (GO:0019787)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.H448Y(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(4)|prostate(1)|skin(1)	14						GATGCAGCAGCACAACATGTC	0.473																																					p.H448Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1342T	15						.						242.0	171.0	195.0					15																	72873198		2198	4297	6495	70660252	SO:0001583	missense	25820	exon12			AF072832	CCDS10244.1	15q24	2013-10-03	2013-10-03		ENSG00000166233	ENSG00000166233			689	protein-coding gene	gene with protein product	"""ariadne, Drosophila, homolog of"""	605624	"""ariadne (Drosophila) homolog, ubiquitin-conjugating enzyme E2-binding protein, 1"", ""ariadne homolog, ubiquitin-conjugating enzyme E2 binding protein, 1 (Drosophila)"""			10521492, 24058416	Standard	NM_005744		Approved	HARI, HHARI, UBCH7BP, ARI	uc002aut.4	Q9Y4X5	OTTHUMG00000133474	ENST00000379887.4:c.1342C>T	15.37:g.72873198C>T	ENSP00000369217:p.His448Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	70660252	NM_005744	B2R6U3|O76026|Q9H3T6|Q9UEN0|Q9UP39	Missense_Mutation	SNP	ENST00000379887.4	37	CCDS10244.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.805761	0.90623	.	.	ENSG00000166233	ENST00000379887;ENST00000299305	D	0.83075	-1.68	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.89389	0.6701	M	0.81239	2.535	0.80722	D	1	D	0.63880	0.993	P	0.54706	0.759	D	0.87326	0.2321	10	0.30854	T	0.27	.	20.0546	0.97648	0.0:1.0:0.0:0.0	.	448	Q9Y4X5	ARI1_HUMAN	Y	448;418	ENSP00000369217:H448Y	ENSP00000299305:H418Y	H	+	1	0	ARIH1	70660252	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.391000	0.79828	2.758000	0.94735	0.644000	0.83932	CAC		0.473	ARIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257350.1	NM_005744	
HCN4	10021	broad.mit.edu	37	15	73622003	73622003	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:73622003C>T	ENST00000261917.3	-	4	2494	c.1501G>A	c.(1501-1503)Gtg>Atg	p.V501M		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	501					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.V501M(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)		GTGGCACCCACGATCATGCTG	0.637																																					p.V501M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1501A	15						.						102.0	89.0	93.0					15																	73622003		2198	4297	6495	71409056	SO:0001583	missense	10021	exon4			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.1501G>A	15.37:g.73622003C>T	ENSP00000261917:p.Val501Met	Somatic		Capture	Illumina HiSeq	Phase_I	71409056	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	37	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.842325	0.91197	.	.	ENSG00000138622	ENST00000261917	D	0.98531	-4.98	4.31	4.31	0.51392	Ion transport (1);	.	.	.	.	D	0.98704	0.9565	M	0.72894	2.215	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.99873	1.1099	9	0.87932	D	0	.	16.7901	0.85586	0.0:1.0:0.0:0.0	.	501	Q9Y3Q4	HCN4_HUMAN	M	501	ENSP00000261917:V501M	ENSP00000261917:V501M	V	-	1	0	HCN4	71409056	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.684000	0.84104	2.105000	0.64084	0.561000	0.74099	GTG		0.637	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
CYP1A1	1543	broad.mit.edu	37	15	75015288	75015288	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:75015288G>A	ENST00000379727.3	-	2	349	c.151C>T	c.(151-153)Cac>Tac	p.H51Y	CYP1A1_ENST00000395049.4_Missense_Mutation_p.H51Y|CYP1A1_ENST00000395048.2_Missense_Mutation_p.H51Y|CYP1A1_ENST00000567032.1_Missense_Mutation_p.H51Y|CYP1A1_ENST00000564596.1_Intron			P04798	CP1A1_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 1	51					9-cis-retinoic acid biosynthetic process (GO:0042904)|aging (GO:0007568)|amine metabolic process (GO:0009308)|arachidonic acid metabolic process (GO:0019369)|camera-type eye development (GO:0043010)|cell proliferation (GO:0008283)|cellular lipid metabolic process (GO:0044255)|cellular response to organic cyclic compound (GO:0071407)|coumarin metabolic process (GO:0009804)|dibenzo-p-dioxin catabolic process (GO:0019341)|digestive tract development (GO:0048565)|drug metabolic process (GO:0017144)|embryo development ending in birth or egg hatching (GO:0009792)|epoxygenase P450 pathway (GO:0019373)|flavonoid metabolic process (GO:0009812)|hepatocyte differentiation (GO:0070365)|hydrogen peroxide biosynthetic process (GO:0050665)|insecticide metabolic process (GO:0017143)|maternal process involved in parturition (GO:0060137)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|response to antibiotic (GO:0046677)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to food (GO:0032094)|response to herbicide (GO:0009635)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to iron(III) ion (GO:0010041)|response to lipopolysaccharide (GO:0032496)|response to nematode (GO:0009624)|response to virus (GO:0009615)|response to vitamin A (GO:0033189)|response to wounding (GO:0009611)|small molecule metabolic process (GO:0044281)|vitamin D metabolic process (GO:0042359)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|demethylase activity (GO:0032451)|flavonoid 3'-monooxygenase activity (GO:0016711)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on diphenols and related substances as donors (GO:0016679)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)|vitamin D 24-hydroxylase activity (GO:0070576)	p.H51Y(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|large_intestine(7)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Acetaminophen(DB00316)|Albendazole(DB00518)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Caffeine(DB00201)|Carvedilol(DB01136)|Chloroquine(DB00608)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Cinnarizine(DB00568)|Clenbuterol(DB01407)|Clobetasol propionate(DB01013)|Clofibrate(DB00636)|Clomifene(DB00882)|Clonidine(DB00575)|Clozapine(DB00363)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Dexamethasone(DB01234)|Dexmedetomidine(DB00633)|Diclofenac(DB00586)|Dicyclomine(DB00804)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Ethanol(DB00898)|Flunarizine(DB04841)|Fluorescein(DB00693)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Granisetron(DB00889)|Haloperidol(DB00502)|Isoprenaline(DB01064)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lorcaserin(DB04871)|Mebendazole(DB00643)|Melatonin(DB01065)|Menadione(DB00170)|Methoxsalen(DB00553)|Nicotine(DB00184)|Nifedipine(DB01115)|Nitroprusside(DB00325)|Norfloxacin(DB01059)|Omeprazole(DB00338)|Ouabain(DB01092)|Oxaliplatin(DB00526)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Prazosin(DB00457)|Primaquine(DB01087)|Progesterone(DB00396)|Propofol(DB00818)|Propranolol(DB00571)|Pyridoxine(DB00165)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Riluzole(DB00740)|Sildenafil(DB00203)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiabendazole(DB00730)|Ticlopidine(DB00208)|Toremifene(DB00539)|Tretinoin(DB00755)|Vitamin A(DB00162)|Warfarin(DB00682)	GTCAGCATGTGCCCAATCAGA	0.582									Endometrial Cancer, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.H51Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C151T	15						.						52.0	49.0	50.0					15																	75015288		2197	4296	6493	72802341	SO:0001583	missense	1543	exon2	Familial Cancer Database	;AIMAH, Cushing disease, Adrenal, Familial	BC023019	CCDS10268.1	15q24.1	2007-12-14	2003-01-14		ENSG00000140465	ENSG00000140465	1.14.14.1	"""Cytochrome P450s"""	2595	protein-coding gene	gene with protein product		108330	"""cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 1"""	CYP1		15128046	Standard	NM_000499		Approved	P450DX, P1-450, P450-C, CP11	uc002ayp.4	P04798	OTTHUMG00000142812	ENST00000379727.3:c.151C>T	15.37:g.75015288G>A	ENSP00000369050:p.His51Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	72802341	NM_000499	A4F3V9|A4F3W0|Q53G18	Missense_Mutation	SNP	ENST00000379727.3	37	CCDS10268.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.403377	0.42613	.	.	ENSG00000140465	ENST00000379727;ENST00000395048;ENST00000395049;ENST00000268062	T;T;T	0.68765	-0.35;-0.35;-0.35	5.64	1.14	0.20703	.	0.128774	0.64402	D	0.000002	T	0.79879	0.4522	M	0.77616	2.38	0.34385	D	0.693538	D;D	0.76494	0.994;0.999	D;D	0.69307	0.944;0.963	D	0.86729	0.1947	10	0.87932	D	0	.	15.2622	0.73634	0.0:0.0:0.2464:0.7536	.	51;51	E7EMT5;P04798	.;CP1A1_HUMAN	Y	51	ENSP00000369050:H51Y;ENSP00000378488:H51Y;ENSP00000378489:H51Y	ENSP00000268062:H51Y	H	-	1	0	CYP1A1	72802341	1.000000	0.71417	0.159000	0.22649	0.287000	0.27160	3.806000	0.55583	0.298000	0.22638	0.655000	0.94253	CAC		0.582	CYP1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286396.1	NM_000499	
LMAN1L	79748	broad.mit.edu	37	15	75108622	75108622	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:75108622G>A	ENST00000309664.5	+	2	439	c.300G>A	c.(298-300)acG>acA	p.T100T	LMAN1L_ENST00000379709.3_Silent_p.T100T	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	100	L-type lectin-like. {ECO:0000255|PROSITE- ProRule:PRU00658}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.T100T(1)		NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGAGGGTGACGGGACTGGGGC	0.687																																					p.T100T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G300A	15						.						32.0	32.0	32.0					15																	75108622		2195	4296	6491	72895675	SO:0001819	synonymous_variant	79748	exon2			AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.300G>A	15.37:g.75108622G>A		Somatic		Capture	Illumina HiSeq	Phase_I	72895675	NM_021819	Q6UWN2	Silent	SNP	ENST00000309664.5	37	CCDS10270.1																																																																																				0.687	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4		
NEIL1	79661	broad.mit.edu	37	15	75641646	75641646	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:75641646G>T	ENST00000564784.1	+	3	1029	c.400G>T	c.(400-402)Ggg>Tgg	p.G134W	NEIL1_ENST00000569035.1_Missense_Mutation_p.G134W|NEIL1_ENST00000567959.1_Intron|NEIL1_ENST00000355059.4_Missense_Mutation_p.G134W			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)	134					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)			breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)	13						GCCGGGCCGCGGGCCCTGTGT	0.647								Base excision repair (BER), DNA glycosylases																													p.G134W												.	.	0			c.G400T	15						.						19.0	22.0	21.0					15																	75641646		2102	4135	6237	73428699	SO:0001583	missense	79661	exon2			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.400G>T	15.37:g.75641646G>T	ENSP00000457352:p.Gly134Trp	None		Capture	Illumina HiSeq	Phase_I	73428699	NM_024608	D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Missense_Mutation	SNP	ENST00000564784.1	37	CCDS10278.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.7|21.7	4.187192|4.187192	0.78789|0.78789	.|.	.|.	ENSG00000140398|ENSG00000140398	ENST00000355059|ENST00000336572	T|.	0.61742|.	0.08|.	5.4|5.4	5.4|5.4	0.78164|0.78164	Ribosomal protein S13-like, H2TH (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.90810|0.90810	0.7114|0.7114	H|H	0.98295|0.98295	4.195|4.195	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.94286|0.94286	0.7524|0.7524	10|6	0.87932|0.87932	D|D	0|0	-37.9817|-37.9817	18.146|18.146	0.89655|0.89655	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	134|.	Q96FI4|.	NEIL1_HUMAN|.	W|L	134|119	ENSP00000347170:G134W|.	ENSP00000347170:G134W|ENSP00000338328:R119L	G|R	+|+	1|2	0|0	NEIL1|NEIL1	73428699|73428699	1.000000|1.000000	0.71417|0.71417	0.994000|0.994000	0.49952|0.49952	0.338000|0.338000	0.28826|0.28826	9.011000|9.011000	0.93618|0.93618	2.525000|2.525000	0.85131|0.85131	0.561000|0.561000	0.74099|0.74099	GGG|CGG		0.647	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608	
MAN2C1	4123	broad.mit.edu	37	15	75653992	75653992	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:75653992G>A	ENST00000267978.5	-	10	1217	c.1171C>T	c.(1171-1173)Cgc>Tgc	p.R391C	MAN2C1_ENST00000563539.1_5'Flank|MAN2C1_ENST00000565683.1_Missense_Mutation_p.R391C|MAN2C1_ENST00000569482.1_Missense_Mutation_p.R391C|MAN2C1_ENST00000563622.1_Missense_Mutation_p.R292C	NM_006715.3	NP_006706.2	Q9NTJ4	MA2C1_HUMAN	mannosidase, alpha, class 2C, member 1	391					mannose metabolic process (GO:0006013)		alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)	p.R391C(1)		central_nervous_system(4)|endometrium(4)|kidney(6)|large_intestine(6)|lung(20)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	44						GTGAGAAAGCGCCTGATGCCA	0.602																																					p.R391C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1171T	15						.						63.0	66.0	65.0					15																	75653992		2197	4294	6491	73441045	SO:0001583	missense	4123	exon10			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.1171C>T	15.37:g.75653992G>A	ENSP00000267978:p.Arg391Cys	Somatic		Capture	Illumina HiSeq	Phase_I	73441045	NM_006715	H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Missense_Mutation	SNP	ENST00000267978.5	37	CCDS32298.1	.	.	.	.	.	.	.	.	.	.	G	11.76	1.733595	0.30684	.	.	ENSG00000140400	ENST00000267978	T	0.79653	-1.29	5.44	0.928	0.19443	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.751173	0.13378	N	0.392392	T	0.69655	0.3135	L	0.49513	1.565	0.09310	N	0.999992	P;B;B	0.38370	0.628;0.014;0.013	B;B;B	0.34779	0.189;0.013;0.015	T	0.56836	-0.7913	10	0.38643	T	0.18	-1.0584	5.294	0.15743	0.2606:0.0:0.603:0.1363	.	173;391;391	B4DVP6;Q68EM8;Q9NTJ4	.;.;MA2C1_HUMAN	C	391	ENSP00000267978:R391C	ENSP00000267978:R391C	R	-	1	0	MAN2C1	73441045	0.011000	0.17503	0.000000	0.03702	0.769000	0.43574	1.334000	0.33827	-0.092000	0.12417	-0.424000	0.05967	CGC		0.602	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1		
PEAK1	79834	broad.mit.edu	37	15	77473598	77473598	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:77473598C>A	ENST00000560626.2	-	4	1146	c.671G>T	c.(670-672)cGg>cTg	p.R224L	PEAK1_ENST00000312493.4_Missense_Mutation_p.R224L|PEAK1_ENST00000558305.1_Missense_Mutation_p.R224L			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	224					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.R224L(2)									GTAACAGAACCGGCCCCCTTC	0.478																																					p.R224L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G671T	15						.						143.0	138.0	139.0					15																	77473598		1918	4119	6037	75260653	SO:0001583	missense	79834	exon3				CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.671G>T	15.37:g.77473598C>A	ENSP00000452796:p.Arg224Leu	Somatic		Capture	Illumina HiSeq	Phase_I	75260653	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	37	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	C	15.97	2.990968	0.54041	.	.	ENSG00000173517	ENST00000312493	T	0.75367	-0.93	5.42	4.51	0.55191	.	0.000000	0.32473	U	0.006045	T	0.68137	0.2968	L	0.29908	0.895	0.44771	D	0.997778	D	0.57899	0.981	P	0.46208	0.507	T	0.72795	-0.4185	10	0.87932	D	0	-7.0019	14.1551	0.65413	0.0:0.9279:0.0:0.0721	.	224	Q9H792	PEAK1_HUMAN	L	224	ENSP00000309230:R224L	ENSP00000309230:R224L	R	-	2	0	AC087465.1	75260653	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.686000	0.61700	1.293000	0.44690	0.650000	0.86243	CGG		0.478	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		
TBC1D2B	23102	broad.mit.edu	37	15	78290633	78290633	+	Missense_Mutation	SNP	G	G	A	rs199780820		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:78290633G>A	ENST00000300584.3	-	13	2760	c.2761C>T	c.(2761-2763)Cgc>Tgc	p.R921C	TBC1D2B_ENST00000492078.1_5'UTR|TBC1D2B_ENST00000409931.3_Silent_p.D903D	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	921							Rab GTPase activator activity (GO:0005097)	p.D903D(1)		breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						TGGTAGGCGCGTCGGTTCCGG	0.612																																					p.R921C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2761T	15						.						40.0	34.0	36.0					15																	78290633		2196	4291	6487	76077688	SO:0001583	missense	23102	exon13			AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.2761C>T	15.37:g.78290633G>A	ENSP00000300584:p.Arg921Cys	Somatic		Capture	Illumina HiSeq	Phase_I	76077688	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Missense_Mutation	SNP	ENST00000300584.3	37	CCDS45314.1	.	.	.	.	.	.	.	.	.	.	g	18.97	3.735618	0.69189	.	.	ENSG00000167202	ENST00000300584	T	0.13089	2.62	4.48	2.27	0.28462	.	.	.	.	.	T	0.35219	0.0924	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.16247	-1.0409	8	0.87932	D	0	.	10.9397	0.47266	0.0:0.0:0.5412:0.4588	.	921	Q9UPU7	TBD2B_HUMAN	C	921	ENSP00000300584:R921C	ENSP00000300584:R921C	R	-	1	0	TBC1D2B	76077688	1.000000	0.71417	0.878000	0.34440	0.839000	0.47603	2.286000	0.43496	0.801000	0.34066	0.479000	0.44913	CGC		0.612	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079	
TBC1D2B	23102	broad.mit.edu	37	15	78295787	78295787	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:78295787G>A	ENST00000300584.3	-	11	2433	c.2434C>T	c.(2434-2436)Cgg>Tgg	p.R812W	TBC1D2B_ENST00000492078.1_5'Flank|TBC1D2B_ENST00000409931.3_Missense_Mutation_p.R812W	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	812	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)	p.R812W(1)		breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						CCATGCAACCGAGGCAGCTTC	0.507																																					p.R812W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2434T	15						.						117.0	100.0	105.0					15																	78295787		2196	4293	6489	76082842	SO:0001583	missense	23102	exon11			AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.2434C>T	15.37:g.78295787G>A	ENSP00000300584:p.Arg812Trp	Somatic		Capture	Illumina HiSeq	Phase_I	76082842	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Missense_Mutation	SNP	ENST00000300584.3	37	CCDS45314.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.105373	0.56291	.	.	ENSG00000167202	ENST00000409931;ENST00000300584	T;T	0.04706	3.57;3.57	5.29	4.35	0.52113	Rab-GAP/TBC domain (5);	0.000000	0.85682	D	0.000000	T	0.29817	0.0745	M	0.93594	3.435	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.40553	-0.9557	10	0.87932	D	0	.	14.1982	0.65684	0.0:0.0:0.8495:0.1505	.	812;264;812	Q9UPU7-2;Q9UPU7-3;Q9UPU7	.;.;TBD2B_HUMAN	W	812	ENSP00000387165:R812W;ENSP00000300584:R812W	ENSP00000300584:R812W	R	-	1	2	TBC1D2B	76082842	1.000000	0.71417	0.065000	0.19835	0.367000	0.29736	6.346000	0.72999	1.164000	0.42652	0.563000	0.77884	CGG		0.507	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079	
TMED3	23423	broad.mit.edu	37	15	79614335	79614335	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:79614335G>A	ENST00000299705.5	+	3	621	c.433G>A	c.(433-435)Gtg>Atg	p.V145M	TMED3_ENST00000536821.1_Intron|TMED3_ENST00000558562.1_3'UTR|TMED3_ENST00000424155.2_Intron	NM_007364.2	NP_031390.1	Q9Y3Q3	TMED3_HUMAN	transmembrane emp24 protein transport domain containing 3	145					protein transport (GO:0015031)	COPI vesicle coat (GO:0030126)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.V145M(1)		large_intestine(3)|lung(4)|ovary(1)|skin(1)	9						GTCCGCCTGCGTGACCATCCA	0.552																																					p.V145M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G433A	15						.						80.0	74.0	76.0					15																	79614335		2196	4293	6489	77401390	SO:0001583	missense	23423	exon3			BC022232	CCDS10310.1, CCDS73768.1	15q24-q25	2011-02-09	2005-08-26	2005-01-07	ENSG00000166557	ENSG00000166557			28889	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 22"", ""transmembrane emp24 domain containing 3"""	C15orf22		12975309	Standard	XM_005254263		Approved	p24B	uc002beu.3	Q9Y3Q3	OTTHUMG00000144170	ENST00000299705.5:c.433G>A	15.37:g.79614335G>A	ENSP00000299705:p.Val145Met	Somatic		Capture	Illumina HiSeq	Phase_I	77401390	NM_007364	A8K069|B4DN05|Q2T9F8	Missense_Mutation	SNP	ENST00000299705.5	37	CCDS10310.1	.	.	.	.	.	.	.	.	.	.	G	18.85	3.711742	0.68730	.	.	ENSG00000166557	ENST00000299705	T	0.16897	2.31	4.86	3.94	0.45596	GOLD (1);	0.078674	0.51477	D	0.000099	T	0.26666	0.0652	L	0.49256	1.55	0.80722	D	1	D	0.56968	0.978	P	0.55161	0.77	T	0.01312	-1.1388	10	0.33141	T	0.24	-12.1075	12.3502	0.55144	0.0:0.0:0.8302:0.1698	.	145	Q9Y3Q3	TMED3_HUMAN	M	145	ENSP00000299705:V145M	ENSP00000299705:V145M	V	+	1	0	TMED3	77401390	1.000000	0.71417	0.996000	0.52242	0.935000	0.57460	7.138000	0.77305	1.245000	0.43885	0.591000	0.81541	GTG		0.552	TMED3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291369.1	NM_007364	
ST20	400410	broad.mit.edu	37	15	80191329	80191329	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:80191329C>T	ENST00000478497.1	-	3	863	c.184G>A	c.(184-186)Ggc>Agc	p.G62S	ST20-MTHFS_ENST00000479961.1_Intron|ST20_ENST00000562759.1_Missense_Mutation_p.G62S|MTHFS_ENST00000559722.1_5'Flank|ST20-MTHFS_ENST00000494999.1_Intron|MTHFS_ENST00000258874.3_5'Flank|ST20_ENST00000485386.1_Missense_Mutation_p.G62S	NM_001100879.1	NP_001094349.1	Q9HBF5	ST20_HUMAN	suppressor of tumorigenicity 20	62					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G62S(1)		kidney(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						AAAATTAGGCCGGTTTCACAA	0.378																																					p.G62S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G184A	15						.						114.0	114.0	114.0					15																	80191329		2202	4300	6502	77978384	SO:0001583	missense	400410	exon3			AF249277	CCDS42067.1	15q25.1	2007-07-16				ENSG00000180953			33520	protein-coding gene	gene with protein product							Standard	NM_001100879		Approved	HCCS-1		Q9HBF5		ENST00000478497.1:c.184G>A	15.37:g.80191329C>T	ENSP00000453502:p.Gly62Ser	Somatic		Capture	Illumina HiSeq	Phase_I	77978384	NM_001100879		Missense_Mutation	SNP	ENST00000478497.1	37	CCDS42067.1	.	.	.	.	.	.	.	.	.	.	C	9.106	1.005402	0.19199	.	.	ENSG00000180953	ENST00000322484;ENST00000417278	.	.	.	2.09	0.873	0.19118	.	.	.	.	.	T	0.20088	0.0483	.	.	.	0.09310	N	1	P	0.36535	0.557	B	0.22880	0.042	T	0.12811	-1.0533	7	0.87932	D	0	.	4.9009	0.13773	0.6642:0.3358:0.0:0.0	.	62	Q9HBF5	ST20_HUMAN	S	62	.	ENSP00000319125:G62S	G	-	1	0	ST20	77978384	0.001000	0.12720	0.058000	0.19502	0.693000	0.40251	-0.007000	0.12810	0.072000	0.16694	0.205000	0.17691	GGC		0.378	ST20-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416728.2		
FAH	2184	broad.mit.edu	37	15	80473419	80473419	+	Silent	SNP	G	G	A	rs35033541	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:80473419G>A	ENST00000407106.1	+	14	1253	c.1098G>A	c.(1096-1098)tcG>tcA	p.S366S	FAH_ENST00000561421.1_Silent_p.S366S|FAH_ENST00000261755.5_Silent_p.S366S|FAH_ENST00000539156.1_Silent_p.S296S			P16930	FAAA_HUMAN	fumarylacetoacetate hydrolase (fumarylacetoacetase)	366			Missing (in TYRSN1). {ECO:0000269|PubMed:9633815}.		arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	fumarylacetoacetase activity (GO:0004334)|metal ion binding (GO:0046872)	p.S366S(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGGAACTGTCGTGGAAGGGAA	0.507									Tyrosinemia, type 1				G|||	13	0.00259585	0.0091	0.0014	5008	,	,		22989	0.0		0.0	False		,,,				2504	0.0				p.S366S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1098A	15						.	G		20,4386	27.2+/-55.0	0,20,2183	147.0	135.0	139.0		1098	-10.6	0.0	15	dbSNP_126	139	0,8600		0,0,4300	no	coding-synonymous	FAH	NM_000137.2		0,20,6483	AA,AG,GG		0.0,0.4539,0.1538		366/420	80473419	20,12986	2203	4300	6503	78260474	SO:0001819	synonymous_variant	2184	exon13	Familial Cancer Database	Fumarylacetoacetase Deficiency, Hepatorenal Tyrosinemia, Hereditary Tyrosinemia 1, HT1	M55150	CCDS10314.1	15q25.1	2012-08-30			ENSG00000103876	ENSG00000103876	3.7.1.2		3579	protein-coding gene	gene with protein product		613871				1998338, 2336361	Standard	NM_000137		Approved		uc002bfm.2	P16930	OTTHUMG00000144187	ENST00000407106.1:c.1098G>A	15.37:g.80473419G>A		Somatic		Capture	Illumina HiSeq	Phase_I	78260474	NM_000137	B2R9X1|D3DW95|Q53XA7	Silent	SNP	ENST00000407106.1	37	CCDS10314.1																																																																																				0.507	FAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291392.2		
MEX3B	84206	broad.mit.edu	37	15	82336308	82336308	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:82336308G>A	ENST00000329713.4	-	2	1338	c.903C>T	c.(901-903)ttC>ttT	p.F301F	MEX3B_ENST00000558133.1_3'UTR|AC026956.1_ENST00000410589.1_RNA	NM_032246.4	NP_115622.2	Q6ZN04	MEX3B_HUMAN	mex-3 RNA binding family member B	301					protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.F301F(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)	19						TCCCGCCGCCGAAATAAGAGT	0.647																																					p.F301F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C903T	15						.						33.0	41.0	38.0					15																	82336308		2199	4291	6490	80123363	SO:0001819	synonymous_variant	84206	exon2			AK131424	CCDS10319.1	15q25.1	2013-08-21	2013-08-21	2007-07-18	ENSG00000183496	ENSG00000183496		"""RING-type (C3HC4) zinc fingers"", ""Mex-3 homologs"""	25297	protein-coding gene	gene with protein product		611008	"""ring finger and KH domain containing 3"", ""mex-3 homolog B (C. elegans)"""	RKHD3		11230166, 17267406	Standard	NM_032246		Approved	DKFZp434J0617, RNF195	uc002bgq.2	Q6ZN04	OTTHUMG00000147356	ENST00000329713.4:c.903C>T	15.37:g.82336308G>A		Somatic		Capture	Illumina HiSeq	Phase_I	80123363	NM_032246	Q4G0W1|Q8IVG2|Q9H0J0	Silent	SNP	ENST00000329713.4	37	CCDS10319.1																																																																																				0.647	MEX3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304000.1	XM_290645	
AP3B2	8120	broad.mit.edu	37	15	83335613	83335613	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:83335613G>A	ENST00000261722.3	-	15	1945	c.1738C>T	c.(1738-1740)Cgc>Tgc	p.R580C	AP3B2_ENST00000535359.1_Missense_Mutation_p.R580C|RP11-752G15.3_ENST00000560650.1_RNA|AP3B2_ENST00000535348.1_Missense_Mutation_p.R548C	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	580					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)	p.R579C(1)		breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			CGGGTGAAGCGCGCCCGGTCG	0.597																																					p.R579R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1737T	15						.						64.0	72.0	70.0					15																	83335613		1955	4133	6088	81132668	SO:0001583	missense	8120	exon15			U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.1738C>T	15.37:g.83335613G>A	ENSP00000261722:p.Arg580Cys	Somatic		Capture	Illumina HiSeq	Phase_I	81132668	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Missense_Mutation	SNP	ENST00000261722.3	37	CCDS45331.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.597330	0.87055	.	.	ENSG00000103723	ENST00000261722;ENST00000535348;ENST00000535359	T;T;T	0.27557	1.66;1.66;1.66	5.84	5.84	0.93424	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68439	0.3001	H	0.96239	3.79	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.963;1.0;1.0	T	0.78142	-0.2319	10	0.87932	D	0	-16.9405	14.9171	0.70807	0.0:0.0:0.8569:0.1431	.	548;580;580	B7ZKR7;B7ZKS0;Q13367	.;.;AP3B2_HUMAN	C	580;548;580	ENSP00000261722:R580C;ENSP00000438721:R548C;ENSP00000440984:R580C	ENSP00000261722:R580C	R	-	1	0	AP3B2	81132668	1.000000	0.71417	0.966000	0.40874	0.852000	0.48524	6.589000	0.74080	2.765000	0.95021	0.655000	0.94253	CGC		0.597	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1		
WHAMM	123720	broad.mit.edu	37	15	83502050	83502050	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:83502050C>T	ENST00000286760.4	+	10	2291	c.2192C>T	c.(2191-2193)gCg>gTg	p.A731V		NM_001080435.1	NP_001073904.1	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules	731	Mediates actin nucleation. {ECO:0000269|PubMed:18614018}.				actin filament organization (GO:0007015)|actin filament reorganization (GO:0090527)|ER to Golgi vesicle-mediated transport (GO:0006888)|focal adhesion assembly (GO:0048041)|lamellipodium assembly (GO:0030032)|membrane tubulation (GO:0097320)|positive regulation of actin nucleation (GO:0051127)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|Golgi membrane (GO:0000139)	Arp2/3 complex binding (GO:0071933)|GTP-Rho binding (GO:0017049)|microtubule binding (GO:0008017)	p.A731V(1)		endometrium(6)|large_intestine(5)|lung(1)|prostate(1)	13						GAAGTGCCGGCGGTGCGCCCT	0.532																																					p.A731V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2192T	15						.						60.0	60.0	60.0					15																	83502050		1990	4145	6135	81299104	SO:0001583	missense	123720	exon10			AK126887	CCDS45333.1	15q25.2	2009-02-18	2009-02-18	2009-02-18	ENSG00000156232	ENSG00000156232			30493	protein-coding gene	gene with protein product		612393	"""WAS protein homology region 2 domain containing 1"""	WHDC1		11853319, 18226259, 18614018, 18812086	Standard	XM_005272422		Approved	KIAA1971	uc002bje.3	Q8TF30		ENST00000286760.4:c.2192C>T	15.37:g.83502050C>T	ENSP00000286760:p.Ala731Val	Somatic		Capture	Illumina HiSeq	Phase_I	81299104	NM_001080435	Q8N1J9	Missense_Mutation	SNP	ENST00000286760.4	37	CCDS45333.1	.	.	.	.	.	.	.	.	.	.	C	11.47	1.648410	0.29336	.	.	ENSG00000156232	ENST00000286760	T	0.33216	1.42	4.94	4.03	0.46877	.	1.048780	0.07400	N	0.890712	T	0.23572	0.0570	L	0.27053	0.805	0.09310	N	1	B	0.16396	0.017	B	0.09377	0.004	T	0.19160	-1.0314	10	0.33141	T	0.24	.	9.5416	0.39255	0.0:0.902:0.0:0.098	.	731	Q8TF30	WHAMM_HUMAN	V	731	ENSP00000286760:A731V	ENSP00000286760:A731V	A	+	2	0	WHAMM	81299104	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.367000	0.20382	1.205000	0.43262	0.557000	0.71058	GCG		0.532	WHAMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418463.1		
WHAMM	123720	broad.mit.edu	37	15	83502209	83502209	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:83502209C>T	ENST00000286760.4	+	10	2450	c.2351C>T	c.(2350-2352)gCg>gTg	p.A784V		NM_001080435.1	NP_001073904.1	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules	784	Mediates actin nucleation. {ECO:0000269|PubMed:18614018}.				actin filament organization (GO:0007015)|actin filament reorganization (GO:0090527)|ER to Golgi vesicle-mediated transport (GO:0006888)|focal adhesion assembly (GO:0048041)|lamellipodium assembly (GO:0030032)|membrane tubulation (GO:0097320)|positive regulation of actin nucleation (GO:0051127)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|Golgi membrane (GO:0000139)	Arp2/3 complex binding (GO:0071933)|GTP-Rho binding (GO:0017049)|microtubule binding (GO:0008017)	p.A758V(1)|p.A784V(1)		endometrium(6)|large_intestine(5)|lung(1)|prostate(1)	13						ATCAAGGCTGCGCTCCAGAGA	0.542																																					p.A784V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2351T	15						.						49.0	51.0	50.0					15																	83502209		2103	4232	6335	81299263	SO:0001583	missense	123720	exon10			AK126887	CCDS45333.1	15q25.2	2009-02-18	2009-02-18	2009-02-18	ENSG00000156232	ENSG00000156232			30493	protein-coding gene	gene with protein product		612393	"""WAS protein homology region 2 domain containing 1"""	WHDC1		11853319, 18226259, 18614018, 18812086	Standard	XM_005272422		Approved	KIAA1971	uc002bje.3	Q8TF30		ENST00000286760.4:c.2351C>T	15.37:g.83502209C>T	ENSP00000286760:p.Ala784Val	Somatic		Capture	Illumina HiSeq	Phase_I	81299263	NM_001080435	Q8N1J9	Missense_Mutation	SNP	ENST00000286760.4	37	CCDS45333.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.974149	0.53720	.	.	ENSG00000156232	ENST00000286760;ENST00000234505	T	0.35789	1.29	5.57	5.57	0.84162	.	0.052882	0.85682	D	0.000000	T	0.58764	0.2145	M	0.70842	2.15	0.46798	D	0.999206	D	0.89917	1.0	D	0.87578	0.998	T	0.59445	-0.7453	10	0.54805	T	0.06	.	13.8582	0.63542	0.0:0.9244:0.0:0.0756	.	784	Q8TF30	WHAMM_HUMAN	V	784;758	ENSP00000286760:A784V	ENSP00000234505:A758V	A	+	2	0	WHAMM	81299263	0.997000	0.39634	0.114000	0.21550	0.052000	0.14988	3.776000	0.55356	2.607000	0.88179	0.557000	0.71058	GCG		0.542	WHAMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418463.1		
ZNF592	9640	broad.mit.edu	37	15	85327839	85327839	+	Missense_Mutation	SNP	G	G	A	rs200137485		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:85327839G>A	ENST00000560079.2	+	4	2221	c.1933G>A	c.(1933-1935)Gtc>Atc	p.V645I	ZNF592_ENST00000299927.3_Missense_Mutation_p.V645I	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	645					cell death (GO:0008219)|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.V645I(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CAAGGGGCTCGTCATGCAGTG	0.602																																					p.V645I												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1933A	15						.						106.0	78.0	87.0					15																	85327839		2203	4299	6502	83128843	SO:0001583	missense	9640	exon4			D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.1933G>A	15.37:g.85327839G>A	ENSP00000452877:p.Val645Ile	Somatic		Capture	Illumina HiSeq	Phase_I	83128843	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.454524	0.43634	.	.	ENSG00000166716	ENST00000299927	T	0.30714	1.52	5.88	5.88	0.94601	.	0.112221	0.64402	D	0.000009	T	0.26376	0.0644	N	0.12569	0.235	0.45108	D	0.998129	D	0.55605	0.972	P	0.53224	0.721	T	0.02437	-1.1159	10	0.27785	T	0.31	-28.2826	11.0631	0.47959	0.0835:0.0:0.9165:0.0	.	645	Q92610	ZN592_HUMAN	I	645	ENSP00000299927:V645I	ENSP00000299927:V645I	V	+	1	0	ZNF592	83128843	1.000000	0.71417	0.970000	0.41538	0.992000	0.81027	4.532000	0.60608	2.774000	0.95407	0.655000	0.94253	GTC		0.602	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630	
ALPK3	57538	broad.mit.edu	37	15	85400119	85400119	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:85400119C>A	ENST00000258888.5	+	6	2923	c.2756C>A	c.(2755-2757)cCc>cAc	p.P919H		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	919					heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.P919H(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GGGAGCGCGCCCACAGCCATG	0.617																																					p.P919H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2756A	15						.						105.0	112.0	109.0					15																	85400119		2203	4299	6502	83201123	SO:0001583	missense	57538	exon6			AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.2756C>A	15.37:g.85400119C>A	ENSP00000258888:p.Pro919His	Somatic		Capture	Illumina HiSeq	Phase_I	83201123	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	.	.	.	.	.	.	.	.	.	.	C	14.95	2.689071	0.48097	.	.	ENSG00000136383	ENST00000258888	T	0.63417	-0.04	4.37	3.33	0.38152	.	1.630770	0.04053	N	0.305081	T	0.56819	0.2011	L	0.34521	1.04	0.09310	N	1	B	0.17465	0.022	B	0.12837	0.008	T	0.49661	-0.8916	10	0.87932	D	0	-10.4975	12.4567	0.55708	0.1797:0.8202:0.0:0.0	.	919	Q96L96	ALPK3_HUMAN	H	919	ENSP00000258888:P919H	ENSP00000258888:P919H	P	+	2	0	ALPK3	83201123	0.037000	0.19845	0.086000	0.20670	0.032000	0.12392	1.463000	0.35277	1.988000	0.58038	0.313000	0.20887	CCC		0.617	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
MFGE8	4240	broad.mit.edu	37	15	89453133	89453133	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:89453133C>T	ENST00000566497.1	-	2	156	c.95G>A	c.(94-96)tGc>tAc	p.C32Y	MFGE8_ENST00000539437.1_Missense_Mutation_p.C24Y|MFGE8_ENST00000268151.7_Missense_Mutation_p.C32Y|MFGE8_ENST00000542878.1_Intron|MFGE8_ENST00000268150.8_Missense_Mutation_p.C32Y|MFGE8_ENST00000559997.1_Intron			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	32	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)	p.C32Y(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					ACCGTTGTGGCAGGGGTTTTT	0.542																																					p.C32Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G95A	15						.						123.0	117.0	119.0					15																	89453133		2200	4299	6499	87254137	SO:0001583	missense	4240	exon2			U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"""sperm surface protein hP47"""	602281	"""sperm associated antigen 10"""	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.95G>A	15.37:g.89453133C>T	ENSP00000456281:p.Cys32Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	87254137	NM_001114614	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Missense_Mutation	SNP	ENST00000566497.1	37	CCDS10347.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.049902	0.75846	.	.	ENSG00000140545	ENST00000268150;ENST00000268151;ENST00000539437	D;D;D	0.99992	-12.4;-12.4;-12.4	5.39	5.39	0.77823	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.99994	0.9999	H	0.95079	3.62	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;1.0;1.0	D	0.99983	1.2799	10	0.46703	T	0.11	-56.7052	18.0846	0.89453	0.0:1.0:0.0:0.0	.	24;24;32;32	B3KTQ2;F5H7N9;Q08431-3;Q08431	.;.;.;MFGM_HUMAN	Y	32;32;24	ENSP00000268150:C32Y;ENSP00000268151:C32Y;ENSP00000442386:C24Y	ENSP00000268150:C32Y	C	-	2	0	MFGE8	87254137	1.000000	0.71417	0.957000	0.39632	0.374000	0.29953	7.330000	0.79181	2.700000	0.92200	0.561000	0.74099	TGC		0.542	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928	
RLBP1	6017	broad.mit.edu	37	15	89760454	89760454	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:89760454C>T	ENST00000268125.5	-	5	682	c.243G>A	c.(241-243)gcG>gcA	p.A81A		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	81					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)	p.A81A(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	CCACGGCCACCGCCAGCTCCT	0.657																																					p.A81A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G243A	15						.						56.0	56.0	56.0					15																	89760454		2200	4299	6499	87561458	SO:0001819	synonymous_variant	6017	exon5			BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"""retinaldehyde-binding protein 1"""			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.243G>A	15.37:g.89760454C>T		Somatic		Capture	Illumina HiSeq	Phase_I	87561458	NM_000326	B2R667	Silent	SNP	ENST00000268125.5	37	CCDS32324.1																																																																																				0.657	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326	
POLG	5428	broad.mit.edu	37	15	89861810	89861810	+	Silent	SNP	G	G	A	rs374937961		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:89861810G>A	ENST00000268124.5	-	21	3777	c.3444C>T	c.(3442-3444)cgC>cgT	p.R1148R	POLG_ENST00000442287.2_Silent_p.R1148R	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	1148					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)	p.R1148R(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			CCAGGGCAGCGCGGTAGCGGT	0.602								DNA polymerases (catalytic subunits)																													p.R1148R	Colon(73;648 1203 11348 18386 27782)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3444T	15						.						75.0	71.0	72.0					15																	89861810		2200	4299	6499	87662814	SO:0001819	synonymous_variant	5428	exon21			X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"""DNA polymerases"""	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.3444C>T	15.37:g.89861810G>A		Somatic		Capture	Illumina HiSeq	Phase_I	87662814	NM_001126131	Q8NFM2|Q92515	Silent	SNP	ENST00000268124.5	37	CCDS10350.1																																																																																				0.602	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693	
POLG	5428	broad.mit.edu	37	15	89870550	89870550	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:89870550C>T	ENST00000268124.5	-	7	1614	c.1281G>A	c.(1279-1281)atG>atA	p.M427I	POLG_ENST00000442287.2_Missense_Mutation_p.M427I	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	427					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)	p.M427I(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			CCATCTCCAGCATGCCGGCCA	0.592								DNA polymerases (catalytic subunits)																													p.M427I	Colon(73;648 1203 11348 18386 27782)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1281A	15						.						42.0	37.0	39.0					15																	89870550		2200	4299	6499	87671554	SO:0001583	missense	5428	exon7			X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"""DNA polymerases"""	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.1281G>A	15.37:g.89870550C>T	ENSP00000268124:p.Met427Ile	Somatic		Capture	Illumina HiSeq	Phase_I	87671554	NM_001126131	Q8NFM2|Q92515	Missense_Mutation	SNP	ENST00000268124.5	37	CCDS10350.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.018407	0.93404	.	.	ENSG00000140521	ENST00000268124;ENST00000442287	D;D	0.92965	-3.14;-3.14	5.0	5.0	0.66597	Ribonuclease H-like (1);	0.104403	0.85682	D	0.000000	D	0.93854	0.8034	M	0.73598	2.24	0.80722	D	1	D	0.59357	0.985	P	0.50314	0.637	D	0.94151	0.7405	10	0.54805	T	0.06	-31.2227	18.4821	0.90815	0.0:1.0:0.0:0.0	.	427	P54098	DPOG1_HUMAN	I	427	ENSP00000268124:M427I;ENSP00000399851:M427I	ENSP00000268124:M427I	M	-	3	0	POLG	87671554	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.439000	0.80444	2.598000	0.87819	0.491000	0.48974	ATG		0.592	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693	
TICRR	90381	broad.mit.edu	37	15	90144735	90144735	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:90144735C>T	ENST00000268138.7	+	11	2368	c.2263C>T	c.(2263-2265)Cgc>Tgc	p.R755C	TICRR_ENST00000560985.1_Missense_Mutation_p.R754C			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	755					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.R755C(1)									AGATTTGCTGCGCATGGTGTG	0.403																																					p.R755C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2263T	15						.						159.0	158.0	158.0					15																	90144735		2004	4202	6206	87945739	SO:0001583	missense	90381	exon11			AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"""TOPBP1-interacting replication-stimulating protein"", ""SLD3 homolog (S. cerevisiae)"""	613298	"""chromosome 15 open reading frame 42"""	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.2263C>T	15.37:g.90144735C>T	ENSP00000268138:p.Arg755Cys	Somatic		Capture	Illumina HiSeq	Phase_I	87945739	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	37	CCDS10352.2	.	.	.	.	.	.	.	.	.	.	C	23.5	4.422626	0.83559	.	.	ENSG00000140534	ENST00000268138	T	0.22743	1.94	5.76	5.76	0.90799	.	0.107659	0.64402	D	0.000004	T	0.47116	0.1428	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.37842	-0.9688	10	0.87932	D	0	-17.7703	15.8811	0.79205	0.136:0.864:0.0:0.0	.	755	Q7Z2Z1	TICRR_HUMAN	C	755	ENSP00000268138:R755C	ENSP00000268138:R755C	R	+	1	0	C15orf42	87945739	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	2.586000	0.46119	2.882000	0.98803	0.655000	0.94253	CGC		0.403	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
ARPIN	348110	broad.mit.edu	37	15	90454001	90454001	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:90454001C>T	ENST00000357484.5	-	2	263	c.143G>A	c.(142-144)aGc>aAc	p.S48N	C15orf38_ENST00000460685.1_5'UTR|C15orf38-AP3S2_ENST00000398333.3_Missense_Mutation_p.S48N	NM_001282380.1|NM_182616.2	NP_001269309.1|NP_872422.1	Q7Z6K5	ARPIN_HUMAN		48					directional locomotion (GO:0033058)|negative regulation of actin nucleation (GO:0051126)|negative regulation of cell migration (GO:0030336)|negative regulation of lamellipodium morphogenesis (GO:2000393)	lamellipodium (GO:0030027)		p.S48N(1)		breast(3)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)	10	Melanoma(11;0.0171)|Lung NSC(78;0.0181)|all_lung(78;0.0384)		BRCA - Breast invasive adenocarcinoma(143;0.0107)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.223)			GTCCAAGATGCTGTGCCGAGA	0.532																																					p.S48N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G143A	15						.						118.0	113.0	115.0					15																	90454001		2129	4235	6364	88255005	SO:0001583	missense	10239	exon2																														ENST00000357484.5:c.143G>A	15.37:g.90454001C>T	ENSP00000350075:p.Ser48Asn	Somatic		Capture	Illumina HiSeq	Phase_I	88255005	NM_182616	E2QRD5	Missense_Mutation	SNP	ENST00000357484.5	37	CCDS42080.1	.	.	.	.	.	.	.	.	.	.	C	9.730	1.161951	0.21538	.	.	ENSG00000250021;ENSG00000242498	ENST00000398333;ENST00000357484	T	0.46063	0.88	5.29	3.13	0.36017	.	1.058690	0.07397	U	0.890149	T	0.26810	0.0656	N	0.17082	0.46	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.14023	0.01;0.003	T	0.35251	-0.9796	10	0.39692	T	0.17	-12.5016	5.9303	0.19134	0.0:0.5503:0.3412:0.1085	.	48;48	Q7Z6K5;E2QRD5	CO038_HUMAN;.	N	48	ENSP00000381377:S48N	ENSP00000381377:S48N	S	-	2	0	C15orf38-AP3S2;C15orf38	88255005	1.000000	0.71417	1.000000	0.80357	0.059000	0.15707	1.580000	0.36547	2.476000	0.83614	0.563000	0.77884	AGC		0.532	C15orf38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335629.1		
IDH2	3418	broad.mit.edu	37	15	90628140	90628140	+	Splice_Site	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:90628140C>T	ENST00000330062.3	-	10	1292	c.1179G>A	c.(1177-1179)agG>agA	p.R393R	IDH2_ENST00000540499.2_Splice_Site_p.R341R|RP11-617F23.1_ENST00000558334.1_RNA|IDH2_ENST00000539790.1_Splice_Site_p.R263R|IDH2_ENST00000559482.1_Intron	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	393					2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R393R(1)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			TCTGGGCAAACCTATGGGGAT	0.627			M		GBM																																p.R393R			Dom	yes		15	15q26.1	3418	"""socitrate dehydrogenase 2 (NADP+), mitochondrial """		M	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1179A	15						.						105.0	103.0	104.0					15																	90628140		2200	4298	6498	88429144	SO:0001630	splice_region_variant	3418	exon10				CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.1179-1G>A	15.37:g.90628140C>T		Somatic		Capture	Illumina HiSeq	Phase_I	88429144	NM_002168	B2R6L6|B4DFL2|Q96GT3	Silent	SNP	ENST00000330062.3	37	CCDS10359.1																																																																																				0.627	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313426.1		Silent
TTLL13	440307	broad.mit.edu	37	15	90801486	90801486	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:90801486G>A	ENST00000339615.5	+	9	1442	c.1152G>A	c.(1150-1152)aaG>aaA	p.K384K	RP11-697E2.6_ENST00000561573.1_3'UTR|TTLL13_ENST00000438251.1_Silent_p.K384K	NM_001029964.2	NP_001025135.2			tubulin tyrosine ligase-like family, member 13									p.K384K(1)		NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)	16	Melanoma(11;0.00551)|Lung NSC(78;0.0178)|all_lung(78;0.0378)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|BRCA - Breast invasive adenocarcinoma(143;0.0323)|Kidney(142;0.0514)			ACAAGTTGAAGCCCTGGCTGC	0.502																																					p.K384K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1152A	15						.						203.0	191.0	195.0					15																	90801486		2199	4298	6497	88602490	SO:0001819	synonymous_variant	440307	exon9			BC036668		15q26.1	2013-02-14				ENSG00000213471		"""Tubulin tyrosine ligase-like family"""	32484	protein-coding gene	gene with protein product						15890843	Standard	NR_104604		Approved	FLJ46079, MGC33417	uc002bpd.1	A6NNM8		ENST00000339615.5:c.1152G>A	15.37:g.90801486G>A		Somatic		Capture	Illumina HiSeq	Phase_I	88602490	NM_001029964		Silent	SNP	ENST00000339615.5	37	CCDS32328.1																																																																																				0.502	TTLL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435854.1	NM_001029964	
FES	2242	broad.mit.edu	37	15	91433079	91433079	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:91433079A>G	ENST00000328850.3	+	8	1078	c.936A>G	c.(934-936)tcA>tcG	p.S312S	FES_ENST00000448367.1_3'UTR|FES_ENST00000394302.1_Silent_p.S254S|FES_ENST00000444422.2_Silent_p.S312S|FES_ENST00000450438.2_Silent_p.S254S|FES_ENST00000394300.3_Silent_p.S254S|FES_ENST00000414248.2_Silent_p.S254S	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	312					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of mast cell degranulation (GO:0043304)|regulation of vesicle-mediated transport (GO:0060627)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule cytoskeleton (GO:0015630)	ATP binding (GO:0005524)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol binding (GO:0035091)|protein tyrosine kinase activity (GO:0004713)	p.S312S(1)		lung(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			GGCTGACCTCAGTGACAGATG	0.607																																					p.S254S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A762G	15						.						120.0	126.0	124.0					15																	91433079		2198	4298	6496	89234083	SO:0001819	synonymous_variant	2242	exon6			X52192	CCDS10365.1, CCDS45349.1, CCDS45350.1, CCDS45351.1	15q26.1	2014-06-26	2014-06-26		ENSG00000182511	ENSG00000182511	2.7.10.1	"""SH2 domain containing"""	3657	protein-coding gene	gene with protein product	"""Oncogene FES, feline sarcoma virus"", ""c-fes/fps protein"""	190030	"""feline sarcoma (Snyder-Theilen) viral (v-fes)/Fujinami avian sarcoma (PRCII) viral (v-fps) oncogene homolog"", ""feline sarcoma oncogene"""			1870997	Standard	NM_002005		Approved	FPS	uc002bpv.3	P07332	OTTHUMG00000044456	ENST00000328850.3:c.936A>G	15.37:g.91433079A>G		Somatic		Capture	Illumina HiSeq	Phase_I	89234083	NM_001143783	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Silent	SNP	ENST00000328850.3	37	CCDS10365.1																																																																																				0.607	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005	
CHD2	1106	broad.mit.edu	37	15	93528836	93528836	+	Missense_Mutation	SNP	C	C	T	rs200013427		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:93528836C>T	ENST00000394196.4	+	26	4414	c.3346C>T	c.(3346-3348)Cgc>Tgc	p.R1116C	CHD2_ENST00000557381.1_Missense_Mutation_p.R1116C	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1116					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)	p.R1116C(1)		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)			GAAGCCAAAGCGCAGAGGGCG	0.527																																					p.R1116C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3346T	15						.						134.0	123.0	127.0					15																	93528836		2197	4298	6495	91329840	SO:0001583	missense	1106	exon26			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.3346C>T	15.37:g.93528836C>T	ENSP00000377747:p.Arg1116Cys	Somatic		Capture	Illumina HiSeq	Phase_I	91329840	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	C	27.4	4.830876	0.91036	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	T;T	0.79940	-1.32;-1.32	5.18	5.18	0.71444	.	0.000000	0.34959	U	0.003553	D	0.85885	0.5801	L	0.48642	1.525	0.80722	D	1	D;D	0.76494	0.997;0.999	P;P	0.61275	0.548;0.886	D	0.87415	0.2378	10	0.87932	D	0	-11.7867	18.6951	0.91598	0.0:1.0:0.0:0.0	.	1116;1116	O14647;O14647-2	CHD2_HUMAN;.	C	1116	ENSP00000377747:R1116C;ENSP00000451366:R1116C	ENSP00000377747:R1116C	R	+	1	0	CHD2	91329840	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.435000	0.59941	2.417000	0.82017	0.650000	0.86243	CGC		0.527	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
IGF1R	3480	broad.mit.edu	37	15	99478220	99478220	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:99478220C>T	ENST00000268035.6	+	16	3735	c.3124C>T	c.(3124-3126)Cgt>Tgt	p.R1042C	IGF1R_ENST00000558762.1_Missense_Mutation_p.R1041C	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	1042	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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.R1042C(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)"""	CGCAAGCATGCGTGAGAGGAT	0.468																																					p.R1042C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3124T	15						.						137.0	122.0	127.0					15																	99478220		2197	4297	6494	97295743	SO:0001583	missense	3480	exon16			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.3124C>T	15.37:g.99478220C>T	ENSP00000268035:p.Arg1042Cys	Somatic		Capture	Illumina HiSeq	Phase_I	97295743	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Missense_Mutation	SNP	ENST00000268035.6	37	CCDS10378.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.095032	0.76870	.	.	ENSG00000140443	ENST00000268035	D	0.83335	-1.71	5.18	4.2	0.49525	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000045	D	0.88455	0.6441	L	0.55481	1.735	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.984;0.997	D	0.89505	0.3767	10	0.87932	D	0	.	14.4688	0.67501	0.1477:0.8523:0.0:0.0	.	1041;1042	C9J5X1;P08069	.;IGF1R_HUMAN	C	1042	ENSP00000268035:R1042C	ENSP00000268035:R1042C	R	+	1	0	IGF1R	97295743	1.000000	0.71417	0.997000	0.53966	0.894000	0.52154	2.458000	0.45014	2.422000	0.82143	0.462000	0.41574	CGT		0.468	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
SYNM	23336	broad.mit.edu	37	15	99671648	99671648	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:99671648A>T	ENST00000560674.1	+	4	2694	c.2225A>T	c.(2224-2226)gAg>gTg	p.E742V	RP11-6O2.4_ENST00000566974.1_RNA|SYNM_ENST00000328642.7_Missense_Mutation_p.E1027V|SYNM_ENST00000336292.6_Missense_Mutation_p.E1027V|SYNM_ENST00000561323.1_3'UTR			O15061	SYNEM_HUMAN	synemin, intermediate filament protein	1028	Tail.				intermediate filament cytoskeleton organization (GO:0045104)	adherens junction (GO:0005912)|costamere (GO:0043034)|intermediate filament (GO:0005882)|membrane (GO:0016020)|neurofilament cytoskeleton (GO:0060053)	intermediate filament binding (GO:0019215)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)	p.E1027V(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(6)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	29						AGTGAGATGGAGAAGGCTGTG	0.612																																					p.R1028X	Pancreas(125;1071 1762 21750 40003 40381)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3082T	15						.						31.0	39.0	36.0					15																	99671648		2164	4269	6433	97489171	SO:0001583	missense	23336	exon4			AK026420	CCDS73786.1, CCDS73787.1	15q26.3	2014-09-17	2008-09-19	2008-09-19	ENSG00000182253	ENSG00000182253		"""A-kinase anchor proteins"", ""Intermediate filaments type IV"""	24466	protein-coding gene	gene with protein product	"""synemin alpha"", ""synemin beta"""	606087	"""desmuslin"""	DMN		11737198, 11454237	Standard	NM_145728		Approved	KIAA0353, SYN	uc002bup.3	O15061		ENST00000560674.1:c.2225A>T	15.37:g.99671648A>T	ENSP00000453040:p.Glu742Val	Somatic		Capture	Illumina HiSeq	Phase_I	97489171	NM_015286	A7E2Y2|Q2TBJ4|Q5NJJ9|Q8TE61|Q8TE62	Missense_Mutation	SNP	ENST00000560674.1	37		.	.	.	.	.	.	.	.	.	.	A	12.56	1.973893	0.34848	.	.	ENSG00000182253	ENST00000336292;ENST00000328642	D;D	0.85556	-1.96;-2.0	5.55	5.55	0.83447	.	.	.	.	.	D	0.90858	0.7128	.	.	.	0.39362	D	0.965934	D;D	0.89917	0.999;1.0	D;D	0.71870	0.96;0.975	D	0.91964	0.5581	8	0.72032	D	0.01	.	9.3836	0.38329	0.9208:0.0:0.0792:0.0	.	1028;1027	O15061;C9JIE4	SYNEM_HUMAN;.	V	1027	ENSP00000336775:E1027V;ENSP00000330469:E1027V	ENSP00000330469:E1027V	E	+	2	0	SYNM	97489171	1.000000	0.71417	0.955000	0.39395	0.107000	0.19398	2.883000	0.48554	2.099000	0.63709	0.533000	0.62120	GAG		0.612	SYNM-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000415698.2	NM_145728	
LRRK1	79705	broad.mit.edu	37	15	101606385	101606385	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:101606385G>A	ENST00000388948.3	+	32	6102	c.5743G>A	c.(5743-5745)Gtc>Atc	p.V1915I	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Missense_Mutation_p.V1912I|LRRK1_ENST00000532145.1_3'UTR	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1									p.V1927I(1)|p.V1915I(1)		breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GATCCTCGCCGTCAGAGACCT	0.642																																					p.V1915I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G5743A	15						.						91.0	96.0	94.0					15																	101606385		2080	4214	6294	99423908	SO:0001583	missense	79705	exon32			AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.5743G>A	15.37:g.101606385G>A	ENSP00000373600:p.Val1915Ile	Somatic		Capture	Illumina HiSeq	Phase_I	99423908	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	37	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.754238	0.89843	.	.	ENSG00000154237	ENST00000388948;ENST00000284395;ENST00000529762;ENST00000542170	T;T	0.79141	-1.18;-1.24	5.46	5.46	0.80206	.	0.150847	0.42172	D	0.000748	D	0.86736	0.6004	M	0.66939	2.045	0.53005	D	0.999969	D	0.76494	0.999	D	0.72982	0.979	D	0.84454	0.0590	10	0.31617	T	0.26	.	18.9136	0.92496	0.0:0.0:1.0:0.0	.	1915	Q38SD2	LRRK1_HUMAN	I	1915;1912;606;469	ENSP00000373600:V1915I;ENSP00000284395:V1912I	ENSP00000284395:V1912I	V	+	1	0	LRRK1	99423908	1.000000	0.71417	0.074000	0.20217	0.799000	0.45148	9.245000	0.95431	2.563000	0.86464	0.655000	0.94253	GTC		0.642	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
FURIN	5045	broad.mit.edu	37	15	91423107	91423108	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	AT	AT	AT	-	AT	AT	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:91423107_91423108delAT	ENST00000268171.3	+	12	1548_1549	c.1269_1270delAT	c.(1267-1272)tcatatfs	p.Y424fs		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	424	Peptidase S8.				cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.Y424fs*72(1)		breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			TGAGCCACTCATATGGCTACGG	0.624																																					p.423_424del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1269_1270del	15						.																																			89224112	SO:0001589	frameshift_variant	5045	exon12			X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"""paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"""	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.1269_1270delAT	15.37:g.91423109_91423110delAT	ENSP00000268171:p.Tyr424fs	Somatic		Capture	Illumina HiSeq	Phase_I	89224111	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Frame_Shift_Del	DEL	ENST00000268171.3	37	CCDS10364.1																																																																																				0.624	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	
CHSY1	22856	broad.mit.edu	37	15	101775584	101775584	+	Silent	SNP	G	G	A	rs143062356	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr15:101775584G>A	ENST00000254190.3	-	2	994	c.519C>T	c.(517-519)gaC>gaT	p.D173D		NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	173					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of ossification (GO:0030279)|response to nutrient levels (GO:0031667)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)	p.D173D(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGATGTACACGTCATCATCTG	0.512																																					p.D173D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C519T	15						.	G		0,4406		0,0,2203	106.0	98.0	101.0		519	-8.8	0.0	15	dbSNP_134	101	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	CHSY1	NM_014918.4		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		173/803	101775584	2,13004	2203	4300	6503	99593107	SO:0001819	synonymous_variant	22856	exon2			AB023207	CCDS10390.1	15q26.3	2013-02-19	2008-01-24	2008-01-24	ENSG00000131873	ENSG00000131873	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	17198	protein-coding gene	gene with protein product		608183	"""carbohydrate (chondroitin) synthase 1"""			11514575	Standard	NM_014918		Approved	KIAA0990, CSS1	uc021sxt.1	Q86X52	OTTHUMG00000149873	ENST00000254190.3:c.519C>T	15.37:g.101775584G>A		Somatic		Capture	Illumina HiSeq	Phase_I	99593107	NM_014918	Q6UX38|Q7LFU5|Q9Y2J5	Silent	SNP	ENST00000254190.3	37	CCDS10390.1																																																																																				0.512	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918	
PALB2	79728	broad.mit.edu	37	16	23632769	23632770	+	Frame_Shift_Ins	INS	-	-	G	rs180177131|rs587776422|rs552354535		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:23632769_23632770insG	ENST00000261584.4	-	10	3178_3179	c.3026_3027insC	c.(3025-3027)cctfs	p.P1009fs	CTD-2196E14.3_ENST00000561764.1_RNA	NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	1009	Interaction with RAD51, BRCA2 and POLH.|Required for interaction with POLH and POLH DNA synthesis stimulation.				DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E1010fs*1(1)		breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		TAGTCTCCTCAGGGGGCATCAA	0.406			"""F, N, Mis"""			"""Wilms tumor, medulloblastoma, AML ,breast"""		Involved in tolerance or repair of DNA crosslinks																													p.P1009fs		yes	Rec		"""Fanconi anaemia N, breast cancer susceptibility """	16	16p12.1	79728	partner and localizer of BRCA2		"""L, O, E"""	.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.3027_3028insC	16						.																																			23540271	SO:0001589	frameshift_variant	79728	exon10				CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"""Fanconi anemia, complementation groups"""	26144	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group N"""	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.3027dupC	16.37:g.23632774_23632774dupG	ENSP00000261584:p.Pro1009fs	Somatic		Capture	Illumina HiSeq	Phase_I	23540270	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Frame_Shift_Ins	INS	ENST00000261584.4	37	CCDS32406.1																																																																																				0.406	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675	
TEKT5	146279	broad.mit.edu	37	16	10729660	10729660	+	Missense_Mutation	SNP	C	C	T	rs549750185		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:10729660C>T	ENST00000283025.2	-	6	1273	c.1202G>A	c.(1201-1203)cGc>cAc	p.R401H	TEKT5_ENST00000574923.1_5'UTR	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	401						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.R401H(2)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						CATGTTGGGGCGCCGGGTCCG	0.627																																					p.R401H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1202A	16						.						96.0	101.0	100.0					16																	10729660		2197	4300	6497	10637161	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.1202G>A	16.37:g.10729660C>T	ENSP00000283025:p.Arg401His	Somatic		Capture	Illumina HiSeq	Phase_I	10637161	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.758177	0.89843	.	.	ENSG00000153060	ENST00000283025	T	0.26660	1.72	4.56	4.56	0.56223	.	0.000000	0.53938	D	0.000041	T	0.58892	0.2154	M	0.90542	3.125	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70004	-0.4991	10	0.87932	D	0	-23.7408	15.9141	0.79496	0.0:1.0:0.0:0.0	.	401	Q96M29	TEKT5_HUMAN	H	401	ENSP00000283025:R401H	ENSP00000283025:R401H	R	-	2	0	TEKT5	10637161	0.996000	0.38824	0.983000	0.44433	0.760000	0.43138	7.225000	0.78051	2.090000	0.63153	0.555000	0.69702	CGC		0.627	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
CIITA	4261	broad.mit.edu	37	16	11001395	11001395	+	Silent	SNP	C	C	T	rs143474425		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:11001395C>T	ENST00000324288.8	+	11	2179	c.2046C>T	c.(2044-2046)tcC>tcT	p.S682S	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	682	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)	p.S682S(1)		central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						AGTTCCCATCCGCAGACGTGA	0.667			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """																																p.S682S			Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2046T	16						.	C		0,4394		0,0,2197	45.0	47.0	46.0		2046	-10.3	0.0	16	dbSNP_134	46	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CIITA	NM_000246.3		0,1,6496	TT,TC,CC		0.0116,0.0,0.0077		682/1131	11001395	1,12993	2197	4300	6497	10908896	SO:0001819	synonymous_variant	4261	exon11			U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.2046C>T	16.37:g.11001395C>T		Somatic		Capture	Illumina HiSeq	Phase_I	10908896	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																				0.667	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
CIITA	4261	broad.mit.edu	37	16	11012358	11012358	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:11012358C>T	ENST00000324288.8	+	16	3257	c.3124C>T	c.(3124-3126)Ctc>Ttc	p.L1042F	CIITA_ENST00000381835.5_Missense_Mutation_p.L458F	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	1042					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)	p.L1042F(1)		central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						CCTGCCTTCGCTCGCTGCATC	0.647			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """						OREG0023606	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1042F			Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3124T	16						.						157.0	151.0	153.0					16																	11012358		2197	4300	6497	10919859	SO:0001583	missense	4261	exon16			U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.3124C>T	16.37:g.11012358C>T	ENSP00000316328:p.Leu1042Phe	Somatic	669	Capture	Illumina HiSeq	Phase_I	10919859	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.711922	0.48517	.	.	ENSG00000179583	ENST00000324288;ENST00000381835	T;T	0.54071	0.59;0.59	5.03	3.07	0.35406	.	0.000000	0.39146	N	0.001443	T	0.54447	0.1859	L	0.31578	0.945	0.09310	N	0.999998	D;D;D	0.89917	1.0;1.0;0.994	D;D;D	0.87578	0.988;0.998;0.968	T	0.35101	-0.9802	10	0.44086	T	0.13	.	6.2032	0.20587	0.0:0.7216:0.0:0.2784	.	458;1042;1042	E9PFE0;A0N0N9;P33076	.;.;C2TA_HUMAN	F	1042;458	ENSP00000316328:L1042F;ENSP00000371257:L458F	ENSP00000316328:L1042F	L	+	1	0	CIITA	10919859	0.699000	0.27786	0.052000	0.19188	0.497000	0.33675	1.156000	0.31712	1.106000	0.41623	0.561000	0.74099	CTC		0.647	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
CACNA1H	8912	broad.mit.edu	37	16	1268393	1268393	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:1268393G>A	ENST00000348261.5	+	33	5877	c.5629G>A	c.(5629-5631)Gac>Aac	p.D1877N	CACNA1H_ENST00000565831.1_Missense_Mutation_p.D1871N|CACNA1H_ENST00000358590.4_Missense_Mutation_p.D1871N	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1877					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)	p.D1871N(1)		breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	TGCGGAGCTGGACGCCGAGAT	0.692																																					p.D1877N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5629A	16						.						43.0	52.0	49.0					16																	1268393		2100	4182	6282	1208394	SO:0001583	missense	8912	exon33			AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.5629G>A	16.37:g.1268393G>A	ENSP00000334198:p.Asp1877Asn	Somatic		Capture	Illumina HiSeq	Phase_I	1208394	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.010845	0.75046	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.97303	-4.33;-4.27	4.1	4.1	0.47936	.	0.293086	0.28790	N	0.014130	D	0.97495	0.9180	L	0.46157	1.445	0.47659	D	0.999487	D;D;D;D;D	0.89917	0.997;0.996;0.998;1.0;0.999	P;D;D;D;D	0.76575	0.888;0.917;0.954;0.988;0.922	D	0.98296	1.0516	10	0.87932	D	0	.	15.8267	0.78711	0.0:0.0:1.0:0.0	.	623;612;618;1871;1877	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	N	1877;1871	ENSP00000334198:D1877N;ENSP00000351401:D1871N	ENSP00000334198:D1877N	D	+	1	0	CACNA1H	1208394	1.000000	0.71417	1.000000	0.80357	0.430000	0.31655	5.336000	0.65935	2.287000	0.76781	0.462000	0.41574	GAC		0.692	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
TPSD1	23430	broad.mit.edu	37	16	1306325	1306325	+	Missense_Mutation	SNP	C	C	T	rs142635848		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:1306325C>T	ENST00000211076.3	+	1	192	c.44C>T	c.(43-45)gCg>gTg	p.A15V	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Missense_Mutation_p.A8V	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	15						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.A15V(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CTGCTGCTGGCGCTGCCCGTC	0.697																																					p.A15V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C44T	16						.	C	VAL/ALA	0,4394		0,0,2197	42.0	53.0	50.0		44	-2.4	0.0	16	dbSNP_134	50	2,8596		0,2,4297	no	missense	TPSD1	NM_012217.2	64	0,2,6494	TT,TC,CC		0.0233,0.0,0.0154	benign	15/243	1306325	2,12990	2197	4299	6496	1246326	SO:0001583	missense	23430	exon1			AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.44C>T	16.37:g.1306325C>T	ENSP00000211076:p.Ala15Val	Somatic		Capture	Illumina HiSeq	Phase_I	1246326	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	.	.	.	.	.	.	.	.	.	.	-	8.821	0.937473	0.18206	0.0	2.33E-4	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.81499	-1.5;-1.5	2.55	-2.41	0.06562	.	0.437392	0.19416	N	0.114808	T	0.61837	0.2379	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45041	-0.9288	10	0.41790	T	0.15	.	6.4267	0.21773	0.0:0.4472:0.0:0.5528	.	15	Q9BZJ3	TRYD_HUMAN	V	8;15	ENSP00000380668:A8V;ENSP00000211076:A15V	ENSP00000211076:A15V	A	+	2	0	TPSD1	1246326	0.000000	0.05858	0.010000	0.14722	0.104000	0.19210	-0.741000	0.04855	-0.768000	0.04626	-1.125000	0.01998	GCG		0.697	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
CLEC16A	23274	broad.mit.edu	37	16	11217664	11217664	+	Silent	SNP	G	G	A	rs201130241		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:11217664G>A	ENST00000409790.1	+	21	2564	c.2334G>A	c.(2332-2334)gcG>gcA	p.A778A	CLEC16A_ENST00000465491.1_3'UTR|CLEC16A_ENST00000381822.2_5'Flank|CLEC16A_ENST00000409552.3_Silent_p.A760A	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.A778A(1)|p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						ACAAGCCTGCGTCCAGCCCCC	0.592													G|||	1	0.000199681	0.0	0.0	5008	,	,		20981	0.0		0.0	False		,,,				2504	0.001				p.A778A												.	.	2	Whole gene deletion(1)|Substitution - coding silent(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.G2334A	16						.						73.0	82.0	79.0					16																	11217664		2134	4242	6376	11125165	SO:0001819	synonymous_variant	23274	exon20			AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2334G>A	16.37:g.11217664G>A		Somatic		Capture	Illumina HiSeq	Phase_I	11125165	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	G	8.584	0.882996	0.17467	.	.	ENSG00000038532	ENST00000428742	.	.	.	5.55	-11.1	0.00147	.	.	.	.	.	T	0.33760	0.0874	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53865	-0.8378	4	.	.	.	-13.722	2.6647	0.05037	0.3441:0.3374:0.1583:0.1601	.	.	.	.	H	22	.	.	R	+	2	0	CLEC16A	11125165	0.000000	0.05858	0.009000	0.14445	0.949000	0.60115	-4.060000	0.00303	-4.463000	0.00047	-2.511000	0.00188	CGT		0.592	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
CPPED1	55313	broad.mit.edu	37	16	12798554	12798554	+	Silent	SNP	G	G	A	rs200745290	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:12798554G>A	ENST00000381774.4	-	3	882	c.642C>T	c.(640-642)gaC>gaT	p.D214D	CPPED1_ENST00000261660.4_Intron|CPPED1_ENST00000433677.2_Intron	NM_018340.2	NP_060810.2	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain containing 1	214	Catalytic.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.D214D(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|urinary_tract(1)	18						CGTCGTCCTCGTCGATGCTCT	0.602																																					p.D214D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C642T	16						.						94.0	96.0	96.0					16																	12798554		2126	4257	6383	12706055	SO:0001819	synonymous_variant	55313	exon3			AK022710	CCDS42119.1, CCDS42120.1	16p13.12	2014-02-12	2009-03-13		ENSG00000103381	ENSG00000103381			25632	protein-coding gene	gene with protein product	"""complete S transactivated protein 1"""	615603				12477932	Standard	NM_018340		Approved	CSTP1, FLJ11151	uc002dca.4	Q9BRF8	OTTHUMG00000167711	ENST00000381774.4:c.642C>T	16.37:g.12798554G>A		Somatic		Capture	Illumina HiSeq	Phase_I	12706055	NM_018340	B4DQ68|Q6MZY9|Q9H9M9|Q9NUT6	Silent	SNP	ENST00000381774.4	37	CCDS42120.1																																																																																				0.602	CPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395795.2	NM_018340	
NOMO1	23420	broad.mit.edu	37	16	14969013	14969013	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:14969013C>T	ENST00000287667.7	+	19	2346	c.2175C>T	c.(2173-2175)ggC>ggT	p.G725G		NM_014287.3	NP_055102.3	Q15155	NOMO1_HUMAN	NODAL modulator 1	725						integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)	p.G725G(1)		endometrium(6)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|skin(2)	30						AGAAAAACGGCAATGAGGAAG	0.577																																					p.G725G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2175T	16						.						216.0	223.0	220.0					16																	14969013		2197	4299	6496	14876514	SO:0001819	synonymous_variant	23420	exon19			X57398	CCDS10556.1	16p13.11	2008-02-05			ENSG00000103512	ENSG00000103512			30060	protein-coding gene	gene with protein product		609157				1310294, 15257293	Standard	NM_014287		Approved	PM5	uc002dcv.3	Q15155	OTTHUMG00000090541	ENST00000287667.7:c.2175C>T	16.37:g.14969013C>T		Somatic		Capture	Illumina HiSeq	Phase_I	14876514	NM_014287	P78421|Q8IW21|Q96DG0	Silent	SNP	ENST00000287667.7	37	CCDS10556.1																																																																																				0.577	NOMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207065.1		
IFT140	9742	broad.mit.edu	37	16	1634276	1634276	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:1634276G>A	ENST00000426508.2	-	11	1664	c.1301C>T	c.(1300-1302)aCg>aTg	p.T434M	LA16c-395F10.2_ENST00000563162.1_RNA|IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	434					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)		p.T434M(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				TGCGACCCCCGTGGACAGGAA	0.627																																					p.T434M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1301T	16						.						48.0	39.0	42.0					16																	1634276		2199	4300	6499	1574277	SO:0001583	missense	9742	exon11			AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.1301C>T	16.37:g.1634276G>A	ENSP00000406012:p.Thr434Met	Somatic		Capture	Illumina HiSeq	Phase_I	1574277	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	.	.	.	.	.	.	.	.	.	.	G	14.97	2.694652	0.48202	.	.	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.70986	-0.53	5.51	3.53	0.40419	.	0.469632	0.23369	N	0.048928	T	0.80864	0.4705	M	0.74258	2.255	0.32800	D	0.500068	D;D	0.89917	0.999;1.0	P;D	0.68621	0.847;0.959	D	0.83790	0.0230	10	0.46703	T	0.11	.	10.6746	0.45778	0.072:0.1327:0.7953:0.0	.	434;159	Q96RY7;B4DR58	IF140_HUMAN;.	M	434	ENSP00000406012:T434M	ENSP00000380562:T434M	T	-	2	0	IFT140	1574277	0.022000	0.18835	0.011000	0.14972	0.172000	0.22775	1.843000	0.39259	0.789000	0.33779	0.655000	0.94253	ACG		0.627	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
MYH11	4629	broad.mit.edu	37	16	15802690	15802690	+	Intron	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:15802690G>T	ENST00000300036.5	-	41	5896				MYH11_ENST00000576790.2_Missense_Mutation_p.P1932H|NDE1_ENST00000396355.1_Intron|NDE1_ENST00000342673.5_Intron|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000396324.3_Intron|MYH11_ENST00000573908.1_Intron|MYH11_ENST00000452625.2_Missense_Mutation_p.P1939H	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle						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.P1932H(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						TTCCTGTGGGGGGGGCCCTCT	0.488			T	CBFB	AML																																p.P1939H			Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5816A	16						.						32.0	32.0	32.0					16																	15802690		2197	4300	6497	15710191	SO:0001627	intron_variant	4629	exon42			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.5787-4710C>A	16.37:g.15802690G>T		Somatic		Capture	Illumina HiSeq	Phase_I	15710191	NM_001040113	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.20|16.20	3.055652|3.055652	0.55325|0.55325	.|.	.|.	ENSG00000133392|ENSG00000133392	ENST00000338282;ENST00000452625|ENST00000396320	D;D|.	0.85484|.	-1.99;-1.99|.	3.78|3.78	2.75|2.75	0.32379|0.32379	.|.	.|.	.|.	.|.	.|.	T|T	0.35278|0.35278	0.0926|0.0926	N|N	0.16368|0.16368	0.405|0.405	0.80722|0.80722	D|D	1|1	P;P;P|.	0.46706|.	0.883;0.705;0.705|.	P;B;B|.	0.46320|.	0.512;0.237;0.237|.	T|T	0.18555|0.18555	-1.0333|-1.0333	9|6	0.40728|0.46703	T|T	0.16|0.11	.|.	2.5483|2.5483	0.04742|0.04742	0.548:0.0:0.452:0.0|0.548:0.0:0.452:0.0	.|.	1939;1932;1939|.	B1PS43;Q3MIV8;Q3MNF0|.	.;.;.|.	H|T	1932;1939|1939	ENSP00000345136:P1932H;ENSP00000407821:P1939H|.	ENSP00000345136:P1932H|ENSP00000379613:P1939T	P|P	-|-	2|1	0|0	MYH11|MYH11	15710191|15710191	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	1.516000|1.516000	0.35856|0.35856	0.977000|0.977000	0.38444|0.38444	0.561000|0.561000	0.74099|0.74099	CCC|CCC		0.488	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
MYH11	4629	broad.mit.edu	37	16	15876283	15876283	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:15876283C>T	ENST00000300036.5	-	6	794	c.685G>A	c.(685-687)Ggc>Agc	p.G229S	MYH11_ENST00000576790.2_Missense_Mutation_p.G229S|MYH11_ENST00000396324.3_Missense_Mutation_p.G236S|MYH11_ENST00000452625.2_Missense_Mutation_p.G236S	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	229	Myosin motor.				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.G229S(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						TTGGCGTTGCCGAAAGCCTCC	0.463			T	CBFB	AML																																p.G236S			Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G706A	16						.						163.0	149.0	154.0					16																	15876283		2197	4300	6497	15783784	SO:0001583	missense	4629	exon7			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.685G>A	16.37:g.15876283C>T	ENSP00000300036:p.Gly229Ser	Somatic		Capture	Illumina HiSeq	Phase_I	15783784	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	C	35	5.509653	0.96386	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.81659	-1.52;-1.52;-1.52;-1.52	5.33	5.33	0.75918	Myosin head, motor domain (3);	0.000000	0.85682	D	0.000000	D	0.94525	0.8237	H	0.99225	4.475	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	1.0;1.0;1.0;1.0;1.0	D	0.96747	0.9551	10	0.87932	D	0	.	17.9519	0.89056	0.0:1.0:0.0:0.0	.	236;229;236;229;236	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	S	229;229;236;236;236	ENSP00000300036:G229S;ENSP00000345136:G229S;ENSP00000379616:G236S;ENSP00000407821:G236S	ENSP00000300036:G229S	G	-	1	0	MYH11	15783784	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.511000	0.81718	2.637000	0.89404	0.561000	0.74099	GGC		0.463	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
MYH11	4629	broad.mit.edu	37	16	15931796	15931796	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:15931796A>G	ENST00000300036.5	-	2	423	c.314T>C	c.(313-315)cTg>cCg	p.L105P	MYH11_ENST00000576790.2_Missense_Mutation_p.L105P|MYH11_ENST00000396324.3_Missense_Mutation_p.L105P|MYH11_ENST00000452625.2_Missense_Mutation_p.L105P	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	105	Myosin motor.				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.L105P(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						CCGCTCCCTCAGGTTGTGTAG	0.517			T	CBFB	AML																																p.L105P			Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T314C	16						.						166.0	141.0	150.0					16																	15931796		2197	4300	6497	15839297	SO:0001583	missense	4629	exon2			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.314T>C	16.37:g.15931796A>G	ENSP00000300036:p.Leu105Pro	Somatic		Capture	Illumina HiSeq	Phase_I	15839297	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	A	20.1	3.935130	0.73442	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.85339	-1.97;-1.97;-1.97;-1.97	5.5	5.5	0.81552	Myosin head, motor domain (2);	0.198452	0.33959	N	0.004383	D	0.96405	0.8827	H	0.99900	4.915	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	1.0;1.0;1.0;1.0;1.0	D	0.98262	1.0499	10	0.87932	D	0	.	14.7863	0.69806	1.0:0.0:0.0:0.0	.	105;105;105;105;105	Q4G140;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	P	105	ENSP00000300036:L105P;ENSP00000345136:L105P;ENSP00000379616:L105P;ENSP00000407821:L105P	ENSP00000300036:L105P	L	-	2	0	MYH11	15839297	1.000000	0.71417	0.989000	0.46669	0.654000	0.38779	9.287000	0.95975	2.091000	0.63221	0.533000	0.62120	CTG		0.517	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
ABCC6	368	broad.mit.edu	37	16	16251615	16251615	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:16251615C>T	ENST00000205557.7	-	27	3816	c.3787G>A	c.(3787-3789)Ggg>Agg	p.G1263R		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1263					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.G1263R(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	TCGATCTGCCCGCCCTGAGGC	0.622																																					p.G1263R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3787A	16	GRCh37	CM080019	ABCC6	M		.						44.0	39.0	41.0					16																	16251615		2197	4300	6497	16159116	SO:0001583	missense	368	exon27			AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.3787G>A	16.37:g.16251615C>T	ENSP00000205557:p.Gly1263Arg	Somatic		Capture	Illumina HiSeq	Phase_I	16159116	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	c	20.9	4.058575	0.76074	.	.	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.91407	-2.84	5.15	4.18	0.49190	.	0.000000	0.47455	U	0.000229	D	0.96043	0.8711	M	0.92604	3.325	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.96541	0.9400	10	0.87932	D	0	.	13.2261	0.59914	0.0:0.9218:0.0:0.0782	.	1263	O95255	MRP6_HUMAN	R	1263;201	ENSP00000205557:G1263R	ENSP00000205557:G1263R	G	-	1	0	ABCC6	16159116	1.000000	0.71417	0.021000	0.16686	0.691000	0.40173	5.822000	0.69265	1.151000	0.42436	0.536000	0.68110	GGG		0.622	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
SMG1	23049	broad.mit.edu	37	16	18840904	18840904	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:18840904C>T	ENST00000446231.2	-	54	9719	c.9307G>A	c.(9307-9309)Gga>Aga	p.G3103R	SMG1_ENST00000389467.3_Missense_Mutation_p.G3103R			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	3103					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.G3099R(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						AGTGTGAGTCCGAGGGCTTGG	0.468																																					p.G3103R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G9307A	16						.						58.0	58.0	58.0					16																	18840904		1919	4134	6053	18748405	SO:0001583	missense	23049	exon54			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.9307G>A	16.37:g.18840904C>T	ENSP00000402515:p.Gly3103Arg	Somatic		Capture	Illumina HiSeq	Phase_I	18748405	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.362410	0.61403	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01821	4.69;4.62	6.07	5.11	0.69529	.	0.000000	0.64402	D	0.000003	T	0.05090	0.0136	L	0.29908	0.895	0.45035	D	0.998058	D	0.76494	0.999	P	0.60236	0.871	T	0.49173	-0.8967	10	0.87932	D	0	.	16.6643	0.85248	0.1309:0.8691:0.0:0.0	.	3103	Q96Q15	SMG1_HUMAN	R	3103	ENSP00000402515:G3103R;ENSP00000374118:G3103R	ENSP00000374118:G3103R	G	-	1	0	SMG1	18748405	1.000000	0.71417	0.940000	0.37924	0.983000	0.72400	5.286000	0.65639	1.545000	0.49373	0.585000	0.79938	GGA		0.468	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
C16orf62	57020	broad.mit.edu	37	16	19663339	19663339	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:19663339G>A	ENST00000251143.5	+	26	2160	c.2148G>A	c.(2146-2148)gcG>gcA	p.A716A	C16orf62_ENST00000448695.1_Silent_p.A566A|C16orf62_ENST00000543152.1_Silent_p.A465A|C16orf62_ENST00000544275.1_3'UTR|C16orf62_ENST00000417362.2_Silent_p.A623A|C16orf62_ENST00000438132.3_Silent_p.A805A|C16orf62_ENST00000542263.1_Silent_p.A712A			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	716						integral component of membrane (GO:0016021)		p.A716A(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	36						CCTCCCTGGCGGGCATCTTCA	0.537																																					p.A805A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2415A	16						.						149.0	114.0	126.0					16																	19663339		2197	4300	6497	19570840	SO:0001819	synonymous_variant	57020	exon26				CCDS32397.1, CCDS32397.2, CCDS73840.1	16p12.3	2012-05-30			ENSG00000103544	ENSG00000103544			24641	protein-coding gene	gene with protein product						10493829	Standard	NM_020314		Approved	MGC16824	uc002dgn.3	Q7Z3J2	OTTHUMG00000167925	ENST00000251143.5:c.2148G>A	16.37:g.19663339G>A		Somatic		Capture	Illumina HiSeq	Phase_I	19570840	NM_020314	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Silent	SNP	ENST00000251143.5	37																																																																																					0.537	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314	
GPR139	124274	broad.mit.edu	37	16	20043248	20043248	+	Missense_Mutation	SNP	G	G	A	rs556069972		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:20043248G>A	ENST00000570682.1	-	2	1171	c.871C>T	c.(871-873)Cgg>Tgg	p.R291W		NM_001002911.2	NP_001002911.1	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	291					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)	p.R291W(1)		autonomic_ganglia(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	30						GTGCGGAACCGCTTGCTGATG	0.502													G|||	1	0.000199681	0.0	0.0	5008	,	,		19797	0.0		0.0	False		,,,				2504	0.001				p.R291W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C871T	16						.						108.0	107.0	107.0					16																	20043248		2203	4300	6503	19950749	SO:0001583	missense	124274	exon2			AY255545	CCDS32398.1	16p13.11	2012-08-21						"""GPCR / Class A : Orphans"""	19995	protein-coding gene	gene with protein product						12679517	Standard	XM_005255114		Approved	PGR3	uc002dgu.1	Q6DWJ6		ENST00000570682.1:c.871C>T	16.37:g.20043248G>A	ENSP00000458791:p.Arg291Trp	Somatic		Capture	Illumina HiSeq	Phase_I	19950749	NM_001002911	A8K5R9|Q86SP2|Q8TDU8	Missense_Mutation	SNP	ENST00000570682.1	37	CCDS32398.1	.	.	.	.	.	.	.	.	.	.	G	17.37	3.373073	0.61624	.	.	ENSG00000180269	ENST00000326571	.	.	.	5.52	3.5	0.40072	.	0.000000	0.85682	D	0.000000	T	0.60625	0.2283	N	0.19112	0.55	0.58432	D	0.999996	D	0.89917	1.0	D	0.69654	0.965	T	0.64373	-0.6423	9	0.87932	D	0	-29.5547	13.4138	0.60958	0.0:0.0:0.5488:0.4512	.	291	Q6DWJ6	GP139_HUMAN	W	291	.	ENSP00000370779:R291W	R	-	1	2	GPR139	19950749	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.409000	0.52657	0.623000	0.30267	0.655000	0.94253	CGG		0.502	GPR139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438522.1	NM_001002911	
GP2	2813	broad.mit.edu	37	16	20329702	20329702	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:20329702G>A	ENST00000381362.4	-	8	1143	c.1067C>T	c.(1066-1068)gCc>gTc	p.A356V	GP2_ENST00000341642.5_Missense_Mutation_p.A206V|GP2_ENST00000573897.1_5'Flank|GP2_ENST00000302555.5_Missense_Mutation_p.A353V|GP2_ENST00000381360.5_Missense_Mutation_p.A209V	NM_001007240.1|NM_001502.2	NP_001007241.2|NP_001493.2	P55259	GP2_HUMAN	glycoprotein 2 (zymogen granule membrane)	356	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				antigen transcytosis by M cells in mucosal-associated lymphoid tissue (GO:0002412)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)	p.A353V(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						TTGGAAGAGGGCCATCCTGAC	0.483																																					p.A206V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C617T	16						.						295.0	245.0	262.0					16																	20329702		2203	4300	6503	20237203	SO:0001583	missense	2813	exon6			U36221	CCDS10582.2, CCDS42128.1, CCDS45432.1, CCDS45433.1	16p12.3	2008-02-05			ENSG00000169347	ENSG00000169347			4441	protein-coding gene	gene with protein product		602977				9605860	Standard	XM_005255259		Approved		uc002dgw.3	P55259	OTTHUMG00000131489	ENST00000381362.4:c.1067C>T	16.37:g.20329702G>A	ENSP00000370767:p.Ala356Val	Somatic		Capture	Illumina HiSeq	Phase_I	20237203	NM_001007242	A6NFM9|A6NJA8|Q13338|Q9UIF1	Missense_Mutation	SNP	ENST00000381362.4	37	CCDS42128.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.619566	0.87460	.	.	ENSG00000169347	ENST00000302555;ENST00000381362;ENST00000381360;ENST00000341642;ENST00000537520	D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62	5.8	4.83	0.62350	Zona pellucida sperm-binding protein (3);	.	.	.	.	D	0.90635	0.7063	M	0.81179	2.53	0.42674	D	0.993521	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.992;0.998;0.998;1.0	D	0.90349	0.4365	9	0.36615	T	0.2	-22.3832	14.5797	0.68278	0.0:0.147:0.853:0.0	.	206;334;353;356	P55259-4;B7Z1G2;P55259-3;P55259	.;.;.;GP2_HUMAN	V	353;356;209;206;334	ENSP00000304044:A353V;ENSP00000370767:A356V;ENSP00000370765:A209V;ENSP00000343861:A206V	ENSP00000304044:A353V	A	-	2	0	GP2	20237203	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	3.109000	0.50345	1.415000	0.47037	0.650000	0.86243	GCC		0.483	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436920.1	NM_016295	
UMOD	7369	broad.mit.edu	37	16	20357532	20357532	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:20357532G>T	ENST00000570689.1	-	5	1244	c.1098C>A	c.(1096-1098)tgC>tgA	p.C366*	UMOD_ENST00000396134.2_Nonsense_Mutation_p.C399*|UMOD_ENST00000424589.1_Nonsense_Mutation_p.C399*|UMOD_ENST00000396142.2_Nonsense_Mutation_p.C366*|UMOD_ENST00000396138.4_Nonsense_Mutation_p.C415*|UMOD_ENST00000302509.4_Nonsense_Mutation_p.C366*			P07911	UROM_HUMAN	uromodulin	366	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				cellular defense response (GO:0006968)|chemical homeostasis (GO:0048878)|excretion (GO:0007588)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte cell-cell adhesion (GO:0007159)|metanephric ascending thin limb development (GO:0072218)|metanephric distal convoluted tubule development (GO:0072221)|metanephric thick ascending limb development (GO:0072233)|negative regulation of cell proliferation (GO:0008285)|neutrophil migration (GO:1990266)|regulation of ion homeostasis (GO:2000021)|response to organic substance (GO:0010033)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|primary cilium (GO:0072372)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|IgG binding (GO:0019864)	p.C366*(1)		endometrium(5)|kidney(1)|large_intestine(7)|lung(20)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						TGAAGCCCGAGCACCGGCTGT	0.592																																					p.C366X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1098A	16						.						58.0	55.0	56.0					16																	20357532		2203	4300	6503	20265033	SO:0001587	stop_gained	7369	exon5			M17778	CCDS10583.1, CCDS61876.1	16p12.3	2008-06-23	2008-06-23		ENSG00000169344	ENSG00000169344			12559	protein-coding gene	gene with protein product	"""Tamm-Horsfall glycoprotein"", ""uromucoid"""	191845	"""uromodulin (uromucoid, Tamm-Horsfall glycoprotein)"""			8382593	Standard	NM_003361		Approved		uc002dha.3	P07911	OTTHUMG00000131488	ENST00000570689.1:c.1098C>A	16.37:g.20357532G>T	ENSP00000460548:p.Cys366*	Somatic		Capture	Illumina HiSeq	Phase_I	20265033	NM_003361	B3KP48|B3KRN9|E9PEA4|Q540J6|Q6ZS84|Q8IYG0	Nonsense_Mutation	SNP	ENST00000570689.1	37	CCDS10583.1	.	.	.	.	.	.	.	.	.	.	G	37	6.475060	0.97598	.	.	ENSG00000169344	ENST00000396138;ENST00000396134;ENST00000424589;ENST00000302509;ENST00000429954;ENST00000396142	.	.	.	4.68	3.61	0.41365	.	0.000000	0.52532	D	0.000071	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-29.6482	7.5584	0.27837	0.1671:0.0:0.8329:0.0	.	.	.	.	X	366;399;399;366;344;366	.	ENSP00000306279:C366X	C	-	3	2	UMOD	20265033	0.941000	0.31946	0.949000	0.38748	0.892000	0.51952	1.527000	0.35975	2.116000	0.64780	0.313000	0.20887	TGC		0.592	UMOD-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436862.1		
DNAH3	55567	broad.mit.edu	37	16	20975351	20975351	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:20975351C>T	ENST00000261383.3	-	53	9854	c.9855G>A	c.(9853-9855)acG>acA	p.T3285T	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3285					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.T3285T(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)		CGTCAATCTGCGTTTCTGTCA	0.498																																					p.T3285T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G9855A	16						.						135.0	135.0	135.0					16																	20975351		2201	4300	6501	20882852	SO:0001819	synonymous_variant	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.9855G>A	16.37:g.20975351C>T		Somatic		Capture	Illumina HiSeq	Phase_I	20882852	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																				0.498	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
ZP2	7783	broad.mit.edu	37	16	21211138	21211138	+	Missense_Mutation	SNP	G	G	A	rs149277141	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:21211138G>A	ENST00000574002.1	-	16	2238	c.1756C>T	c.(1756-1758)Cat>Tat	p.H586Y	ZP2_ENST00000219593.4_Missense_Mutation_p.H586Y|ZP2_ENST00000574091.1_Missense_Mutation_p.H577Y|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	586	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)	p.H586Y(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		TGATCAGGATGGGTCACAGAG	0.512																																					p.H586Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1756T	16						.						115.0	109.0	111.0					16																	21211138		2200	4300	6500	21118639	SO:0001583	missense	7783	exon15			M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"""Zona pellucida glycoproteins"""	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.1756C>T	16.37:g.21211138G>A	ENSP00000460971:p.His586Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	21118639	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	CCDS10596.1	.	.	.	.	.	.	.	.	.	.	G	0.423	-0.907531	0.02434	.	.	ENSG00000103310	ENST00000219593	D	0.81996	-1.56	5.52	-1.04	0.10068	Zona pellucida sperm-binding protein (3);	0.778291	0.11810	N	0.527225	T	0.48554	0.1506	N	0.01289	-0.905	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.50004	-0.8878	10	0.02654	T	1	-1.9676	4.644	0.12563	0.5839:0.0:0.1381:0.278	.	577;586	Q4VAP1;Q05996	.;ZP2_HUMAN	Y	586	ENSP00000219593:H586Y	ENSP00000219593:H586Y	H	-	1	0	ZP2	21118639	0.975000	0.34042	0.196000	0.23383	0.851000	0.48451	0.359000	0.20233	-0.069000	0.12931	0.579000	0.79373	CAT		0.512	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2		
TRAF7	84231	broad.mit.edu	37	16	2221294	2221294	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:2221294G>A	ENST00000326181.6	+	6	510	c.378G>A	c.(376-378)tcG>tcA	p.S126S		NM_032271.2	NP_115647.2	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7, E3 ubiquitin protein ligase	126					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.S126S(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						AGCAGCCCTCGGTGAAGCTGT	0.682																																					p.S126S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G378A	16						.						24.0	19.0	21.0					16																	2221294		2165	4249	6414	2161295	SO:0001819	synonymous_variant	84231	exon6			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.378G>A	16.37:g.2221294G>A		Somatic		Capture	Illumina HiSeq	Phase_I	2161295	NM_032271	Q9H073	Silent	SNP	ENST00000326181.6	37	CCDS10461.1																																																																																				0.682	TRAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250762.1	NM_032271	
MLST8	64223	broad.mit.edu	37	16	2256583	2256583	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:2256583G>A	ENST00000569417.1	+	4	621	c.267G>A	c.(265-267)gcG>gcA	p.A89A	MLST8_ENST00000561651.1_3'UTR|MLST8_ENST00000565250.1_Silent_p.A89A|MLST8_ENST00000301725.7_Silent_p.A108A|AC009065.3_ENST00000517149.1_RNA|MLST8_ENST00000382450.4_Silent_p.A88A|MLST8_ENST00000397124.1_Silent_p.A89A|MLST8_ENST00000301724.10_Silent_p.A89A|MLST8_ENST00000564088.1_Silent_p.A89A	NM_022372.4	NP_071767.3	Q9BVC4	LST8_HUMAN	MTOR associated protein, LST8 homolog (S. cerevisiae)	89					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)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of TOR signaling (GO:0032008)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Rac GTPase activity (GO:0032314)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.A89A(2)		large_intestine(3)|lung(2)|skin(1)	6						AGAACATCGCGTCTGTGGGCT	0.597																																					p.A89A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G267A	16						.						159.0	162.0	161.0					16																	2256583		2079	4211	6290	2196584	SO:0001819	synonymous_variant	64223	exon4				CCDS10462.2, CCDS58409.1	16p13.3	2013-01-09			ENSG00000167965	ENSG00000167965		"""WD repeat domain containing"""	24825	protein-coding gene	gene with protein product	"""G protein beta subunit like"""	612190				12477932	Standard	NM_022372		Approved	Lst8, Pop3, GBL, GbetaL	uc002cpc.3	Q9BVC4	OTTHUMG00000128827	ENST00000569417.1:c.267G>A	16.37:g.2256583G>A		Somatic		Capture	Illumina HiSeq	Phase_I	2196584	NM_001199174	B3KMM4|B4DY00|D3DU88|Q5M800|Q86Y18|Q8WUI5|Q9HA66|Q9UJV6	Silent	SNP	ENST00000569417.1	37	CCDS10462.2																																																																																				0.597	MLST8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250763.2	NM_022372	
ABCA3	21	broad.mit.edu	37	16	2367376	2367376	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:2367376C>T	ENST00000301732.5	-	10	1719	c.1019G>A	c.(1018-1020)cGc>cAc	p.R340H	ABCA3_ENST00000382381.3_Missense_Mutation_p.R340H	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	340					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.R340H(1)		breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	GGGGTCGCTGCGGGACAGCAC	0.622																																					p.R340H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1019A	16						.						120.0	102.0	108.0					16																	2367376		2198	4300	6498	2307377	SO:0001583	missense	21	exon10			U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"""ATP binding cassette transporters / subfamily A"""	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.1019G>A	16.37:g.2367376C>T	ENSP00000301732:p.Arg340His	Somatic		Capture	Illumina HiSeq	Phase_I	2307377	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	C	8.061	0.768166	0.15983	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.86956	-2.19	4.88	-1.94	0.07571	.	1.270590	0.04811	N	0.435283	T	0.62307	0.2417	N	0.00325	-1.645	0.44515	D	0.997464	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45381	-0.9265	10	0.15066	T	0.55	.	12.1434	0.54010	0.0:0.5912:0.0:0.4088	.	340;402;340	A7MBM9;Q4LE27;Q99758	.;.;ABCA3_HUMAN	H	340;402	ENSP00000301732:R340H	ENSP00000301732:R340H	R	-	2	0	ABCA3	2307377	0.031000	0.19500	0.008000	0.14137	0.012000	0.07955	0.241000	0.18065	-0.576000	0.05974	-0.367000	0.07326	CGC		0.622	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
ZP2	7783	broad.mit.edu	37	16	21222704	21222704	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:21222704C>T	ENST00000574002.1	-	3	557	c.75G>A	c.(73-75)tcG>tcA	p.S25S	ZP2_ENST00000219593.4_Silent_p.S25S|ZP2_ENST00000574091.1_Silent_p.S25S			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	25					binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)	p.S25S(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		AGAGAGAAATCGACCTGTAGG	0.463																																					p.S25S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G75A	16						.						153.0	151.0	152.0					16																	21222704		2199	4300	6499	21130205	SO:0001819	synonymous_variant	7783	exon2			M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"""Zona pellucida glycoproteins"""	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.75G>A	16.37:g.21222704C>T		Somatic		Capture	Illumina HiSeq	Phase_I	21130205	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Silent	SNP	ENST00000574002.1	37	CCDS10596.1																																																																																				0.463	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2		
SCNN1G	6340	broad.mit.edu	37	16	23200707	23200707	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:23200707C>T	ENST00000300061.2	+	3	476	c.333C>T	c.(331-333)cgC>cgT	p.R111R		NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	111					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)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)	p.R111R(1)		NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	GCACCGTTCGCCACCTTCTAG	0.602																																					p.R111R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C333T	16						.						66.0	71.0	69.0					16																	23200707		2197	4300	6497	23108208	SO:0001819	synonymous_variant	6340	exon3			U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10602	protein-coding gene	gene with protein product		600761	"""sodium channel, nonvoltage-gated 1, gamma"", ""sodium channel, non-voltage-gated 1, gamma"""			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.333C>T	16.37:g.23200707C>T		Somatic		Capture	Illumina HiSeq	Phase_I	23108208	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Silent	SNP	ENST00000300061.2	37	CCDS10608.1																																																																																				0.602	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039	
COG7	91949	broad.mit.edu	37	16	23457240	23457240	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:23457240C>T	ENST00000307149.5	-	2	397	c.212G>A	c.(211-213)cGt>cAt	p.R71H	CTD-2270L9.2_ENST00000561624.2_RNA	NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	71					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.R71H(1)		breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		TTCAACATCACGGAGCACTTT	0.388																																					p.R71H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G212A	16						.						118.0	105.0	109.0					16																	23457240		2197	4300	6497	23364741	SO:0001583	missense	91949	exon2			AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"""Components of oligomeric golgi complex"""	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.212G>A	16.37:g.23457240C>T	ENSP00000305442:p.Arg71His	Somatic		Capture	Illumina HiSeq	Phase_I	23364741	NM_153603	Q6UWU7	Missense_Mutation	SNP	ENST00000307149.5	37	CCDS10610.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.877893	0.91664	.	.	ENSG00000168434	ENST00000307149	T	0.54479	0.57	5.64	5.64	0.86602	.	0.110655	0.64402	D	0.000007	T	0.69540	0.3122	M	0.68317	2.08	0.80722	D	1	D	0.69078	0.997	D	0.63488	0.915	T	0.66280	-0.5963	10	0.34782	T	0.22	-11.6458	18.689	0.91576	0.0:1.0:0.0:0.0	.	71	P83436	COG7_HUMAN	H	71	ENSP00000305442:R71H	ENSP00000305442:R71H	R	-	2	0	COG7	23364741	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.908000	0.69916	2.633000	0.89246	0.637000	0.83480	CGT		0.388	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1		
TNRC6A	27327	broad.mit.edu	37	16	24804927	24804927	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:24804927G>A	ENST00000395799.3	+	7	3438	c.3309G>A	c.(3307-3309)acG>acA	p.T1103T	TNRC6A_ENST00000315183.7_Silent_p.T1103T	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1103	Sufficient for interaction with AGO1 and AGO4.|Sufficient for interaction with AGO2.				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.T1103T(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)		GCACATCCACGTGGGGCTCCA	0.527																																					p.T1103T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3309A	16						.						88.0	89.0	88.0					16																	24804927		2197	4300	6497	24712428	SO:0001819	synonymous_variant	27327	exon7			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.3309G>A	16.37:g.24804927G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24712428	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	37	CCDS10624.2																																																																																				0.527	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
SRRM2	23524	broad.mit.edu	37	16	2816345	2816345	+	Missense_Mutation	SNP	C	C	T	rs563699936		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:2816345C>T	ENST00000301740.8	+	11	6365	c.5816C>T	c.(5815-5817)aCg>aTg	p.T1939M		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1939	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)	p.T1939M(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						AGGTCTAGAACGCCAACAACA	0.587													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16061	0.0		0.0	False		,,,				2504	0.0				p.T1939M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5816T	16						.						74.0	77.0	76.0					16																	2816345		2198	4300	6498	2756346	SO:0001583	missense	23524	exon11			AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.5816C>T	16.37:g.2816345C>T	ENSP00000301740:p.Thr1939Met	Somatic		Capture	Illumina HiSeq	Phase_I	2756346	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	2.277	-0.365649	0.05069	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.28666	1.6	5.24	5.24	0.73138	.	0.094910	0.46442	D	0.000286	T	0.26268	0.0641	N	0.08118	0	0.32751	N	0.506373	D	0.65815	0.995	P	0.50231	0.635	T	0.35943	-0.9768	10	0.62326	D	0.03	-11.1268	16.3084	0.82859	0.0:1.0:0.0:0.0	.	1939	Q9UQ35	SRRM2_HUMAN	M	1939;1939;1191	ENSP00000301740:T1939M	ENSP00000301740:T1939M	T	+	2	0	SRRM2	2756346	0.326000	0.24669	0.762000	0.31397	0.544000	0.35116	1.878000	0.39608	2.454000	0.82982	0.650000	0.86243	ACG		0.587	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
SRRM2	23524	broad.mit.edu	37	16	2819142	2819142	+	Silent	SNP	T	T	C	rs374269313	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:2819142T>C	ENST00000301740.8	+	12	8427	c.7878T>C	c.(7876-7878)tcT>tcC	p.S2626S	AC092117.2_ENST00000581119.1_RNA|SRRM2_ENST00000574593.1_3'UTR	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2626	Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)	p.S2626S(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						cctcctcctcttcttcctcct	0.592													T|||	11	0.00219649	0.003	0.0043	5008	,	,		17730	0.002		0.002	False		,,,				2504	0.0				p.S2626S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T7878C	16						.	T		9,4387	9.9+/-24.2	0,9,2189	140.0	120.0	127.0		7878	-3.8	0.8	16		127	9,8591	7.7+/-29.5	0,9,4291	no	coding-synonymous	SRRM2	NM_016333.3		0,18,6480	CC,CT,TT		0.1047,0.2047,0.1385		2626/2753	2819142	18,12978	2198	4300	6498	2759143	SO:0001819	synonymous_variant	23524	exon12			AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.7878T>C	16.37:g.2819142T>C		Somatic		Capture	Illumina HiSeq	Phase_I	2759143	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	37	CCDS32373.1																																																																																				0.592	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
GTF3C1	2975	broad.mit.edu	37	16	27492455	27492455	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:27492455C>T	ENST00000356183.4	-	27	4156	c.4141G>A	c.(4141-4143)Gcc>Acc	p.A1381T	GTF3C1_ENST00000561623.1_Missense_Mutation_p.A1381T	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1381					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)	p.A1381T(1)		breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						TTCCTTAGGGCTGAACTGAAC	0.473																																					p.A1381T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4141A	16						.						138.0	125.0	129.0					16																	27492455		2197	4300	6497	27399956	SO:0001583	missense	2975	exon27			U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.4141G>A	16.37:g.27492455C>T	ENSP00000348510:p.Ala1381Thr	Somatic		Capture	Illumina HiSeq	Phase_I	27399956	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.168850	0.38315	.	.	ENSG00000077235	ENST00000356183;ENST00000388971	T	0.21932	1.98	5.49	-0.308	0.12773	.	0.616092	0.17506	N	0.171791	T	0.09247	0.0228	N	0.20483	0.58	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.09377	0.004;0.003	T	0.32771	-0.9894	10	0.15499	T	0.54	-9.6655	3.6497	0.08198	0.3623:0.2091:0.0:0.4287	.	1381;1381	Q12789;Q12789-3	TF3C1_HUMAN;.	T	1381;1377	ENSP00000348510:A1381T	ENSP00000348510:A1381T	A	-	1	0	GTF3C1	27399956	0.010000	0.17322	0.017000	0.16124	0.998000	0.95712	0.267000	0.18552	-0.068000	0.12953	0.655000	0.94253	GCC		0.473	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
XPO6	23214	broad.mit.edu	37	16	28123191	28123191	+	Missense_Mutation	SNP	C	C	T	rs145368246		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:28123191C>T	ENST00000304658.5	-	17	2788	c.2288G>A	c.(2287-2289)cGc>cAc	p.R763H	XPO6_ENST00000565698.1_Missense_Mutation_p.R749H	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	763					protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)	p.R763H(1)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25						CTTCAGGTTGCGATAGTCCCG	0.592																																					p.R763H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2288A	16						.						78.0	84.0	82.0					16																	28123191		2115	4230	6345	28030692	SO:0001583	missense	23214	exon17			AY026388	CCDS42135.1, CCDS59266.1	16p11.2	2011-04-13	2003-03-11	2003-03-14		ENSG00000169180		"""Exportins"""	19733	protein-coding gene	gene with protein product		608411	"""RAN binding protein 20"""	RANBP20		14592989	Standard	NM_001270940		Approved	KIAA0370, FLJ22519	uc002dpa.2	Q96QU8		ENST00000304658.5:c.2288G>A	16.37:g.28123191C>T	ENSP00000302790:p.Arg763His	Somatic		Capture	Illumina HiSeq	Phase_I	28030692	NM_015171	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Missense_Mutation	SNP	ENST00000304658.5	37	CCDS42135.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	17.14	3.314311	0.60414	.	.	ENSG00000169180	ENST00000304658	T	0.67698	-0.28	5.77	3.81	0.43845	Armadillo-type fold (1);	0.051278	0.85682	N	0.000000	T	0.51295	0.1666	L	0.45581	1.43	0.49582	D	0.999807	P;P	0.50369	0.934;0.678	B;B	0.33295	0.161;0.054	T	0.50923	-0.8770	10	0.42905	T	0.14	-5.1394	10.0234	0.42057	0.0:0.8337:0.0:0.1663	.	763;763	B7ZM10;Q96QU8	.;XPO6_HUMAN	H	763	ENSP00000302790:R763H	ENSP00000302790:R763H	R	-	2	0	XPO6	28030692	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	2.995000	0.49441	0.784000	0.33661	0.650000	0.86243	CGC		0.592	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195	
ATP2A1	487	broad.mit.edu	37	16	28909415	28909415	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:28909415G>A	ENST00000357084.3	+	13	1781	c.1514G>A	c.(1513-1515)cGg>cAg	p.R505Q	ATP2A1_ENST00000395503.4_Missense_Mutation_p.R505Q|ATP2A1_ENST00000536376.1_Missense_Mutation_p.R380Q	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	505					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)	p.R505Q(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						AAATCTTCCCGGGCTGCTGTG	0.537																																					p.R505Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1514A	16						.						81.0	84.0	83.0					16																	28909415		2197	4300	6497	28816916	SO:0001583	missense	487	exon13				CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"""ATPases / P-type"""	811	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 1"", ""calcium pump 1"""	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.1514G>A	16.37:g.28909415G>A	ENSP00000349595:p.Arg505Gln	Somatic		Capture	Illumina HiSeq	Phase_I	28816916	NM_004320	A8K5J9|B3KY17|O14984	Missense_Mutation	SNP	ENST00000357084.3	37	CCDS10643.1	.	.	.	.	.	.	.	.	.	.	G	15.96	2.986857	0.53934	.	.	ENSG00000196296	ENST00000357084;ENST00000395503;ENST00000395498;ENST00000536376	D;D;D	0.82433	-1.61;-1.61;-1.61	5.35	4.39	0.52855	ATPase, cation-transporting, domain N (1);ATPase, P-type, cytoplasmic domain N (1);	0.225614	0.36101	N	0.002783	T	0.68384	0.2995	N	0.10874	0.06	0.34033	D	0.654016	B;B;B	0.12013	0.001;0.003;0.005	B;B;B	0.06405	0.002;0.002;0.001	T	0.70114	-0.4961	10	0.41790	T	0.15	.	12.897	0.58106	0.0805:0.0:0.9195:0.0	.	380;505;505	B3KY17;O14983;O14983-2	.;AT2A1_HUMAN;.	Q	505;505;542;380	ENSP00000349595:R505Q;ENSP00000378879:R505Q;ENSP00000443101:R380Q	ENSP00000349595:R505Q	R	+	2	0	ATP2A1	28816916	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.227000	0.58612	1.243000	0.43853	0.655000	0.94253	CGG		0.537	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320	
ATP2A1	487	broad.mit.edu	37	16	28913337	28913337	+	Missense_Mutation	SNP	G	G	A	rs201798363		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:28913337G>A	ENST00000357084.3	+	16	2521	c.2254G>A	c.(2254-2256)Gcc>Acc	p.A752T	ATP2A1_ENST00000395503.4_Missense_Mutation_p.A752T|ATP2A1_ENST00000536376.1_Missense_Mutation_p.A627T	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	752					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)	p.A752T(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						GGAGGGCCGCGCCATCTACAA	0.602																																					p.A752T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2254A	16						.						156.0	113.0	127.0					16																	28913337		2197	4300	6497	28820838	SO:0001583	missense	487	exon16				CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"""ATPases / P-type"""	811	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 1"", ""calcium pump 1"""	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.2254G>A	16.37:g.28913337G>A	ENSP00000349595:p.Ala752Thr	Somatic		Capture	Illumina HiSeq	Phase_I	28820838	NM_004320	A8K5J9|B3KY17|O14984	Missense_Mutation	SNP	ENST00000357084.3	37	CCDS10643.1	.	.	.	.	.	.	.	.	.	.	G	32	5.131323	0.94473	.	.	ENSG00000196296	ENST00000357084;ENST00000395503;ENST00000395498;ENST00000536376	D;D;D	0.98060	-2.48;-2.48;-4.69	5.23	5.23	0.72850	ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.96228	0.8770	N	0.05592	-0.015	0.80722	D	1	D;P;P	0.76494	0.999;0.723;0.906	P;B;P	0.59595	0.86;0.204;0.449	D	0.97919	1.0313	10	0.72032	D	0.01	.	17.5662	0.87920	0.0:0.0:1.0:0.0	.	627;752;752	B3KY17;O14983;O14983-2	.;AT2A1_HUMAN;.	T	752;752;789;627	ENSP00000349595:A752T;ENSP00000378879:A752T;ENSP00000443101:A627T	ENSP00000349595:A752T	A	+	1	0	ATP2A1	28820838	1.000000	0.71417	0.950000	0.38849	0.980000	0.70556	9.766000	0.98957	2.450000	0.82876	0.561000	0.74099	GCC		0.602	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320	
SPNS1	83985	broad.mit.edu	37	16	28992841	28992841	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:28992841G>A	ENST00000311008.11	+	6	1091	c.714G>A	c.(712-714)gtG>gtA	p.V238V	SPNS1_ENST00000323081.8_Silent_p.V165V|RP11-264B17.3_ENST00000569969.1_RNA|RP11-264B17.4_ENST00000567209.1_RNA|SPNS1_ENST00000565975.1_Silent_p.V283V|SPNS1_ENST00000334536.8_Silent_p.V238V|SPNS1_ENST00000352260.7_Silent_p.V216V|SPNS1_ENST00000561868.1_3'UTR	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	238					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)		p.V238V(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						TCCTGGTAGTGCGGGAGCCGC	0.622											OREG0023712	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V216V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G648A	16						.						55.0	58.0	57.0					16																	28992841		2197	4300	6497	28900342	SO:0001819	synonymous_variant	83985	exon5			BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.714G>A	16.37:g.28992841G>A		Somatic	806	Capture	Illumina HiSeq	Phase_I	28900342	NM_001142449	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Silent	SNP	ENST00000311008.11	37	CCDS10646.1																																																																																				0.622	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038	
PAQR4	124222	broad.mit.edu	37	16	3021659	3021659	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:3021659G>A	ENST00000318782.8	+	3	962	c.532G>A	c.(532-534)Gga>Aga	p.G178R	PKMYT1_ENST00000571102.1_5'Flank|PAQR4_ENST00000576565.1_Missense_Mutation_p.G111R|PKMYT1_ENST00000431515.2_Intron|PAQR4_ENST00000293978.8_Missense_Mutation_p.G139R|PAQR4_ENST00000574988.1_Missense_Mutation_p.G111R|PAQR4_ENST00000572687.1_Missense_Mutation_p.G104R	NM_001284513.1|NM_152341.3	NP_001271442.1|NP_689554.2	Q8N4S7	PAQR4_HUMAN	progestin and adipoQ receptor family member IV	178						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.G178R(1)		kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	8						CCGGGCATTTGGATGGCAGGC	0.701																																					p.G178R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G532A	16						.						28.0	34.0	32.0					16																	3021659		2198	4296	6494	2961660	SO:0001583	missense	124222	exon3				CCDS10485.1, CCDS66911.1, CCDS66912.1, CCDS73814.1	16p13	2008-05-02			ENSG00000162073	ENSG00000162073			26386	protein-coding gene	gene with protein product		614578				12477932	Standard	XM_005255112		Approved	FLJ30002	uc002csj.4	Q8N4S7	OTTHUMG00000128977	ENST00000318782.8:c.532G>A	16.37:g.3021659G>A	ENSP00000321804:p.Gly178Arg	Somatic		Capture	Illumina HiSeq	Phase_I	2961660	NM_152341	A8K5Q8|D3DUA2|D3DUA3|Q8NAS6|Q96NW1	Missense_Mutation	SNP	ENST00000318782.8	37	CCDS10485.1	.	.	.	.	.	.	.	.	.	.	g	15.48	2.847187	0.51164	.	.	ENSG00000162073	ENST00000318782;ENST00000293978	T	0.29655	1.56	4.32	4.32	0.51571	.	0.230476	0.33916	N	0.004437	T	0.26666	0.0652	N	0.20685	0.6	0.46396	D	0.999028	D;P;P	0.59767	0.986;0.799;0.586	P;B;B	0.53861	0.736;0.366;0.377	T	0.02424	-1.1161	10	0.02654	T	1	-10.096	14.3666	0.66810	0.0:0.0:1.0:0.0	.	103;139;178	Q8N4S7-3;Q8N4S7-2;Q8N4S7	.;.;PAQR4_HUMAN	R	178;104	ENSP00000321804:G178R	ENSP00000293978:G104R	G	+	1	0	PAQR4	2961660	1.000000	0.71417	0.999000	0.59377	0.238000	0.25445	8.708000	0.91372	2.228000	0.72767	0.450000	0.29827	GGA		0.701	PAQR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250966.1	NM_152341	
SPNS1	83985	broad.mit.edu	37	16	28993844	28993844	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:28993844G>A	ENST00000311008.11	+	8	1510	c.1133G>A	c.(1132-1134)cGt>cAt	p.R378H	SPNS1_ENST00000323081.8_Missense_Mutation_p.R305H|LAT_ENST00000454369.2_5'Flank|LAT_ENST00000395456.2_5'Flank|RP11-264B17.3_ENST00000569969.1_RNA|SPNS1_ENST00000565975.1_Missense_Mutation_p.R423H|LAT_ENST00000354453.4_5'Flank|SPNS1_ENST00000334536.8_Missense_Mutation_p.R326H|SPNS1_ENST00000352260.7_Missense_Mutation_p.R304H|LAT_ENST00000566177.1_5'Flank|LAT_ENST00000395461.3_5'Flank|LAT_ENST00000564277.1_5'Flank|LAT_ENST00000360872.5_5'Flank	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	378					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)		p.R378H(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						GCCTGCGCCCGTGGTAGCATC	0.657																																					p.R304H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G911A	16						.						68.0	61.0	63.0					16																	28993844		2197	4300	6497	28901345	SO:0001583	missense	83985	exon6			BC006156	CCDS10646.1, CCDS45452.1, CCDS45453.1, CCDS45454.1	16p11.2	2007-04-12			ENSG00000169682	ENSG00000169682			30621	protein-coding gene	gene with protein product		612583				11340170, 12815463	Standard	NM_032038		Approved	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT	uc010vdi.1	Q9H2V7	OTTHUMG00000131762	ENST00000311008.11:c.1133G>A	16.37:g.28993844G>A	ENSP00000309945:p.Arg378His	Somatic		Capture	Illumina HiSeq	Phase_I	28901345	NM_001142449	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Missense_Mutation	SNP	ENST00000311008.11	37	CCDS10646.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.477651	0.44044	.	.	ENSG00000169682	ENST00000311008;ENST00000334536;ENST00000352260;ENST00000323081	T;T;T;T	0.57595	0.42;0.39;0.39;0.42	4.14	0.86	0.19042	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.428938	0.25050	N	0.033532	T	0.33147	0.0853	N	0.05230	-0.09	0.35260	D	0.779465	B;B;B;D	0.54207	0.006;0.014;0.018;0.965	B;B;B;P	0.51016	0.005;0.015;0.026;0.656	T	0.36286	-0.9754	10	0.32370	T	0.25	.	5.4493	0.16554	0.4855:0.0:0.5145:0.0	.	305;304;378;326	Q9H2V7-4;Q9H2V7-3;Q9H2V7;Q9H2V7-2	.;.;SPNS1_HUMAN;.	H	378;326;304;305	ENSP00000309945:R378H;ENSP00000335494:R326H;ENSP00000306050:R304H;ENSP00000318228:R305H	ENSP00000309945:R378H	R	+	2	0	SPNS1	28901345	1.000000	0.71417	0.973000	0.42090	0.924000	0.55760	4.065000	0.57513	0.410000	0.25675	0.462000	0.41574	CGT		0.657	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038	
SEZ6L2	26470	broad.mit.edu	37	16	29889661	29889661	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:29889661G>A	ENST00000308713.5	-	10	2186	c.1659C>T	c.(1657-1659)tgC>tgT	p.C553C	SEZ6L2_ENST00000346932.5_Silent_p.C439C|SEZ6L2_ENST00000537485.1_Silent_p.C509C|SEZ6L2_ENST00000350527.3_Silent_p.C483C	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	553	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.C553C(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CGCCCCACACGCAGTCTTGGC	0.607																																					p.C439C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1317T	16						.						106.0	87.0	94.0					16																	29889661		2197	4300	6497	29797162	SO:0001819	synonymous_variant	26470	exon8			AY358404	CCDS10658.1, CCDS10659.1, CCDS45458.1, CCDS58447.1, CCDS73865.1	16p12.1	2008-02-05			ENSG00000174938	ENSG00000174938			30844	protein-coding gene	gene with protein product	"""type I transmembrane receptor (seizure related protein)"""					12975309	Standard	NM_012410		Approved	PSK-1, FLJ90517	uc010vec.2	Q6UXD5	OTTHUMG00000132112	ENST00000308713.5:c.1659C>T	16.37:g.29889661G>A		Somatic		Capture	Illumina HiSeq	Phase_I	29797162	NM_001114100	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Silent	SNP	ENST00000308713.5	37	CCDS10659.1																																																																																				0.607	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410	
TAOK2	9344	broad.mit.edu	37	16	29993194	29993194	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:29993194G>A	ENST00000308893.4	+	10	1807	c.764G>A	c.(763-765)cGg>cAg	p.R255Q	TAOK2_ENST00000543033.1_Missense_Mutation_p.R255Q|TAOK2_ENST00000416441.2_Missense_Mutation_p.R82Q|TAOK2_ENST00000279394.3_Missense_Mutation_p.R255Q	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	255	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)	p.R255Q(1)		breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						GAGTACTTCCGGAATTTTGTC	0.552																																					p.R255Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G764A	16						.						64.0	64.0	64.0					16																	29993194		2197	4300	6497	29900695	SO:0001583	missense	9344	exon10			AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.764G>A	16.37:g.29993194G>A	ENSP00000310094:p.Arg255Gln	Somatic		Capture	Illumina HiSeq	Phase_I	29900695	NM_004783	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Missense_Mutation	SNP	ENST00000308893.4	37	CCDS10663.1	.	.	.	.	.	.	.	.	.	.	G	34	5.332107	0.95733	.	.	ENSG00000149930	ENST00000416441;ENST00000308893;ENST00000543033;ENST00000279394	D;D;D	0.90133	-2.62;-2.62;-2.62	5.91	5.91	0.95273	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	0.92945	0.7755	L	0.38953	1.18	0.80722	D	1	P;D;D;D;P	0.76494	0.954;0.999;0.999;0.998;0.936	P;D;D;D;P	0.79108	0.533;0.992;0.958;0.964;0.823	D	0.91555	0.5260	9	.	.	.	.	19.0726	0.93145	0.0:0.0:1.0:0.0	.	439;82;255;255;255	Q86V37;Q9UL54-3;Q9UL54-2;A0PJ48;Q9UL54	.;.;.;.;TAOK2_HUMAN	Q	255	ENSP00000310094:R255Q;ENSP00000440336:R255Q;ENSP00000279394:R255Q	.	R	+	2	0	TAOK2	29900695	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.809000	0.96659	0.555000	0.69702	CGG		0.552	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151	
TAOK2	9344	broad.mit.edu	37	16	29994201	29994201	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:29994201C>T	ENST00000308893.4	+	11	2021	c.978C>T	c.(976-978)gcC>gcT	p.A326A	TAOK2_ENST00000543033.1_Silent_p.A326A|TAOK2_ENST00000416441.2_Silent_p.A153A|TAOK2_ENST00000279394.3_Silent_p.A326A	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	326					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)	p.A326A(1)		breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						GCCCTGGTGCCGAGGCCCCAG	0.612																																					p.A326A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C978T	16						.						95.0	87.0	89.0					16																	29994201		2197	4300	6497	29901702	SO:0001819	synonymous_variant	9344	exon11			AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.978C>T	16.37:g.29994201C>T		Somatic		Capture	Illumina HiSeq	Phase_I	29901702	NM_004783	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Silent	SNP	ENST00000308893.4	37	CCDS10663.1																																																																																				0.612	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151	
HIRIP3	8479	broad.mit.edu	37	16	30004676	30004676	+	Missense_Mutation	SNP	C	C	T	rs376313895		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:30004676C>T	ENST00000279392.3	-	7	2353	c.1523G>A	c.(1522-1524)cGt>cAt	p.R508H	HIRIP3_ENST00000564026.1_3'UTR|INO80E_ENST00000567705.1_5'Flank|INO80E_ENST00000304516.7_5'Flank|HIRIP3_ENST00000566471.1_5'Flank|INO80E_ENST00000563197.1_5'Flank|INO80E_ENST00000567254.1_5'Flank	NM_003609.4	NP_003600.2	Q9BW71	HIRP3_HUMAN	HIRA interacting protein 3	508					chromatin assembly or disassembly (GO:0006333)	nucleus (GO:0005634)		p.R508H(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(9)	17						CCAGGCTGTACGTCTGCGTGG	0.622																																					p.R508H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1523A	16						.	C	HIS/ARG	0,4394		0,0,2197	68.0	71.0	70.0		1523	4.9	1.0	16		70	1,8599	1.2+/-3.3	0,1,4299	no	missense	HIRIP3	NM_003609.4	29	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	508/557	30004676	1,12993	2197	4300	6497	29912177	SO:0001583	missense	8479	exon7			AJ223351	CCDS10664.1, CCDS58449.1	16p12.1	2008-02-05	2001-11-29		ENSG00000149929	ENSG00000149929			4917	protein-coding gene	gene with protein product		603365	"""HIRA-interacting protein 3"""			9710638	Standard	NM_003609		Approved		uc002dve.3	Q9BW71	OTTHUMG00000132118	ENST00000279392.3:c.1523G>A	16.37:g.30004676C>T	ENSP00000279392:p.Arg508His	Somatic		Capture	Illumina HiSeq	Phase_I	29912177	NM_003609	H3BSR3|O75707|O75708	Missense_Mutation	SNP	ENST00000279392.3	37	CCDS10664.1	.	.	.	.	.	.	.	.	.	.	C	31	5.062152	0.93846	0.0	1.16E-4	ENSG00000149929	ENST00000279392;ENST00000352552	T	0.52526	0.66	4.91	4.91	0.64330	Histone chaperone domain CHZ (1);	0.068795	0.53938	D	0.000043	T	0.57140	0.2033	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.67231	0.95	T	0.60687	-0.7214	10	0.87932	D	0	-3.9232	15.6441	0.77033	0.0:1.0:0.0:0.0	.	508	Q9BW71	HIRP3_HUMAN	H	508;195	ENSP00000279392:R508H	ENSP00000279392:R508H	R	-	2	0	HIRIP3	29912177	0.999000	0.42202	0.954000	0.39281	0.980000	0.70556	2.938000	0.48987	2.559000	0.86315	0.650000	0.86243	CGT		0.622	HIRIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255160.2	NM_003609	
SEPT1	1731	broad.mit.edu	37	16	30390793	30390793	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:30390793C>T	ENST00000571393.1	-	9	909	c.723G>A	c.(721-723)ccG>ccA	p.P241P	SEPT1_ENST00000605106.1_Silent_p.P246P|SEPT1_ENST00000321367.3_Silent_p.P288P			Q8WYJ6	SEPT1_HUMAN	septin 1	241	Septin-type G.			RP -> GL (in Ref. 1; AAL40393). {ECO:0000305}.	cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)	p.P241P(1)		breast(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)|urinary_tract(1)	24			Colorectal(24;0.193)			GTCCCCTCACCGGCCGGTTCC	0.682																																					p.P241P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G723A	16						.						74.0	70.0	71.0					16																	30390793		2197	4300	6497	30298294	SO:0001819	synonymous_variant	1731	exon9			AF308288	CCDS10678.1, CCDS10678.2, CCDS10678.3	16p11.2	2013-01-21		2001-09-10	ENSG00000180096	ENSG00000180096	3.1.5.1	"""Septins"""	2879	protein-coding gene	gene with protein product		612897		DIFF6		8697812	Standard	NM_052838		Approved	PNUTL3	uc002dxy.4	Q8WYJ6	OTTHUMG00000176984	ENST00000571393.1:c.723G>A	16.37:g.30390793C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30298294	NM_052838	B4DVE6|Q658T1|Q8NEZ1|Q96EL4|Q9H285	Silent	SNP	ENST00000571393.1	37																																																																																					0.682	SEPT1-201	KNOWN	basic	protein_coding	protein_coding		NM_052838	
SEPT1	1731	broad.mit.edu	37	16	30392466	30392466	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:30392466G>T	ENST00000571393.1	-	7	726	c.540C>A	c.(538-540)acC>acA	p.T180T	SEPT1_ENST00000605106.1_Silent_p.T185T|SEPT1_ENST00000570039.1_5'Flank|SEPT1_ENST00000321367.3_Silent_p.T227T			Q8WYJ6	SEPT1_HUMAN	septin 1	180	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)	p.T180T(1)		breast(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)|urinary_tract(1)	24			Colorectal(24;0.193)			TGAGGGCCTGGGTTTCCTGGG	0.537																																					p.T180T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C540A	16						.						192.0	177.0	182.0					16																	30392466		2197	4300	6497	30299967	SO:0001819	synonymous_variant	1731	exon7			AF308288	CCDS10678.1, CCDS10678.2, CCDS10678.3	16p11.2	2013-01-21		2001-09-10	ENSG00000180096	ENSG00000180096	3.1.5.1	"""Septins"""	2879	protein-coding gene	gene with protein product		612897		DIFF6		8697812	Standard	NM_052838		Approved	PNUTL3	uc002dxy.4	Q8WYJ6	OTTHUMG00000176984	ENST00000571393.1:c.540C>A	16.37:g.30392466G>T		Somatic		Capture	Illumina HiSeq	Phase_I	30299967	NM_052838	B4DVE6|Q658T1|Q8NEZ1|Q96EL4|Q9H285	Silent	SNP	ENST00000571393.1	37																																																																																					0.537	SEPT1-201	KNOWN	basic	protein_coding	protein_coding		NM_052838	
SEPT1	1731	broad.mit.edu	37	16	30392661	30392661	+	Splice_Site	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:30392661C>A	ENST00000571393.1	-	6	625	c.439G>T	c.(439-441)Ggg>Tgg	p.G147W	SEPT1_ENST00000605106.1_Splice_Site_p.G152W|SEPT1_ENST00000570039.1_5'Flank|SEPT1_ENST00000321367.3_Splice_Site_p.G194W			Q8WYJ6	SEPT1_HUMAN	septin 1	147	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)	p.G147W(1)		breast(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)|urinary_tract(1)	24			Colorectal(24;0.193)			CCACCAGACCCCCGGCCGAAG	0.627																																					p.G147W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G439T	16						.						46.0	50.0	48.0					16																	30392661		2197	4300	6497	30300162	SO:0001630	splice_region_variant	1731	exon6			AF308288	CCDS10678.1, CCDS10678.2, CCDS10678.3	16p11.2	2013-01-21		2001-09-10	ENSG00000180096	ENSG00000180096	3.1.5.1	"""Septins"""	2879	protein-coding gene	gene with protein product		612897		DIFF6		8697812	Standard	NM_052838		Approved	PNUTL3	uc002dxy.4	Q8WYJ6	OTTHUMG00000176984	ENST00000571393.1:c.440+1G>T	16.37:g.30392661C>A		Somatic		Capture	Illumina HiSeq	Phase_I	30300162	NM_052838	B4DVE6|Q658T1|Q8NEZ1|Q96EL4|Q9H285	Missense_Mutation	SNP	ENST00000571393.1	37		.	.	.	.	.	.	.	.	.	.	C	16.51	3.142695	0.57044	.	.	ENSG00000180096	ENST00000321367	.	.	.	5.74	5.74	0.90152	.	0.090422	0.49305	D	0.000152	D	0.84506	0.5487	M	0.85041	2.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85923	0.1447	9	0.87932	D	0	.	19.0821	0.93186	0.0:1.0:0.0:0.0	.	194;147	B4E0I4;Q8WYJ6	.;SEPT1_HUMAN	W	147	.	ENSP00000324511:G147W	G	-	1	0	SEPT1	30300162	1.000000	0.71417	1.000000	0.80357	0.037000	0.13140	7.689000	0.84165	2.884000	0.98904	0.655000	0.94253	GGG		0.627	SEPT1-201	KNOWN	basic	protein_coding	protein_coding		NM_052838	Missense_Mutation
ITGAL	3683	broad.mit.edu	37	16	30485551	30485551	+	Silent	SNP	C	C	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:30485551C>G	ENST00000356798.6	+	2	276	c.96C>G	c.(94-96)ggC>ggG	p.G32G	Y_RNA_ENST00000410769.1_RNA|RP11-297C4.2_ENST00000569459.1_RNA|ITGAL_ENST00000454514.2_Silent_p.G32G|ITGAL_ENST00000433423.2_Silent_p.G32G|ITGAL_ENST00000358164.5_Silent_p.G32G	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	32					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.G32G(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)	ACGTGCGGGGCGCGCGGAGCT	0.697																																					p.G32G	NSCLC(110;1462 1641 3311 33990 49495)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C96G	16						.						18.0	20.0	19.0					16																	30485551		2188	4274	6462	30393052	SO:0001819	synonymous_variant	3683	exon2				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.96C>G	16.37:g.30485551C>G		Somatic		Capture	Illumina HiSeq	Phase_I	30393052	NM_001114380	O43746|Q45H73|Q96HB1|Q9UBC8	Silent	SNP	ENST00000356798.6	37	CCDS32433.1																																																																																				0.697	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2		
SRCAP	10847	broad.mit.edu	37	16	30745016	30745016	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:30745016G>A	ENST00000262518.4	+	29	6776	c.6391G>A	c.(6391-6393)Gac>Aac	p.D2131N	SRCAP_ENST00000344771.4_Missense_Mutation_p.D1973N|SRCAP_ENST00000395059.2_Missense_Mutation_p.D2069N	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2131	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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.D2131N(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)			GACAGGAGCAGACACTGTTGT	0.527																																					p.D2131N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6391A	16						.						114.0	113.0	113.0					16																	30745016		2197	4300	6497	30652517	SO:0001583	missense	10847	exon29			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.6391G>A	16.37:g.30745016G>A	ENSP00000262518:p.Asp2131Asn	Somatic		Capture	Illumina HiSeq	Phase_I	30652517	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	15.43	2.830159	0.50845	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.92199	-2.99;-2.99;-2.99	5.24	4.29	0.51040	Helicase, C-terminal (3);	0.000000	0.50627	D	0.000117	D	0.91171	0.7219	N	0.12663	0.25	0.37913	D	0.931437	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.93140	0.6540	10	0.62326	D	0.03	-13.7523	12.8207	0.57692	0.0797:0.0:0.9203:0.0	.	2069;2131	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	N	2131;2069;1973	ENSP00000262518:D2131N;ENSP00000378499:D2069N;ENSP00000343042:D1973N	ENSP00000262518:D2131N	D	+	1	0	SRCAP	30652517	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.578000	0.98200	1.441000	0.47550	0.563000	0.77884	GAC		0.527	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
SRCAP	10847	broad.mit.edu	37	16	30750809	30750809	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:30750809G>A	ENST00000262518.4	+	34	9833	c.9448G>A	c.(9448-9450)Ggg>Agg	p.G3150R	SRCAP_ENST00000344771.4_Missense_Mutation_p.G2992R|RP11-2C24.4_ENST00000483578.1_lincRNA|SRCAP_ENST00000395059.2_Missense_Mutation_p.G3088R	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	3150					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.G3150R(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)			TGGGAGTCCTGGGCTGGCAAA	0.652																																					p.G3150R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G9448A	16						.						20.0	23.0	22.0					16																	30750809		2197	4299	6496	30658310	SO:0001583	missense	10847	exon34			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.9448G>A	16.37:g.30750809G>A	ENSP00000262518:p.Gly3150Arg	Somatic		Capture	Illumina HiSeq	Phase_I	30658310	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	6.652	0.488753	0.12641	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.92299	-2.96;-3.01;-3.0	4.76	4.76	0.60689	.	0.144732	0.31760	N	0.007117	T	0.81894	0.4919	N	0.08118	0	0.09310	N	1	B;B	0.12630	0.006;0.003	B;B	0.08055	0.003;0.001	T	0.72571	-0.4253	10	0.72032	D	0.01	-12.5182	8.829	0.35072	0.1005:0.0:0.8994:0.0	.	3088;3150	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	R	3150;3088;2992	ENSP00000262518:G3150R;ENSP00000378499:G3088R;ENSP00000343042:G2992R	ENSP00000262518:G3150R	G	+	1	0	SRCAP	30658310	1.000000	0.71417	0.912000	0.35992	0.981000	0.71138	3.078000	0.50096	2.473000	0.83533	0.462000	0.41574	GGG		0.652	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
RNF40	9810	broad.mit.edu	37	16	30779659	30779659	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:30779659C>G	ENST00000324685.6	+	13	2222	c.1787C>G	c.(1786-1788)gCc>gGc	p.A596G	RNF40_ENST00000563683.1_Missense_Mutation_p.A556G|RNF40_ENST00000357890.5_Missense_Mutation_p.A496G|RNF40_ENST00000402121.3_Missense_Mutation_p.A288G	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	596					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.A596G(1)		central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			ACCCCTGGGGCCCAGGGCCCT	0.637																																					p.A596G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1787G	16						.						22.0	25.0	24.0					16																	30779659		2197	4299	6496	30687160	SO:0001583	missense	9810	exon13			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.1787C>G	16.37:g.30779659C>G	ENSP00000325677:p.Ala596Gly	Somatic		Capture	Illumina HiSeq	Phase_I	30687160	NM_014771	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Missense_Mutation	SNP	ENST00000324685.6	37	CCDS10691.1	.	.	.	.	.	.	.	.	.	.	C	11.46	1.644238	0.29246	.	.	ENSG00000103549	ENST00000324685;ENST00000357890;ENST00000402121	T;T;T	0.30981	1.51;1.51;1.51	5.97	5.97	0.96955	.	0.892392	0.09872	N	0.744811	T	0.25044	0.0608	N	0.24115	0.695	0.20196	N	0.999927	B;B;B;B	0.11235	0.004;0.004;0.002;0.002	B;B;B;B	0.14023	0.006;0.01;0.004;0.004	T	0.10567	-1.0624	10	0.30078	T	0.28	-1.2827	14.0852	0.64951	0.1507:0.8493:0.0:0.0	.	288;496;596;596	F8W8Z4;O75150-4;A8K6K1;O75150	.;.;.;BRE1B_HUMAN	G	596;496;288	ENSP00000325677:A596G;ENSP00000350563:A496G;ENSP00000384942:A288G	ENSP00000325677:A596G	A	+	2	0	RNF40	30687160	0.610000	0.26983	0.973000	0.42090	0.867000	0.49689	1.127000	0.31357	2.837000	0.97791	0.655000	0.94253	GCC		0.637	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771	
ZNF629	23361	broad.mit.edu	37	16	30795140	30795140	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:30795140C>T	ENST00000262525.4	-	3	716	c.509G>A	c.(508-510)cGc>cAc	p.R170H		NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	170					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.R170H(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			CGTGTGGATGCGCTGGTGCCG	0.687																																					p.R170H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G509A	16						.						33.0	36.0	35.0					16																	30795140		2197	4299	6496	30702641	SO:0001583	missense	23361	exon3			AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"""Zinc fingers, C2H2-type"""	29008	protein-coding gene	gene with protein product			"""zinc finger protein 65"""	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.509G>A	16.37:g.30795140C>T	ENSP00000262525:p.Arg170His	Somatic		Capture	Illumina HiSeq	Phase_I	30702641	NM_001080417	Q15938	Missense_Mutation	SNP	ENST00000262525.4	37	CCDS45463.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.031478	0.75504	.	.	ENSG00000102870	ENST00000262525	T	0.58506	0.33	5.16	5.16	0.70880	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45361	D	0.000377	T	0.75451	0.3851	M	0.71581	2.175	0.48395	D	0.999646	D	0.89917	1.0	D	0.74674	0.984	T	0.78013	-0.2370	10	0.72032	D	0.01	-56.1425	17.7785	0.88516	0.0:1.0:0.0:0.0	.	170	Q9UEG4	ZN629_HUMAN	H	170	ENSP00000262525:R170H	ENSP00000262525:R170H	R	-	2	0	ZNF629	30702641	0.009000	0.17119	1.000000	0.80357	0.945000	0.59286	2.005000	0.40864	2.566000	0.86566	0.561000	0.74099	CGC		0.687	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309	
CTF1	1489	broad.mit.edu	37	16	30910812	30910812	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:30910812G>A	ENST00000279804.2	+	2	139	c.102G>A	c.(100-102)gcG>gcA	p.A34A	CTF1_ENST00000395019.3_Silent_p.A33A	NM_001142544.1|NM_001330.3	NP_001136016.1|NP_001321.1	Q16619	CTF1_HUMAN	cardiotrophin 1	34					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|leukemia inhibitory factor signaling pathway (GO:0048861)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|neuron development (GO:0048666)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	leukemia inhibitory factor receptor binding (GO:0005146)	p.A34A(1)		large_intestine(1)|urinary_tract(1)	2			Colorectal(24;0.198)			ACAGCCTTGCGCACCTCCTCA	0.592																																					p.A33A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G99A	16						.						87.0	76.0	80.0					16																	30910812		2197	4300	6497	30818313	SO:0001819	synonymous_variant	1489	exon2			U43030	CCDS10694.1, CCDS45464.1	16p11.2	2014-09-17			ENSG00000150281	ENSG00000150281			2499	protein-coding gene	gene with protein product		600435				8833032	Standard	NM_001330		Approved	CT-1, CT1	uc002dzw.3	Q16619	OTTHUMG00000132413	ENST00000279804.2:c.102G>A	16.37:g.30910812G>A		Somatic		Capture	Illumina HiSeq	Phase_I	30818313	NM_001142544	A8MVX4|Q5U5Y7	Silent	SNP	ENST00000279804.2	37	CCDS10694.1																																																																																				0.592	CTF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255550.1	NM_001330	
ZNF205	7755	broad.mit.edu	37	16	3169811	3169811	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:3169811C>T	ENST00000382192.3	+	7	1355	c.1150C>T	c.(1150-1152)Cgc>Tgc	p.R384C	RP11-473M20.14_ENST00000575139.1_RNA|ZNF205_ENST00000219091.4_Missense_Mutation_p.R384C|RP11-473M20.14_ENST00000576490.1_RNA	NM_001278158.1|NM_003456.2	NP_001265087.1|NP_003447.2	O95201	ZN205_HUMAN	zinc finger protein 205	384					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hydrogen peroxide biosynthetic process (GO:0010729)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R384C(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20						TCAGCACCAGCGCATCCACAC	0.667																																					p.R384C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1150T	16						.						65.0	69.0	68.0					16																	3169811		2197	4300	6497	3109812	SO:0001583	missense	7755	exon7			AF060865	CCDS10494.2	16p13.3	2013-01-08			ENSG00000122386	ENSG00000122386		"""Zinc fingers, C2H2-type"", ""-"""	12996	protein-coding gene	gene with protein product		603436		ZNF210		9787081	Standard	NM_003456		Approved	Zfp13	uc002cub.3	O95201	OTTHUMG00000148676	ENST00000382192.3:c.1150C>T	16.37:g.3169811C>T	ENSP00000371627:p.Arg384Cys	Somatic		Capture	Illumina HiSeq	Phase_I	3109812	NM_001042428	A8MZK0|D3DUB4|Q9BU95	Missense_Mutation	SNP	ENST00000382192.3	37	CCDS10494.2	.	.	.	.	.	.	.	.	.	.	C	15.79	2.938683	0.52972	.	.	ENSG00000122386	ENST00000382192;ENST00000219091	T;T	0.25749	1.78;1.78	5.42	3.26	0.37387	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.48286	D	0.000200	T	0.47948	0.1473	M	0.74546	2.27	0.43708	D	0.996173	D	0.89917	1.0	D	0.85130	0.997	T	0.50668	-0.8801	10	0.87932	D	0	-36.349	11.3865	0.49789	0.3324:0.6676:0.0:0.0	.	384	O95201	ZN205_HUMAN	C	384	ENSP00000371627:R384C;ENSP00000219091:R384C	ENSP00000219091:R384C	R	+	1	0	ZNF205	3109812	0.001000	0.12720	1.000000	0.80357	0.819000	0.46315	-0.054000	0.11826	2.544000	0.85801	0.561000	0.74099	CGC		0.667	ZNF205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309057.1	NM_003456	
STX4	6810	broad.mit.edu	37	16	31049314	31049314	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:31049314G>A	ENST00000313843.3	+	6	761	c.446G>A	c.(445-447)cGg>cAg	p.R149Q	STX4_ENST00000493902.1_3'UTR|STX4_ENST00000394998.1_Missense_Mutation_p.R147Q	NM_004604.3	NP_004595.2	Q12846	STX4_HUMAN	syntaxin 4	149					blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|neurotransmitter transport (GO:0006836)|platelet activation (GO:0030168)|post-Golgi vesicle-mediated transport (GO:0006892)|SNARE complex assembly (GO:0035493)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|membrane (GO:0016020)|myelin sheath adaxonal region (GO:0035749)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|specific granule (GO:0042581)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)		p.R149Q(1)		NS(2)|breast(1)|large_intestine(3)|lung(3)	9						TCCGAATACCGGGAGAAGAAC	0.552																																					p.R149Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G446A	16						.						120.0	123.0	122.0					16																	31049314		2197	4300	6497	30956815	SO:0001583	missense	6810	exon6			AF026007	CCDS10700.1, CCDS61916.1	16p11.2	2008-02-05	2006-04-25	2006-04-25	ENSG00000103496	ENSG00000103496			11439	protein-coding gene	gene with protein product		186591	"""syntaxin 4A (placental)"""	STX4A		8206394, 16339081	Standard	NM_001272095		Approved	p35-2	uc002eak.4	Q12846	OTTHUMG00000132404	ENST00000313843.3:c.446G>A	16.37:g.31049314G>A	ENSP00000317714:p.Arg149Gln	Somatic		Capture	Illumina HiSeq	Phase_I	30956815	NM_004604	A8MXY0|Q15525|Q6FHE8	Missense_Mutation	SNP	ENST00000313843.3	37	CCDS10700.1	.	.	.	.	.	.	.	.	.	.	g	36	5.744121	0.96882	.	.	ENSG00000103496	ENST00000394998;ENST00000313843	T;T	0.22539	1.95;1.95	5.57	5.57	0.84162	t-SNARE (1);Syntaxin, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.46405	0.1391	M	0.69248	2.105	0.46798	D	0.999209	D;D	0.89917	1.0;1.0	D;D	0.69654	0.965;0.944	T	0.40251	-0.9573	10	0.87932	D	0	.	18.3784	0.90442	0.0:0.0:1.0:0.0	.	149;147	Q12846;A8MXY0	STX4_HUMAN;.	Q	147;149	ENSP00000378447:R147Q;ENSP00000317714:R149Q	ENSP00000317714:R149Q	R	+	2	0	STX4	30956815	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.962000	0.93254	2.643000	0.89663	0.550000	0.68814	CGG		0.552	STX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255538.3	NM_004604	
ITGAM	3684	broad.mit.edu	37	16	31332931	31332931	+	Missense_Mutation	SNP	G	G	A	rs368823511		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:31332931G>A	ENST00000287497.8	+	16	2060	c.1985G>A	c.(1984-1986)cGg>cAg	p.R662Q	ITGAM_ENST00000544665.3_Missense_Mutation_p.R663Q			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	662					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)	p.R662Q(1)		endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						AAGAGCACACGGGATCGGCTA	0.527																																					p.R662Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1985A	16						.	G	GLN/ARG,GLN/ARG	0,4322		0,0,2161	109.0	115.0	113.0		1985,1988	-3.8	0.0	16		113	1,8557		0,1,4278	no	missense,missense	ITGAM	NM_000632.3,NM_001145808.1	43,43	0,1,6439	AA,AG,GG		0.0117,0.0,0.0078	possibly-damaging,possibly-damaging	662/1153,663/1154	31332931	1,12879	2161	4279	6440	31240432	SO:0001583	missense	3684	exon16			J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"""CD molecules"", ""Complement system"", ""Integrins"""	6149	protein-coding gene	gene with protein product		120980	"""integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"""	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.1985G>A	16.37:g.31332931G>A	ENSP00000287497:p.Arg662Gln	Somatic		Capture	Illumina HiSeq	Phase_I	31240432	NM_000632	Q4VAK0|Q4VAK1|Q4VAK2	Missense_Mutation	SNP	ENST00000287497.8	37	CCDS45470.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.618132	0.46736	0.0	1.17E-4	ENSG00000169896	ENST00000544665;ENST00000287497	T;T	0.44482	0.92;0.92	4.83	-3.84	0.04256	Integrin alpha-2 (1);	.	.	.	.	T	0.17534	0.0421	L	0.31065	0.9	0.09310	N	1	P;P;P	0.37398	0.593;0.593;0.593	B;B;B	0.29524	0.103;0.072;0.072	T	0.21586	-1.0241	9	0.17832	T	0.49	.	0.1566	0.00098	0.2702:0.2616:0.2028:0.2655	.	68;662;662	B3KXM6;Q4VAK1;P11215	.;.;ITAM_HUMAN	Q	663;662	ENSP00000441691:R663Q;ENSP00000287497:R662Q	ENSP00000287497:R662Q	R	+	2	0	ITGAM	31240432	0.004000	0.15560	0.010000	0.14722	0.932000	0.56968	-0.434000	0.06939	-0.279000	0.09167	0.655000	0.94253	CGG		0.527	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632	
ITGAX	3687	broad.mit.edu	37	16	31374640	31374640	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:31374640C>T	ENST00000268296.4	+	14	1776	c.1655C>T	c.(1654-1656)gCt>gTt	p.A552V	ITGAX_ENST00000562522.1_Missense_Mutation_p.A552V	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	552					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.A552V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						AACCGGGGTGCTGTCTACCTG	0.617																																					p.A552V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1655T	16						.						113.0	117.0	116.0					16																	31374640		2197	4300	6497	31282141	SO:0001583	missense	3687	exon14			BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1655C>T	16.37:g.31374640C>T	ENSP00000268296:p.Ala552Val	Somatic		Capture	Illumina HiSeq	Phase_I	31282141	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.542998	0.45280	.	.	ENSG00000140678	ENST00000268296	T	0.18657	2.2	4.14	4.14	0.48551	.	.	.	.	.	T	0.44117	0.1278	M	0.65975	2.015	0.30788	N	0.741239	D	0.89917	1.0	D	0.74348	0.983	T	0.47736	-0.9094	9	0.87932	D	0	.	13.6863	0.62517	0.0:1.0:0.0:0.0	.	552	P20702	ITAX_HUMAN	V	552	ENSP00000268296:A552V	ENSP00000268296:A552V	A	+	2	0	ITGAX	31282141	0.996000	0.38824	0.987000	0.45799	0.205000	0.24178	3.602000	0.54066	2.012000	0.59069	0.460000	0.39030	GCT		0.617	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
ITGAX	3687	broad.mit.edu	37	16	31391611	31391611	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:31391611C>T	ENST00000268296.4	+	27	3206	c.3085C>T	c.(3085-3087)Cgg>Tgg	p.R1029W	ITGAX_ENST00000562522.1_Missense_Mutation_p.R1029W	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	1029					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.R1029W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						TGGCTGCCTGCGGTTCCGCTG	0.592																																					p.R1029W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3085T	16						.						51.0	40.0	44.0					16																	31391611		2197	4300	6497	31299112	SO:0001583	missense	3687	exon27			BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.3085C>T	16.37:g.31391611C>T	ENSP00000268296:p.Arg1029Trp	Somatic		Capture	Illumina HiSeq	Phase_I	31299112	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	CCDS10711.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.933633	0.52866	.	.	ENSG00000140678	ENST00000268296	T	0.50277	0.75	4.7	-2.28	0.06826	Integrin alpha-2 (1);	.	.	.	.	T	0.46718	0.1407	L	0.54323	1.7	0.09310	N	1	D;D	0.67145	0.996;0.968	P;B	0.49477	0.612;0.37	T	0.47522	-0.9111	9	0.87932	D	0	.	8.9892	0.36012	0.2705:0.6006:0.0:0.1289	.	1029;214	P20702;Q8TES5	ITAX_HUMAN;.	W	1029	ENSP00000268296:R1029W	ENSP00000268296:R1029W	R	+	1	2	ITGAX	31299112	0.010000	0.17322	0.186000	0.23195	0.872000	0.50106	0.080000	0.14802	-0.542000	0.06249	-0.467000	0.05162	CGG		0.592	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
ITGAD	3681	broad.mit.edu	37	16	31424472	31424472	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:31424472C>T	ENST00000389202.2	+	16	1950	c.1901C>T	c.(1900-1902)gCt>gTt	p.A634V		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	634					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.A634V(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						GTGGCCAAGGCTGTGTACCGG	0.612																																					p.A634V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1901T	16						.						124.0	107.0	113.0					16																	31424472		2197	4300	6497	31331973	SO:0001583	missense	3681	exon16			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.1901C>T	16.37:g.31424472C>T	ENSP00000373854:p.Ala634Val	Somatic		Capture	Illumina HiSeq	Phase_I	31331973	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	37	CCDS32438.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.065126	0.36470	.	.	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.46451	0.87	5.24	5.24	0.73138	Integrin alpha-2 (1);	.	.	.	.	T	0.49966	0.1588	L	0.55481	1.735	0.09310	N	0.999997	P;P	0.37276	0.589;0.589	P;P	0.46208	0.507;0.507	T	0.46442	-0.9191	9	0.48119	T	0.1	.	14.3124	0.66424	0.0:1.0:0.0:0.0	.	650;634	Q59H14;Q13349	.;ITAD_HUMAN	V	650;634	ENSP00000373854:A634V	ENSP00000373854:A634V	A	+	2	0	ITGAD	31331973	0.000000	0.05858	0.394000	0.26270	0.001000	0.01503	0.204000	0.17335	2.460000	0.83146	0.604000	0.83254	GCT		0.612	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
ZNF174	7727	broad.mit.edu	37	16	3458608	3458608	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:3458608C>T	ENST00000268655.4	+	3	1498	c.913C>T	c.(913-915)Cgg>Tgg	p.R305W	ZNF174_ENST00000571936.1_Missense_Mutation_p.R305W	NM_003450.2	NP_003441.1	Q15697	ZN174_HUMAN	zinc finger protein 174	305					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.R305W(1)		endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|urinary_tract(2)	12						AGGAGGTAAACGGAGTCTGAG	0.498																																					p.R305W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C913T	16						.						82.0	78.0	79.0					16																	3458608		2197	4300	6497	3398609	SO:0001583	missense	7727	exon3			U31248	CCDS10504.1, CCDS32380.1	16p13	2013-01-09			ENSG00000103343	ENSG00000103343		"""-"", ""Zinc fingers, C2H2-type"""	12963	protein-coding gene	gene with protein product		603900					Standard	NM_003450		Approved	ZSCAN8	uc002cvc.3	Q15697	OTTHUMG00000129358	ENST00000268655.4:c.913C>T	16.37:g.3458608C>T	ENSP00000268655:p.Arg305Trp	Somatic		Capture	Illumina HiSeq	Phase_I	3398609	NM_003450	Q53Y68|Q9BQ34	Missense_Mutation	SNP	ENST00000268655.4	37	CCDS10504.1	.	.	.	.	.	.	.	.	.	.	C	9.314	1.056205	0.19907	.	.	ENSG00000103343	ENST00000268655	T	0.01051	5.4	4.11	3.02	0.34903	.	0.173869	0.27052	N	0.021169	T	0.02494	0.0076	N	0.24115	0.695	0.25479	N	0.987752	D	0.89917	1.0	D	0.83275	0.996	T	0.43294	-0.9400	10	0.87932	D	0	.	7.7205	0.28729	0.7698:0.2302:0.0:0.0	.	305	Q15697	ZN174_HUMAN	W	305	ENSP00000268655:R305W	ENSP00000268655:R305W	R	+	1	2	ZNF174	3398609	0.021000	0.18746	0.049000	0.19019	0.469000	0.32828	1.105000	0.31086	0.943000	0.37553	-0.457000	0.05445	CGG		0.498	ZNF174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251510.1	NM_003450	
NAA60	79903	broad.mit.edu	37	16	3526273	3526273	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:3526273C>T	ENST00000407558.4	+	3	349	c.46C>T	c.(46-48)Cgc>Tgc	p.R16C	NAA60_ENST00000575076.1_Missense_Mutation_p.R16C|NAA60_ENST00000576916.1_Missense_Mutation_p.R16C|NAA60_ENST00000577013.1_Missense_Mutation_p.R16C|NAA60_ENST00000414063.2_Missense_Mutation_p.R16C|NAA60_ENST00000573580.1_Intron|NAA60_ENST00000572942.1_Missense_Mutation_p.R16C|NAA60_ENST00000608722.1_Missense_Mutation_p.R16C|NAA60_ENST00000424546.2_Intron|NAA60_ENST00000610180.1_Missense_Mutation_p.R16C|NAA60_ENST00000608993.1_Intron|NAA60_ENST00000572584.1_Missense_Mutation_p.R16C|NAA60_ENST00000570819.1_Missense_Mutation_p.R16C|NAA60_ENST00000570551.1_Intron|LA16c-306E5.3_ENST00000574423.2_RNA|NAA60_ENST00000421765.3_Missense_Mutation_p.R16C|NAA60_ENST00000360862.5_Intron			Q9H7X0	NAA60_HUMAN	N(alpha)-acetyltransferase 60, NatF catalytic subunit	16	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|histone H4 acetylation (GO:0043967)|N-terminal peptidyl-methionine acetylation (GO:0017196)|nucleosome assembly (GO:0006334)	Golgi membrane (GO:0000139)	H4 histone acetyltransferase activity (GO:0010485)|peptide alpha-N-acetyltransferase activity (GO:0004596)	p.R16C(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)	7						GGTCAGCCTGCGCCTCCTCTG	0.627																																					p.R16C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C46T	16						.						56.0	61.0	59.0					16																	3526273		2195	4294	6489	3466274	SO:0001583	missense	79903	exon2				CCDS45396.1	16p13.3	2012-07-13	2011-08-02	2011-08-02	ENSG00000122390	ENSG00000122390	2.3.1.48, 2.3.1.88	"""N(alpha)-acetyltransferase subunits"""	25875	protein-coding gene	gene with protein product		614246	"""N-acetyltransferase 15 (GCN5-related, putative)"""	NAT15		12975309, 21750686	Standard	NM_001083600		Approved	FLJ14154	uc010btm.3	Q9H7X0	OTTHUMG00000150268	ENST00000407558.4:c.46C>T	16.37:g.3526273C>T	ENSP00000385903:p.Arg16Cys	Somatic		Capture	Illumina HiSeq	Phase_I	3466274	NM_001083600	B3KRQ0|B4DLZ0|B4DPZ8|B4DYC4|D3DUC2|E7EQ65|Q6IA31|Q6UX26	Missense_Mutation	SNP	ENST00000407558.4	37	CCDS45396.1	.	.	.	.	.	.	.	.	.	.	C	33	5.275806	0.95459	.	.	ENSG00000122390	ENST00000407558;ENST00000414063;ENST00000421765	T;T	0.58358	0.34;0.34	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.75664	0.3880	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77739	-0.2475	10	0.72032	D	0.01	.	18.9669	0.92700	0.0:1.0:0.0:0.0	.	16	Q9H7X0	NAA60_HUMAN	C	16	ENSP00000385903:R16C;ENSP00000393224:R16C	ENSP00000385903:R16C	R	+	1	0	NAA60	3466274	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.316000	0.79007	2.733000	0.93635	0.561000	0.74099	CGC		0.627	NAA60-001	KNOWN	NMD_exception|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317235.2	NM_024845	
SLX4	84464	broad.mit.edu	37	16	3640824	3640824	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:3640824G>A	ENST00000294008.3	-	12	3455	c.2815C>T	c.(2815-2817)Cgg>Tgg	p.R939W		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	939	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.R939W(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						TCTGCTCCCCGTGCCCCTGAG	0.667								Direct reversal of damage																													p.R939W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2815T	16						.						54.0	59.0	57.0					16																	3640824		2197	4300	6497	3580825	SO:0001583	missense	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.2815C>T	16.37:g.3640824G>A	ENSP00000294008:p.Arg939Trp	Somatic		Capture	Illumina HiSeq	Phase_I	3580825	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	G	11.44	1.639450	0.29157	.	.	ENSG00000188827	ENST00000294008	T	0.01159	5.25	4.99	-0.82	0.10826	.	3.254390	0.01044	N	0.004351	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48864	-0.8997	10	0.59425	D	0.04	.	0.6058	0.00752	0.256:0.3079:0.1227:0.3134	.	939	Q8IY92	SLX4_HUMAN	W	939	ENSP00000294008:R939W	ENSP00000294008:R939W	R	-	1	2	SLX4	3580825	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.378000	0.07446	-0.035000	0.13691	-1.332000	0.01269	CGG		0.667	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
CREBBP	1387	broad.mit.edu	37	16	3781317	3781317	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:3781317C>T	ENST00000262367.5	-	30	5857	c.5048G>A	c.(5047-5049)cGc>cAc	p.R1683H	CREBBP_ENST00000382070.3_Missense_Mutation_p.R1645H	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1683	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Interaction with TRERF1.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|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 transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R1683H(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CCACTTGGAGCGGCGCAAGGA	0.642			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.R1683H			Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5048A	16						.						87.0	61.0	70.0					16																	3781317		2197	4300	6497	3721318	SO:0001583	missense	1387	exon30			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.5048G>A	16.37:g.3781317C>T	ENSP00000262367:p.Arg1683His	Somatic		Capture	Illumina HiSeq	Phase_I	3721318	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	c	19.82	3.897914	0.72639	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.92647	-3.08;-2.98	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.97365	0.9138	M	0.93808	3.46	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.991	D	0.97530	1.0079	10	0.66056	D	0.02	-23.6306	20.2192	0.98319	0.0:1.0:0.0:0.0	.	1713;1683	Q4LE28;Q92793	.;CBP_HUMAN	H	1683;1713;1645;218	ENSP00000262367:R1683H;ENSP00000371502:R1645H	ENSP00000262367:R1683H	R	-	2	0	CREBBP	3721318	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.818000	0.86416	2.780000	0.95670	0.655000	0.94253	CGC		0.642	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
SLC5A2	6524	broad.mit.edu	37	16	31500231	31500231	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:31500231G>A	ENST00000330498.3	+	11	1330	c.1311G>A	c.(1309-1311)tcG>tcA	p.S437S	AC026471.6_ENST00000565137.1_RNA	NM_003041.3	NP_003032.1	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 2	437					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-affinity glucose:sodium symporter activity (GO:0005362)	p.S437S(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	25					Canagliflozin(DB08907)|Dapagliflozin(DB06292)	TGGTAGTGTCGGTGGCCTGGC	0.697																																					p.S437S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1311A	16						.						56.0	52.0	53.0					16																	31500231		2197	4299	6496	31407732	SO:0001819	synonymous_variant	6524	exon11				CCDS10714.1	16p11.2	2013-05-22			ENSG00000140675	ENSG00000140675		"""Solute carriers"""	11037	protein-coding gene	gene with protein product		182381		SGLT2		8244402	Standard	NM_003041		Approved		uc002ecf.4	P31639	OTTHUMG00000176620	ENST00000330498.3:c.1311G>A	16.37:g.31500231G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31407732	NM_003041	A2RRD2	Silent	SNP	ENST00000330498.3	37	CCDS10714.1																																																																																				0.697	SLC5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255627.2		
SHCBP1	79801	broad.mit.edu	37	16	46629469	46629469	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:46629469C>T	ENST00000303383.3	-	10	1725	c.1459G>A	c.(1459-1461)Gcc>Acc	p.A487T		NM_024745.4	NP_079021	Q8NEM2	SHCBP_HUMAN	SHC SH2-domain binding protein 1	487					fibroblast growth factor receptor signaling pathway (GO:0008543)|regulation of neural precursor cell proliferation (GO:2000177)			p.A487T(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(37;0.00404)|all_epithelial(9;0.00527)|all_lung(18;0.0413)|Lung NSC(13;0.213)				TCTACCTTGGCGCCATATAAA	0.438																																					p.A487T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1459A	16						.						111.0	99.0	103.0					16																	46629469		2203	4300	6503	45186970	SO:0001583	missense	79801	exon10			AK055931	CCDS10720.1	16q11	2008-02-05			ENSG00000171241	ENSG00000171241			29547	protein-coding gene	gene with protein product		611027				10086341	Standard	NM_024745		Approved	FLJ22009	uc002eec.4	Q8NEM2	OTTHUMG00000132540	ENST00000303383.3:c.1459G>A	16.37:g.46629469C>T	ENSP00000306473:p.Ala487Thr	Somatic		Capture	Illumina HiSeq	Phase_I	45186970	NM_024745	Q96N60|Q9BVS0|Q9H6P6	Missense_Mutation	SNP	ENST00000303383.3	37	CCDS10720.1	.	.	.	.	.	.	.	.	.	.	C	18.92	3.724678	0.68959	.	.	ENSG00000171241	ENST00000303383	T	0.41400	1.0	4.03	4.03	0.46877	Pectin lyase fold/virulence factor (1);Pectin lyase fold (1);	0.053366	0.85682	D	0.000000	T	0.55752	0.1940	L	0.59436	1.845	0.54753	D	0.999988	D	0.71674	0.998	P	0.58130	0.833	T	0.61633	-0.7023	10	0.59425	D	0.04	-12.3701	16.374	0.83379	0.0:1.0:0.0:0.0	.	487	Q8NEM2	SHCBP_HUMAN	T	487	ENSP00000306473:A487T	ENSP00000306473:A487T	A	-	1	0	SHCBP1	45186970	1.000000	0.71417	0.998000	0.56505	0.310000	0.27922	4.891000	0.63185	2.085000	0.62840	0.655000	0.94253	GCC		0.438	SHCBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255740.1	NM_024745	
GLYR1	84656	broad.mit.edu	37	16	4862113	4862113	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:4862113G>A	ENST00000321919.9	-	13	1332	c.1256C>T	c.(1255-1257)gCg>gTg	p.A419V	GLYR1_ENST00000436648.5_Missense_Mutation_p.A338V|GLYR1_ENST00000381983.3_Missense_Mutation_p.A402V|GLYR1_ENST00000591451.1_Missense_Mutation_p.A413V	NM_032569.3	NP_115958	Q49A26	GLYR1_HUMAN	glyoxylate reductase 1 homolog (Arabidopsis)	419				A -> T (in Ref. 7; AAH47223). {ECO:0000305}.	pentose-phosphate shunt (GO:0006098)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)	p.A419V(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	19						CTTCCCCATCGCCTGGAAGCA	0.572																																					p.A419V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1256T	16						.						78.0	65.0	69.0					16																	4862113		2197	4300	6497	4802114	SO:0001583	missense	84656	exon13			AF244907	CCDS10524.1	16p13.3	2010-02-17			ENSG00000140632	ENSG00000140632			24434	protein-coding gene	gene with protein product	"""nuclear protein 60kDa"""	610660				16352664	Standard	NM_032569		Approved	BM045, HIBDL, NP60, N-PAC	uc002cxx.4	Q49A26	OTTHUMG00000129530	ENST00000321919.9:c.1256C>T	16.37:g.4862113G>A	ENSP00000322716:p.Ala419Val	Somatic		Capture	Illumina HiSeq	Phase_I	4802114	NM_032569	B4DL47|C9JJ40|C9JJ60|Q5U632|Q6P1Q2|Q6V3W7|Q9BTI1|Q9BXK2	Missense_Mutation	SNP	ENST00000321919.9	37	CCDS10524.1	.	.	.	.	.	.	.	.	.	.	G	19.64	3.865499	0.71949	.	.	ENSG00000140632	ENST00000321919;ENST00000381983;ENST00000436648	T;T;T	0.71103	-0.22;-0.21;-0.54	4.84	4.84	0.62591	6-phosphogluconate dehydrogenase, NADP-binding (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.72358	0.3450	N	0.12853	0.265	0.80722	D	1	P;D;P;D	0.89917	0.753;0.98;0.753;1.0	B;B;B;D	0.83275	0.152;0.378;0.1;0.996	T	0.76280	-0.3017	10	0.49607	T	0.09	-11.9028	17.2337	0.86992	0.0:0.0:1.0:0.0	.	338;413;402;419	Q49A26-5;Q49A26-3;Q49A26-2;Q49A26	.;.;.;GLYR1_HUMAN	V	419;402;338	ENSP00000322716:A419V;ENSP00000371413:A402V;ENSP00000390276:A338V	ENSP00000322716:A419V	A	-	2	0	GLYR1	4802114	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.340000	0.79292	2.667000	0.90743	0.655000	0.94253	GCG		0.572	GLYR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251717.2	NM_032569	
VPS35	55737	broad.mit.edu	37	16	46712944	46712944	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:46712944G>A	ENST00000299138.7	-	6	689	c.631C>T	c.(631-633)Cga>Tga	p.R211*	VPS35_ENST00000568642.1_5'UTR	NM_018206.4	NP_060676.2	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35 homolog (S. cerevisiae)	211					cell death (GO:0008219)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|retromer complex (GO:0030904)		p.R211*(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|pancreas(1)|prostate(1)|urinary_tract(1)	23		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				TGTCTTTCTCGTTCTCTTTTT	0.408																																					p.R211X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C631T	16						.						180.0	173.0	175.0					16																	46712944		2203	4300	6503	45270445	SO:0001587	stop_gained	55737	exon6			AF175265	CCDS10721.1	16q12	2012-06-27	2006-12-19		ENSG00000069329	ENSG00000069329		"""Parkinson disease"""	13487	protein-coding gene	gene with protein product		601501	"""vacuolar protein sorting 35 (yeast homolog)"", ""vacuolar protein sorting 35 (yeast)"""			11112353, 21763482	Standard	NM_018206		Approved	FLJ10752, MEM3, PARK17	uc002eef.4	Q96QK1	OTTHUMG00000132542	ENST00000299138.7:c.631C>T	16.37:g.46712944G>A	ENSP00000299138:p.Arg211*	Somatic		Capture	Illumina HiSeq	Phase_I	45270445	NM_018206	Q561W2|Q9H016|Q9H096|Q9H4P3|Q9H8J0|Q9NRS7|Q9NVG2|Q9NX80|Q9NZK2	Nonsense_Mutation	SNP	ENST00000299138.7	37	CCDS10721.1	.	.	.	.	.	.	.	.	.	.	.	37	6.165042	0.97338	.	.	ENSG00000069329	ENST00000299138;ENST00000541330	.	.	.	5.35	0.865	0.19074	.	0.060291	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	-11.279	15.1447	0.72641	0.0:0.0:0.5322:0.4678	.	.	.	.	X	211;76	.	ENSP00000299138:R211X	R	-	1	2	VPS35	45270445	1.000000	0.71417	0.995000	0.50966	0.983000	0.72400	3.329000	0.52060	0.013000	0.14918	-0.740000	0.03531	CGA		0.408	VPS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255742.3		
PPL	5493	broad.mit.edu	37	16	4940287	4940287	+	Silent	SNP	G	G	A	rs146862092		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:4940287G>A	ENST00000345988.2	-	18	2300	c.2211C>T	c.(2209-2211)cgC>cgT	p.R737R	PPL_ENST00000590782.2_Silent_p.R735R	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	737					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.R737R(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						GGTCATGGCCGCGGTGGAAGT	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		18994	0.0		0.0	False		,,,				2504	0.001				p.R737R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2211T	16						.	G		2,4392	4.2+/-10.8	0,2,2195	123.0	98.0	106.0		2211	-4.8	0.0	16	dbSNP_134	106	0,8600		0,0,4300	no	coding-synonymous	PPL	NM_002705.4		0,2,6495	AA,AG,GG		0.0,0.0455,0.0154		737/1757	4940287	2,12992	2197	4300	6497	4880288	SO:0001819	synonymous_variant	5493	exon18			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.2211C>T	16.37:g.4940287G>A		Somatic		Capture	Illumina HiSeq	Phase_I	4880288	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																				0.602	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
PPL	5493	broad.mit.edu	37	16	4943575	4943575	+	Missense_Mutation	SNP	G	G	A	rs563190051		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:4943575G>A	ENST00000345988.2	-	13	1548	c.1459C>T	c.(1459-1461)Cgg>Tgg	p.R487W	PPL_ENST00000590782.2_Missense_Mutation_p.R485W	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	487					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.R487W(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						ACCTCATACCGCTGCTGCAGC	0.667													g|||	1	0.000199681	0.0	0.0014	5008	,	,		18529	0.0		0.0	False		,,,				2504	0.0				p.R487W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1459T	16						.						43.0	41.0	42.0					16																	4943575		2195	4300	6495	4883576	SO:0001583	missense	5493	exon13			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.1459C>T	16.37:g.4943575G>A	ENSP00000340510:p.Arg487Trp	Somatic		Capture	Illumina HiSeq	Phase_I	4883576	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	.	.	.	.	.	.	.	.	.	.	g	18.51	3.638838	0.67130	.	.	ENSG00000118898	ENST00000345988	T	0.70631	-0.5	4.78	4.78	0.61160	.	0.163783	0.41823	D	0.000810	T	0.71256	0.3318	L	0.43152	1.355	0.45777	D	0.998665	D	0.71674	0.998	P	0.53185	0.72	T	0.73987	-0.3809	10	0.66056	D	0.02	.	11.8463	0.52387	0.0:0.0:0.8253:0.1747	.	487	O60437	PEPL_HUMAN	W	487	ENSP00000340510:R487W	ENSP00000340510:R487W	R	-	1	2	PPL	4883576	1.000000	0.71417	1.000000	0.80357	0.377000	0.30045	2.594000	0.46189	2.496000	0.84212	0.457000	0.33378	CGG		0.667	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
ZNF423	23090	broad.mit.edu	37	16	49671193	49671193	+	Missense_Mutation	SNP	C	C	T	rs369619436		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:49671193C>T	ENST00000561648.1	-	4	1923	c.1870G>A	c.(1870-1872)Gcc>Acc	p.A624T	ZNF423_ENST00000535559.1_Missense_Mutation_p.A507T|ZNF423_ENST00000563137.2_Missense_Mutation_p.A564T|ZNF423_ENST00000567169.1_Missense_Mutation_p.A507T|ZNF423_ENST00000562520.1_Missense_Mutation_p.A564T|ZNF423_ENST00000262383.2_Missense_Mutation_p.A624T|ZNF423_ENST00000562871.1_Missense_Mutation_p.A564T	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	624					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A624T(2)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				ATGGAGTTGGCGCTTGCTGAG	0.577																																					p.A624T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1870A	16						.						79.0	71.0	74.0					16																	49671193		2198	4300	6498	48228694	SO:0001583	missense	23090	exon5			AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1870G>A	16.37:g.49671193C>T	ENSP00000455426:p.Ala624Thr	Somatic		Capture	Illumina HiSeq	Phase_I	48228694	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	4.151	0.026347	0.08054	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.09073	3.02;3.05	4.78	1.32	0.21799	.	0.528716	0.22074	N	0.064999	T	0.04048	0.0113	N	0.14661	0.345	0.09310	N	0.999999	B	0.18863	0.031	B	0.11329	0.006	T	0.43228	-0.9404	9	.	.	.	.	6.8571	0.24046	0.0:0.5661:0.2613:0.1726	.	624	Q2M1K9	ZN423_HUMAN	T	624;507	ENSP00000262383:A624T;ENSP00000442321:A507T	.	A	-	1	0	ZNF423	48228694	0.001000	0.12720	0.785000	0.31869	0.860000	0.49131	-0.209000	0.09358	1.021000	0.39600	0.561000	0.74099	GCC		0.577	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
CHD9	80205	broad.mit.edu	37	16	53301952	53301952	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:53301952G>A	ENST00000398510.3	+	21	4718	c.4631G>A	c.(4630-4632)cGa>cAa	p.R1544Q	CHD9_ENST00000566029.1_Missense_Mutation_p.R1544Q|CHD9_ENST00000564845.1_Missense_Mutation_p.R1544Q|CHD9_ENST00000447540.1_Missense_Mutation_p.R1544Q			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1544					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R1544Q(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				GTTCACTACCGAGGAGATGAG	0.408																																					p.R1544Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4631A	16						.						106.0	98.0	100.0					16																	53301952		1863	4112	5975	51859453	SO:0001583	missense	80205	exon22			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.4631G>A	16.37:g.53301952G>A	ENSP00000381522:p.Arg1544Gln	Somatic		Capture	Illumina HiSeq	Phase_I	51859453	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	37		.	.	.	.	.	.	.	.	.	.	G	36	5.850100	0.97023	.	.	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000219084	D;D	0.87491	-2.26;-2.26	5.64	5.64	0.86602	.	0.000000	0.48286	D	0.000194	D	0.92512	0.7622	L	0.60904	1.88	0.80722	D	1	B;P;D;D	0.76494	0.42;0.943;0.999;0.999	B;P;D;D	0.77557	0.062;0.576;0.978;0.99	D	0.92156	0.5732	10	0.54805	T	0.06	-10.3434	19.7167	0.96124	0.0:0.0:1.0:0.0	.	1070;1544;1544;1544	B4DR07;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	Q	1544;1544;1070	ENSP00000396345:R1544Q;ENSP00000381522:R1544Q	ENSP00000219084:R1070Q	R	+	2	0	CHD9	51859453	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.683000	0.74533	2.673000	0.90976	0.650000	0.86243	CGA		0.408	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134	
CHD9	80205	broad.mit.edu	37	16	53338084	53338084	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:53338084C>A	ENST00000398510.3	+	30	6253	c.6166C>A	c.(6166-6168)Cct>Act	p.P2056T	CHD9_ENST00000566029.1_Missense_Mutation_p.P2056T|CHD9_ENST00000564845.1_Missense_Mutation_p.P2056T|CHD9_ENST00000447540.1_Missense_Mutation_p.P2056T			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2056					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.P2056T(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				TAAAGAGGAGCCTCAGTCTTC	0.403																																					p.P2056T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6166A	16						.						42.0	39.0	40.0					16																	53338084		1842	4082	5924	51895585	SO:0001583	missense	80205	exon31			AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.6166C>A	16.37:g.53338084C>A	ENSP00000381522:p.Pro2056Thr	Somatic		Capture	Illumina HiSeq	Phase_I	51895585	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	37		.	.	.	.	.	.	.	.	.	.	C	11.44	1.638156	0.29157	.	.	ENSG00000177200	ENST00000447540;ENST00000398510	D;D	0.86164	-1.99;-2.08	6.16	5.2	0.72013	.	0.207171	0.34178	N	0.004181	T	0.82195	0.4984	L	0.53249	1.67	0.29813	N	0.831515	B;P;B;B	0.37276	0.421;0.589;0.281;0.403	B;B;B;B	0.33392	0.115;0.163;0.06;0.128	T	0.79186	-0.1907	10	0.37606	T	0.19	-12.6628	10.7987	0.46476	0.2239:0.5506:0.2255:0.0	.	2056;2056;2056;2056	B7ZML1;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	T	2056	ENSP00000396345:P2056T;ENSP00000381522:P2056T	ENSP00000381522:P2056T	P	+	1	0	CHD9	51895585	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	1.902000	0.39848	1.582000	0.49881	0.650000	0.86243	CCT		0.403	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134	
RHBDF1	64285	broad.mit.edu	37	16	114721	114721	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:114721G>A	ENST00000262316.6	-	3	366	c.224C>T	c.(223-225)aCg>aTg	p.T75M	RHBDF1_ENST00000454039.2_Missense_Mutation_p.T75M	NM_022450.3	NP_071895.3	Q96CC6	RHDF1_HUMAN	rhomboid 5 homolog 1 (Drosophila)	75					cell migration (GO:0016477)|cell proliferation (GO:0008283)|negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)|proteolysis (GO:0006508)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)		p.T75M(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	18		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				TGTGATGGACGTCTGGCGTTG	0.642																																					p.T75M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C224T	16						.						121.0	123.0	122.0					16																	114721		2203	4300	6503	54721	SO:0001583	missense	64285	exon3			BC014425	CCDS32344.1	16p13.3	2008-02-05	2006-02-22		ENSG00000007384	ENSG00000007384			20561	protein-coding gene	gene with protein product		614403	"""chromosome 16 open reading frame 8"", ""rhomboid family 1 (Drosophila)"""	C16orf8		8318735, 15965977	Standard	NM_022450		Approved	EGFR-RS, FLJ2235, Dist1	uc002cfl.4	Q96CC6	OTTHUMG00000060719	ENST00000262316.6:c.224C>T	16.37:g.114721G>A	ENSP00000262316:p.Thr75Met	Somatic		Capture	Illumina HiSeq	Phase_I	54721	NM_022450	Q04842|Q1W6H2|Q4TT59|Q96S34|Q9H6E1	Missense_Mutation	SNP	ENST00000262316.6	37	CCDS32344.1	.	.	.	.	.	.	.	.	.	.	.	14.98	2.696694	0.48202	.	.	ENSG00000007384	ENST00000262316;ENST00000454039;ENST00000338527;ENST00000450643;ENST00000420545;ENST00000419764	T;T;D	0.87103	0.62;-0.24;-2.21	5.62	1.02	0.19986	.	0.441651	0.26792	N	0.022479	T	0.78091	0.4229	L	0.50333	1.59	0.34281	D	0.682129	B;B;B	0.33103	0.286;0.397;0.009	B;B;B	0.20955	0.022;0.032;0.014	T	0.72693	-0.4216	10	0.28530	T	0.3	-2.7937	8.6806	0.34207	0.3504:0.0:0.6496:0.0	.	75;98;75	F5GWL4;B4E3Q0;Q96CC6	.;.;RHDF1_HUMAN	M	75	ENSP00000262316:T75M;ENSP00000392133:T75M;ENSP00000408915:T75M	ENSP00000262316:T75M	T	-	2	0	RHBDF1	54721	0.998000	0.40836	0.252000	0.24328	0.985000	0.73830	3.425000	0.52771	-0.041000	0.13558	-0.136000	0.14681	ACG		0.642	RHBDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134178.2	NM_022450	
RBL2	5934	broad.mit.edu	37	16	53524068	53524068	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:53524068A>G	ENST00000262133.6	+	22	3413	c.3276A>G	c.(3274-3276)atA>atG	p.I1092M	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Missense_Mutation_p.I471M	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	1092					chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)	p.I1092M(1)		breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						ATAGTATGATACGCACAGGAG	0.338																																					p.I1092M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3276G	16						.						62.0	65.0	64.0					16																	53524068		2198	4300	6498	52081569	SO:0001583	missense	5934	exon22			X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.3276A>G	16.37:g.53524068A>G	ENSP00000262133:p.Ile1092Met	Somatic		Capture	Illumina HiSeq	Phase_I	52081569	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	37	CCDS10748.1	.	.	.	.	.	.	.	.	.	.	A	18.11	3.550185	0.65311	.	.	ENSG00000103479	ENST00000262133;ENST00000379935;ENST00000544545	T;T	0.56103	0.48;0.48	5.63	0.318	0.15867	.	0.000000	0.85682	D	0.000000	T	0.54515	0.1863	M	0.64997	1.995	0.22240	N	0.999262	P;P;D	0.57899	0.952;0.905;0.981	P;P;P	0.52758	0.526;0.566;0.708	T	0.49370	-0.8947	10	0.37606	T	0.19	-28.9185	8.9891	0.36012	0.2412:0.5191:0.0:0.2397	.	471;802;1092	B7Z913;E9PG04;Q08999	.;.;RBL2_HUMAN	M	1092;802;471	ENSP00000262133:I1092M;ENSP00000444685:I471M	ENSP00000262133:I1092M	I	+	3	3	RBL2	52081569	0.983000	0.35010	1.000000	0.80357	0.995000	0.86356	0.242000	0.18087	0.120000	0.18254	0.533000	0.62120	ATA		0.338	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611	
OGFOD1	55239	broad.mit.edu	37	16	56501908	56501908	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:56501908T>A	ENST00000566157.1	+	8	1001	c.878T>A	c.(877-879)aTt>aAt	p.I293N	OGFOD1_ENST00000568397.1_Missense_Mutation_p.I250N	NM_018233.3	NP_060703.3	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 1	293					cell proliferation (GO:0008283)|peptidyl-proline hydroxylation (GO:0019511)|protein hydroxylation (GO:0018126)|regulation of translational termination (GO:0006449)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|peptidyl-proline 3-dioxygenase activity (GO:0031544)|peptidyl-proline dioxygenase activity (GO:0031543)	p.I293N(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8					Vitamin C(DB00126)	AGTTCTGAAATTCTCCTGAAG	0.368																																					p.I293N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T878A	16						.						69.0	68.0	68.0					16																	56501908		2198	4300	6498	55059409	SO:0001583	missense	55239	exon8			BC032919	CCDS10761.2	16q12.2	2010-11-23			ENSG00000087263	ENSG00000087263			25585	protein-coding gene	gene with protein product	"""TPA1, termination and polyadenylation 1, homolog (S. cerevisiae)"""	615857				10997877	Standard	NM_018233		Approved	KIAA1612, FLJ10826, TPA1	uc002ejb.3	Q8N543	OTTHUMG00000133237	ENST00000566157.1:c.878T>A	16.37:g.56501908T>A	ENSP00000457258:p.Ile293Asn	Somatic		Capture	Illumina HiSeq	Phase_I	55059409	NM_018233	H3BUQ2|Q9H7U5|Q9H9J9|Q9HA87|Q9HCG0|Q9NVB6	Missense_Mutation	SNP	ENST00000566157.1	37	CCDS10761.2	.	.	.	.	.	.	.	.	.	.	T	22.8	4.337658	0.81911	.	.	ENSG00000087263	ENST00000336111;ENST00000540727	.	.	.	5.98	4.88	0.63580	Oxoglutarate/iron-dependent oxygenase, C-terminal degradation domain (1);	0.136179	0.64402	D	0.000002	T	0.79690	0.4489	M	0.84948	2.725	0.80722	D	1	D	0.65815	0.995	D	0.69142	0.962	T	0.82366	-0.0493	9	0.87932	D	0	-19.0409	12.7048	0.57054	0.1234:0.0:0.0:0.8765	.	293	Q8N543	OGFD1_HUMAN	N	293;137	.	ENSP00000337196:I293N	I	+	2	0	OGFOD1	55059409	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.530000	0.67141	1.072000	0.40860	0.524000	0.50904	ATT		0.368	OGFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256976.3	NM_018233	
NUP93	9688	broad.mit.edu	37	16	56792470	56792470	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:56792470G>A	ENST00000308159.5	+	3	321	c.200G>A	c.(199-201)cGg>cAg	p.R67Q	NUP93_ENST00000569842.1_Missense_Mutation_p.R67Q	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	67					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)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)	p.R67Q(1)		breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						CTCGGGTCTCGGGGACTTGAC	0.463																																					p.R67Q	Colon(33;610 796 1305 1705 38917)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G200A	16						.						100.0	89.0	92.0					16																	56792470		2198	4300	6498	55349971	SO:0001583	missense	9688	exon3			D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.200G>A	16.37:g.56792470G>A	ENSP00000310668:p.Arg67Gln	Somatic		Capture	Illumina HiSeq	Phase_I	55349971	NM_014669	B3KPQ8|Q14705	Missense_Mutation	SNP	ENST00000308159.5	37	CCDS10769.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.865417	0.51588	.	.	ENSG00000102900	ENST00000308159	T	0.42513	0.97	5.17	5.17	0.71159	.	0.048135	0.85682	D	0.000000	T	0.32164	0.0820	L	0.41710	1.295	0.80722	D	1	B	0.25390	0.125	B	0.13407	0.009	T	0.09314	-1.0680	10	0.15066	T	0.55	-17.1652	14.0153	0.64521	0.075:0.0:0.925:0.0	.	67	Q8N1F7	NUP93_HUMAN	Q	67	ENSP00000310668:R67Q	ENSP00000310668:R67Q	R	+	2	0	NUP93	55349971	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	5.302000	0.65733	2.401000	0.81631	0.555000	0.69702	CGG		0.463	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669	
CPNE2	221184	broad.mit.edu	37	16	57171187	57171187	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:57171187C>T	ENST00000535318.2	+	15	1656	c.1295C>T	c.(1294-1296)aCg>aTg	p.T432M	CPNE2_ENST00000565951.1_Intron|CPNE2_ENST00000565874.1_Missense_Mutation_p.T432M|CPNE2_ENST00000290776.8_Missense_Mutation_p.T432M|CPNE2_ENST00000537605.1_Missense_Mutation_p.T330M			Q96FN4	CPNE2_HUMAN	copine II	432	VWFA.					extracellular vesicular exosome (GO:0070062)		p.T432M(1)		central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(5)	21		all_neural(199;0.224)				CAACAGCGGACGGCCACGGTG	0.597																																					p.T432M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1295T	16						.						61.0	41.0	47.0					16																	57171187		2198	4300	6498	55728688	SO:0001583	missense	221184	exon14				CCDS10774.1	16q13	2008-02-05			ENSG00000140848	ENSG00000140848			2315	protein-coding gene	gene with protein product		604206				9430674	Standard	NM_152727		Approved	CPN2	uc002eks.2	Q96FN4	OTTHUMG00000133471	ENST00000535318.2:c.1295C>T	16.37:g.57171187C>T	ENSP00000439018:p.Thr432Met	Somatic		Capture	Illumina HiSeq	Phase_I	55728688	NM_152727	Q68D19|Q719H8|Q86XP9	Missense_Mutation	SNP	ENST00000535318.2	37	CCDS10774.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.031510	0.54790	.	.	ENSG00000140848	ENST00000290776;ENST00000537605;ENST00000535318	T;T;T	0.22743	1.94;1.94;1.94	5.88	4.88	0.63580	von Willebrand factor, type A (1);Copine (1);	0.332477	0.31450	N	0.007628	T	0.33118	0.0852	L	0.60067	1.865	0.38590	D	0.950393	B;P	0.47034	0.216;0.889	B;P	0.50109	0.06;0.631	T	0.06807	-1.0806	10	0.48119	T	0.1	-32.2113	16.5258	0.84330	0.0:0.8695:0.1305:0.0	.	432;432	A8K8A4;Q96FN4	.;CPNE2_HUMAN	M	432;330;432	ENSP00000290776:T432M;ENSP00000445468:T330M;ENSP00000439018:T432M	ENSP00000290776:T432M	T	+	2	0	CPNE2	55728688	0.407000	0.25352	0.997000	0.53966	0.836000	0.47400	1.054000	0.30455	2.782000	0.95742	0.655000	0.94253	ACG		0.597	CPNE2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432986.2	NM_152727	
FAM192A	80011	broad.mit.edu	37	16	57188277	57188277	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:57188277G>A	ENST00000309137.8	-	7	948	c.690C>T	c.(688-690)agC>agT	p.S230S	FAM192A_ENST00000567439.1_Silent_p.S230S|FAM192A_ENST00000389447.5_Silent_p.S230S|FAM192A_ENST00000564108.1_Silent_p.S230S|FAM192A_ENST00000569266.1_Silent_p.S230S|FAM192A_ENST00000566077.1_Silent_p.S153S	NM_024946.2	NP_079222.1	Q9GZU8	F192A_HUMAN	family with sequence similarity 192, member A	230						nucleus (GO:0005634)		p.S230S(1)		endometrium(2)|large_intestine(3)|lung(4)|prostate(2)	11						TGGTGCCTTCGCTGTCTGAGC	0.602																																					p.S230S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C690T	16						.						61.0	71.0	68.0					16																	57188277		2044	4203	6247	55745778	SO:0001819	synonymous_variant	80011	exon7				CCDS42168.1	16q13	2009-08-19	2009-08-19	2009-08-19		ENSG00000172775			29856	protein-coding gene	gene with protein product	"""NEFA interacting nuclear protein NIP30"""		"""chromosome 16 open reading frame 94"""	C16orf94		12477932	Standard	NM_024946		Approved	NIP30	uc021tiy.1	Q9GZU8		ENST00000309137.8:c.690C>T	16.37:g.57188277G>A		Somatic		Capture	Illumina HiSeq	Phase_I	55745778	NM_024946		Silent	SNP	ENST00000309137.8	37	CCDS42168.1																																																																																				0.602	FAM192A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433022.2	NM_024946	
ARL2BP	23568	broad.mit.edu	37	16	57282555	57282555	+	Splice_Site	SNP	C	C	T	rs201489348		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:57282555C>T	ENST00000219204.3	+	3	477	c.207C>T	c.(205-207)taC>taT	p.Y69Y	RP11-407G23.4_ENST00000562409.1_RNA|RP11-407G23.3_ENST00000564376.1_RNA|ARL2BP_ENST00000562023.1_Intron	NM_012106.3	NP_036238.1	Q9Y2Y0	AR2BP_HUMAN	ADP-ribosylation factor-like 2 binding protein	69					maintenance of protein location in nucleus (GO:0051457)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of catalytic activity (GO:0050790)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	centrosome (GO:0005813)|cilium (GO:0005929)|midbody (GO:0030496)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	small GTPase regulator activity (GO:0005083)|transcription coactivator activity (GO:0003713)	p.Y69*(1)|p.Y69Y(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|urinary_tract(1)	12						TTAATGAATACGTAAGTAGAT	0.318																																					p.Y69Y												.	.	2	Substitution - Nonsense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	c.C207T	16						.	C		0,4396		0,0,2198	67.0	67.0	67.0		207	1.1	1.0	16		67	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous-near-splice	ARL2BP	NM_012106.3		0,1,6497	TT,TC,CC		0.0116,0.0,0.0077		69/164	57282555	1,12995	2198	4300	6498	55840056	SO:0001630	splice_region_variant	23568	exon3			AF126062	CCDS10776.1	16q13	2014-01-30			ENSG00000102931	ENSG00000102931			17146	protein-coding gene	gene with protein product	"""binder of Arl2"""	615407	"""retinitis pigmentosa 66 (autosomal recessive)"""	RP66		10488091, 18981177, 23849777	Standard	NM_012106		Approved	BART1, BART	uc002elf.1	Q9Y2Y0	OTTHUMG00000133459	ENST00000219204.3:c.207+1C>T	16.37:g.57282555C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55840056	NM_012106	B3KQJ5|Q504R0	Silent	SNP	ENST00000219204.3	37	CCDS10776.1																																																																																				0.318	ARL2BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257334.2	NM_012106	Silent
CIAPIN1	57019	broad.mit.edu	37	16	57474721	57474721	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:57474721G>A	ENST00000569979.1	-	1	166	c.120C>T	c.(118-120)ggC>ggT	p.G40G	CIAPIN1_ENST00000569370.1_Silent_p.G40G|CIAPIN1_ENST00000567518.1_Silent_p.G40G|CIAPIN1_ENST00000569246.1_5'UTR|CIAPIN1_ENST00000394391.4_Silent_p.G40G|CIAPIN1_ENST00000568940.1_Silent_p.G40G|CIAPIN1_ENST00000565961.1_Silent_p.G40G					cytokine induced apoptosis inhibitor 1									p.G40G(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						CAGACACGCGGCCCTCATTGC	0.527																																					p.G40G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C120T	16						.						93.0	91.0	92.0					16																	57474721		1978	4164	6142	56032222	SO:0001819	synonymous_variant	57019	exon2			AF248964	CCDS10781.2	16q21	2012-09-20			ENSG00000005194	ENSG00000005194			28050	protein-coding gene	gene with protein product		608943				10493829, 11230166	Standard	XM_005256061		Approved	Anamorsin	uc002ell.1	Q6FI81	OTTHUMG00000133457	ENST00000569979.1:c.120C>T	16.37:g.57474721G>A		Somatic		Capture	Illumina HiSeq	Phase_I	56032222	NM_020313		Silent	SNP	ENST00000569979.1	37																																																																																					0.527	CIAPIN1-010	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432580.1	NM_020313	
GPR56	9289	broad.mit.edu	37	16	57689373	57689373	+	Silent	SNP	G	G	A	rs552642182		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:57689373G>A	ENST00000388812.4	+	6	1271	c.831G>A	c.(829-831)acG>acA	p.T277T	GPR56_ENST00000538815.1_Silent_p.T277T|GPR56_ENST00000379696.3_Silent_p.T277T|GPR56_ENST00000544297.1_Silent_p.T102T|GPR56_ENST00000456916.1_Silent_p.T277T|GPR56_ENST00000568908.1_Silent_p.T277T|GPR56_ENST00000540164.2_Silent_p.T277T|GPR56_ENST00000379694.4_Silent_p.T107T|GPR56_ENST00000388813.5_Silent_p.T277T|GPR56_ENST00000562558.1_Silent_p.T277T|GPR56_ENST00000562631.1_Silent_p.T277T|GPR56_ENST00000568909.1_Silent_p.T277T|GPR56_ENST00000567835.1_Silent_p.T277T			Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56	277					angiogenesis (GO:0001525)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cerebral cortex radial glia guided migration (GO:0021801)|G-protein coupled receptor signaling pathway (GO:0007186)|layer formation in cerebral cortex (GO:0021819)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell adhesion (GO:0045785)|positive regulation of Rho protein signal transduction (GO:0035025)|protein kinase C signaling (GO:0070528)|Rho protein signal transduction (GO:0007266)|vascular endothelial growth factor production (GO:0010573)	extracellular vesicular exosome (GO:0070062)|glial limiting end-foot (GO:0097451)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|G-protein coupled receptor activity (GO:0004930)	p.T277T(1)		kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	15						TCCAGAGGACGAAAGGCCGGA	0.612																																					p.T277T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G831A	16						.						53.0	57.0	56.0					16																	57689373		2198	4300	6498	56246874	SO:0001819	synonymous_variant	9289	exon7			AJ011001	CCDS32460.1, CCDS32461.1, CCDS73893.1	16q13	2014-08-08				ENSG00000205336		"""-"", ""GPCR / Class B : Orphans"""	4512	protein-coding gene	gene with protein product		604110				10049584, 10100861	Standard	XM_005256237		Approved	TM7LN4, TM7XN1	uc002emb.2	Q9Y653		ENST00000388812.4:c.831G>A	16.37:g.57689373G>A		Somatic		Capture	Illumina HiSeq	Phase_I	56246874	NM_001145774	A6NIT7|A6NJV9|B0M0K4|B4DR54|O95966|Q6ZMP1|Q8NGB3|Q96HB4	Silent	SNP	ENST00000388812.4	37	CCDS32460.1																																																																																				0.612	GPR56-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433436.3		
GPR56	9289	broad.mit.edu	37	16	57691292	57691292	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:57691292C>T	ENST00000388812.4	+	10	1615	c.1175C>T	c.(1174-1176)tCg>tTg	p.S392L	GPR56_ENST00000538815.1_Missense_Mutation_p.S392L|GPR56_ENST00000379696.3_Missense_Mutation_p.S392L|GPR56_ENST00000544297.1_Missense_Mutation_p.S217L|GPR56_ENST00000456916.1_Missense_Mutation_p.S392L|GPR56_ENST00000568908.1_Missense_Mutation_p.S392L|GPR56_ENST00000540164.2_Missense_Mutation_p.S392L|GPR56_ENST00000379694.4_Missense_Mutation_p.S222L|GPR56_ENST00000388813.5_Missense_Mutation_p.S392L|GPR56_ENST00000562558.1_Missense_Mutation_p.S392L|GPR56_ENST00000562631.1_Missense_Mutation_p.S392L|GPR56_ENST00000568909.1_Missense_Mutation_p.S392L|GPR56_ENST00000567835.1_Missense_Mutation_p.S392L			Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56	392	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cerebral cortex radial glia guided migration (GO:0021801)|G-protein coupled receptor signaling pathway (GO:0007186)|layer formation in cerebral cortex (GO:0021819)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell adhesion (GO:0045785)|positive regulation of Rho protein signal transduction (GO:0035025)|protein kinase C signaling (GO:0070528)|Rho protein signal transduction (GO:0007266)|vascular endothelial growth factor production (GO:0010573)	extracellular vesicular exosome (GO:0070062)|glial limiting end-foot (GO:0097451)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|G-protein coupled receptor activity (GO:0004930)	p.S392L(1)		kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	15						CAGGTCTCCTCGGTGGAGGTG	0.652																																					p.S392L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1175T	16						.						114.0	103.0	106.0					16																	57691292		2198	4300	6498	56248793	SO:0001583	missense	9289	exon11			AJ011001	CCDS32460.1, CCDS32461.1, CCDS73893.1	16q13	2014-08-08				ENSG00000205336		"""-"", ""GPCR / Class B : Orphans"""	4512	protein-coding gene	gene with protein product		604110				10049584, 10100861	Standard	XM_005256237		Approved	TM7LN4, TM7XN1	uc002emb.2	Q9Y653		ENST00000388812.4:c.1175C>T	16.37:g.57691292C>T	ENSP00000373464:p.Ser392Leu	Somatic		Capture	Illumina HiSeq	Phase_I	56248793	NM_001145774	A6NIT7|A6NJV9|B0M0K4|B4DR54|O95966|Q6ZMP1|Q8NGB3|Q96HB4	Missense_Mutation	SNP	ENST00000388812.4	37	CCDS32460.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.381239	0.61845	.	.	ENSG00000205336	ENST00000388813;ENST00000388812;ENST00000538815;ENST00000456916;ENST00000540164;ENST00000544297;ENST00000379694;ENST00000379696	T;T;T;T;T;T;T;T	0.51071	0.75;0.72;0.75;0.72;0.75;1.6;0.99;0.72	5.11	5.11	0.69529	GPS domain (2);	0.217978	0.32719	N	0.005738	T	0.53061	0.1773	M	0.79475	2.455	0.32972	D	0.522538	P;P;B;P;D	0.53745	0.951;0.952;0.334;0.952;0.962	B;B;B;B;B	0.43680	0.371;0.349;0.063;0.349;0.427	T	0.70565	-0.4837	10	0.46703	T	0.11	.	15.2842	0.73814	0.0:1.0:0.0:0.0	.	217;397;392;392;222	F5H144;B4DR54;Q9Y653-2;Q9Y653;E7ENB2	.;.;.;GPR56_HUMAN;.	L	392;392;392;392;392;217;222;392	ENSP00000373465:S392L;ENSP00000373464:S392L;ENSP00000444415:S392L;ENSP00000398034:S392L;ENSP00000444911:S392L;ENSP00000438006:S217L;ENSP00000369016:S222L;ENSP00000369018:S392L	ENSP00000369016:S222L	S	+	2	0	GPR56	56248793	0.844000	0.29557	0.412000	0.26496	0.395000	0.30598	3.344000	0.52174	2.375000	0.81037	0.491000	0.48974	TCG		0.652	GPR56-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433436.3		
CNGB1	1258	broad.mit.edu	37	16	57931389	57931389	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:57931389T>C	ENST00000251102.8	-	31	3214	c.3154A>G	c.(3154-3156)Acc>Gcc	p.T1052A	CNGB1_ENST00000564448.1_Missense_Mutation_p.T1046A	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	1052					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)	p.T1052A(1)		breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						AAGAGGTTGGTAAACCCGTGC	0.552																																					p.T1052A	Colon(156;1293 1853 16336 28962 38659)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3154G	16						.						47.0	48.0	48.0					16																	57931389		1906	4114	6020	56488890	SO:0001583	missense	1258	exon31			AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.3154A>G	16.37:g.57931389T>C	ENSP00000251102:p.Thr1052Ala	Somatic		Capture	Illumina HiSeq	Phase_I	56488890	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	37	CCDS42169.1	.	.	.	.	.	.	.	.	.	.	T	10.31	1.315289	0.23908	.	.	ENSG00000070729	ENST00000251102	D	0.96992	-4.2	5.23	2.9	0.33743	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.070802	0.64402	D	0.000020	D	0.88672	0.6500	N	0.17674	0.51	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.11329	0.003;0.006	T	0.76597	-0.2901	10	0.08381	T	0.77	.	4.4042	0.11400	0.1473:0.1725:0.0:0.6802	.	424;1052	Q14028-2;Q14028	.;CNGB1_HUMAN	A	1052	ENSP00000251102:T1052A	ENSP00000251102:T1052A	T	-	1	0	CNGB1	56488890	0.997000	0.39634	0.982000	0.44146	0.874000	0.50279	3.256000	0.51492	0.272000	0.22027	-0.604000	0.04097	ACC		0.552	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
CNGB1	1258	broad.mit.edu	37	16	57949164	57949164	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:57949164G>T	ENST00000251102.8	-	23	2353	c.2293C>A	c.(2293-2295)Cgc>Agc	p.R765S	CNGB1_ENST00000564448.1_Missense_Mutation_p.R759S	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	765					cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)	p.R765S(1)		breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						TTTAAACAGCGGGGCAGGCGG	0.597																																					p.R765S	Colon(156;1293 1853 16336 28962 38659)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2293A	16						.						38.0	43.0	42.0					16																	57949164		1934	4122	6056	56506665	SO:0001583	missense	1258	exon23			AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.2293C>A	16.37:g.57949164G>T	ENSP00000251102:p.Arg765Ser	Somatic		Capture	Illumina HiSeq	Phase_I	56506665	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	37	CCDS42169.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.711213	0.89112	.	.	ENSG00000070729	ENST00000251102	D	0.98777	-5.13	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.99399	0.9788	H	0.94385	3.53	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.993;0.995	D	0.98650	1.0679	10	0.87932	D	0	.	18.0549	0.89361	0.0:0.0:1.0:0.0	.	137;765	Q14028-2;Q14028	.;CNGB1_HUMAN	S	765	ENSP00000251102:R765S	ENSP00000251102:R765S	R	-	1	0	CNGB1	56506665	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	7.521000	0.81832	2.497000	0.84241	0.655000	0.94253	CGC		0.597	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
CNOT1	23019	broad.mit.edu	37	16	58559250	58559250	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:58559250G>T	ENST00000317147.5	-	46	6949	c.6617C>A	c.(6616-6618)cCt>cAt	p.P2206H	CNOT1_ENST00000569240.1_Missense_Mutation_p.P2201H|CNOT1_ENST00000245138.4_Missense_Mutation_p.P1057H	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	2206					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|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 stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)	p.P2206H(1)		breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		GCGATTCCCAGGTTCATTGGA	0.473																																					p.P2206H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6617A	16						.						157.0	122.0	134.0					16																	58559250		2198	4300	6498	57116751	SO:0001583	missense	23019	exon46			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.6617C>A	16.37:g.58559250G>T	ENSP00000320949:p.Pro2206His	Somatic		Capture	Illumina HiSeq	Phase_I	57116751	NM_016284	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.780373	0.90195	.	.	ENSG00000125107	ENST00000317147;ENST00000422872;ENST00000546037;ENST00000245138	T	0.48522	0.81	5.98	5.98	0.97165	CCR4-Not complex component, Not1, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70684	0.3252	M	0.76838	2.35	0.80722	D	1	D;D;D	0.76494	0.999;0.994;0.998	P;D;D	0.68353	0.885;0.957;0.951	T	0.70941	-0.4735	10	0.56958	D	0.05	-18.4244	19.4402	0.94817	0.0:0.0:1.0:0.0	.	1057;2206;2201	B5MDN3;A5YKK6;A5YKK6-2	.;CNOT1_HUMAN;.	H	2206;900;211;1057	ENSP00000320949:P2206H	ENSP00000245138:P1057H	P	-	2	0	CNOT1	57116751	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	9.572000	0.98179	2.838000	0.97847	0.591000	0.81541	CCT		0.473	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
CNOT1	23019	broad.mit.edu	37	16	58577759	58577759	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:58577759C>T	ENST00000317147.5	-	31	4518	c.4186G>A	c.(4186-4188)Gca>Aca	p.A1396T	CNOT1_ENST00000569240.1_Missense_Mutation_p.A1391T|CNOT1_ENST00000441024.2_Missense_Mutation_p.A1396T|CNOT1_ENST00000245138.4_Missense_Mutation_p.A247T	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1396	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|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 stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)	p.A1396T(1)		breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		CGTTCAATTGCCTGACGCACA	0.483																																					p.A1396T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4186A	16						.						62.0	53.0	56.0					16																	58577759		2198	4300	6498	57135260	SO:0001583	missense	23019	exon31			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.4186G>A	16.37:g.58577759C>T	ENSP00000320949:p.Ala1396Thr	Somatic		Capture	Illumina HiSeq	Phase_I	57135260	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.827100	0.90955	.	.	ENSG00000125107	ENST00000317147;ENST00000245138;ENST00000394200;ENST00000441024	T;T	0.68903	-0.36;-0.24	5.3	5.3	0.74995	CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819 (1);	0.051164	0.85682	D	0.000000	D	0.85978	0.5823	M	0.93462	3.42	0.80722	D	1	D;P;P;P	0.65815	0.995;0.51;0.933;0.917	D;B;P;P	0.63957	0.92;0.23;0.737;0.619	D	0.89364	0.3670	10	0.62326	D	0.03	-19.7967	18.9405	0.92604	0.0:1.0:0.0:0.0	.	247;1396;1396;1391	B5MDN3;A5YKK6-4;A5YKK6;A5YKK6-2	.;.;CNOT1_HUMAN;.	T	1396;247;1391;1396	ENSP00000320949:A1396T;ENSP00000413113:A1396T	ENSP00000245138:A247T	A	-	1	0	CNOT1	57135260	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.826000	0.62715	2.461000	0.83175	0.585000	0.79938	GCA		0.483	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
CDH8	1006	broad.mit.edu	37	16	61851414	61851414	+	Missense_Mutation	SNP	G	G	A	rs548909736		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:61851414G>A	ENST00000577390.1	-	7	2200	c.1246C>T	c.(1246-1248)Cgt>Tgt	p.R416C	CDH8_ENST00000299345.6_Missense_Mutation_p.R416C|CDH8_ENST00000584337.1_Missense_Mutation_p.R416C|CDH8_ENST00000577730.1_Missense_Mutation_p.R416C	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	416	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)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)	p.R416C(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		TCAGGGTCACGAGCAGTCACT	0.423													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19653	0.0		0.0	False		,,,				2504	0.0				p.R416C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1246T	16						.						82.0	76.0	78.0					16																	61851414		2203	4300	6503	60408915	SO:0001583	missense	1006	exon7			L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"""Cadherins / Major cadherins"""	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1246C>T	16.37:g.61851414G>A	ENSP00000462701:p.Arg416Cys	Somatic		Capture	Illumina HiSeq	Phase_I	60408915	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	G	19.63	3.864252	0.71949	.	.	ENSG00000150394	ENST00000299345	T	0.01787	4.64	6.17	6.17	0.99709	Cadherin (4);Cadherin-like (1);	0.043054	0.85682	D	0.000000	T	0.13157	0.0319	M	0.87269	2.87	0.80722	D	1	D;D	0.65815	0.995;0.987	P;P	0.62382	0.901;0.846	T	0.00027	-1.2306	10	0.56958	D	0.05	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	232;416	Q3LID3;P55286	.;CADH8_HUMAN	C	416	ENSP00000299345:R416C	ENSP00000299345:R416C	R	-	1	0	CDH8	60408915	0.994000	0.37717	0.999000	0.59377	0.973000	0.67179	3.320000	0.51991	2.941000	0.99782	0.655000	0.94253	CGT		0.423	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796	
CES2	8824	broad.mit.edu	37	16	66974398	66974398	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:66974398C>T	ENST00000317091.4	+	5	1792	c.808C>T	c.(808-810)Cgc>Tgc	p.R270C	CES2_ENST00000417689.1_Missense_Mutation_p.R270C|RP11-361L15.4_ENST00000566869.1_RNA	NM_003869.5	NP_003860.2	O00748	EST2_HUMAN	carboxylesterase 2	206					catabolic process (GO:0009056)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)	p.R270C(1)		breast(1)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|urinary_tract(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0663)|Epithelial(162;0.166)	Dabigatran etexilate(DB06695)|Irinotecan(DB00762)|Mycophenolate mofetil(DB00688)|Prasugrel(DB06209)	GGCTGCACTACGCTGGGTCCA	0.592																																					p.R270C	Ovarian(70;1230 1691 37888 38351)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C808T	16						.						133.0	109.0	117.0					16																	66974398		2200	4300	6500	65531899	SO:0001583	missense	8824	exon5			BC032095	CCDS10825.1, CCDS45507.1	16q22.1	2010-10-12	2010-10-12		ENSG00000172831	ENSG00000172831		"""Carboxylesterases"""	1864	protein-coding gene	gene with protein product		605278	"""carboxylesterase 2 (intestine, liver)"""			9169443, 9144407, 20931200	Standard	NM_198061		Approved	CE-2, iCE, CES2A1	uc002eqr.3	O00748	OTTHUMG00000137517	ENST00000317091.4:c.808C>T	16.37:g.66974398C>T	ENSP00000317842:p.Arg270Cys	Somatic		Capture	Illumina HiSeq	Phase_I	65531899	NM_198061	A8K367|Q16859|Q5MAB8|Q7Z366|Q8IUP4|Q8TCP8	Missense_Mutation	SNP	ENST00000317091.4	37	CCDS10825.1	.	.	.	.	.	.	.	.	.	.	C	14.73	2.623802	0.46840	.	.	ENSG00000172831	ENST00000417689;ENST00000317091	T;T	0.71222	-0.55;-0.55	5.29	4.29	0.51040	Carboxylesterase, type B (1);	0.564254	0.17110	N	0.186650	T	0.75503	0.3858	M	0.90814	3.15	0.36000	D	0.837298	B;B	0.33413	0.411;0.411	B;B	0.33690	0.168;0.117	T	0.83070	-0.0143	10	0.62326	D	0.03	.	12.3611	0.55203	0.2878:0.7122:0.0:0.0	.	206;270	O00748;A8K367	EST2_HUMAN;.	C	270	ENSP00000394452:R270C;ENSP00000317842:R270C	ENSP00000317842:R270C	R	+	1	0	CES2	65531899	0.001000	0.12720	0.825000	0.32803	0.567000	0.35839	1.083000	0.30815	2.756000	0.94617	0.650000	0.86243	CGC		0.592	CES2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268838.2	NM_003869	
ELMO3	79767	broad.mit.edu	37	16	67235908	67235908	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:67235908G>A	ENST00000360833.1	+	11	1244	c.1187G>A	c.(1186-1188)cGc>cAc	p.R396H	MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000393997.2_Missense_Mutation_p.R413H|ELMO3_ENST00000477898.1_Missense_Mutation_p.R247H			Q96BJ8	ELMO3_HUMAN	engulfment and cell motility 3	360	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				apoptotic process (GO:0006915)|phagocytosis (GO:0006909)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R413H(1)		cervix(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	18		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00067)|Epithelial(162;0.00442)|all cancers(182;0.0417)		GACCTGGAGCGCGTGCCCCCC	0.662																																					p.R413H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1238A	16						.						46.0	56.0	53.0					16																	67235908		1978	4150	6128	65793409	SO:0001583	missense	79767	exon12				CCDS10833.2	16q22.1	2010-03-18	2006-01-20		ENSG00000102890	ENSG00000102890		"""Engulfment and cell motility proteins"""	17289	protein-coding gene	gene with protein product		606422	"""engulfment and cell motility 3 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_024712		Approved	FLJ13824, CED12, ELMO-3, CED-12	uc002esa.3	Q96BJ8	OTTHUMG00000133570	ENST00000360833.1:c.1187G>A	16.37:g.67235908G>A	ENSP00000354077:p.Arg396His	Somatic		Capture	Illumina HiSeq	Phase_I	65793409	NM_024712	B4DV86|Q9H8A5	Missense_Mutation	SNP	ENST00000360833.1	37		.	.	.	.	.	.	.	.	.	.	G	13.85	2.361609	0.41801	.	.	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.30981	1.51;1.51	5.39	4.44	0.53790	Engulfment/cell motility, ELMO (2);	0.105080	0.64402	D	0.000002	T	0.26231	0.0640	L	0.51422	1.61	0.54753	D	0.999985	P;P;P	0.39443	0.561;0.674;0.674	B;B;B	0.36766	0.139;0.232;0.085	T	0.05566	-1.0877	10	0.59425	D	0.04	-10.7437	8.0891	0.30790	0.081:0.0:0.7624:0.1565	.	360;396;413	Q96BJ8;F8W9E7;Q96BJ8-3	ELMO3_HUMAN;.;.	H	396;413	ENSP00000354077:R396H;ENSP00000377566:R413H	ENSP00000354077:R396H	R	+	2	0	ELMO3	65793409	0.668000	0.27493	0.888000	0.34837	0.694000	0.40290	1.525000	0.35953	1.290000	0.44636	0.563000	0.77884	CGC		0.662	ELMO3-001	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000257667.2	NM_024712	
SLC9A5	6553	broad.mit.edu	37	16	67286675	67286675	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:67286675G>A	ENST00000299798.11	+	2	483	c.418G>A	c.(418-420)Gtg>Atg	p.V140M	SLC9A5_ENST00000561472.2_Intron	NM_004594.2	NP_004585.1	Q14940	SL9A5_HUMAN	solute carrier family 9, subfamily A (NHE5, cation proton antiporter 5), member 5	140					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)	p.V140M(1)		breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)		CACCTATGCCGTGGTAGGCAC	0.552																																					p.V140M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G418A	16						.						76.0	74.0	75.0					16																	67286675		2069	4223	6292	65844176	SO:0001583	missense	6553	exon2				CCDS42178.1	16q22.1	2013-05-22	2012-03-22		ENSG00000135740	ENSG00000135740		"""Solute carriers"""	11078	protein-coding gene	gene with protein product		600477	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 5"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 5"""			7759094, 9933642	Standard	NM_004594		Approved	NHE5	uc002esm.3	Q14940	OTTHUMG00000172935	ENST00000299798.11:c.418G>A	16.37:g.67286675G>A	ENSP00000299798:p.Val140Met	Somatic		Capture	Illumina HiSeq	Phase_I	65844176	NM_004594	A5PKY7|Q9Y626	De_novo_Start_OutOfFrame	SNP	ENST00000299798.11	37	CCDS42178.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.888563	0.91814	.	.	ENSG00000135740	ENST00000299798	T	0.17370	2.28	5.16	5.16	0.70880	Cation/H+ exchanger (1);	0.000000	0.85682	D	0.000000	T	0.45236	0.1332	M	0.78916	2.43	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.47522	-0.9111	10	0.87932	D	0	.	17.2221	0.86960	0.0:0.0:1.0:0.0	.	140	Q14940	SL9A5_HUMAN	M	140	ENSP00000299798:V140M	ENSP00000299798:V140M	V	+	1	0	SLC9A5	65844176	1.000000	0.71417	0.932000	0.37286	0.971000	0.66376	9.858000	0.99539	2.405000	0.81733	0.655000	0.94253	GTG		0.552	SLC9A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421386.1		
WDR24	84219	broad.mit.edu	37	16	739515	739515	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:739515G>A	ENST00000248142.6	-	3	311	c.312C>T	c.(310-312)gtC>gtT	p.V104V	LA16c-313D11.12_ENST00000566927.1_RNA|WDR24_ENST00000293883.4_Silent_p.V42V			Q96S15	WDR24_HUMAN	WD repeat domain 24	104								p.V104V(1)|p.V42V(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(3)	19		Hepatocellular(780;0.0218)				GGCCTGCCACGACCACCTGGG	0.617																																					p.V42V												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C126T	16						.						58.0	54.0	55.0					16																	739515		2200	4300	6500	679516	SO:0001819	synonymous_variant	84219	exon1			AL136863	CCDS10420.1	16p13.3	2013-01-09			ENSG00000127580	ENSG00000127580		"""WD repeat domain containing"""	20852	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 21"""	C16orf21		11230166	Standard	NM_032259		Approved	DKFZp434F054, JFP7	uc002ciz.1	Q96S15	OTTHUMG00000090421	ENST00000248142.6:c.312C>T	16.37:g.739515G>A		Somatic		Capture	Illumina HiSeq	Phase_I	679516	NM_032259	A2IDB8|D3DU59|Q96GC7|Q9H0B7	Silent	SNP	ENST00000248142.6	37																																																																																					0.617	WDR24-201	KNOWN	basic	protein_coding	protein_coding		NM_032259	
SLC7A6OS	84138	broad.mit.edu	37	16	68344511	68344511	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:68344511T>C	ENST00000263997.6	-	2	216	c.198A>G	c.(196-198)gaA>gaG	p.E66E	PRMT7_ENST00000449359.3_5'Flank|PRMT7_ENST00000339507.5_5'Flank|PRMT7_ENST00000441236.1_5'Flank|snoU13_ENST00000458872.1_RNA|PRMT7_ENST00000348497.4_5'Flank	NM_032178.2	NP_115554.2	Q96CW6	S7A6O_HUMAN	solute carrier family 7, member 6 opposite strand	66					hematopoietic progenitor cell differentiation (GO:0002244)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E66E(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.106)		GCTGGACTGGTTCCTCCTAGG	0.682																																					p.E66E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A198G	16						.						11.0	12.0	12.0					16																	68344511		2181	4282	6463	66902012	SO:0001819	synonymous_variant	84138	exon2				CCDS10865.1	16q22.1	2010-03-11			ENSG00000103061	ENSG00000103061			25807	protein-coding gene	gene with protein product							Standard	NM_032178		Approved	FLJ13291	uc002evw.2	Q96CW6	OTTHUMG00000137558	ENST00000263997.6:c.198A>G	16.37:g.68344511T>C		Somatic		Capture	Illumina HiSeq	Phase_I	66902012	NM_032178	Q8TCZ3|Q9H8R8	Silent	SNP	ENST00000263997.6	37	CCDS10865.1																																																																																				0.682	SLC7A6OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268894.3	NM_032178	
FUK	197258	broad.mit.edu	37	16	70503207	70503207	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:70503207C>T	ENST00000288078.6	+	10	1168	c.936C>T	c.(934-936)cgC>cgT	p.R312R	FUK_ENST00000378912.2_Silent_p.R344R|FUK_ENST00000571514.1_Intron	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	312						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|fucokinase activity (GO:0050201)	p.R312R(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(11)|ovary(2)|prostate(2)	23		Ovarian(137;0.0694)				GGGAGCTTCGCGATCAGCCCC	0.637																																					p.R312R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C936T	16						.						57.0	63.0	61.0					16																	70503207		1956	4143	6099	69060708	SO:0001819	synonymous_variant	197258	exon10				CCDS10891.2	16q22.1	2008-02-05			ENSG00000157353	ENSG00000157353	2.7.1.52		29500	protein-coding gene	gene with protein product	"""L-fucose kinase"""	608675				12056818	Standard	XM_006721161		Approved	FLJ39408	uc002eyy.3	Q8N0W3	OTTHUMG00000074085	ENST00000288078.6:c.936C>T	16.37:g.70503207C>T		Somatic		Capture	Illumina HiSeq	Phase_I	69060708	NM_145059	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Silent	SNP	ENST00000288078.6	37	CCDS10891.2																																																																																				0.637	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059	
HYDIN	54768	broad.mit.edu	37	16	70913324	70913324	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:70913324G>A	ENST00000393567.2	-	62	10583	c.10433C>T	c.(10432-10434)aCg>aTg	p.T3478M		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3478					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.T3429M(1)|p.T3477M(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CCGCACAACCGTCACTCGAGG	0.547																																					p.T3477M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C10430T	16						.						21.0	23.0	22.0					16																	70913324		1838	4084	5922	69470825	SO:0001583	missense	54768	exon62			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.10433C>T	16.37:g.70913324G>A	ENSP00000377197:p.Thr3478Met	Somatic		Capture	Illumina HiSeq	Phase_I	69470825	NM_032821	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	14.15	2.450914	0.43531	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01068	5.38	5.19	0.992	0.19819	.	0.000000	0.33792	U	0.004556	T	0.02767	0.0083	M	0.71581	2.175	0.47994	D	0.999567	D	0.60575	0.988	P	0.52424	0.698	T	0.54801	-0.8239	10	0.59425	D	0.04	.	7.517	0.27606	0.1654:0.2242:0.6104:0.0	.	3477	F8WD23	.	M	3478;3477	ENSP00000377197:T3478M	ENSP00000313052:T3477M	T	-	2	0	HYDIN	69470825	0.123000	0.22298	0.751000	0.31187	0.173000	0.22820	0.291000	0.18994	1.081000	0.41110	0.511000	0.50034	ACG		0.547	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
HYDIN	54768	broad.mit.edu	37	16	70975620	70975620	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:70975620G>A	ENST00000393567.2	-	43	6922	c.6772C>T	c.(6772-6774)Cgg>Tgg	p.R2258W		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2258					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.R2209W(1)|p.R2257W(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				ATATGCTCCCGGCTGCCAATG	0.552																																					p.R2257W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C6769T	16						.						63.0	67.0	65.0					16																	70975620		1922	4119	6041	69533121	SO:0001583	missense	54768	exon43			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.6772C>T	16.37:g.70975620G>A	ENSP00000377197:p.Arg2258Trp	Somatic		Capture	Illumina HiSeq	Phase_I	69533121	NM_032821	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.069108	0.76301	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01228	5.14	5.32	4.35	0.52113	.	0.000000	0.30593	U	0.009287	T	0.08670	0.0215	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.01617	-1.1311	10	0.87932	D	0	.	15.2526	0.73559	0.0:0.0:0.8581:0.1419	.	2257	F8WD23	.	W	2258;2257	ENSP00000377197:R2258W	ENSP00000313052:R2257W	R	-	1	2	HYDIN	69533121	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	3.880000	0.56145	1.345000	0.45676	0.508000	0.49915	CGG		0.552	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
HYDIN	54768	broad.mit.edu	37	16	70989434	70989434	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:70989434C>T	ENST00000393567.2	-	40	6310	c.6160G>A	c.(6160-6162)Gtt>Att	p.V2054I		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2054					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.V2005I(1)|p.V2053I(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GCCACGCTAACGGCATTGGCT	0.537																																					p.V2053I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G6157A	16						.						22.0	20.0	21.0					16																	70989434		1828	4047	5875	69546935	SO:0001583	missense	54768	exon40			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.6160G>A	16.37:g.70989434C>T	ENSP00000377197:p.Val2054Ile	Somatic		Capture	Illumina HiSeq	Phase_I	69546935	NM_032821	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	0.125	-1.120873	0.01785	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.21734	1.99	4.66	-2.43	0.06522	.	0.636054	0.11461	N	0.561683	T	0.13329	0.0323	L	0.38531	1.155	0.09310	N	1	B	0.15141	0.012	B	0.10450	0.005	T	0.41413	-0.9510	10	0.10377	T	0.69	.	10.5625	0.45154	0.0:0.553:0.0:0.447	.	2053	F8WD23	.	I	2054;2053	ENSP00000377197:V2054I	ENSP00000310485:V345I	V	-	1	0	HYDIN	69546935	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.022000	0.12480	-0.363000	0.08101	-0.409000	0.06214	GTT		0.537	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
HYDIN	54768	broad.mit.edu	37	16	70993592	70993592	+	Missense_Mutation	SNP	G	G	A	rs201606263		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:70993592G>A	ENST00000393567.2	-	39	6250	c.6100C>T	c.(6100-6102)Cgg>Tgg	p.R2034W		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2034					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.R1985W(1)|p.R2033W(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				ATGCCTTTCCGGTTCTTGGCC	0.527													G|||	1	0.000199681	0.0	0.0	5008	,	,		12827	0.0		0.001	False		,,,				2504	0.0				p.R2033W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C6097T	16						.						12.0	40.0	32.0					16																	70993592		1577	4020	5597	69551093	SO:0001583	missense	54768	exon39			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.6100C>T	16.37:g.70993592G>A	ENSP00000377197:p.Arg2034Trp	Somatic		Capture	Illumina HiSeq	Phase_I	69551093	NM_032821	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.225963	0.79576	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.44083	0.93	4.6	3.63	0.41609	.	0.000000	0.31221	U	0.008023	T	0.59636	0.2208	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.63703	0.917	T	0.63972	-0.6516	10	0.87932	D	0	.	12.7716	0.57423	0.0:0.0:0.834:0.166	.	2033	F8WD23	.	W	2034;2033	ENSP00000377197:R2034W	ENSP00000310485:R325W	R	-	1	2	HYDIN	69551093	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	5.632000	0.67819	0.912000	0.36772	0.505000	0.49811	CGG		0.527	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
ZNF19	7567	broad.mit.edu	37	16	71510031	71510031	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:71510031T>C	ENST00000288177.5	-	6	674	c.419A>G	c.(418-420)gAc>gGc	p.D140G	ZNF19_ENST00000567225.1_Intron|ZNF19_ENST00000564230.1_Missense_Mutation_p.D140G|ZNF19_ENST00000565100.2_Missense_Mutation_p.D70G|ZNF19_ENST00000565637.1_Missense_Mutation_p.D98G|AC010547.9_ENST00000561908.1_Intron	NM_006961.3	NP_008892.2	P17023	ZNF19_HUMAN	zinc finger protein 19	140					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.D140G(1)		NS(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|prostate(1)|stomach(1)	22		Ovarian(137;0.00965)		BRCA - Breast invasive adenocarcinoma(221;0.0161)|Kidney(780;0.0598)		TGTGGGGATGTCCTGGTGCTT	0.448																																					p.D140G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A419G	16						.						143.0	131.0	135.0					16																	71510031		2198	4300	6498	70067532	SO:0001583	missense	7567	exon6			X52343	CCDS10901.1	16q22	2013-01-08	2006-05-10		ENSG00000157429	ENSG00000157429		"""Zinc fingers, C2H2-type"", ""-"""	12981	protein-coding gene	gene with protein product		194525	"""zinc finger protein 19 (KOX 12)"""			1505991, 1946370	Standard	NM_006961		Approved	KOX12, MGC51021	uc002fam.1	P17023	OTTHUMG00000137593	ENST00000288177.5:c.419A>G	16.37:g.71510031T>C	ENSP00000288177:p.Asp140Gly	Somatic		Capture	Illumina HiSeq	Phase_I	70067532	NM_006961	A8K895|Q86Y66|Q8NDE2|Q96M79|Q96NE5	Missense_Mutation	SNP	ENST00000288177.5	37	CCDS10901.1	.	.	.	.	.	.	.	.	.	.	T	4.949	0.176372	0.09443	.	.	ENSG00000157429	ENST00000288177	T	0.05319	3.46	3.24	-0.39	0.12450	.	1.095610	0.07150	N	0.848913	T	0.03095	0.0091	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46789	-0.9166	10	0.27785	T	0.31	.	3.7403	0.08527	0.0:0.3575:0.2122:0.4303	.	140	P17023	ZNF19_HUMAN	G	140	ENSP00000288177:D140G	ENSP00000288177:D140G	D	-	2	0	ZNF19	70067532	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.137000	0.10389	-0.105000	0.12132	-0.250000	0.11733	GAC		0.448	ZNF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268993.2	NM_006961	
MARVELD3	91862	broad.mit.edu	37	16	71674434	71674434	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:71674434G>A	ENST00000299952.4	+	3	780	c.737G>A	c.(736-738)gGc>gAc	p.G246D	MARVELD3_ENST00000561682.1_Intron|MARVELD3_ENST00000565261.1_3'UTR|PHLPP2_ENST00000540628.1_3'UTR	NM_001017967.3|NM_001271329.1	NP_001017967.2|NP_001258258.1	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	249	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)		p.G246D(1)		NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				CCGTTCGAGGGCACTGAGCTA	0.587																																					p.G246D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G737A	16						.						104.0	87.0	93.0					16																	71674434		2198	4300	6498	70231935	SO:0001583	missense	91862	exon3			BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"""MARVEL (membrane-associating) domain containing 3"""	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000299952.4:c.737G>A	16.37:g.71674434G>A	ENSP00000299952:p.Gly246Asp	Somatic		Capture	Illumina HiSeq	Phase_I	70231935	NM_001017967	A8K820|H3BQM5|Q96MJ4	Missense_Mutation	SNP	ENST00000299952.4	37	CCDS32478.1	.	.	.	.	.	.	.	.	.	.	G	32	5.113343	0.94339	.	.	ENSG00000140832	ENST00000299952	D	0.86562	-2.14	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.93766	0.8007	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94114	0.7373	9	0.87932	D	0	-8.1668	17.5152	0.87771	0.0:0.0:1.0:0.0	.	246	Q96A59-2	.	D	246	ENSP00000299952:G246D	ENSP00000299952:G246D	G	+	2	0	MARVELD3	70231935	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.708000	0.91372	2.735000	0.93741	0.650000	0.86243	GGC		0.587	MARVELD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268990.1	NM_052858	
DHODH	1723	broad.mit.edu	37	16	72046117	72046117	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:72046117C>A	ENST00000219240.4	+	2	211	c.190C>A	c.(190-192)Ctg>Atg	p.L64M	DHODH_ENST00000572887.1_Missense_Mutation_p.L64M	NM_001361.4	NP_001352.2	Q02127	PYRD_HUMAN	dihydroorotate dehydrogenase (quinone)	64					'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207)|'de novo' UMP biosynthetic process (GO:0044205)|female pregnancy (GO:0007565)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of apoptotic process (GO:0043065)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of mitochondrial fission (GO:0090140)|response to caffeine (GO:0031000)|response to drug (GO:0042493)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|neuronal cell body (GO:0043025)	dihydroorotate dehydrogenase activity (GO:0004152)|dihydroorotate oxidase activity (GO:0004158)|drug binding (GO:0008144)|FMN binding (GO:0010181)|ubiquinone binding (GO:0048039)	p.L64M(1)		breast(1)|endometrium(2)|large_intestine(4)|ovary(1)|skin(1)|stomach(1)	10		Ovarian(137;0.125)			Atovaquone(DB01117)|Leflunomide(DB01097)|Teriflunomide(DB08880)	CTTCACCTCCCTGGGGCTCCT	0.572																																					p.L64M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C190A	16						.						57.0	64.0	61.0					16																	72046117		2155	4274	6429	70603618	SO:0001583	missense	1723	exon2				CCDS42192.1	16q22.2	2012-10-02	2011-09-05		ENSG00000102967	ENSG00000102967	1.3.5.2		2867	protein-coding gene	gene with protein product		126064	"""dihydroorotate dehydrogenase"""			8211381	Standard	NM_001361		Approved		uc002fbp.3	Q02127	OTTHUMG00000178093	ENST00000219240.4:c.190C>A	16.37:g.72046117C>A	ENSP00000219240:p.Leu64Met	Somatic		Capture	Illumina HiSeq	Phase_I	70603618	NM_001361	A8K8C8|Q6P176	Missense_Mutation	SNP	ENST00000219240.4	37	CCDS42192.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.270511	0.23221	.	.	ENSG00000102967	ENST00000219240	D	0.94537	-3.45	4.73	2.61	0.31194	Aldolase-type TIM barrel (1);	0.146450	0.46442	D	0.000288	D	0.91123	0.7205	M	0.68317	2.08	0.46564	D	0.999102	B	0.14012	0.009	B	0.14578	0.011	D	0.86269	0.1660	10	0.35671	T	0.21	-10.8652	6.0823	0.19948	0.1637:0.6594:0.0:0.1769	.	64	Q02127	PYRD_HUMAN	M	64	ENSP00000219240:L64M	ENSP00000219240:L64M	L	+	1	2	DHODH	70603618	0.771000	0.28555	1.000000	0.80357	0.846000	0.48090	0.246000	0.18160	1.198000	0.43158	0.462000	0.41574	CTG		0.572	DHODH-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001361	
HP	3240	broad.mit.edu	37	16	72094681	72094681	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:72094681G>A	ENST00000355906.5	+	7	1171	c.1113G>A	c.(1111-1113)gcG>gcA	p.A371A	HP_ENST00000398131.2_Silent_p.A312A|HP_ENST00000357763.4_Silent_p.A407A|HPR_ENST00000540303.2_5'Flank|HPR_ENST00000561690.1_5'Flank|HP_ENST00000565574.1_Silent_p.A312A|HP_ENST00000570083.1_Silent_p.A312A|HP_ENST00000562526.1_3'UTR|HPR_ENST00000356967.5_Intron	NM_005143.3	NP_005134.1	P00738	HPT_HUMAN	haptoglobin	371	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acute-phase response (GO:0006953)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|immune system process (GO:0002376)|negative regulation of hydrogen peroxide catabolic process (GO:2000296)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of cell death (GO:0010942)|response to hydrogen peroxide (GO:0042542)	blood microparticle (GO:0072562)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|haptoglobin-hemoglobin complex (GO:0031838)	antioxidant activity (GO:0016209)|hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)	p.A371A(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|urinary_tract(1)	7		Renal(780;9.67e-05)|Ovarian(137;0.00327)|Hepatocellular(780;0.114)		BRCA - Breast invasive adenocarcinoma(221;0.00015)|Kidney(780;0.000529)		CCTGGTATGCGACTGGGATCT	0.527																																					p.A312A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G936A	16						.						223.0	216.0	219.0					16																	72094681		2127	4236	6363	70652182	SO:0001819	synonymous_variant	3240	exon5				CCDS45524.1, CCDS45525.1	16q22.2	2012-10-02			ENSG00000257017	ENSG00000257017			5141	protein-coding gene	gene with protein product		140100				11109501, 9352226	Standard	NM_005143		Approved		uc002fbr.4	P00738		ENST00000355906.5:c.1113G>A	16.37:g.72094681G>A		Somatic		Capture	Illumina HiSeq	Phase_I	70652182	NM_001126102	B0AZL5|P00737|Q0VAC4|Q0VAC5|Q2PP15|Q3B7J0|Q6LBY9|Q9UC67	Silent	SNP	ENST00000355906.5	37	CCDS45524.1																																																																																				0.527	HP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421680.1	NM_005143	
DHX38	9785	broad.mit.edu	37	16	72143343	72143343	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:72143343C>T	ENST00000268482.3	+	25	3920	c.3411C>T	c.(3409-3411)gaC>gaT	p.D1137D	DHX38_ENST00000536867.1_Silent_p.D449D	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	1137					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|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)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.D1137D(1)		endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				CCGCTGTGGACGGGGAGTGGC	0.612																																					p.D1137D	Melanoma(97;711 1442 7855 13832 28836)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3411T	16						.						68.0	52.0	58.0					16																	72143343		2198	4300	6498	70700844	SO:0001819	synonymous_variant	9785	exon25			AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"""DEAH-boxes"""	17211	protein-coding gene	gene with protein product		605584	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"""	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.3411C>T	16.37:g.72143343C>T		Somatic		Capture	Illumina HiSeq	Phase_I	70700844	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																				0.612	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
ZFHX3	463	broad.mit.edu	37	16	72828024	72828024	+	Missense_Mutation	SNP	C	C	T	rs200701402		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:72828024C>T	ENST00000268489.5	-	9	9229	c.8557G>A	c.(8557-8559)Gca>Aca	p.A2853T	ZFHX3_ENST00000397992.5_Missense_Mutation_p.A1939T|RP5-991G20.4_ENST00000569195.1_RNA	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2853					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.A2853T(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)				TCGTTATCTGCGTTGCCCTCG	0.473																																					p.A2853T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8557A	16						.	C	THR/ALA,THR/ALA	0,4396		0,0,2198	272.0	224.0	241.0		5815,8557	6.0	1.0	16		241	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	ZFHX3	NM_001164766.1,NM_006885.3	58,58	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	1939/2790,2853/3704	72828024	1,12995	2198	4300	6498	71385525	SO:0001583	missense	463	exon9			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.8557G>A	16.37:g.72828024C>T	ENSP00000268489:p.Ala2853Thr	Somatic		Capture	Illumina HiSeq	Phase_I	71385525	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.671655	0.29693	0.0	1.16E-4	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.73897	-0.79;-0.77	5.96	5.96	0.96718	.	0.000000	0.49916	D	0.000136	T	0.54598	0.1868	N	0.14661	0.345	0.42677	D	0.993535	P	0.48640	0.913	B	0.34038	0.174	T	0.58929	-0.7549	10	0.09590	T	0.72	.	20.4043	0.99006	0.0:1.0:0.0:0.0	.	2853	Q15911	ZFHX3_HUMAN	T	2853;1939	ENSP00000268489:A2853T;ENSP00000438926:A1939T	ENSP00000268489:A2853T	A	-	1	0	ZFHX3	71385525	0.993000	0.37304	0.991000	0.47740	0.882000	0.50991	3.289000	0.51747	2.823000	0.97156	0.650000	0.86243	GCA		0.473	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
NARFL	64428	broad.mit.edu	37	16	783355	783355	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:783355G>A	ENST00000251588.2	-	7	782	c.766C>T	c.(766-768)Ccc>Tcc	p.P256S	NARFL_ENST00000568545.1_Missense_Mutation_p.P154S|NARFL_ENST00000540986.1_Missense_Mutation_p.P154S|NARFL_ENST00000562862.1_5'UTR|HAGHL_ENST00000569604.1_Intron|NARFL_ENST00000301694.5_3'UTR	NM_022493.1	NP_071938.1	Q9H6Q4	NARFL_HUMAN	nuclear prelamin A recognition factor-like	256					hematopoietic progenitor cell differentiation (GO:0002244)|iron-sulfur cluster assembly (GO:0016226)|oxygen homeostasis (GO:0032364)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	CIA complex (GO:0097361)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)	p.P256S(1)		autonomic_ganglia(1)|large_intestine(1)|lung(7)	9		Hepatocellular(780;0.0218)				AAAAAGTCGGGTCTGGAGGCT	0.557																																					p.P256S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C766T	16						.						126.0	110.0	116.0					16																	783355		2200	4298	6498	723356	SO:0001583	missense	64428	exon7			AY129231	CCDS10425.1	16p13.3	2009-12-17			ENSG00000103245	ENSG00000103245			14179	protein-coding gene	gene with protein product	"""iron-only hydrogenase-like protein 1"""	611118				16956324	Standard	NM_022493		Approved	FLJ21988, PRN, HPRN, IOP1	uc002cjr.3	Q9H6Q4	OTTHUMG00000122093	ENST00000251588.2:c.766C>T	16.37:g.783355G>A	ENSP00000251588:p.Pro256Ser	Somatic		Capture	Illumina HiSeq	Phase_I	723356	NM_022493	A1L385|B3KTJ3|Q53GC6|Q96S10|Q9H6J8	Missense_Mutation	SNP	ENST00000251588.2	37	CCDS10425.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.255572	0.39896	.	.	ENSG00000103245	ENST00000251588;ENST00000540986	T;T	0.46063	0.88;0.88	4.84	2.84	0.33178	Iron hydrogenase, large subunit, C-terminal (1);Iron hydrogenase (1);	0.268407	0.43260	N	0.000599	T	0.28732	0.0712	L	0.33189	0.99	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.07233	-1.0783	10	0.22109	T	0.4	-23.0948	10.4321	0.44413	0.1622:0.0:0.8378:0.0	.	256	Q9H6Q4	NARFL_HUMAN	S	256;154	ENSP00000251588:P256S;ENSP00000444008:P154S	ENSP00000251588:P256S	P	-	1	0	NARFL	723356	1.000000	0.71417	0.488000	0.27440	0.958000	0.62258	2.558000	0.45879	1.288000	0.44600	0.555000	0.69702	CCC		0.557	NARFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242855.1	NM_022493	
RBFOX1	54715	broad.mit.edu	37	16	7383010	7383010	+	Intron	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:7383010C>T	ENST00000550418.1	+	5	1015				RBFOX1_ENST00000552089.1_Intron|RBFOX1_ENST00000311745.5_Missense_Mutation_p.A3V|RBFOX1_ENST00000422070.4_Intron|RBFOX1_ENST00000535565.2_Intron|RBFOX1_ENST00000547372.1_Intron|RBFOX1_ENST00000547338.1_Intron|RBFOX1_ENST00000436368.2_Missense_Mutation_p.A3V|RBFOX1_ENST00000553186.1_Intron|RBFOX1_ENST00000355637.4_Missense_Mutation_p.A3V|RBFOX1_ENST00000340209.4_5'UTR	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1						mRNA processing (GO:0006397)|neuromuscular process controlling balance (GO:0050885)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	nucleotide binding (GO:0000166)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)	p.A3V(2)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|lung(17)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)	55						AGCATGCTGGCGTCTCAAGGA	0.473																																					p.A3V	Ovarian(157;934 2567 15163 39509)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C8T	16						.						231.0	186.0	201.0					16																	7383010		2197	4300	6497	7323011	SO:0001627	intron_variant	54715	exon1			AF107203	CCDS10531.1, CCDS10532.1, CCDS45405.1, CCDS55983.1, CCDS55984.1	16p13.3	2013-02-12			ENSG00000078328	ENSG00000078328		"""RNA binding motif (RRM) containing"""	18222	protein-coding gene	gene with protein product	"""ataxin 2-binding protein 1"", ""hexaribonucleotide binding protein 1"""	605104				10814712, 16260614	Standard	NM_018723		Approved	A2BP1, FOX-1, HRNBP1	uc002cyy.2	Q9NWB1	OTTHUMG00000129551	ENST00000550418.1:c.28-185139C>T	16.37:g.7383010C>T		Somatic		Capture	Illumina HiSeq	Phase_I	7323011	NM_145893	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Missense_Mutation	SNP	ENST00000550418.1	37	CCDS55983.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.252886	0.59212	.	.	ENSG00000078328	ENST00000436368;ENST00000311745;ENST00000355637;ENST00000352951	T;T;T	0.32272	1.46;1.66;1.6	5.75	5.75	0.90469	.	0.927283	0.09030	N	0.858899	T	0.23014	0.0556	N	0.08118	0	0.80722	D	1	B;B;B;B	0.27765	0.188;0.188;0.188;0.188	B;B;B;B	0.20384	0.024;0.016;0.024;0.029	T	0.23119	-1.0197	10	0.52906	T	0.07	2.7554	19.9564	0.97221	0.0:1.0:0.0:0.0	.	3;3;3;3	F8WAC5;Q9NWB1-2;Q9NWB1-4;Q9NWB1-5	.;.;.;.	V	3	ENSP00000402745:A3V;ENSP00000309117:A3V;ENSP00000347855:A3V	ENSP00000309117:A3V	A	+	2	0	RBFOX1	7323011	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	5.987000	0.70571	2.708000	0.92522	0.650000	0.86243	GCG		0.473	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891	
ZFHX3	463	broad.mit.edu	37	16	72923739	72923739	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:72923739C>T	ENST00000268489.5	-	4	4011	c.3339G>A	c.(3337-3339)caG>caA	p.Q1113Q	ZFHX3_ENST00000397992.5_Silent_p.Q199Q	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1113					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.Q1113Q(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)				TCTCGCTTCGCTGGTGCTTCA	0.597																																					p.Q1113Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3339A	16						.						79.0	60.0	67.0					16																	72923739		2198	4300	6498	71481240	SO:0001819	synonymous_variant	463	exon4			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.3339G>A	16.37:g.72923739C>T		Somatic		Capture	Illumina HiSeq	Phase_I	71481240	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																				0.597	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
BCAR1	9564	broad.mit.edu	37	16	75268928	75268928	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:75268928G>A	ENST00000162330.5	-	5	1995	c.1869C>T	c.(1867-1869)ccC>ccT	p.P623P	BCAR1_ENST00000542031.2_Silent_p.P621P|BCAR1_ENST00000535626.2_Silent_p.P475P|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000420641.3_Silent_p.P641P|BCAR1_ENST00000418647.3_Silent_p.P669P|BCAR1_ENST00000538440.2_Silent_p.P623P|BCAR1_ENST00000546196.1_Silent_p.P594P|BCAR1_ENST00000393420.6_Silent_p.P641P|BCAR1_ENST00000393422.2_Silent_p.P641P	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	623					actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.P623P(1)|p.P641P(1)		breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		CAGTGGGGTTGGGGTGCAGGG	0.652																																					p.P641P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1923T	16						.						57.0	56.0	56.0					16																	75268928		2198	4299	6497	73826429	SO:0001819	synonymous_variant	9564	exon5			AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"""Cas scaffolding proteins"""	971	protein-coding gene	gene with protein product	"""Crk-associated substrate"", ""Cas scaffolding protein family member 1"""	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.1869C>T	16.37:g.75268928G>A		Somatic		Capture	Illumina HiSeq	Phase_I	73826429	NM_001170716	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Silent	SNP	ENST00000162330.5	37	CCDS10915.1																																																																																				0.652	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567	
TMEM231	79583	broad.mit.edu	37	16	75576514	75576514	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:75576514T>C	ENST00000258173.6	-	5	726	c.650A>G	c.(649-651)tAc>tGc	p.Y217C	RP11-77K12.7_ENST00000460606.1_Missense_Mutation_p.T49A|TMEM231_ENST00000565067.1_Missense_Mutation_p.Y169C|RP11-77K12.8_ENST00000564489.1_RNA|TMEM231_ENST00000569294.1_5'UTR|TMEM231_ENST00000568377.1_Missense_Mutation_p.Y246C	NM_001077418.1	NP_001070886.1	Q9H6L2	TM231_HUMAN	transmembrane protein 231	217					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)		p.Y246C(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						CCTCTCCTGGTAGGCAGCAAC	0.557																																					p.Y246C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A737G	16						.						109.0	103.0	105.0					16																	75576514		1988	4176	6164	74134015	SO:0001583	missense	79583	exon4				CCDS45530.1	16q23.1	2014-01-28			ENSG00000205084	ENSG00000205084			37234	protein-coding gene	gene with protein product		614949				23012439	Standard	NM_001077416		Approved	FLJ22167, ALYE870, PRO1886, JBTS20, MKS11	uc002fek.4	Q9H6L2		ENST00000258173.6:c.650A>G	16.37:g.75576514T>C	ENSP00000258173:p.Tyr217Cys	Somatic		Capture	Illumina HiSeq	Phase_I	74134015	NM_001077416	A0JLU1|A6NDZ6|B3KU85|G5E9E3|Q6P450|Q6UWW5	Missense_Mutation	SNP	ENST00000258173.6	37	CCDS45530.1	.	.	.	.	.	.	.	.	.	.	T	18.74	3.687973	0.68271	.	.	ENSG00000205084	ENST00000258173;ENST00000398114	T;T	0.66099	-0.19;-0.19	4.33	4.33	0.51752	.	0.218264	0.40222	U	0.001147	T	0.77644	0.4161	M	0.77820	2.39	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.998	T	0.80625	-0.1299	10	0.87932	D	0	-3.9032	11.758	0.51886	0.0:0.0:0.0:1.0	.	246;217;246	B3KU85;Q9H6L2;G5E9E3	.;TM231_HUMAN;.	C	217;246	ENSP00000258173:Y217C;ENSP00000381184:Y246C	ENSP00000258173:Y217C	Y	-	2	0	TMEM231	74134015	1.000000	0.71417	0.997000	0.53966	0.854000	0.48673	6.623000	0.74238	1.743000	0.51761	0.383000	0.25322	TAC		0.557	TMEM231-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435481.2	NM_001077416	
KARS	3735	broad.mit.edu	37	16	75663411	75663411	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:75663411G>A	ENST00000302445.3	-	12	1492	c.1453C>T	c.(1453-1455)Cgc>Tgc	p.R485C	KARS_ENST00000319410.5_Missense_Mutation_p.R513C|KARS_ENST00000568378.1_Intron	NM_005548.2	NP_005539.1	Q15046	SYK_HUMAN	lysyl-tRNA synthetase	485					cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|lysyl-tRNA aminoacylation (GO:0006430)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)|viral process (GO:0016032)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|microtubule cytoskeleton (GO:0015630)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid binding (GO:0016597)|ATP binding (GO:0005524)|lysine-tRNA ligase activity (GO:0004824)|metal ion binding (GO:0046872)|tRNA binding (GO:0000049)	p.R485C(1)		kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	18					L-Lysine(DB00123)	AGCTCAAAGCGCTCAGTCAGA	0.463																																					p.R513C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1537T	16						.						165.0	168.0	167.0					16																	75663411		2198	4300	6498	74220912	SO:0001583	missense	3735	exon13			AF285758	CCDS10923.1, CCDS45532.1	16q23.1	2014-09-17			ENSG00000065427	ENSG00000065427	6.1.1.6	"""Aminoacyl tRNA synthetases / Class II"""	6215	protein-coding gene	gene with protein product	"""lysine tRNA ligase"""	601421	"""deafness, autosomal recessive 89"""	DFNB89		8812440, 9278442, 23768514	Standard	NM_005548		Approved	KARS2, KARS1	uc002fer.3	Q15046	OTTHUMG00000137609	ENST00000302445.3:c.1453C>T	16.37:g.75663411G>A	ENSP00000303043:p.Arg485Cys	Somatic		Capture	Illumina HiSeq	Phase_I	74220912	NM_001130089	A8MSK1|D3DUK4|O14946|Q96J25|Q9HB23	Missense_Mutation	SNP	ENST00000302445.3	37	CCDS10923.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.807210	0.90623	.	.	ENSG00000065427	ENST00000319410;ENST00000302445	D;D	0.86030	-2.06;-2.06	5.81	5.81	0.92471	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.000000	0.85682	D	0.000000	D	0.96303	0.8794	H	0.99927	4.965	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.97431	1.0015	10	0.87932	D	0	0.1363	13.6144	0.62099	0.0:0.0:0.8449:0.1551	.	513;485	Q15046-2;Q15046	.;SYK_HUMAN	C	513;485	ENSP00000325448:R513C;ENSP00000303043:R485C	ENSP00000303043:R485C	R	-	1	0	KARS	74220912	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.838000	0.86804	2.752000	0.94435	0.557000	0.71058	CGC		0.463	KARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269023.1	NM_005548	
CNTNAP4	85445	broad.mit.edu	37	16	76573703	76573703	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:76573703T>C	ENST00000476707.1	+	19	3456	c.3317T>C	c.(3316-3318)cTt>cCt	p.L1106P	CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.L1030P|CNTNAP4_ENST00000377504.4_Missense_Mutation_p.L1054P|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.L1102P			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	1103	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)		p.L1030P(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						GATGGACAACTTCACCACATA	0.358																																					p.F1103L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3307C	16						.						97.0	100.0	99.0					16																	76573703		2082	4268	6350	75131204	SO:0001583	missense	85445	exon20			AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.3317T>C	16.37:g.76573703T>C	ENSP00000417628:p.Leu1106Pro	Somatic		Capture	Illumina HiSeq	Phase_I	75131204	NM_033401	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	37		.	.	.	.	.	.	.	.	.	.	T	13.35	2.211002	0.39102	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13	5.03	3.92	0.45320	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.205122	0.24282	N	0.039884	D	0.85230	0.5649	.	.	.	0.80722	D	1	P;P;D	0.89917	0.941;0.871;1.0	P;P;D	0.85130	0.808;0.596;0.997	T	0.82902	-0.0227	9	0.30854	T	0.27	.	11.5707	0.50832	0.1337:0.0:0.0:0.8662	.	1030;1106;1103	E9PFZ6;E9PDN6;Q9C0A0	.;.;CNTP4_HUMAN	P	1102;1054;1030;1106	ENSP00000306893:L1102P;ENSP00000439733:L1054P;ENSP00000418741:L1030P;ENSP00000417628:L1106P	ENSP00000306893:L1102P	L	+	2	0	CNTNAP4	75131204	1.000000	0.71417	0.993000	0.49108	0.652000	0.38707	4.598000	0.61069	1.023000	0.39654	-0.336000	0.08194	CTT		0.358	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401	
PKD1L2	114780	broad.mit.edu	37	16	81232565	81232565	+	RNA	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:81232565C>T	ENST00000525539.1	-	0	1244				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)	p.Q415Q(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CCATCAGTTTCTGGGTTTCTC	0.552																																					p.Q415Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1245A	16						.						136.0	138.0	137.0					16																	81232565		1963	4147	6110	79790066			114780	exon7			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81232565C>T		Somatic		Capture	Illumina HiSeq	Phase_I	79790066	NM_052892	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000525539.1	37																																																																																					0.552	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
GAN	8139	broad.mit.edu	37	16	81388170	81388170	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:81388170A>G	ENST00000568107.2	+	3	605	c.443A>G	c.(442-444)cAc>cGc	p.H148R		NM_022041.3	NP_071324.1	Q9H2C0	GAN_HUMAN	gigaxonin	148	BACK.				cell death (GO:0008219)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.H148R(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)	25		Colorectal(91;0.153)				TGCCTCCATCACGTTCATTAC	0.463																																					p.H148R	GBM(106;1239 1507 7582 9741 33976)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A443G	16						.						216.0	191.0	200.0					16																	81388170		2202	4300	6502	79945671	SO:0001583	missense	8139	exon3			AF291673	CCDS10935.1	16q24.1	2014-09-17	2008-08-01		ENSG00000261609	ENSG00000261609		"""Kelch-like"", ""BTB/POZ domain containing"""	4137	protein-coding gene	gene with protein product	"""kelch-like family member 16"""	605379	"""giant axonal neuropathy (gigaxonin)"""			9450783, 11062483	Standard	NM_022041		Approved	GAN1, KLHL16	uc002fgo.3	Q9H2C0	OTTHUMG00000137627	ENST00000568107.2:c.443A>G	16.37:g.81388170A>G	ENSP00000476795:p.His148Arg	Somatic		Capture	Illumina HiSeq	Phase_I	79945671	NM_022041		Missense_Mutation	SNP	ENST00000568107.2	37	CCDS10935.1	.	.	.	.	.	.	.	.	.	.	A	17.20	3.328567	0.60743	.	.	ENSG00000127688	ENST00000248272	T	0.67171	-0.25	5.96	5.96	0.96718	BTB/Kelch-associated (2);	0.000000	0.85682	D	0.000000	T	0.57257	0.2041	N	0.16602	0.42	0.80722	D	1	P	0.39216	0.664	B	0.41723	0.365	T	0.63139	-0.6704	10	0.62326	D	0.03	.	16.4484	0.83959	1.0:0.0:0.0:0.0	.	148	Q9H2C0	GAN_HUMAN	R	148	ENSP00000248272:H148R	ENSP00000248272:H148R	H	+	2	0	GAN	79945671	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	8.962000	0.93254	2.285000	0.76669	0.533000	0.62120	CAC		0.463	GAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269050.3		
NECAB2	54550	broad.mit.edu	37	16	84012099	84012099	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:84012099G>A	ENST00000305202.4	+	3	294	c.277G>A	c.(277-279)Gtc>Atc	p.V93I	NECAB2_ENST00000565691.1_Silent_p.A18A	NM_019065.2	NP_061938.2	Q7Z6G3	NECA2_HUMAN	N-terminal EF-hand calcium binding protein 2	93	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)	p.V93I(1)		endometrium(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19						TGCAGATGGCGTCCTTAATGA	0.512																																					p.V93I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G277A	16						.						158.0	140.0	146.0					16																	84012099		2200	4300	6500	82569600	SO:0001583	missense	54550	exon3			AY299331	CCDS10940.1	16q23.3-q24.1	2013-01-10	2007-12-06	2007-12-06	ENSG00000103154	ENSG00000103154		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	23746	protein-coding gene	gene with protein product			"""EF-hand calcium binding protein 2"""	EFCBP2		12044471	Standard	NM_019065		Approved		uc002fhd.3	Q7Z6G3	OTTHUMG00000137636	ENST00000305202.4:c.277G>A	16.37:g.84012099G>A	ENSP00000307449:p.Val93Ile	Somatic		Capture	Illumina HiSeq	Phase_I	82569600	NM_019065	A2RRG3|O75547|Q6ZSK0	Missense_Mutation	SNP	ENST00000305202.4	37	CCDS10940.1	.	.	.	.	.	.	.	.	.	.	G	9.925	1.213309	0.22289	.	.	ENSG00000103154	ENST00000305202	T	0.70986	-0.53	4.84	4.84	0.62591	EF-hand-like domain (1);	0.167445	0.40144	N	0.001175	T	0.60983	0.2311	N	0.05306	-0.075	0.80722	D	1	D	0.71674	0.998	P	0.62014	0.897	T	0.58183	-0.7681	10	0.17832	T	0.49	-3.8488	9.1535	0.36978	0.0993:0.0:0.9007:0.0	.	93	Q7Z6G3	NECA2_HUMAN	I	93	ENSP00000307449:V93I	ENSP00000307449:V93I	V	+	1	0	NECAB2	82569600	1.000000	0.71417	1.000000	0.80357	0.684000	0.39900	4.614000	0.61183	2.249000	0.74217	0.591000	0.81541	GTC		0.512	NECAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269077.2	NM_019065	
DNAAF1	123872	broad.mit.edu	37	16	84199398	84199398	+	Silent	SNP	G	G	A	rs149704838	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:84199398G>A	ENST00000378553.5	+	7	997	c.873G>A	c.(871-873)gcG>gcA	p.A291A	DNAAF1_ENST00000334315.5_Silent_p.A291A|DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	291	LRRCT.				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.A291A(1)		NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						GAGCTTGTGCGGAGGCCTGGG	0.478													G|||	4	0.000798722	0.0	0.0058	5008	,	,		15639	0.0		0.0	False		,,,				2504	0.0				p.A291A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G873A	16						.	G		1,4399	2.1+/-5.4	0,1,2199	113.0	121.0	118.0		873	-11.1	0.2	16	dbSNP_134	118	0,8600		0,0,4300	no	coding-synonymous	DNAAF1	NM_178452.4		0,1,6499	AA,AG,GG		0.0,0.0227,0.0077		291/726	84199398	1,12999	2200	4300	6500	82756899	SO:0001819	synonymous_variant	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.873G>A	16.37:g.84199398G>A		Somatic		Capture	Illumina HiSeq	Phase_I	82756899	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Silent	SNP	ENST00000378553.5	37	CCDS10943.2																																																																																				0.478	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
KCNG4	93107	broad.mit.edu	37	16	84270675	84270675	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:84270675G>A	ENST00000308251.4	-	2	485	c.417C>T	c.(415-417)tgC>tgT	p.C139C	KCNG4_ENST00000568181.1_Silent_p.C139C	NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	139					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.C139C(2)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						AGGACAGCGCGCACATCTCCT	0.652																																					p.C139C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C417T	16						.						47.0	49.0	48.0					16																	84270675		2200	4300	6500	82828176	SO:0001819	synonymous_variant	93107	exon2			AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.417C>T	16.37:g.84270675G>A		Somatic		Capture	Illumina HiSeq	Phase_I	82828176	NM_172347	Q96H24	Silent	SNP	ENST00000308251.4	37	CCDS10945.1																																																																																				0.652	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347	
USP10	9100	broad.mit.edu	37	16	84778553	84778553	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:84778553C>T	ENST00000219473.7	+	4	579	c.466C>T	c.(466-468)Cca>Tca	p.P156S	USP10_ENST00000562743.1_3'UTR|USP10_ENST00000570191.1_Missense_Mutation_p.P160S	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	156					autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.P156S(1)		endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						GAAAAAGCGGCCACCTGGATA	0.473																																					p.P156S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C466T	16						.						38.0	36.0	37.0					16																	84778553		1893	4120	6013	83336054	SO:0001583	missense	9100	exon4			D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"""Ubiquitin-specific peptidases"""	12608	protein-coding gene	gene with protein product		609818	"""ubiquitin specific protease 10"""			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.466C>T	16.37:g.84778553C>T	ENSP00000219473:p.Pro156Ser	Somatic		Capture	Illumina HiSeq	Phase_I	83336054	NM_005153	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Missense_Mutation	SNP	ENST00000219473.7	37	CCDS45537.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.466166	0.84425	.	.	ENSG00000103194	ENST00000219473	T	0.13657	2.57	5.17	5.17	0.71159	.	0.256833	0.35013	N	0.003503	T	0.37100	0.0991	M	0.69823	2.125	0.58432	D	0.999999	D;D	0.76494	0.999;0.998	D;D	0.72625	0.978;0.952	T	0.13124	-1.0521	10	0.87932	D	0	-14.2693	15.8288	0.78736	0.0:1.0:0.0:0.0	.	160;156	Q14694-3;Q14694	.;UBP10_HUMAN	S	156	ENSP00000219473:P156S	ENSP00000219473:P156S	P	+	1	0	USP10	83336054	1.000000	0.71417	0.993000	0.49108	0.990000	0.78478	6.862000	0.75484	2.403000	0.81681	0.491000	0.48974	CCA		0.473	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
CRISPLD2	83716	broad.mit.edu	37	16	84884184	84884184	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:84884184C>T	ENST00000262424.5	+	5	727	c.503C>T	c.(502-504)gCc>gTc	p.A168V	CRISPLD2_ENST00000567845.1_Missense_Mutation_p.A168V|CRISPLD2_ENST00000566431.1_3'UTR|CRISPLD2_ENST00000564567.1_Missense_Mutation_p.A168V|AC025280.1_ENST00000584136.1_RNA	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	168	SCP.				extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|lung development (GO:0030324)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|transport vesicle (GO:0030133)	heparin binding (GO:0008201)	p.A168V(1)		endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)	18						ATAGTTTGGGCCACCACCAAC	0.478																																					p.A168V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C503T	16						.						139.0	127.0	131.0					16																	84884184		2199	4300	6499	83441685	SO:0001583	missense	83716	exon5			AL136861	CCDS10949.1	16q24.1	2008-02-05	2005-02-16	2005-02-16	ENSG00000103196	ENSG00000103196			25248	protein-coding gene	gene with protein product		612434	"""LCCL domain containing cysteine-rich secretory protein 2"""	LCRISP2		11230166	Standard	NM_031476		Approved	DKFZP434B044	uc010voh.1	Q9H0B8	OTTHUMG00000137644	ENST00000262424.5:c.503C>T	16.37:g.84884184C>T	ENSP00000262424:p.Ala168Val	Somatic		Capture	Illumina HiSeq	Phase_I	83441685	NM_031476	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Missense_Mutation	SNP	ENST00000262424.5	37	CCDS10949.1	.	.	.	.	.	.	.	.	.	.	C	35	5.567625	0.96540	.	.	ENSG00000103196	ENST00000262424	T	0.11712	2.75	5.94	5.94	0.96194	CAP domain (3);	0.000000	0.85682	D	0.000000	T	0.45796	0.1360	M	0.92738	3.34	0.80722	D	1	D;D;D	0.89917	0.985;0.998;1.0	D;D;D	0.91635	0.993;0.992;0.999	T	0.54860	-0.8230	10	0.87932	D	0	.	18.9413	0.92607	0.0:1.0:0.0:0.0	.	168;168;168	Q9H0B8;Q9H0B8-2;Q9H0B8-3	CRLD2_HUMAN;.;.	V	168	ENSP00000262424:A168V	ENSP00000262424:A168V	A	+	2	0	CRISPLD2	83441685	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.389000	0.79806	2.826000	0.97356	0.561000	0.74099	GCC		0.478	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476	
IRF8	3394	broad.mit.edu	37	16	85953768	85953768	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:85953768C>T	ENST00000268638.5	+	8	1464	c.1042C>T	c.(1042-1044)Ctg>Ttg	p.L348L	IRF8_ENST00000562492.1_Silent_p.L144L	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	348					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)	p.L348L(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				CAGGGTGGTGCTGTGCTTTGG	0.507																																					p.L348L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1042T	16						.						65.0	58.0	61.0					16																	85953768		2198	4300	6498	84511269	SO:0001819	synonymous_variant	3394	exon8			M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.1042C>T	16.37:g.85953768C>T		Somatic		Capture	Illumina HiSeq	Phase_I	84511269	NM_002163	A0AV82	Silent	SNP	ENST00000268638.5	37	CCDS10956.1																																																																																				0.507	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163	
MTHFSD	64779	broad.mit.edu	37	16	86565886	86565886	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:86565886C>A	ENST00000360900.6	-	8	908	c.883G>T	c.(883-885)Ggc>Tgc	p.G295C	MTHFSD_ENST00000381214.5_Missense_Mutation_p.G295C|MTHFSD_ENST00000543303.2_Missense_Mutation_p.G294C|MTHFSD_ENST00000546093.1_Missense_Mutation_p.G132C|MTHFSD_ENST00000322911.6_Missense_Mutation_p.G294C	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	295							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G294C(1)		endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						GGTGGGGAGCCAGGGGCTGCC	0.667																																					p.G294C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G880T	16						.						13.0	17.0	16.0					16																	86565886		1877	4095	5972	85123387	SO:0001583	missense	64779	exon8			AK023060	CCDS54047.1, CCDS54048.1, CCDS58490.1	16q24.1	2013-02-12				ENSG00000103248		"""RNA binding motif (RRM) containing"""	25778	protein-coding gene	gene with protein product						12477932	Standard	NM_022764		Approved	FLJ12998	uc010vor.2	Q2M296		ENST00000360900.6:c.883G>T	16.37:g.86565886C>A	ENSP00000354152:p.Gly295Cys	Somatic		Capture	Illumina HiSeq	Phase_I	85123387	NM_022764	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Missense_Mutation	SNP	ENST00000360900.6	37	CCDS54047.1	.	.	.	.	.	.	.	.	.	.	C	11.80	1.747284	0.30955	.	.	ENSG00000103248	ENST00000543303;ENST00000381214;ENST00000360900;ENST00000322911;ENST00000546093	T;T;T;T	0.19394	2.4;2.41;2.41;2.15	5.28	-0.888	0.10583	.	3.709200	0.00855	U	0.001874	T	0.15262	0.0368	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.13145	0.004;0.004;0.007;0.006	B;B;B;B	0.09377	0.002;0.002;0.004;0.004	T	0.19877	-1.0292	10	0.39692	T	0.17	-13.1252	3.6612	0.08240	0.3726:0.2931:0.0:0.3343	.	295;294;295;294	E9PAM1;B7ZLC0;Q2M296;Q2M296-2	.;.;MTHSD_HUMAN;.	C	293;295;295;294;132	ENSP00000370612:G295C;ENSP00000354152:G295C;ENSP00000326777:G294C;ENSP00000438761:G132C	ENSP00000326777:G294C	G	-	1	0	MTHFSD	85123387	0.000000	0.05858	0.001000	0.08648	0.193000	0.23685	-0.599000	0.05700	-0.060000	0.13132	0.609000	0.83330	GGC		0.667	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764	
FBXO31	79791	broad.mit.edu	37	16	87364959	87364959	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:87364959C>T	ENST00000311635.7	-	9	1567	c.1555G>A	c.(1555-1557)Gca>Aca	p.A519T	RP11-178L8.4_ENST00000568879.1_Intron	NM_001282683.1|NM_024735.3	NP_001269612.1|NP_079011.3	Q5XUX0	FBX31_HUMAN	F-box protein 31	519					cellular response to DNA damage stimulus (GO:0006974)|cyclin catabolic process (GO:0008054)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)	p.A347T(1)|p.A519T(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0272)		GGCGCATCTGCGTTCCGGAAG	0.617																																					p.A519T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1555A	16						.						79.0	61.0	68.0					16																	87364959		2198	4300	6498	85922460	SO:0001583	missense	79791	exon9			BC002985	CCDS32501.1, CCDS73922.1	16q24	2008-12-18	2004-05-27			ENSG00000103264		"""F-boxes /  ""other"""""	16510	protein-coding gene	gene with protein product		609102	"""F-box only protein 31"""				Standard	NM_024735		Approved	FBX14, FBXO14, Fbx31, MGC15419	uc002fjw.3	Q5XUX0		ENST00000311635.7:c.1555G>A	16.37:g.87364959C>T	ENSP00000310841:p.Ala519Thr	Somatic		Capture	Illumina HiSeq	Phase_I	85922460	NM_024735	Q5K680|Q8WYV1|Q96D73|Q9UFV4	Missense_Mutation	SNP	ENST00000311635.7	37	CCDS32501.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.570621	0.86542	.	.	ENSG00000103264	ENST00000311635	.	.	.	4.86	4.86	0.63082	.	0.053997	0.64402	D	0.000001	T	0.60881	0.2303	L	0.51422	1.61	0.80722	D	1	D;D	0.63046	0.986;0.992	P;P	0.51266	0.463;0.664	T	0.65409	-0.6175	9	0.72032	D	0.01	-13.0525	13.3377	0.60526	0.158:0.842:0.0:0.0	.	519;411	Q5XUX0;Q5XUX0-2	FBX31_HUMAN;.	T	519	.	ENSP00000310841:A519T	A	-	1	0	FBXO31	85922460	1.000000	0.71417	0.676000	0.29932	0.844000	0.47949	5.400000	0.66320	2.404000	0.81709	0.561000	0.74099	GCA		0.617	FBXO31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430799.2	NM_024735	
FBXO31	79791	broad.mit.edu	37	16	87365026	87365026	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:87365026G>A	ENST00000311635.7	-	9	1500	c.1488C>T	c.(1486-1488)ttC>ttT	p.F496F	RP11-178L8.4_ENST00000568879.1_Intron	NM_001282683.1|NM_024735.3	NP_001269612.1|NP_079011.3	Q5XUX0	FBX31_HUMAN	F-box protein 31	496					cellular response to DNA damage stimulus (GO:0006974)|cyclin catabolic process (GO:0008054)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)	p.F324F(1)|p.F496F(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0272)		AGACGAACCCGAAGCGGTCCT	0.617																																					p.F496F												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1488T	16						.						45.0	43.0	44.0					16																	87365026		2198	4300	6498	85922527	SO:0001819	synonymous_variant	79791	exon9			BC002985	CCDS32501.1, CCDS73922.1	16q24	2008-12-18	2004-05-27			ENSG00000103264		"""F-boxes /  ""other"""""	16510	protein-coding gene	gene with protein product		609102	"""F-box only protein 31"""				Standard	NM_024735		Approved	FBX14, FBXO14, Fbx31, MGC15419	uc002fjw.3	Q5XUX0		ENST00000311635.7:c.1488C>T	16.37:g.87365026G>A		Somatic		Capture	Illumina HiSeq	Phase_I	85922527	NM_024735	Q5K680|Q8WYV1|Q96D73|Q9UFV4	Silent	SNP	ENST00000311635.7	37	CCDS32501.1																																																																																				0.617	FBXO31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430799.2	NM_024735	
ZC3H18	124245	broad.mit.edu	37	16	88696898	88696898	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:88696898C>T	ENST00000301011.5	+	17	2772	c.2572C>T	c.(2572-2574)Cgg>Tgg	p.R858W	ZC3H18_ENST00000452588.2_Missense_Mutation_p.R882W	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	858						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R858W(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		CCCAGGTTCTCGGGACCGGAA	0.622																																					p.R858W	Ovarian(121;375 2276 20373 38669)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2572T	16						.						54.0	50.0	51.0					16																	88696898		2197	4300	6497	87224399	SO:0001583	missense	124245	exon17			BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"""Zinc fingers, CCCH-type domain containing"""	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.2572C>T	16.37:g.88696898C>T	ENSP00000301011:p.Arg858Trp	Somatic		Capture	Illumina HiSeq	Phase_I	87224399	NM_144604	Q96DG4|Q96MP7	Missense_Mutation	SNP	ENST00000301011.5	37	CCDS10967.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.270317	0.80469	.	.	ENSG00000158545	ENST00000301011;ENST00000452588	T;T	0.39592	1.07;1.07	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.60612	0.2282	L	0.54323	1.7	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.62364	-0.6870	10	0.72032	D	0.01	-20.6347	15.8382	0.78814	0.0:1.0:0.0:0.0	.	882;858	E7ERS3;Q86VM9	.;ZCH18_HUMAN	W	858;882	ENSP00000301011:R858W;ENSP00000416951:R882W	ENSP00000301011:R858W	R	+	1	2	ZC3H18	87224399	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	4.751000	0.62169	2.517000	0.84864	0.462000	0.41574	CGG		0.622	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604	
ANKRD11	29123	broad.mit.edu	37	16	89346978	89346978	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:89346978G>T	ENST00000301030.4	-	9	6432	c.5972C>A	c.(5971-5973)cCa>cAa	p.P1991Q	ANKRD11_ENST00000378330.2_Missense_Mutation_p.P1991Q	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1991	Pro-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P1991Q(1)		breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		GAAACGCTTTGGGGACTCGGG	0.692																																					p.P1991Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5972A	16						.						18.0	21.0	20.0					16																	89346978		2143	4162	6305	87874479	SO:0001583	missense	29123	exon9			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.5972C>A	16.37:g.89346978G>T	ENSP00000301030:p.Pro1991Gln	Somatic		Capture	Illumina HiSeq	Phase_I	87874479	NM_013275	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	37	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	g	13.89	2.370656	0.42003	.	.	ENSG00000167522	ENST00000301030;ENST00000378330	T;T	0.41065	1.01;1.01	5.29	5.29	0.74685	.	0.620836	0.15207	N	0.274687	T	0.54967	0.1891	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	D	0.63597	0.916	T	0.57505	-0.7800	10	0.87932	D	0	.	18.565	0.91114	0.0:0.0:1.0:0.0	.	1991	Q6UB99	ANR11_HUMAN	Q	1991	ENSP00000301030:P1991Q;ENSP00000367581:P1991Q	ENSP00000301030:P1991Q	P	-	2	0	ANKRD11	87874479	1.000000	0.71417	0.943000	0.38184	0.015000	0.08874	3.954000	0.56708	2.475000	0.83589	0.450000	0.29827	CCA		0.692	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275	
ANKRD11	29123	broad.mit.edu	37	16	89349263	89349263	+	Silent	SNP	C	C	T	rs374974445		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:89349263C>T	ENST00000301030.4	-	9	4147	c.3687G>A	c.(3685-3687)acG>acA	p.T1229T	ANKRD11_ENST00000378330.2_Silent_p.T1229T	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1229	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.T1229T(1)		breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		TCTTATCTTGCGTGGAGTCCA	0.438																																					p.T1229T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3687A	16						.						64.0	71.0	69.0					16																	89349263		2198	4300	6498	87876764	SO:0001819	synonymous_variant	29123	exon9			AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.3687G>A	16.37:g.89349263C>T		Somatic		Capture	Illumina HiSeq	Phase_I	87876764	NM_013275	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	37	CCDS32513.1																																																																																				0.438	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275	
DPEP1	1800	broad.mit.edu	37	16	89696820	89696820	+	Start_Codon_SNP	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:89696820T>C	ENST00000393092.3	+	2	293	c.2T>C	c.(1-3)aTg>aCg	p.M1T	DPEP1_ENST00000421184.1_Start_Codon_SNP_p.M1T|DPEP1_ENST00000261615.4_Start_Codon_SNP_p.M1T	NM_004413.3	NP_004404.1	P16444	DPEP1_HUMAN	dipeptidase 1 (renal)	1					antibiotic metabolic process (GO:0016999)|arachidonic acid metabolic process (GO:0019369)|cellular lactam catabolic process (GO:0072340)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to nitric oxide (GO:0071732)|glutathione metabolic process (GO:0006749)|homocysteine metabolic process (GO:0050667)|leukotriene metabolic process (GO:0006691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|dipeptidyl-peptidase activity (GO:0008239)|GPI anchor binding (GO:0034235)|metallodipeptidase activity (GO:0070573)|metalloexopeptidase activity (GO:0008235)|modified amino acid binding (GO:0072341)|zinc ion binding (GO:0008270)	p.M1T(1)		large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	14		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)	GACCCCACCATGTGGAGCGGA	0.637																																					p.M1T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2C	16						.						63.0	64.0	64.0					16																	89696820		2198	4300	6498	88224321	SO:0001582	initiator_codon_variant	1800	exon2				CCDS10982.1	16q24	2011-07-22			ENSG00000015413	ENSG00000015413	3.4.13.19		3002	protein-coding gene	gene with protein product		179780					Standard	NM_004413		Approved		uc002fnr.4	P16444	OTTHUMG00000138052	ENST00000393092.3:c.2T>C	16.37:g.89696820T>C	ENSP00000376807:p.Met1Thr	Somatic		Capture	Illumina HiSeq	Phase_I	88224321	NM_004413	D3DX80|Q96AK2	Missense_Mutation	SNP	ENST00000393092.3	37	CCDS10982.1	.	.	.	.	.	.	.	.	.	.	T	6.115	0.389399	0.11581	.	.	ENSG00000015413	ENST00000421184;ENST00000393092;ENST00000261615	T;T;T	0.22743	1.94;1.94;1.94	3.82	2.73	0.32206	.	0.694788	0.14973	N	0.287668	T	0.16854	0.0405	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.05386	-1.0888	9	0.87932	D	0	-1.7129	7.4231	0.27083	0.0:0.1048:0.0:0.8952	.	1	P16444	DPEP1_HUMAN	T	1	ENSP00000397313:M1T;ENSP00000376807:M1T;ENSP00000261615:M1T	ENSP00000261615:M1T	M	+	2	0	DPEP1	88224321	0.267000	0.24122	0.109000	0.21407	0.001000	0.01503	0.614000	0.24314	0.823000	0.34589	-0.256000	0.11100	ATG		0.637	DPEP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423058.1	NM_001128141	Missense_Mutation
GRIN2A	2903	broad.mit.edu	37	16	10032355	10032355	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:10032355C>T	ENST00000396573.2	-	4	777	c.468G>A	c.(466-468)acG>acA	p.T156T	GRIN2A_ENST00000562109.1_Silent_p.T156T|GRIN2A_ENST00000566670.1_5'UTR|GRIN2A_ENST00000330684.3_Silent_p.T156T|GRIN2A_ENST00000404927.2_Silent_p.T156T|GRIN2A_ENST00000535259.1_5'UTR|GRIN2A_ENST00000396575.2_Silent_p.T156T	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	156					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.T156T(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)	TCAGCATGACCGTGGCTTGCT	0.507																																					p.T156T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G468A	16						.						73.0	65.0	68.0					16																	10032355		2197	4300	6497	9939856	SO:0001819	synonymous_variant	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.468G>A	16.37:g.10032355C>T		Somatic		Capture	Illumina HiSeq	Phase_I	9939856	NM_001134408	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	CCDS10539.1																																																																																				0.507	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
ITGAX	3687	broad.mit.edu	37	16	31373986	31373986	+	Frame_Shift_Del	DEL	C	C	-	rs150562711		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:31373986delC	ENST00000268296.4	+	12	1392	c.1271delC	c.(1270-1272)gccfs	p.A424fs	ITGAX_ENST00000562522.1_Frame_Shift_Del_p.A424fs	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	424					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.R426fs*20(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						GTCCTGGGGGCCCCCCGCTAC	0.662																																					p.A424fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1271delC	16						.						25.0	25.0	25.0					16																	31373986		2197	4299	6496	31281487	SO:0001589	frameshift_variant	3687	exon12			BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1271delC	16.37:g.31373986delC	ENSP00000268296:p.Ala424fs	Somatic		Capture	Illumina HiSeq	Phase_I	31281487	NM_000887	Q8IVA6	Frame_Shift_Del	DEL	ENST00000268296.4	37	CCDS10711.1																																																																																				0.662	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
ZNF276	92822	broad.mit.edu	37	16	89800365	89800365	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:89800365C>T	ENST00000443381.2	+	9	1490	c.1393C>T	c.(1393-1395)Cgg>Tgg	p.R465W	ZNF276_ENST00000289816.5_Missense_Mutation_p.R390W|ZNF276_ENST00000568064.1_Missense_Mutation_p.R373W|ZNF276_ENST00000446326.2_Missense_Mutation_p.R251W	NM_001113525.1	NP_001106997.1	Q8N554	ZN276_HUMAN	zinc finger protein 276	465					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.R390W(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)	14		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		GGTCCGGGAGCGGCCCTGCCC	0.627																																					p.R465W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1393T	16						.						66.0	57.0	60.0					16																	89800365		2198	4300	6498	88327866	SO:0001583	missense	92822	exon9			AK026482	CCDS10986.1, CCDS45554.1	16q24.3	2014-02-17	2006-02-10	2006-02-10	ENSG00000158805	ENSG00000158805		"""Zinc fingers, C2H2-type"""	23330	protein-coding gene	gene with protein product	"""centromere protein Z"", ""zinc finger, AD-type"""	608460	"""zinc finger protein 276 homolog (mouse)"""	ZFP276		10936049, 20813266	Standard	NM_152287		Approved	MGC45417, ZNF477, CENPZ, CENP-Z, ZADT	uc002fos.4	Q8N554	OTTHUMG00000138050	ENST00000443381.2:c.1393C>T	16.37:g.89800365C>T	ENSP00000415836:p.Arg465Trp	Somatic		Capture	Illumina HiSeq	Phase_I	88327866	NM_001113525	Q0VGA1|Q2TBE8|Q3B7H7	Missense_Mutation	SNP	ENST00000443381.2	37	CCDS45554.1	.	.	.	.	.	.	.	.	.	.	C	18.94	3.729184	0.69074	.	.	ENSG00000158805	ENST00000446326;ENST00000289816;ENST00000443381	T;T;T	0.78816	-1.21;2.45;2.45	5.64	0.57	0.17347	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.72510	0.3469	N	0.08118	0	0.42234	D	0.991901	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79784	0.971;0.993;0.971;0.984	T	0.72207	-0.4360	10	0.87932	D	0	-34.5114	9.5671	0.39405	0.4094:0.5213:0.0693:0.0	.	303;465;251;390	B4DIT3;Q8N554;A8K186;Q8N554-2	.;ZN276_HUMAN;.;.	W	251;390;465	ENSP00000415999:R251W;ENSP00000289816:R390W;ENSP00000415836:R465W	ENSP00000289816:R390W	R	+	1	2	ZNF276	88327866	1.000000	0.71417	0.979000	0.43373	0.851000	0.48451	1.228000	0.32588	-0.190000	0.10465	-0.397000	0.06425	CGG		0.627	ZNF276-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422517.1	NM_152287	
PRDM7	11105	broad.mit.edu	37	16	90124736	90124736	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr16:90124736delT	ENST00000449207.2	-	10	1459	c.1440delA	c.(1438-1440)aaafs	p.K480fs	PRDM7_ENST00000407825.1_3'UTR|PRDM7_ENST00000325921.6_3'UTR	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	480					regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleic acid binding (GO:0003676)	p.K480fs*15(1)		lung(2)|ovary(2)|stomach(1)	5		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		TGACCTTTGGTTTTGTCATTA	0.463																																					p.K480fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1440delA	16						.						73.0	74.0	74.0					16																	90124736		2198	4300	6498	88652237	SO:0001589	frameshift_variant	11105	exon10			AF274347	CCDS45557.1	16q24.3	2013-01-09			ENSG00000126856	ENSG00000126856		"""Zinc fingers, C2H2-type"", ""-"""	9351	protein-coding gene	gene with protein product		609759				17916234	Standard	NM_001098173		Approved	ZNF910	uc010cje.3	Q9NQW5	OTTHUMG00000138990	ENST00000449207.2:c.1440delA	16.37:g.90124736delT	ENSP00000396732:p.Lys480fs	Somatic		Capture	Illumina HiSeq	Phase_I	88652237	NM_001098173	A4Q9G8|Q08EM4|Q9NQW4	Frame_Shift_Del	DEL	ENST00000449207.2	37	CCDS45557.1																																																																																				0.463	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1		
TMEM256-PLSCR3	100529211	broad.mit.edu	37	17	7297141	7297142	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:7297141_7297142insG	ENST00000576362.1	-	2	178_179	c.21_22insC	c.(19-24)cccaaafs	p.K8fs	TMEM256-PLSCR3_ENST00000535512.1_Frame_Shift_Ins_p.K8fs|TMEM256-PLSCR3_ENST00000576201.1_Frame_Shift_Ins_p.K8fs|TMEM256-PLSCR3_ENST00000324822.11_Frame_Shift_Ins_p.K8fs|C17orf61-PLSCR3_ENST00000573331.1_3'UTR|TMEM256-PLSCR3_ENST00000574401.1_Frame_Shift_Ins_p.K8fs					TMEM256-PLSCR3 readthrough (NMD candidate)									p.K8fs*76(1)									GCGTAGCCTTTGGGGGGCAAGT	0.663																																					p.K8fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.22_23insC	17						.																																			7237866	SO:0001589	frameshift_variant	57048	exon3					17p13.1	2013-09-25			ENSG00000187838	ENSG00000187838			49186	other	readthrough							Standard	NR_037719		Approved				OTTHUMG00000178150	ENST00000576362.1:c.22dupC	17.37:g.7297147_7297147dupG	ENSP00000460800:p.Lys8fs	Somatic		Capture	Illumina HiSeq	Phase_I	7237865	NM_020360		Frame_Shift_Ins	INS	ENST00000576362.1	37																																																																																					0.663	TMEM256-PLSCR3-008	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000440808.1		
MYH8	4626	broad.mit.edu	37	17	10302878	10302878	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:10302878G>A	ENST00000403437.2	-	28	3938	c.3844C>T	c.(3844-3846)Cgc>Tgc	p.R1282C	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1282					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)	p.R1282C(1)		NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						GTCTGCAGGCGCGCTCTCTGT	0.473									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.R1282C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3844T	17						.						135.0	128.0	130.0					17																	10302878		2203	4300	6503	10243603	SO:0001583	missense	4626	exon28	Familial Cancer Database	Carney Complex Variant		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.3844C>T	17.37:g.10302878G>A	ENSP00000384330:p.Arg1282Cys	Somatic		Capture	Illumina HiSeq	Phase_I	10243603	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	G	15.48	2.846749	0.51164	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	D	0.84146	-1.81	5.38	5.38	0.77491	Myosin tail (1);	0.165634	0.28510	U	0.015085	D	0.94971	0.8373	H	0.95884	3.735	0.34461	D	0.701704	D	0.76494	0.999	D	0.67548	0.952	D	0.98503	1.0615	10	0.87932	D	0	.	19.317	0.94218	0.0:0.0:1.0:0.0	.	1282	P13535	MYH8_HUMAN	C	1282	ENSP00000384330:R1282C	ENSP00000252173:R1282C	R	-	1	0	MYH8	10243603	0.023000	0.18921	0.901000	0.35422	0.492000	0.33523	2.004000	0.40854	2.806000	0.96561	0.655000	0.94253	CGC		0.473	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
MYH2	4620	broad.mit.edu	37	17	10430095	10430095	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:10430095C>T	ENST00000245503.5	-	30	4392	c.4008G>A	c.(4006-4008)gcG>gcA	p.A1336A	MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000397183.2_Silent_p.A1336A|RP11-799N11.1_ENST00000581304.1_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1336					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.A1336A(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						GCAGGGCATGCGCCAGGGCGT	0.493																																					p.A1336A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4008A	17						.						90.0	85.0	87.0					17																	10430095		2203	4300	6503	10370820	SO:0001819	synonymous_variant	4620	exon30				CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.4008G>A	17.37:g.10430095C>T		Somatic		Capture	Illumina HiSeq	Phase_I	10370820	NM_001100112	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	37	CCDS11156.1																																																																																				0.493	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534	
MYH3	4621	broad.mit.edu	37	17	10555851	10555851	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:10555851G>A	ENST00000583535.1	-	4	321	c.234C>T	c.(232-234)taC>taT	p.Y78Y	MYH3_ENST00000226209.7_Silent_p.Y78Y	NM_002470.3	NP_002461.2	P11055	MYH3_HUMAN	myosin, heavy chain 3, skeletal muscle, embryonic	78					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|embryonic limb morphogenesis (GO:0030326)|face morphogenesis (GO:0060325)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|sarcomere organization (GO:0045214)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)	p.Y78Y(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(5)|large_intestine(18)|lung(30)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	83						GGTTCATGGCGTACACATCCT	0.468																																					p.Y78Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C234T	17						.						136.0	123.0	127.0					17																	10555851		2203	4300	6503	10496576	SO:0001819	synonymous_variant	4621	exon3				CCDS11157.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109063	ENSG00000109063		"""Myosins / Myosin superfamily : Class II"""	7573	protein-coding gene	gene with protein product	"""myosin, skeletal, heavy chain, embryonic 1"", ""muscle embryonic myosin heavy chain 3"""	160720	"""myosin, heavy polypeptide 3, skeletal muscle, embryonic"""			2726495	Standard	NM_002470		Approved	MYHC-EMB, MYHSE1, HEMHC, SMHCE	uc002gmq.2	P11055	OTTHUMG00000130367	ENST00000583535.1:c.234C>T	17.37:g.10555851G>A		Somatic		Capture	Illumina HiSeq	Phase_I	10496576	NM_002470	Q15492	Silent	SNP	ENST00000583535.1	37	CCDS11157.1																																																																																				0.468	MYH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252734.2	NM_002470	
PIRT	644139	broad.mit.edu	37	17	10728794	10728794	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:10728794C>T	ENST00000580256.2	-	2	807	c.169G>A	c.(169-171)Gtt>Att	p.V57I		NM_001101387.1	NP_001094857.1	P0C851	PIRT_HUMAN	phosphoinositide-interacting regulator of transient receptor potential channels	57						integral component of membrane (GO:0016021)		p.V57I(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)	8						GACATGATAACGATGGGCTTG	0.582																																					p.V57I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G169A	17						.						64.0	66.0	65.0					17																	10728794		2085	4200	6285	10669519	SO:0001583	missense	644139	exon2			AK021549	CCDS45614.1	17p12	2010-06-04			ENSG00000233670	ENSG00000233670			37239	protein-coding gene	gene with protein product	"""phosphoinositide-interacting regulator of TRPV1"""	612068				18455988	Standard	NM_001101387		Approved		uc010col.3	P0C851		ENST00000580256.2:c.169G>A	17.37:g.10728794C>T	ENSP00000462046:p.Val57Ile	Somatic		Capture	Illumina HiSeq	Phase_I	10669519	NM_001101387	B7Z648	Missense_Mutation	SNP	ENST00000580256.2	37	CCDS45614.1	.	.	.	.	.	.	.	.	.	.	C	5.202	0.222831	0.09863	.	.	ENSG00000233670	ENST00000441732	.	.	.	5.46	-6.01	0.02199	.	.	.	.	.	T	0.15522	0.0374	N	0.02916	-0.46	0.20403	N	0.99991	B	0.09022	0.002	B	0.04013	0.001	T	0.45056	-0.9287	8	0.02654	T	1	-11.2584	15.8545	0.78965	0.0:0.1629:0.0:0.8371	.	57	P0C851	PIRT_HUMAN	I	57	.	ENSP00000408936:V57I	V	-	1	0	PIRT	10669519	0.000000	0.05858	0.503000	0.27626	0.990000	0.78478	-1.591000	0.02100	-0.995000	0.03459	0.655000	0.94253	GTT		0.582	PIRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441078.2	NM_001101387	
DNAH9	1770	broad.mit.edu	37	17	11593737	11593737	+	Missense_Mutation	SNP	G	G	A	rs143638477		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:11593737G>A	ENST00000262442.4	+	20	4666	c.4598G>A	c.(4597-4599)cGg>cAg	p.R1533Q	DNAH9_ENST00000454412.2_Missense_Mutation_p.R1533Q	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1533	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.R1533Q(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GAAGATATTCGGGCACAGCTA	0.488																																					p.R1533Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4598A	17						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	53.0	53.0	53.0		4598	5.6	1.0	17	dbSNP_134	53	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DNAH9	NM_001372.3	43	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging	1533/4487	11593737	3,13003	2203	4300	6503	11534462	SO:0001583	missense	1770	exon20			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.4598G>A	17.37:g.11593737G>A	ENSP00000262442:p.Arg1533Gln	Somatic		Capture	Illumina HiSeq	Phase_I	11534462	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.923485	0.92319	2.27E-4	2.33E-4	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.60920	0.15;0.15	5.57	5.57	0.84162	Dynein heavy chain, domain-2 (1);	0.000000	0.64402	D	0.000001	T	0.77974	0.4211	M	0.79926	2.475	0.80722	D	1	D	0.76494	0.999	D	0.67900	0.954	T	0.80535	-0.1339	10	0.87932	D	0	.	19.557	0.95354	0.0:0.0:1.0:0.0	.	1533	Q9NYC9	DYH9_HUMAN	Q	1533;1533;115	ENSP00000262442:R1533Q;ENSP00000414874:R1533Q	ENSP00000262442:R1533Q	R	+	2	0	DNAH9	11534462	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.457000	0.80775	2.630000	0.89119	0.655000	0.94253	CGG		0.488	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
DNAH9	1770	broad.mit.edu	37	17	11650929	11650929	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:11650929C>T	ENST00000262442.4	+	32	6524	c.6456C>T	c.(6454-6456)ggC>ggT	p.G2152G	DNAH9_ENST00000454412.2_Silent_p.G2152G	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2152	AAA 2. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.G2152G(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TGGTGGGTGGCGCTGGTACCG	0.587																																					p.G2152G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C6456T	17						.						71.0	67.0	68.0					17																	11650929		2203	4300	6503	11591654	SO:0001819	synonymous_variant	1770	exon32			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6456C>T	17.37:g.11650929C>T		Somatic		Capture	Illumina HiSeq	Phase_I	11591654	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																				0.587	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
DNAH9	1770	broad.mit.edu	37	17	11865429	11865429	+	Silent	SNP	G	G	T	rs550364927		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:11865429G>T	ENST00000262442.4	+	68	13157	c.13089G>T	c.(13087-13089)acG>acT	p.T4363T	RP11-1096G20.5_ENST00000580270.1_RNA|DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000608377.1_Silent_p.T675T|DNAH9_ENST00000454412.2_Silent_p.T4287T	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4363					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.T4363T(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TGCAGTCCACGGCTCGCAAGA	0.557																																					p.T675T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2025T	17						.						68.0	64.0	65.0					17																	11865429		2203	4300	6503	11806154	SO:0001819	synonymous_variant	1770	exon14			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.13089G>T	17.37:g.11865429G>T		Somatic		Capture	Illumina HiSeq	Phase_I	11806154	NM_004662	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																				0.557	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
MAP2K4	6416	broad.mit.edu	37	17	12032481	12032481	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:12032481C>A	ENST00000353533.5	+	9	980	c.917C>A	c.(916-918)cCt>cAt	p.P306H	MAP2K4_ENST00000415385.3_Missense_Mutation_p.P317H	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	306	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|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)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|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)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.P306H(1)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		GGCCGATTTCCTTATCCAAAG	0.443			"""D, Mis, N"""		"""pancreatic, breast, colorectal"""																																p.P306H			Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	.	.	12	Whole gene deletion(10)|Substitution - Missense(1)|Unknown(1)	breast(4)|ovary(4)|biliary_tract(1)|large_intestine(1)|lung(1)|pancreas(1)	c.C917A	17						.						67.0	62.0	64.0					17																	12032481		2203	4300	6503	11973206	SO:0001583	missense	6416	exon9			L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.917C>A	17.37:g.12032481C>A	ENSP00000262445:p.Pro306His	Somatic		Capture	Illumina HiSeq	Phase_I	11973206	NM_003010	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Missense_Mutation	SNP	ENST00000353533.5	37	CCDS11162.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.816596	0.90790	.	.	ENSG00000065559	ENST00000353533;ENST00000415385;ENST00000538465;ENST00000536413	T;T	0.34072	1.38;1.38	5.1	5.1	0.69264	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	0.74473	0.3721	H	0.97540	4.025	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	0.83852	0.0263	10	0.87932	D	0	.	17.8069	0.88604	0.0:1.0:0.0:0.0	.	178;317;306	B7ZA62;P45985-2;P45985	.;.;MP2K4_HUMAN	H	306;317;283;178	ENSP00000262445:P306H;ENSP00000410402:P317H	ENSP00000262445:P306H	P	+	2	0	MAP2K4	11973206	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.597000	0.82733	2.805000	0.96524	0.655000	0.94253	CCT		0.443	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1		
ELAC2	60528	broad.mit.edu	37	17	12896297	12896297	+	Silent	SNP	G	G	A	rs550032568		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:12896297G>A	ENST00000338034.4	-	24	2558	c.2319C>T	c.(2317-2319)ggC>ggT	p.G773G	ELAC2_ENST00000395962.2_Silent_p.G754G|RP11-597M12.1_ENST00000582915.1_RNA|ELAC2_ENST00000426905.3_Silent_p.G733G	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	773					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.G773G(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						CCTCGATGTCGCCAGCAAACA	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		17849	0.001		0.0	False		,,,				2504	0.0				p.G733G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2199T	17						.						66.0	67.0	67.0					17																	12896297		2203	4300	6503	12837022	SO:0001819	synonymous_variant	60528	exon23			AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"""tRNase Z (long form)"""	605367	"""elaC (E. coli) homolog 2"", ""elaC homolog 2 (E. coli)"""			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.2319C>T	17.37:g.12896297G>A		Somatic		Capture	Illumina HiSeq	Phase_I	12837022	NM_001165962	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Silent	SNP	ENST00000338034.4	37	CCDS11164.1																																																																																				0.602	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5		
CDRT15	146822	broad.mit.edu	37	17	14139996	14139996	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:14139996A>G	ENST00000420162.2	-	1	170	c.155T>C	c.(154-156)cTg>cCg	p.L52P	CDRT15_ENST00000431716.2_Intron	NM_001007530.1	NP_001007531.1	Q96T59	CDRTF_HUMAN	CMT1A duplicated region transcript 15	52								p.L52P(1)		endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	6				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		GGCCTGCCCCAGGCTGTCCTG	0.602																																					p.L52P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T155C	17						.						9.0	9.0	9.0					17																	14139996		2180	4243	6423	14080721	SO:0001583	missense	146822	exon1			AF355097	CCDS32569.1	17p12	2012-11-19			ENSG00000223510	ENSG00000223510			14395	protein-coding gene	gene with protein product						11381029	Standard	NM_001007530		Approved		uc010vvu.2	Q96T59	OTTHUMG00000179686	ENST00000420162.2:c.155T>C	17.37:g.14139996A>G	ENSP00000402355:p.Leu52Pro	Somatic		Capture	Illumina HiSeq	Phase_I	14080721	NM_001007530	B2RUU5	Missense_Mutation	SNP	ENST00000420162.2	37	CCDS32569.1	.	.	.	.	.	.	.	.	.	.	a	0.023	-1.398317	0.01175	.	.	ENSG00000223510	ENST00000420162	T	0.49139	0.79	0.675	-0.987	0.10249	.	.	.	.	.	T	0.17619	0.0423	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16158	-1.0412	8	0.16896	T	0.51	.	.	.	.	.	52	Q96T59	CDRTF_HUMAN	P	52	ENSP00000402355:L52P	ENSP00000402355:L52P	L	-	2	0	CDRT15	14080721	0.131000	0.22433	0.000000	0.03702	0.005000	0.04900	-2.871000	0.00720	-1.104000	0.03015	-1.039000	0.02377	CTG		0.602	CDRT15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252853.1	NM_001007530	
SCARF1	8578	broad.mit.edu	37	17	1551208	1551208	+	5'Flank	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:1551208C>T	ENST00000263071.4	-	0	0				SCARF1_ENST00000348987.3_5'Flank|SCARF1_ENST00000571272.1_5'Flank|RILP_ENST00000301336.6_Missense_Mutation_p.A289T	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1						cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)	p.A289T(1)		cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		ACCTTCATGGCCTCGAGCAGA	0.607																																					p.A289T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G865A	17						.						124.0	91.0	102.0					17																	1551208		2203	4300	6503	1497958	SO:0001631	upstream_gene_variant	83547	exon6			D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"""scavenger receptor expressed by endothelial cells"", ""acetyl LDL receptor"""	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555		17.37:g.1551208C>T	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	1497958	NM_031430	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	.	.	.	.	.	.	.	.	.	.	C	35	5.519894	0.96416	.	.	ENSG00000167705	ENST00000301336	T	0.43688	0.94	5.6	5.6	0.85130	.	0.000000	0.64402	D	0.000002	T	0.58666	0.2138	L	0.46157	1.445	0.48185	D	0.999607	D	0.89917	1.0	D	0.76071	0.987	T	0.54596	-0.8270	10	0.42905	T	0.14	-15.1323	17.4134	0.87493	0.0:1.0:0.0:0.0	.	289	Q96NA2	RILP_HUMAN	T	289	ENSP00000301336:A289T	ENSP00000301336:A289T	A	-	1	0	RILP	1497958	0.997000	0.39634	1.000000	0.80357	0.897000	0.52465	3.876000	0.56115	2.636000	0.89361	0.655000	0.94253	GCC		0.607	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693	
HS3ST3B1	9953	broad.mit.edu	37	17	14248393	14248393	+	Silent	SNP	G	G	A	rs143567288	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:14248393G>A	ENST00000360954.2	+	2	1039	c.603G>A	c.(601-603)acG>acA	p.T201T		NM_006041.1	NP_006032.1	Q9Y662	HS3SB_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	201	Substrate binding. {ECO:0000250}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)	p.T201T(1)		large_intestine(3)|lung(3)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)		TGGAGAAGACGCCCAGTTACT	0.627																																					p.T201T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G603A	17						.						66.0	52.0	57.0					17																	14248393		2203	4299	6502	14189118	SO:0001819	synonymous_variant	9953	exon2			AF105377	CCDS11167.1	17p12	2007-04-02			ENSG00000125430	ENSG00000125430	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5198	protein-coding gene	gene with protein product		604058				9988767	Standard	NM_006041		Approved	3OST3B1, 30ST3B1	uc002goh.1	Q9Y662	OTTHUMG00000058810	ENST00000360954.2:c.603G>A	17.37:g.14248393G>A		Somatic		Capture	Illumina HiSeq	Phase_I	14189118	NM_006041	B3KN58|D3DTS6	Silent	SNP	ENST00000360954.2	37	CCDS11167.1																																																																																				0.627	HS3ST3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129998.1	NM_006041	
TEKT3	64518	broad.mit.edu	37	17	15231348	15231348	+	Silent	SNP	G	G	A	rs140014086	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:15231348G>A	ENST00000395930.1	-	4	810	c.624C>T	c.(622-624)atC>atT	p.I208I	TEKT3_ENST00000338696.2_Silent_p.I208I	NM_031898.2	NP_114104.1	Q9BXF9	TEKT3_HUMAN	tektin 3	208					cilium morphogenesis (GO:0060271)|regulation of fertilization (GO:0080154)|sperm motility (GO:0030317)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)		p.I208I(1)		endometrium(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	23				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		GAACTAGGTCGATTCCCATTC	0.408																																					p.I208I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C624T	17						.	G		1,4405	2.1+/-5.4	0,1,2202	228.0	180.0	197.0		624	-8.8	0.5	17	dbSNP_134	197	0,8600		0,0,4300	no	coding-synonymous	TEKT3	NM_031898.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		208/491	15231348	1,13005	2203	4300	6503	15172073	SO:0001819	synonymous_variant	64518	exon4			AF334676	CCDS11169.1	17p12	2011-05-23			ENSG00000125409	ENSG00000125409			14293	protein-coding gene	gene with protein product		612683				11381029, 14735490	Standard	NM_031898		Approved	FLJ32828	uc002gon.3	Q9BXF9	OTTHUMG00000058965	ENST00000395930.1:c.624C>T	17.37:g.15231348G>A		Somatic		Capture	Illumina HiSeq	Phase_I	15172073	NM_031898	B2RAS7|D3DTT0|Q8N5R5|Q96M48	Silent	SNP	ENST00000395930.1	37	CCDS11169.1																																																																																				0.408	TEKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130385.2	NM_031898	
RAI1	10743	broad.mit.edu	37	17	17699435	17699435	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:17699435G>A	ENST00000353383.1	+	3	3642	c.3173G>A	c.(3172-3174)cGt>cAt	p.R1058H	RAI1_ENST00000261641.6_Missense_Mutation_p.R1058H	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1058					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)	p.R1058H(1)		breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		ATGTGTACTCGTTCTCTCACG	0.706																																					p.R1058H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3173A	17						.						6.0	8.0	7.0					17																	17699435		2140	4218	6358	17640160	SO:0001583	missense	10743	exon3			AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.3173G>A	17.37:g.17699435G>A	ENSP00000323074:p.Arg1058His	Somatic		Capture	Illumina HiSeq	Phase_I	17640160	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	37	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.868163	0.51588	.	.	ENSG00000108557	ENST00000353383;ENST00000395776;ENST00000261641;ENST00000315321	T;T	0.80909	-1.43;-0.88	3.63	3.63	0.41609	.	0.000000	0.56097	D	0.000022	D	0.87208	0.6120	L	0.60455	1.87	0.39893	D	0.973799	D	0.89917	1.0	D	0.83275	0.996	D	0.89295	0.3622	10	0.62326	D	0.03	.	15.447	0.75238	0.0:0.0:1.0:0.0	.	1058	Q7Z5J4	RAI1_HUMAN	H	1058;1058;1058;1010	ENSP00000323074:R1058H;ENSP00000261641:R1058H	ENSP00000261641:R1058H	R	+	2	0	RAI1	17640160	1.000000	0.71417	0.914000	0.36105	0.345000	0.29048	6.335000	0.72949	1.867000	0.54127	0.491000	0.48974	CGT		0.706	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
MYO15A	51168	broad.mit.edu	37	17	18039938	18039938	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:18039938G>A	ENST00000205890.5	+	15	5055	c.4717G>A	c.(4717-4719)Gcg>Acg	p.A1573T		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	1573	Myosin motor.				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.A1573T(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)					CAGGGTCAACGCGCTGGTGTC	0.617																																					p.A1573T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4717A	17						.						59.0	62.0	61.0					17																	18039938		2180	4270	6450	17980663	SO:0001583	missense	51168	exon14			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.4717G>A	17.37:g.18039938G>A	ENSP00000205890:p.Ala1573Thr	Somatic		Capture	Illumina HiSeq	Phase_I	17980663	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	G	11.74	1.727387	0.30593	.	.	ENSG00000091536	ENST00000205890	D	0.87103	-2.21	5.7	2.23	0.28157	Myosin head, motor domain (2);	.	.	.	.	T	0.65407	0.2688	N	0.05124	-0.11	0.80722	D	1	P	0.34724	0.465	B	0.23716	0.048	T	0.61207	-0.7109	9	0.49607	T	0.09	.	2.4666	0.04554	0.2069:0.0:0.2901:0.503	.	1573	Q9UKN7	MYO15_HUMAN	T	1573	ENSP00000205890:A1573T	ENSP00000205890:A1573T	A	+	1	0	MYO15A	17980663	0.273000	0.24181	0.766000	0.31476	0.209000	0.24338	2.369000	0.44231	0.741000	0.32674	-0.314000	0.08810	GCG		0.617	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
FLII	2314	broad.mit.edu	37	17	18148540	18148540	+	Missense_Mutation	SNP	C	C	T	rs374452292		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:18148540C>T	ENST00000327031.4	-	30	3947	c.3722G>A	c.(3721-3723)cGg>cAg	p.R1241Q	FLII_ENST00000379450.4_Missense_Mutation_p.R1155Q|FLII_ENST00000545457.2_Missense_Mutation_p.R1186Q|FLII_ENST00000579294.1_Missense_Mutation_p.R1230Q|FLII_ENST00000578558.1_Missense_Mutation_p.G651S	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	1241					multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)	p.R1241Q(1)		central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					CAGGCGCAGCCGGCGCGGCCG	0.652													C|||	1	0.000199681	0.0	0.0	5008	,	,		19095	0.0		0.0	False		,,,				2504	0.001				p.R1241Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3722A	17						.	C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	83.0	88.0	86.0		3722	3.5	1.0	17		86	0,8600		0,0,4300	no	missense	FLII	NM_002018.2	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	1241/1270	18148540	1,13005	2203	4300	6503	18089265	SO:0001583	missense	2314	exon30			U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"""flightless I (Drosophila) homolog"""			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.3722G>A	17.37:g.18148540C>T	ENSP00000324573:p.Arg1241Gln	Somatic		Capture	Illumina HiSeq	Phase_I	18089265	NM_002018	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	37	CCDS11192.1	.	.	.	.	.	.	.	.	.	.	C	18.44	3.624108	0.66901	2.27E-4	0.0	ENSG00000177731	ENST00000327031;ENST00000545457;ENST00000379450	T;T	0.55413	0.52;0.52	5.54	3.53	0.40419	Gelsolin domain (1);	0.143577	0.45606	D	0.000359	T	0.24586	0.0596	N	0.02247	-0.625	0.38281	D	0.942434	B;B;B;B	0.32507	0.373;0.373;0.092;0.197	B;B;B;B	0.32677	0.15;0.15;0.021;0.044	T	0.15378	-1.0439	10	0.40728	T	0.16	-14.32	7.7116	0.28682	0.0:0.6562:0.0:0.3438	.	1155;1155;1241;1210	E7EPM0;B4DIL0;Q13045;B4DIX0	.;.;FLII_HUMAN;.	Q	1241;1120;1155	ENSP00000324573:R1241Q;ENSP00000368763:R1155Q	ENSP00000324573:R1241Q	R	-	2	0	FLII	18089265	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	3.864000	0.56024	1.349000	0.45751	0.655000	0.94253	CGG		0.652	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018	
FLII	2314	broad.mit.edu	37	17	18157444	18157444	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:18157444G>A	ENST00000327031.4	-	7	853	c.628C>T	c.(628-630)Cgc>Tgc	p.R210C	FLII_ENST00000379450.4_Missense_Mutation_p.R125C|FLII_ENST00000584444.1_5'UTR|FLII_ENST00000545457.2_Missense_Mutation_p.R156C|FLII_ENST00000579294.1_Missense_Mutation_p.R199C|FLII_ENST00000578558.1_Missense_Mutation_p.R210C	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	210	Interaction with LRRFIP1 and LRRFIP2.				multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)	p.R210C(1)		central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					CTCTGGGTGCGCTGGGTGCTC	0.706																																					p.R210C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C628T	17						.						32.0	32.0	32.0					17																	18157444		2201	4297	6498	18098169	SO:0001583	missense	2314	exon7			U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"""flightless I (Drosophila) homolog"""			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.628C>T	17.37:g.18157444G>A	ENSP00000324573:p.Arg210Cys	Somatic		Capture	Illumina HiSeq	Phase_I	18098169	NM_002018	B4DIL0|F5H407|J3QLG3	Missense_Mutation	SNP	ENST00000327031.4	37	CCDS11192.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.879761	0.72294	.	.	ENSG00000177731	ENST00000327031;ENST00000545457;ENST00000379450	T;T	0.24538	1.85;1.85	4.91	3.94	0.45596	.	0.000000	0.85682	D	0.000000	T	0.49029	0.1533	M	0.78049	2.395	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	1.0;1.0;0.999;1.0;0.999	T	0.51725	-0.8669	10	0.87932	D	0	-27.9968	9.916	0.41434	0.0742:0.0:0.7878:0.138	.	125;125;210;210;179	E7EPM0;B4DIL0;F5H407;Q13045;B4DIX0	.;.;.;FLII_HUMAN;.	C	210;210;125	ENSP00000324573:R210C;ENSP00000368763:R125C	ENSP00000324573:R210C	R	-	1	0	FLII	18098169	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	5.113000	0.64640	1.208000	0.43306	-0.136000	0.14681	CGC		0.706	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018	
MNT	4335	broad.mit.edu	37	17	2290542	2290542	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:2290542C>T	ENST00000174618.4	-	6	1807	c.1402G>A	c.(1402-1404)Gcc>Acc	p.A468T	RP1-59D14.1_ENST00000571775.1_RNA|MNT_ENST00000575374.1_5'Flank	NM_020310.2	NP_064706.1	Q99583	MNT_HUMAN	MAX network transcriptional repressor	468					cell aging (GO:0007569)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cell cycle (GO:0051726)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|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 coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.A468T(1)		endometrium(4)|large_intestine(5)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	12				Colorectal(2;1.37e-05)|READ - Rectum adenocarcinoma(2;8.68e-05)		GCGATGTGGGCGATGTGCTTG	0.662																																					p.A468T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1402A	17						.						49.0	46.0	47.0					17																	2290542		2200	4296	6496	2237292	SO:0001583	missense	4335	exon6			Y13444	CCDS11018.1	17p13.3	2013-11-15	2013-11-15		ENSG00000070444	ENSG00000070444		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	7188	protein-coding gene	gene with protein product	"""myc antagonist"", ""Max-interacting protein"""	603039	"""MAX binding protein"", ""MNT, MAX dimerization protein"""			9598315	Standard	NM_020310		Approved	ROX, MXD6, MAD6, bHLHd3	uc002fur.3	Q99583	OTTHUMG00000090603	ENST00000174618.4:c.1402G>A	17.37:g.2290542C>T	ENSP00000174618:p.Ala468Thr	Somatic		Capture	Illumina HiSeq	Phase_I	2237292	NM_020310	A8K6D1|D3DTI7|Q1ED38	Missense_Mutation	SNP	ENST00000174618.4	37	CCDS11018.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.107252	0.77096	.	.	ENSG00000070444	ENST00000174618;ENST00000404961	D	0.84516	-1.86	4.91	4.91	0.64330	.	0.000000	0.64402	D	0.000005	T	0.81678	0.4873	L	0.47716	1.5	0.58432	D	0.999991	D	0.52996	0.957	B	0.41332	0.354	D	0.83441	0.0043	10	0.45353	T	0.12	-16.4448	17.0679	0.86564	0.0:1.0:0.0:0.0	.	468	Q99583	MNT_HUMAN	T	468	ENSP00000174618:A468T	ENSP00000174618:A468T	A	-	1	0	MNT	2237292	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.491000	0.60326	2.274000	0.75844	0.591000	0.81541	GCC		0.662	MNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207158.1	NM_020310	
METTL16	79066	broad.mit.edu	37	17	2324079	2324079	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:2324079C>T	ENST00000263092.6	-	9	1135	c.1008G>A	c.(1006-1008)gcG>gcA	p.A336A	METTL16_ENST00000571669.2_5'UTR|METTL16_ENST00000538844.1_Silent_p.A118A	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	336							methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)	p.A336A(2)		kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						CTATGCCTTCCGCCGTCTCCG	0.448																																					p.A336A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1008A	17						.						183.0	176.0	178.0					17																	2324079		1936	4143	6079	2270829	SO:0001819	synonymous_variant	79066	exon9			AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"""methyltransferase 10 domain containing"""	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.1008G>A	17.37:g.2324079C>T		Somatic		Capture	Illumina HiSeq	Phase_I	2270829	NM_024086	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Silent	SNP	ENST00000263092.6	37	CCDS42232.1																																																																																				0.448	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086	
TOP3A	7156	broad.mit.edu	37	17	18194328	18194328	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:18194328C>T	ENST00000321105.5	-	12	1509	c.1295G>A	c.(1294-1296)cGa>cAa	p.R432Q	TOP3A_ENST00000542570.1_Missense_Mutation_p.R337Q|TOP3A_ENST00000540524.1_5'UTR	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	432					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.R432Q(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						CTCGTACAGTCGCTGTTCATC	0.517																																					p.R432Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1295A	17						.						82.0	79.0	80.0					17																	18194328		2203	4300	6503	18135053	SO:0001583	missense	7156	exon12			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.1295G>A	17.37:g.18194328C>T	ENSP00000321636:p.Arg432Gln	Somatic		Capture	Illumina HiSeq	Phase_I	18135053	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Missense_Mutation	SNP	ENST00000321105.5	37	CCDS11194.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.720396	0.68959	.	.	ENSG00000177302	ENST00000321105;ENST00000542570	T;T	0.24350	1.86;1.99	5.85	5.85	0.93711	DNA topoisomerase, type IA, core domain (1);DNA topoisomerase, type IA, central region, subdomain 3 (1);DNA topoisomerase, type IA, central (1);DNA topoisomerase, type IA, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.58906	0.2155	M	0.84433	2.695	0.80722	D	1	D;D	0.89917	0.994;1.0	P;D	0.77557	0.903;0.99	T	0.62647	-0.6810	10	0.72032	D	0.01	-11.4954	20.1577	0.98120	0.0:1.0:0.0:0.0	.	337;432	B4DK80;Q13472	.;TOP3A_HUMAN	Q	432;337	ENSP00000321636:R432Q;ENSP00000442336:R337Q	ENSP00000321636:R432Q	R	-	2	0	TOP3A	18135053	1.000000	0.71417	0.992000	0.48379	0.898000	0.52572	7.745000	0.85046	2.767000	0.95098	0.655000	0.94253	CGA		0.517	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2		
NOS2	4843	broad.mit.edu	37	17	26093545	26093545	+	Missense_Mutation	SNP	G	G	A	rs377596177		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:26093545G>A	ENST00000313735.6	-	19	2470	c.2237C>T	c.(2236-2238)cCg>cTg	p.P746L		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	746	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)	p.P746L(1)|p.P746Q(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	CCTGGATGTCGGACTTTGTAG	0.478																																					p.P746L												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C2237T	17						.	G	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	305.0	265.0	278.0		2237	-3.8	0.0	17		278	0,8600		0,0,4300	no	missense	NOS2	NM_000625.4	98	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	746/1154	26093545	1,13005	2203	4300	6503	23117672	SO:0001583	missense	4843	exon19			U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.2237C>T	17.37:g.26093545G>A	ENSP00000327251:p.Pro746Leu	Somatic		Capture	Illumina HiSeq	Phase_I	23117672	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Missense_Mutation	SNP	ENST00000313735.6	37	CCDS11223.1	.	.	.	.	.	.	.	.	.	.	G	0.020	-1.443201	0.01089	2.27E-4	0.0	ENSG00000007171	ENST00000313735;ENST00000379105	T	0.69806	-0.43	4.82	-3.75	0.04372	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.800727	0.11198	N	0.589197	T	0.46619	0.1402	L	0.41710	1.295	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.28138	-1.0053	10	0.36615	T	0.2	.	1.6762	0.02822	0.2817:0.1072:0.3853:0.2259	.	746	P35228	NOS2_HUMAN	L	746;707	ENSP00000327251:P746L	ENSP00000327251:P746L	P	-	2	0	NOS2	23117672	0.004000	0.15560	0.000000	0.03702	0.011000	0.07611	-0.054000	0.11826	-0.687000	0.05162	-2.681000	0.00142	CCG		0.478	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
NOS2	4843	broad.mit.edu	37	17	26106046	26106046	+	Silent	SNP	G	G	A	rs201471682		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:26106046G>A	ENST00000313735.6	-	10	1274	c.1041C>T	c.(1039-1041)taC>taT	p.Y347Y		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	347					arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)	p.Y347Y(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	CAGGCAGGGCGTACCACTTTA	0.498																																					p.Y347Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1041T	17						.						60.0	58.0	59.0					17																	26106046		2203	4300	6503	23130173	SO:0001819	synonymous_variant	4843	exon10			U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.1041C>T	17.37:g.26106046G>A		Somatic		Capture	Illumina HiSeq	Phase_I	23130173	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	37	CCDS11223.1																																																																																				0.498	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
KIAA0100	9703	broad.mit.edu	37	17	26961787	26961787	+	Missense_Mutation	SNP	G	G	A	rs117034424		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:26961787G>A	ENST00000528896.2	-	16	2892	c.2818C>T	c.(2818-2820)Cgc>Tgc	p.R940C	RP11-192H23.7_ENST00000577814.1_RNA|KIAA0100_ENST00000544884.1_Missense_Mutation_p.R797C|KIAA0100_ENST00000389003.3_Missense_Mutation_p.R797C|RP11-192H23.7_ENST00000583787.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	940						extracellular region (GO:0005576)		p.R940C(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)					ATGTTTTTGCGTTCCAAAGAG	0.527													G|||	1	0.000199681	0.0	0.0	5008	,	,		20377	0.0		0.001	False		,,,				2504	0.0				p.R940C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2818T	17						.	G	CYS/ARG	0,4406		0,0,2203	161.0	167.0	165.0		2818	5.9	1.0	17	dbSNP_133	165	2,8598	2.2+/-6.3	0,2,4298	yes	missense	KIAA0100	NM_014680.3	180	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	940/2236	26961787	2,13004	2203	4300	6503	23985914	SO:0001583	missense	9703	exon16			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.2818C>T	17.37:g.26961787G>A	ENSP00000436773:p.Arg940Cys	Somatic		Capture	Illumina HiSeq	Phase_I	23985914	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	15.06	2.720224	0.48728	0.0	2.33E-4	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.24538	1.85;1.85	5.9	5.9	0.94986	.	0.166906	0.47852	D	0.000208	T	0.22513	0.0543	L	0.39898	1.24	0.51233	D	0.99991	P	0.49635	0.926	B	0.39660	0.306	T	0.01516	-1.1335	10	0.72032	D	0.01	5.3312	13.196	0.59738	0.0:0.0:0.7376:0.2624	.	940	Q14667	K0100_HUMAN	C	940;910;940;797	ENSP00000436773:R940C;ENSP00000446443:R797C	ENSP00000005905:R940C	R	-	1	0	KIAA0100	23985914	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.414000	0.52693	2.796000	0.96246	0.563000	0.77884	CGC		0.527	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680	
SUPT6H	6830	broad.mit.edu	37	17	27014352	27014352	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:27014352G>A	ENST00000314616.6	+	23	3152	c.2869G>A	c.(2869-2871)Gcc>Acc	p.A957T	SUPT6H_ENST00000347486.4_Missense_Mutation_p.A957T	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	957	Interaction with KDM6A. {ECO:0000250}.				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.A957T(2)		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)					GCTGCTCAACGCCTTGTACTG	0.527																																					p.A957T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2869A	17						.						114.0	101.0	105.0					17																	27014352		2203	4300	6503	24038479	SO:0001583	missense	6830	exon23			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		ENST00000314616.6:c.2869G>A	17.37:g.27014352G>A	ENSP00000319104:p.Ala957Thr	Somatic		Capture	Illumina HiSeq	Phase_I	24038479	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	G	17.29	3.351701	0.61183	.	.	ENSG00000109111	ENST00000314616	.	.	.	5.83	4.85	0.62838	Tex-like domain (1);	0.051425	0.85682	D	0.000000	T	0.37320	0.0999	L	0.39147	1.195	0.58432	D	0.999999	P	0.42620	0.785	B	0.30943	0.122	T	0.18555	-1.0333	9	0.19590	T	0.45	-11.4847	13.8003	0.63196	0.0:0.0:0.7208:0.2792	.	957	Q7KZ85	SPT6H_HUMAN	T	957	.	ENSP00000319104:A957T	A	+	1	0	SUPT6H	24038479	1.000000	0.71417	0.958000	0.39756	0.975000	0.68041	4.175000	0.58263	1.432000	0.47375	0.557000	0.71058	GCC		0.527	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
SUPT6H	6830	broad.mit.edu	37	17	27024961	27024961	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:27024961A>C	ENST00000314616.6	+	32	4644	c.4361A>C	c.(4360-4362)aAg>aCg	p.K1454T	SUPT6H_ENST00000347486.4_Missense_Mutation_p.K1454T	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1454					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.K1454T(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)					AAGAAGGAGAAGCCCACCTTC	0.532																																					p.K1454T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4361C	17						.						105.0	99.0	101.0					17																	27024961		2203	4300	6503	24049088	SO:0001583	missense	6830	exon32			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		ENST00000314616.6:c.4361A>C	17.37:g.27024961A>C	ENSP00000319104:p.Lys1454Thr	Somatic		Capture	Illumina HiSeq	Phase_I	24049088	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	A	16.62	3.172885	0.57584	.	.	ENSG00000109111	ENST00000314616	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.53077	0.1774	L	0.29908	0.895	0.80722	D	1	B	0.22276	0.067	B	0.22601	0.04	T	0.51795	-0.8660	9	0.56958	D	0.05	-22.5459	15.7888	0.78332	1.0:0.0:0.0:0.0	.	1454	Q7KZ85	SPT6H_HUMAN	T	1454	.	ENSP00000319104:K1454T	K	+	2	0	SUPT6H	24049088	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.852000	0.92215	2.144000	0.66660	0.460000	0.39030	AAG		0.532	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
SUPT6H	6830	broad.mit.edu	37	17	27028638	27028638	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:27028638C>T	ENST00000314616.6	+	37	5459	c.5176C>T	c.(5176-5178)Cgg>Tgg	p.R1726W	PROCA1_ENST00000579650.1_5'Flank|SUPT6H_ENST00000347486.4_Missense_Mutation_p.R1726W	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1726	Interaction with histone H2B and H3.				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.R1726W(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)					CGAGATGGATCGGTAGGGGGC	0.632																																					p.R1726W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5176T	17						.						44.0	41.0	42.0					17																	27028638		2202	4296	6498	24052765	SO:0001583	missense	6830	exon37			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		ENST00000314616.6:c.5176C>T	17.37:g.27028638C>T	ENSP00000319104:p.Arg1726Trp	Somatic		Capture	Illumina HiSeq	Phase_I	24052765	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.850505	0.91277	.	.	ENSG00000109111	ENST00000314616;ENST00000347486	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.72977	0.3528	L	0.51422	1.61	0.80722	D	1	D	0.76494	0.999	P	0.59171	0.853	T	0.75491	-0.3299	9	0.87932	D	0	.	19.2404	0.93879	0.0:1.0:0.0:0.0	.	1726	Q7KZ85	SPT6H_HUMAN	W	1726;726	.	ENSP00000319104:R1726W	R	+	1	2	SUPT6H	24052765	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.301000	0.78850	2.554000	0.86153	0.462000	0.41574	CGG		0.632	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
TRAF4	9618	broad.mit.edu	37	17	27074909	27074909	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:27074909C>T	ENST00000262395.5	+	3	373	c.244C>T	c.(244-246)Cgc>Tgc	p.R82C	TRAF4_ENST00000444415.3_Missense_Mutation_p.R82C|AC010761.10_ENST00000579468.1_RNA|AC010761.9_ENST00000577325.1_RNA|TRAF4_ENST00000262396.6_Missense_Mutation_p.R82C	NM_004295.3	NP_004286.2	Q9BUZ4	TRAF4_HUMAN	TNF receptor-associated factor 4	82					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein kinase activity (GO:0045860)|regulation of apoptotic process (GO:0042981)|respiratory gaseous exchange (GO:0007585)|respiratory tube development (GO:0030323)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	DNA binding (GO:0003677)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|WW domain binding (GO:0050699)|zinc ion binding (GO:0008270)	p.R82C(1)		endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10	Lung NSC(42;0.01)		Epithelial(11;3.26e-05)|all cancers(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.235)			CCTGCCTATCCGCTGCATCCA	0.622																																					p.R82C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C244T	17						.						69.0	56.0	60.0					17																	27074909		2203	4299	6502	24099036	SO:0001583	missense	9618	exon3			X80200	CCDS11243.1	17q11-q21.3	2013-01-09			ENSG00000076604	ENSG00000076604		"""RING-type (C3HC4) zinc fingers"""	12034	protein-coding gene	gene with protein product		602464				7592751, 7490069	Standard	NM_004295		Approved	CART1, MLN62, RNF83	uc002hcs.3	Q9BUZ4	OTTHUMG00000132677	ENST00000262395.5:c.244C>T	17.37:g.27074909C>T	ENSP00000262395:p.Arg82Cys	Somatic		Capture	Illumina HiSeq	Phase_I	24099036	NM_004295	O75615|Q14848|Q2KJU4|Q2PJN8	Missense_Mutation	SNP	ENST00000262395.5	37	CCDS11243.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.036073	0.54896	.	.	ENSG00000076604	ENST00000262395;ENST00000454852;ENST00000422344;ENST00000444415;ENST00000262396	T;T;T;T	0.27104	1.73;1.73;1.73;1.69	5.19	4.2	0.49525	TRAF-like (1);Seven In Absentia Homolog-type (1);	0.053822	0.85682	D	0.000000	T	0.41143	0.1146	L	0.58428	1.81	0.80722	D	1	D;P	0.76494	0.999;0.938	P;B	0.59487	0.858;0.287	T	0.20273	-1.0280	10	0.39692	T	0.17	.	13.4029	0.60893	0.0:0.8409:0.1591:0.0	.	82;82	Q9BUZ4;Q9BUZ4-2	TRAF4_HUMAN;.	C	82;82;89;82;82	ENSP00000262395:R82C;ENSP00000415789:R89C;ENSP00000438154:R82C;ENSP00000262396:R82C	ENSP00000262395:R82C	R	+	1	0	TRAF4	24099036	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.024000	0.57218	1.380000	0.46344	0.555000	0.69702	CGC		0.622	TRAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255944.2	NM_145751	
FAM222B	55731	broad.mit.edu	37	17	27085689	27085689	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:27085689T>C	ENST00000341217.5	-	3	1503	c.1288A>G	c.(1288-1290)Acc>Gcc	p.T430A	FAM222B_ENST00000452648.3_Missense_Mutation_p.T430A|FAM222B_ENST00000581407.1_Missense_Mutation_p.T430A|FAM222B_ENST00000582266.1_3'UTR	NM_018182.2	NP_060652.2	Q8WU58	F222B_HUMAN	family with sequence similarity 222, member B	430								p.T430A(1)									GGGGATGGGGTCGGCTTTTCC	0.612																																					p.R429R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1287G	17						.						14.0	14.0	14.0					17																	27085689		1987	4144	6131	24109816	SO:0001583	missense	55731	exon3			AK001562	CCDS45637.1, CCDS74022.1	17q11.2	2012-04-27	2012-04-27	2012-04-27	ENSG00000173065	ENSG00000173065			25563	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 63"""	C17orf63			Standard	NM_001288631		Approved	FLJ10700	uc010way.1	Q8WU58		ENST00000341217.5:c.1288A>G	17.37:g.27085689T>C	ENSP00000343115:p.Thr430Ala	Somatic		Capture	Illumina HiSeq	Phase_I	24109816	NM_001077498	Q9H6F3|Q9NVJ4|Q9NXN6	Missense_Mutation	SNP	ENST00000341217.5	37	CCDS45637.1	.	.	.	.	.	.	.	.	.	.	T	14.20	2.465713	0.43839	.	.	ENSG00000173065	ENST00000341217;ENST00000452648	T;T	0.31510	1.49;1.49	4.9	4.9	0.64082	.	0.053520	0.64402	D	0.000001	T	0.47857	0.1468	L	0.47716	1.5	0.80722	D	1	D	0.67145	0.996	D	0.75484	0.986	T	0.46331	-0.9199	10	0.59425	D	0.04	-10.8651	13.8577	0.63540	0.0:0.0:0.0:1.0	.	430	Q8WU58	CQ063_HUMAN	A	430	ENSP00000343115:T430A;ENSP00000413645:T430A	ENSP00000343115:T430A	T	-	1	0	C17orf63	24109816	1.000000	0.71417	0.974000	0.42286	0.884000	0.51177	3.776000	0.55356	2.046000	0.60703	0.533000	0.62120	ACC		0.612	FAM222B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446703.1	NM_018182	
CLUH	23277	broad.mit.edu	37	17	2594934	2594934	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:2594934C>T	ENST00000570628.2	-	25	3820	c.3715G>A	c.(3715-3717)Gtc>Atc	p.V1239I	CLUH_ENST00000538975.1_Missense_Mutation_p.V1239I|RP11-74E22.6_ENST00000608984.1_lincRNA|CLUH_ENST00000435359.1_Missense_Mutation_p.V1239I			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	1239					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)		p.V1240I(1)									CCGTTAATGACGTTCAGCTGC	0.667																																					p.V1239I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3715A	17						.						24.0	28.0	27.0					17																	2594934		2002	4159	6161	2541684	SO:0001583	missense	23277	exon25			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.3715G>A	17.37:g.2594934C>T	ENSP00000458986:p.Val1239Ile	Somatic		Capture	Illumina HiSeq	Phase_I	2541684	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	37	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	C	10.95	1.496613	0.26861	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	T;T	0.80653	-1.4;-1.4	4.94	2.91	0.33838	.	0.121318	0.53938	N	0.000046	T	0.52468	0.1736	N	0.03608	-0.345	0.33110	D	0.540343	B;B	0.13594	0.008;0.006	B;B	0.08055	0.003;0.003	T	0.51576	-0.8688	10	0.11182	T	0.66	.	6.2449	0.20811	0.0:0.6381:0.0:0.3619	.	1239;1240	O75153;C9J6D7	K0664_HUMAN;.	I	1239;1240;1239	ENSP00000388872:V1239I;ENSP00000439628:V1239I	ENSP00000320468:V1240I	V	-	1	0	KIAA0664	2541684	1.000000	0.71417	0.999000	0.59377	0.939000	0.58152	3.700000	0.54786	1.305000	0.44909	0.591000	0.81541	GTC		0.667	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	
CLUH	23277	broad.mit.edu	37	17	2597803	2597803	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:2597803G>A	ENST00000570628.2	-	17	2896	c.2791C>T	c.(2791-2793)Cgg>Tgg	p.R931W	CLUH_ENST00000538975.1_Missense_Mutation_p.R931W|CLUH_ENST00000435359.1_Missense_Mutation_p.R931W			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	931					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)		p.R932W(1)									GAGATCTCCCGCAGGAGCGTT	0.667																																					p.R931W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2791T	17						.						52.0	56.0	55.0					17																	2597803		2005	4158	6163	2544553	SO:0001583	missense	23277	exon17			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.2791C>T	17.37:g.2597803G>A	ENSP00000458986:p.Arg931Trp	Somatic		Capture	Illumina HiSeq	Phase_I	2544553	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Missense_Mutation	SNP	ENST00000570628.2	37	CCDS45572.1	.	.	.	.	.	.	.	.	.	.	g	22.4	4.285594	0.80803	.	.	ENSG00000132361	ENST00000435359;ENST00000322335;ENST00000538975	D;D	0.91792	-2.91;-2.91	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	D	0.96605	0.8892	M	0.92026	3.265	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97099	0.9796	10	0.87932	D	0	.	13.0928	0.59174	0.0:0.0:0.8397:0.1603	.	931;932	O75153;C9J6D7	K0664_HUMAN;.	W	931;932;931	ENSP00000388872:R931W;ENSP00000439628:R931W	ENSP00000320468:R932W	R	-	1	2	KIAA0664	2544553	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	5.550000	0.67268	2.520000	0.84964	0.556000	0.70494	CGG		0.667	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	
EFCAB5	374786	broad.mit.edu	37	17	28320332	28320332	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:28320332A>C	ENST00000394835.3	+	5	1109	c.917A>C	c.(916-918)aAg>aCg	p.K306T	EFCAB5_ENST00000378738.3_Missense_Mutation_p.K306T|EFCAB5_ENST00000536908.2_Missense_Mutation_p.K250T|EFCAB5_ENST00000541045.1_Intron|EFCAB5_ENST00000320856.5_Missense_Mutation_p.K306T|EFCAB5_ENST00000394832.2_Missense_Mutation_p.K306T|EFCAB5_ENST00000534836.2_3'UTR	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	306							calcium ion binding (GO:0005509)	p.K306T(1)		breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						ATGATTCCTAAGTCAGTGGTA	0.438																																					p.K250T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A749C	17						.						86.0	80.0	82.0					17																	28320332		1858	4112	5970	25344458	SO:0001583	missense	374786	exon5			AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"""EF-hand domain containing"""	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.917A>C	17.37:g.28320332A>C	ENSP00000378312:p.Lys306Thr	Somatic		Capture	Illumina HiSeq	Phase_I	25344458	NM_001145053	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	37	CCDS11254.2	.	.	.	.	.	.	.	.	.	.	A	10.58	1.389350	0.25118	.	.	ENSG00000176927	ENST00000536908;ENST00000534836;ENST00000394835;ENST00000320856;ENST00000394832;ENST00000378738;ENST00000423598;ENST00000419434	T;T;T;T;T;T	0.69435	0.94;0.94;-0.4;0.94;0.94;0.94	5.26	3.04	0.35103	EF-hand-like domain (1);	0.965679	0.08532	N	0.931870	T	0.42562	0.1208	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.22800	0.044;0.044;0.075;0.0;0.018	B;B;B;B;B	0.18871	0.023;0.014;0.023;0.001;0.014	T	0.28902	-1.0029	10	0.26408	T	0.33	-0.5522	4.4323	0.11533	0.1752:0.0919:0.0:0.7329	.	250;306;306;306;306	F5GYL2;A8MSY9;B5MEA3;E7EVS9;A4FU69	.;.;.;.;EFCB5_HUMAN	T	250;47;306;306;306;306;250;112	ENSP00000440619:K250T;ENSP00000378312:K306T;ENSP00000322003:K306T;ENSP00000378309:K306T;ENSP00000368012:K306T;ENSP00000417009:K112T	ENSP00000322003:K306T	K	+	2	0	EFCAB5	25344458	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.254000	0.18314	0.454000	0.26884	-0.302000	0.09304	AAG		0.438	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
ATAD5	79915	broad.mit.edu	37	17	29220855	29220855	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:29220855C>A	ENST00000321990.4	+	21	5362	c.4984C>A	c.(4984-4986)Ctt>Att	p.L1662I		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1662					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)	p.L1662I(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				CTTAGATGCACTTTTAACTGA	0.358																																					p.L1662I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4984A	17						.						186.0	191.0	189.0					17																	29220855		2203	4300	6503	26244981	SO:0001583	missense	79915	exon21				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.4984C>A	17.37:g.29220855C>A	ENSP00000313171:p.Leu1662Ile	Somatic		Capture	Illumina HiSeq	Phase_I	26244981	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	.	.	.	.	.	.	.	.	.	.	C	13.53	2.263403	0.39995	.	.	ENSG00000176208	ENST00000321990	T	0.06608	3.28	6.08	1.63	0.23807	.	0.896444	0.09667	N	0.771625	T	0.07773	0.0195	L	0.60455	1.87	0.20074	N	0.999939	P	0.42456	0.78	B	0.38106	0.265	T	0.30327	-0.9982	10	0.56958	D	0.05	.	6.5439	0.22394	0.0:0.3892:0.3828:0.228	.	1662	Q96QE3	ATAD5_HUMAN	I	1662	ENSP00000313171:L1662I	ENSP00000313171:L1662I	L	+	1	0	ATAD5	26244981	0.198000	0.23374	0.480000	0.27341	0.991000	0.79684	0.356000	0.20181	0.433000	0.26313	0.591000	0.81541	CTT		0.358	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
C17orf97	400566	broad.mit.edu	37	17	263194	263194	+	Missense_Mutation	SNP	G	G	A	rs141704289		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:263194G>A	ENST00000360127.6	+	2	576	c.560G>A	c.(559-561)cGc>cAc	p.R187H	C17orf97_ENST00000571106.1_Intron|AC108004.3_ENST00000466740.2_RNA	NM_001013672.4	NP_001013694.4	Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	187								p.R187H(1)		breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						GAAAGGATTCGCATCTATAAA	0.567																																					p.R187H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G560A	17						.	G	HIS/ARG	0,4406		0,0,2203	69.0	77.0	74.0		560	4.0	0.8	17	dbSNP_134	74	2,8598	2.2+/-6.3	0,2,4298	no	missense	C17orf97	NM_001013672.4	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging	187/424	263194	2,13004	2203	4300	6503	263510	SO:0001583	missense	400566	exon2			AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000360127.6:c.560G>A	17.37:g.263194G>A	ENSP00000353245:p.Arg187His	Somatic		Capture	Illumina HiSeq	Phase_I	263510	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Missense_Mutation	SNP	ENST00000360127.6	37	CCDS32519.2	.	.	.	.	.	.	.	.	.	.	G	18.24	3.580784	0.65992	0.0	2.33E-4	ENSG00000187624	ENST00000360127;ENST00000491373	T;T	0.58210	0.97;0.35	5.02	4.04	0.47022	.	0.000000	0.42053	D	0.000771	T	0.56321	0.1977	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.52026	-0.8630	10	0.40728	T	0.16	-9.5216	8.414	0.32659	0.1021:0.0:0.8979:0.0	.	187	Q6ZQX7-4	.	H	187;181	ENSP00000353245:R187H;ENSP00000419482:R181H	ENSP00000353245:R187H	R	+	2	0	C17orf97	263510	0.864000	0.29904	0.841000	0.33234	0.478000	0.33099	2.096000	0.41738	2.715000	0.92844	0.655000	0.94253	CGC		0.567	C17orf97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255648.4	NM_001013672	
ADAP2	55803	broad.mit.edu	37	17	29283267	29283267	+	Silent	SNP	C	C	T	rs547065779		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:29283267C>T	ENST00000330889.3	+	10	1226	c.891C>T	c.(889-891)ttC>ttT	p.F297F	AC091177.1_ENST00000442757.1_RNA|ADAP2_ENST00000580525.1_Silent_p.F303F	NM_018404.2	NP_060874.1	Q9NPF8	ADAP2_HUMAN	ArfGAP with dual PH domains 2	297	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				heart development (GO:0007507)|regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|mitochondrial envelope (GO:0005740)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)	p.F297F(1)|p.?(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						AGGATGCCTTCGAGCAGGGCC	0.567																																					p.F297F												.	.	2	Unknown(1)|Substitution - coding silent(1)	large_intestine(1)|central_nervous_system(1)	c.C891T	17						.						47.0	45.0	45.0					17																	29283267		2203	4300	6503	26307393	SO:0001819	synonymous_variant	55803	exon10			AJ238994	CCDS11261.1	17q11.2	2013-01-10	2008-09-22	2008-09-22	ENSG00000184060	ENSG00000184060		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16487	protein-coding gene	gene with protein product		608635	"""centaurin, alpha 2"""	CENTA2			Standard	XM_005258008		Approved		uc002hfx.3	Q9NPF8	OTTHUMG00000132868	ENST00000330889.3:c.891C>T	17.37:g.29283267C>T		Somatic		Capture	Illumina HiSeq	Phase_I	26307393	NM_018404	Q8N4Q6|Q96SD5	Silent	SNP	ENST00000330889.3	37	CCDS11261.1																																																																																				0.567	ADAP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256346.1	NM_018404	
RAB11FIP4	84440	broad.mit.edu	37	17	29848319	29848319	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:29848319C>T	ENST00000325874.8	+	5	928	c.699C>T	c.(697-699)tgC>tgT	p.C233C	RN7SL45P_ENST00000578050.1_RNA|RAB11FIP4_ENST00000394744.2_Silent_p.C131C	NM_032932.3	NP_116321.2	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	233	Necessary for interaction with RAB11A, subcellular location, homo- or heterooligomerization.				cytokinesis (GO:0000910)|transport (GO:0006810)|viral process (GO:0016032)	cleavage furrow (GO:0032154)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|midbody (GO:0030496)|recycling endosome membrane (GO:0055038)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.C233C(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				GCAGCCCTTGCCCCGATGATG	0.567																																					p.C233C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C699T	17						.						141.0	107.0	118.0					17																	29848319		2203	4300	6503	26872439	SO:0001819	synonymous_variant	84440	exon5			AB058724	CCDS11267.1	17q11.2	2013-01-10			ENSG00000131242	ENSG00000131242		"""EF-hand domain containing"""	30267	protein-coding gene	gene with protein product		611999				11347906, 11468690	Standard	NM_032932		Approved	RAB11-FIP4, KIAA1821, MGC11316, FLJ00131	uc002hgn.1	Q86YS3	OTTHUMG00000132787	ENST00000325874.8:c.699C>T	17.37:g.29848319C>T		Somatic		Capture	Illumina HiSeq	Phase_I	26872439	NM_032932	Q52LI1|Q8N829|Q8NDT7|Q969D8	Silent	SNP	ENST00000325874.8	37	CCDS11267.1																																																																																				0.567	RAB11FIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256195.2	NM_032932	
CDK5R1	8851	broad.mit.edu	37	17	30815051	30815051	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:30815051C>T	ENST00000313401.3	+	2	1102	c.413C>T	c.(412-414)aCg>aTg	p.T138M		NM_003885.2	NP_003876.1	Q15078	CD5R1_HUMAN	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	138					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|brain development (GO:0007420)|cell proliferation (GO:0008283)|cerebellum development (GO:0021549)|embryo development (GO:0009790)|ephrin receptor signaling pathway (GO:0048013)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|hippocampus development (GO:0021766)|ionotropic glutamate receptor signaling pathway (GO:0035235)|layer formation in cerebral cortex (GO:0021819)|negative regulation of axon extension (GO:0030517)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein targeting to membrane (GO:0090314)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of neuron differentiation (GO:0045664)|rhythmic process (GO:0048511)|serine phosphorylation of STAT3 protein (GO:0033136)|superior olivary nucleus maturation (GO:0021722)	axon (GO:0030424)|contractile fiber (GO:0043292)|cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|cyclin-dependent protein kinase 5 activator activity (GO:0016534)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)	p.T138M(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.0938)			TCCGCAGGGACGCCCAAACGG	0.687																																					p.T138M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C413T	17						.						35.0	39.0	38.0					17																	30815051		2203	4300	6503	27839164	SO:0001583	missense	8851	exon2			X80343	CCDS11273.1	17q12	2006-03-28			ENSG00000176749	ENSG00000176749			1775	protein-coding gene	gene with protein product		603460				8090221	Standard	NM_003885		Approved	p35nck5a, Nck5a	uc002hhn.3	Q15078	OTTHUMG00000132814	ENST00000313401.3:c.413C>T	17.37:g.30815051C>T	ENSP00000318486:p.Thr138Met	Somatic		Capture	Illumina HiSeq	Phase_I	27839164	NM_003885	E1P664|Q5U0G3	De_novo_Start_OutOfFrame	SNP	ENST00000313401.3	37	CCDS11273.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.613603	0.87359	.	.	ENSG00000176749	ENST00000313401	T	0.77489	-1.1	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000001	D	0.83220	0.5207	L	0.50333	1.59	0.54753	D	0.999989	D	0.63880	0.993	P	0.60236	0.871	T	0.82335	-0.0508	10	0.41790	T	0.15	-17.1575	16.9953	0.86366	0.0:1.0:0.0:0.0	.	138	Q15078	CD5R1_HUMAN	M	138	ENSP00000318486:T138M	ENSP00000318486:T138M	T	+	2	0	CDK5R1	27839164	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.293000	0.78740	2.609000	0.88269	0.557000	0.71058	ACG		0.687	CDK5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256264.1	NM_003885	
MYO1D	4642	broad.mit.edu	37	17	31048090	31048090	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:31048090G>A	ENST00000318217.5	-	15	2168	c.1864C>T	c.(1864-1866)Cgt>Tgt	p.R622C	MYO1D_ENST00000579584.1_Missense_Mutation_p.R622C|MYO1D_ENST00000394649.4_Missense_Mutation_p.R534C	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	622	Myosin motor.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.R622C(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			CCTGCCCGACGCACTCTCACA	0.468																																					p.R622C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1864T	17						.						151.0	151.0	151.0					17																	31048090		2203	4300	6503	28072203	SO:0001583	missense	4642	exon15			AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"""Myosins / Myosin superfamily : Class I"""	7598	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 108"""	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.1864C>T	17.37:g.31048090G>A	ENSP00000324527:p.Arg622Cys	Somatic		Capture	Illumina HiSeq	Phase_I	28072203	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	37	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	G	33	5.260918	0.95368	.	.	ENSG00000176658	ENST00000318217	T	0.73469	-0.75	5.21	5.21	0.72293	Myosin head, motor domain (2);	0.000000	0.36703	U	0.002460	D	0.85362	0.5679	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.86569	0.1846	10	0.87932	D	0	.	16.289	0.82738	0.0:0.0:1.0:0.0	.	533;622	Q7Z3N6;O94832	.;MYO1D_HUMAN	C	622	ENSP00000324527:R622C	ENSP00000324527:R622C	R	-	1	0	MYO1D	28072203	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	6.331000	0.72929	2.716000	0.92895	0.561000	0.74099	CGT		0.468	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1		
SLFN11	91607	broad.mit.edu	37	17	33689956	33689956	+	Missense_Mutation	SNP	G	G	A	rs114962374	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:33689956G>A	ENST00000394566.1	-	4	1143	c.871C>T	c.(871-873)Cgc>Tgc	p.R291C	SLFN11_ENST00000308377.4_Missense_Mutation_p.R291C	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	291					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.R291C(1)		autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GTTATCGGGCGTTGGGGTTGG	0.423													G|||	16	0.00319489	0.0121	0.0	5008	,	,		20181	0.0		0.0	False		,,,				2504	0.0				p.R291C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C871T	17						.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	34,4372	39.2+/-71.8	0,34,2169	198.0	198.0	198.0		871,871,871,871,871	-8.6	0.0	17	dbSNP_132	198	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	SLFN11	NM_001104587.1,NM_001104588.1,NM_001104589.1,NM_001104590.1,NM_152270.3	180,180,180,180,180	0,34,6469	AA,AG,GG		0.0,0.7717,0.2614	benign,benign,benign,benign,benign	291/902,291/902,291/902,291/902,291/902	33689956	34,12972	2203	4300	6503	30714069	SO:0001583	missense	91607	exon3			AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.871C>T	17.37:g.33689956G>A	ENSP00000378067:p.Arg291Cys	Somatic		Capture	Illumina HiSeq	Phase_I	30714069	NM_001104589	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	6.455	0.452023	0.12283	0.007717	0.0	ENSG00000172716	ENST00000308377;ENST00000394566	T;T	0.59638	0.25;0.25	4.32	-8.65	0.00870	.	6.153270	0.00550	N	0.000256	T	0.12305	0.0299	N	0.01705	-0.755	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.13899	-1.0492	10	0.45353	T	0.12	.	1.855	0.03177	0.1698:0.2828:0.3442:0.2032	.	291	Q7Z7L1	SLN11_HUMAN	C	291	ENSP00000312402:R291C;ENSP00000378067:R291C	ENSP00000312402:R291C	R	-	1	0	SLFN11	30714069	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.766000	0.00372	-1.793000	0.01258	-0.966000	0.02617	CGC		0.423	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270	
MYO19	80179	broad.mit.edu	37	17	34856777	34856777	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:34856777C>T	ENST00000431794.3	-	23	2792	c.2270G>A	c.(2269-2271)cGt>cAt	p.R757H	MYO19_ENST00000268852.9_Missense_Mutation_p.R557H	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	757	Myosin motor.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R757H(1)		endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CACCCGGGCACGCCCACATTC	0.662																																					p.R757H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2270A	17						.						21.0	25.0	24.0					17																	34856777		2121	4239	6360	31930890	SO:0001583	missense	80179	exon24			BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"""Myosins / Myosin superfamily : Class XIX"""	26234	protein-coding gene	gene with protein product			"""myosin head domain containing 1"""	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.2270G>A	17.37:g.34856777C>T	ENSP00000409936:p.Arg757His	Somatic		Capture	Illumina HiSeq	Phase_I	31930890	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.967170	0.92855	.	.	ENSG00000141140	ENST00000431794;ENST00000268852	T;T	0.68181	-0.31;-0.31	5.12	5.12	0.69794	Myosin head, motor domain (1);	0.000000	0.38605	N	0.001627	D	0.83792	0.5331	M	0.87269	2.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.915;0.999	D	0.86672	0.1911	10	0.87932	D	0	.	15.6285	0.76882	0.0:1.0:0.0:0.0	.	757;557	Q96H55;Q96H55-4	MYO19_HUMAN;.	H	757;557	ENSP00000409936:R757H;ENSP00000268852:R557H	ENSP00000268852:R557H	R	-	2	0	MYO19	31930890	0.997000	0.39634	0.993000	0.49108	0.832000	0.47134	6.319000	0.72871	2.532000	0.85374	0.462000	0.41574	CGT		0.662	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
SYNRG	11276	broad.mit.edu	37	17	35936514	35936514	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:35936514C>T	ENST00000339208.6	-	8	966	c.826G>A	c.(826-828)Gtg>Atg	p.V276M	SYNRG_ENST00000394378.2_Missense_Mutation_p.V198M|SYNRG_ENST00000345615.4_Missense_Mutation_p.V198M|SYNRG_ENST00000591288.1_Missense_Mutation_p.V198M|SYNRG_ENST00000585472.1_Missense_Mutation_p.V197M|SYNRG_ENST00000588194.1_5'UTR|SYNRG_ENST00000502449.2_Missense_Mutation_p.V198M|SYNRG_ENST00000346661.4_Missense_Mutation_p.V276M	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	276					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)	p.V276M(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						AATACTCCCACACCTAGAAGG	0.433																																					p.V276M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G826A	17						.						67.0	67.0	67.0					17																	35936514		2203	4300	6503	33010627	SO:0001583	missense	11276	exon8			AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"""gamma-synergin"", ""adaptor-related protein complex 1 gamma subunit-binding protein 1"""	607291	"""AP1 gamma subunit binding protein 1"""	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.826G>A	17.37:g.35936514C>T	ENSP00000343610:p.Val276Met	Somatic		Capture	Illumina HiSeq	Phase_I	33010627	NM_007247	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	37	CCDS11321.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.382281	0.82792	.	.	ENSG00000006114	ENST00000346661;ENST00000339208;ENST00000345615;ENST00000502449;ENST00000394378	T;T;T	0.52295	1.09;0.67;0.7	5.92	4.96	0.65561	EF-hand-like domain (1);	0.188038	0.46758	N	0.000276	T	0.64821	0.2633	M	0.61703	1.905	0.58432	D	0.999998	B;D;D;D;D;D	0.89917	0.222;1.0;1.0;1.0;1.0;1.0	B;D;D;D;D;D	0.91635	0.117;0.999;0.999;0.999;0.998;0.998	T	0.66224	-0.5977	10	0.51188	T	0.08	-7.8526	13.2643	0.60125	0.0:0.9271:0.0:0.0729	.	198;198;198;198;276;276	B7ZKZ2;Q9UMZ2-3;A8MWU4;Q9UMZ2-4;Q9UMZ2-5;Q9UMZ2	.;.;.;.;.;SYNRG_HUMAN	M	276;198;276;198;198	ENSP00000005279:V276M;ENSP00000424893:V198M;ENSP00000377903:V198M	ENSP00000343610:V198M	V	-	1	0	SYNRG	33010627	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.783000	0.68982	1.523000	0.49018	0.585000	0.79938	GTG		0.433	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247	
MRPL45	84311	broad.mit.edu	37	17	36478167	36478167	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:36478167G>T	ENST00000312513.5	+	7	980	c.819G>T	c.(817-819)aaG>aaT	p.K273N		NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	273						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)	p.K273N(1)		breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CACCCCCTAAGCAGCCCATCC	0.527											OREG0024353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K273N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G819T	17						.						82.0	73.0	76.0					17																	36478167		2203	4300	6503	33731694	SO:0001583	missense	84311	exon7			BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"""Mitochondrial ribosomal proteins / large subunits"""	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.819G>T	17.37:g.36478167G>T	ENSP00000308901:p.Lys273Asn	Somatic	863	Capture	Illumina HiSeq	Phase_I	33731694	NM_032351	A1L436|Q6ZMJ5	Missense_Mutation	SNP	ENST00000312513.5	37	CCDS11326.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.723192	0.30503	.	.	ENSG00000174100	ENST00000312513	T	0.34667	1.35	5.97	3.88	0.44766	.	0.044963	0.85682	D	0.000000	T	0.39489	0.1080	L	0.34521	1.04	0.58432	D	0.999999	D	0.71674	0.998	P	0.60682	0.878	T	0.27905	-1.0060	10	0.62326	D	0.03	-9.1706	5.9153	0.19052	0.2179:0.1434:0.6387:0.0	.	273	Q9BRJ2	RM45_HUMAN	N	273	ENSP00000308901:K273N	ENSP00000308901:K273N	K	+	3	2	MRPL45	33731694	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.699000	0.37804	1.542000	0.49330	0.536000	0.68110	AAG		0.527	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351	
TRPV1	7442	broad.mit.edu	37	17	3493653	3493653	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:3493653C>T	ENST00000571088.1	-	5	851	c.638G>A	c.(637-639)cGc>cAc	p.R213H	TRPV1_ENST00000399759.3_Missense_Mutation_p.R213H|TRPV1_ENST00000174621.6_Missense_Mutation_p.R211H|TRPV1_ENST00000425167.2_Missense_Mutation_p.R213H|TRPV1_ENST00000576351.1_Missense_Mutation_p.R213H|SHPK_ENST00000572705.1_Missense_Mutation_p.R213H|TRPV1_ENST00000399756.4_Missense_Mutation_p.R213H|TRPV1_ENST00000310522.5_Missense_Mutation_p.R213H	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	213					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.R213H(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)	GGCCATGTTGCGTCTCTCGAT	0.632																																					p.R213H	Melanoma(38;962 1762 15789)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G638A	17						.						70.0	75.0	73.0					17																	3493653		2160	4267	6427	3440402	SO:0001583	missense	7442	exon5			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.638G>A	17.37:g.3493653C>T	ENSP00000461007:p.Arg213His	Somatic		Capture	Illumina HiSeq	Phase_I	3440402	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Missense_Mutation	SNP	ENST00000571088.1	37	CCDS45576.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.943877	0.92593	.	.	ENSG00000196689	ENST00000399759;ENST00000399756;ENST00000174621;ENST00000425167;ENST00000310522	T;T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.12;-0.12	5.29	5.29	0.74685	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.77909	0.4201	L	0.28740	0.885	0.58432	D	0.999999	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;0.999	T	0.80388	-0.1403	10	0.87932	D	0	-6.3421	18.2953	0.90143	0.0:1.0:0.0:0.0	.	213;211;213;213	Q8NER1;E7EQ80;E7ESJ2;E7EQ78	TRPV1_HUMAN;.;.;.	H	213;213;211;213;213	ENSP00000382661:R213H;ENSP00000382659:R213H;ENSP00000174621:R211H;ENSP00000409627:R213H;ENSP00000311692:R213H	ENSP00000174621:R211H	R	-	2	0	TRPV1	3440402	1.000000	0.71417	1.000000	0.80357	0.648000	0.38561	7.366000	0.79548	2.641000	0.89580	0.591000	0.81541	CGC		0.632	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727	
PIP4K2B	8396	broad.mit.edu	37	17	36936775	36936775	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:36936775C>T	ENST00000269554.3	-	4	917	c.437G>A	c.(436-438)cGc>cAc	p.R146H	PIP4K2B_ENST00000311500.6_5'UTR	NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	146	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cell surface receptor signaling pathway (GO:0007166)|intracellular signal transduction (GO:0035556)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|receptor signaling protein activity (GO:0005057)	p.R146H(1)		endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						GATGACAAAGCGCCGGTCGTA	0.552																																					p.R146H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G437A	17						.						105.0	93.0	97.0					17																	36936775		2203	4300	6503	34190301	SO:0001583	missense	8396	exon4			U85245	CCDS11329.1	17q21.2	2007-08-14	2007-08-14	2007-08-14		ENSG00000276293	2.7.1.149		8998	protein-coding gene	gene with protein product		603261	"""phosphatidylinositol-4-phosphate 5-kinase, type II, beta"""	PIP5K2B		9038203, 14691457, 9367159	Standard	NM_003559		Approved	PIP5KIIB, PIP5KIIbeta	uc002hqs.3	P78356		ENST00000269554.3:c.437G>A	17.37:g.36936775C>T	ENSP00000269554:p.Arg146His	Somatic		Capture	Illumina HiSeq	Phase_I	34190301	NM_003559	Q5U0E8|Q8TBP2	Missense_Mutation	SNP	ENST00000269554.3	37	CCDS11329.1	.	.	.	.	.	.	.	.	.	.	C	36	5.677777	0.96764	.	.	ENSG00000141720	ENST00000269554;ENST00000311500	T	0.36157	1.27	5.21	5.21	0.72293	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.65302	0.2678	M	0.88570	2.965	0.80722	D	1	D;D;D	0.71674	0.99;0.988;0.998	P;P;D	0.65140	0.826;0.733;0.932	T	0.71255	-0.4647	10	0.59425	D	0.04	-16.7364	17.4822	0.87675	0.0:1.0:0.0:0.0	.	146;146;146	C9JMM2;P78356-2;P78356	.;.;PI42B_HUMAN	H	146	ENSP00000269554:R146H	ENSP00000269554:R146H	R	-	2	0	PIP4K2B	34190301	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.491000	0.60326	2.716000	0.92895	0.561000	0.74099	CGC		0.552	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1	NM_003559	
CACNB1	782	broad.mit.edu	37	17	37340008	37340008	+	Silent	SNP	C	C	T	rs532308568		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:37340008C>T	ENST00000394303.3	-	11	1215	c.1008G>A	c.(1006-1008)tcG>tcA	p.S336S	CACNB1_ENST00000394310.3_Silent_p.S336S|CACNB1_ENST00000344140.5_Silent_p.S381S|CACNB1_ENST00000582877.1_5'Flank	NM_000723.4	NP_000714.3	Q02641	CACB1_HUMAN	calcium channel, voltage-dependent, beta 1 subunit	336					axon guidance (GO:0007411)|protein targeting to membrane (GO:0006612)|transport (GO:0006810)	sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.S381S(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	16					Dronedarone(DB04855)|Ibutilide(DB00308)|Magnesium Sulfate(DB00653)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	TGGGGGCCAGCGAGGTCTTGG	0.577													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18214	0.0		0.0	False		,,,				2504	0.0				p.S336S	Esophageal Squamous(5;100 366 38393 41452 45827)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1008A	17						.						53.0	43.0	47.0					17																	37340008		2203	4300	6503	34593534	SO:0001819	synonymous_variant	782	exon11				CCDS11334.1, CCDS42311.1, CCDS45665.1	17q21-q22	2013-03-20			ENSG00000067191	ENSG00000067191		"""Calcium channel subunits"""	1401	protein-coding gene	gene with protein product		114207		CACNLB1		8381767, 8395940	Standard	NM_000723		Approved		uc002hrm.2	Q02641	OTTHUMG00000133217	ENST00000394303.3:c.1008G>A	17.37:g.37340008C>T		Somatic		Capture	Illumina HiSeq	Phase_I	34593534	NM_000723	A8K114|O15331|Q02639|Q02640|Q8N3X9|Q9C085|Q9UD79	Silent	SNP	ENST00000394303.3	37	CCDS42311.1																																																																																				0.577	CACNB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256945.3		
CDK12	51755	broad.mit.edu	37	17	37686993	37686993	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:37686993C>T	ENST00000447079.4	+	14	3930	c.3897C>T	c.(3895-3897)gcC>gcT	p.A1299A	CDK12_ENST00000430627.2_Silent_p.A1290A	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1299					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.A1299A(1)		NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						CCGTGACAGCCGCCTTGCTGC	0.652			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)																											p.A1299A			Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3897T	17						.						94.0	104.0	101.0					17																	37686993		2203	4300	6503	34940519	SO:0001819	synonymous_variant	51755	exon14			AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.3897C>T	17.37:g.37686993C>T		Somatic		Capture	Illumina HiSeq	Phase_I	34940519	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Silent	SNP	ENST00000447079.4	37	CCDS11337.1																																																																																				0.652	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507	
CDK12	51755	broad.mit.edu	37	17	37687362	37687362	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:37687362G>T	ENST00000447079.4	+	14	4299	c.4266G>T	c.(4264-4266)aaG>aaT	p.K1422N	CDK12_ENST00000430627.2_Missense_Mutation_p.K1413N	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1422					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.K1422N(1)		NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						CATTCCTGAAGGCTGAGGGAA	0.592			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)																											p.K1422N			Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4266T	17						.						71.0	76.0	74.0					17																	37687362		2203	4300	6503	34940888	SO:0001583	missense	51755	exon14			AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.4266G>T	17.37:g.37687362G>T	ENSP00000398880:p.Lys1422Asn	Somatic		Capture	Illumina HiSeq	Phase_I	34940888	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	G	6.515	0.463231	0.12402	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.70164	-0.46;-0.44	5.54	3.46	0.39613	.	0.000000	0.51477	D	0.000088	T	0.50154	0.1599	N	0.14661	0.345	0.31259	N	0.693092	P;P	0.46784	0.816;0.884	B;P	0.48677	0.382;0.586	T	0.52472	-0.8571	10	0.29301	T	0.29	-12.2885	4.8543	0.13552	0.3698:0.0:0.6301:0.0	.	1422;1413	Q9NYV4;Q9NYV4-2	CDK12_HUMAN;.	N	1413;1422	ENSP00000407720:K1413N;ENSP00000398880:K1422N	ENSP00000407720:K1413N	K	+	3	2	CDK12	34940888	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	1.620000	0.36976	1.581000	0.49865	0.650000	0.86243	AAG		0.592	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507	
ERBB2	2064	broad.mit.edu	37	17	37866621	37866621	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:37866621T>C	ENST00000269571.5	+	7	947	c.788T>C	c.(787-789)aTc>aCc	p.I263T	ERBB2_ENST00000584601.1_Missense_Mutation_p.I233T|ERBB2_ENST00000584450.1_Missense_Mutation_p.I263T|ERBB2_ENST00000406381.2_Missense_Mutation_p.I233T|ERBB2_ENST00000578199.1_Missense_Mutation_p.I233T|ERBB2_ENST00000540147.1_Missense_Mutation_p.I233T|ERBB2_ENST00000541774.1_Missense_Mutation_p.I248T|ERBB2_ENST00000445658.2_Intron|ERBB2_ENST00000540042.1_Missense_Mutation_p.I233T			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	263					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.I263T(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	CACAGTGGCATCTGTGAGCTG	0.602		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)																											p.I233T			Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T698C	17						.						94.0	76.0	82.0					17																	37866621		2203	4300	6503	35120147	SO:0001583	missense	2064	exon10			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.788T>C	17.37:g.37866621T>C	ENSP00000269571:p.Ile263Thr	Somatic		Capture	Illumina HiSeq	Phase_I	35120147	NM_001005862	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	T	12.71	2.020085	0.35606	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000269571;ENST00000540147;ENST00000540042	T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08	5.82	3.64	0.41730	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	.	.	.	.	T	0.29355	0.0731	N	0.04508	-0.205	0.35711	D	0.816394	B;B;B;B	0.12013	0.004;0.004;0.001;0.005	B;B;B;B	0.16722	0.016;0.01;0.002;0.016	T	0.21518	-1.0243	9	0.07325	T	0.83	.	8.878	0.35356	0.0:0.1536:0.0:0.8464	.	233;248;263;263	F5H1T4;P04626-4;P04626;Q9UK79	.;.;ERBB2_HUMAN;.	T	233;248;263;233;233	ENSP00000385185:I233T;ENSP00000446466:I248T;ENSP00000269571:I263T;ENSP00000443562:I233T;ENSP00000446382:I233T	ENSP00000269571:I263T	I	+	2	0	ERBB2	35120147	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.116000	0.31221	1.050000	0.40346	0.482000	0.46254	ATC		0.602	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
GRB7	2886	broad.mit.edu	37	17	37899684	37899684	+	Silent	SNP	C	C	T	rs545599174	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:37899684C>T	ENST00000309156.4	+	6	881	c.624C>T	c.(622-624)ctC>ctT	p.L208L	GRB7_ENST00000394211.3_Silent_p.L208L|GRB7_ENST00000309185.3_Silent_p.L208L|GRB7_ENST00000578702.1_3'UTR|GRB7_ENST00000394209.2_Silent_p.L208L|GRB7_ENST00000394204.1_Silent_p.L208L|GRB7_ENST00000445327.2_Silent_p.L231L	NM_005310.3	NP_005301.2	Q14451	GRB7_HUMAN	growth factor receptor-bound protein 7	208					blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|leukocyte migration (GO:0050900)|negative regulation of translation (GO:0017148)|positive regulation of cell migration (GO:0030335)|positive regulation of signal transduction (GO:0009967)|stress granule assembly (GO:0034063)	cell projection (GO:0042995)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)|SH3/SH2 adaptor activity (GO:0005070)	p.S206fs*16(1)|p.L208L(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;6.86e-60)|all cancers(3;1.65e-53)|BRCA - Breast invasive adenocarcinoma(8;2.03e-43)|STAD - Stomach adenocarcinoma(3;1.43e-12)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CCAGCTGTCTCGATGCACACA	0.557													C|||	2	0.000399361	0.0	0.0	5008	,	,		18973	0.0		0.0	False		,,,				2504	0.002				p.L208L												.	.	2	Deletion - Frameshift(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	c.C624T	17						.						138.0	120.0	126.0					17																	37899684		2203	4300	6503	35153210	SO:0001819	synonymous_variant	2886	exon6			D43772	CCDS11345.1, CCDS56028.1	17q12	2013-02-14			ENSG00000141738	ENSG00000141738		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4567	protein-coding gene	gene with protein product		601522					Standard	NM_005310		Approved		uc021twu.1	Q14451	OTTHUMG00000133253	ENST00000309156.4:c.624C>T	17.37:g.37899684C>T		Somatic		Capture	Illumina HiSeq	Phase_I	35153210	NM_005310	B2RAV1|B3KNL0|B3KWP9|B7WP75|J3KQM4|Q53YD3|Q92568|Q96DF9|Q9Y220	Silent	SNP	ENST00000309156.4	37	CCDS11345.1																																																																																				0.557	GRB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257024.2	NM_005310	
NR1D1	9572	broad.mit.edu	37	17	38251196	38251196	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:38251196T>C	ENST00000246672.3	-	6	2056	c.1426A>G	c.(1426-1428)Acc>Gcc	p.T476A		NM_021724.3	NP_068370.1	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	476	Ligand-binding.				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.T476A(1)		endometrium(1)|large_intestine(5)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	11	Colorectal(19;0.000442)					ACCTCAAAGGTGCCAGCCTTA	0.532																																					p.T476A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1426G	17						.						79.0	63.0	68.0					17																	38251196		2203	4300	6503	35504722	SO:0001583	missense	9572	exon6			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.1426A>G	17.37:g.38251196T>C	ENSP00000246672:p.Thr476Ala	Somatic		Capture	Illumina HiSeq	Phase_I	35504722	NM_021724	Q0P5Z4|Q15304	Missense_Mutation	SNP	ENST00000246672.3	37	CCDS11361.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.955340	0.73902	.	.	ENSG00000126368	ENST00000246672	D	0.96619	-4.07	4.77	4.77	0.60923	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.202193	0.40640	N	0.001058	D	0.94918	0.8357	L	0.37800	1.135	0.51012	D	0.999901	P;P	0.45594	0.862;0.862	P;P	0.50109	0.631;0.631	D	0.94259	0.7500	10	0.39692	T	0.17	.	13.4491	0.61161	0.0:0.0:0.0:1.0	.	476;476	F1D8S3;P20393	.;NR1D1_HUMAN	A	476	ENSP00000246672:T476A	ENSP00000246672:T476A	T	-	1	0	NR1D1	35504722	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.770000	0.85390	2.030000	0.59900	0.454000	0.30748	ACC		0.532	NR1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257135.1		
NR1D1	9572	broad.mit.edu	37	17	38252039	38252039	+	Silent	SNP	G	G	A	rs150627138		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:38252039G>A	ENST00000246672.3	-	5	1536	c.906C>T	c.(904-906)taC>taT	p.Y302Y		NM_021724.3	NP_068370.1	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	302	Ligand-binding.				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.Y302Y(1)		endometrium(1)|large_intestine(5)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	11	Colorectal(19;0.000442)					TGTCATGGGCGTAGGTGAAGA	0.597																																					p.Y302Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C906T	17						.	G		1,4405	2.1+/-5.4	0,1,2202	92.0	75.0	81.0		906	0.8	1.0	17	dbSNP_134	81	0,8600		0,0,4300	no	coding-synonymous	NR1D1	NM_021724.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		302/615	38252039	1,13005	2203	4300	6503	35505565	SO:0001819	synonymous_variant	9572	exon5			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.906C>T	17.37:g.38252039G>A		Somatic		Capture	Illumina HiSeq	Phase_I	35505565	NM_021724	Q0P5Z4|Q15304	Silent	SNP	ENST00000246672.3	37	CCDS11361.1																																																																																				0.597	NR1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257135.1		
KRTAP3-1	83896	broad.mit.edu	37	17	39165109	39165109	+	Missense_Mutation	SNP	G	G	A	rs370223389		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:39165109G>A	ENST00000391588.1	-	1	257	c.218C>T	c.(217-219)cCg>cTg	p.P73L	KRTAP3-1_ENST00000581033.1_5'UTR	NM_031958.1	NP_114164.1	Q9BYR8	KRA31_HUMAN	keratin associated protein 3-1	73						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.P73L(1)|p.P73Q(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	8		Breast(137;0.00043)				TCCGGGAGTCGGGTGACAGTT	0.587																																					p.P73L												.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.C218T	17						.						69.0	60.0	63.0					17																	39165109		2203	4296	6499	36418635	SO:0001583	missense	83896	exon1			AJ406931	CCDS32645.1	17q21.2	2013-06-25			ENSG00000212901	ENSG00000212901		"""Keratin associated proteins"""	16778	protein-coding gene	gene with protein product						11279113	Standard	NM_031958		Approved	KAP3.1	uc002hvt.1	Q9BYR8	OTTHUMG00000133595	ENST00000391588.1:c.218C>T	17.37:g.39165109G>A	ENSP00000375430:p.Pro73Leu	Somatic		Capture	Illumina HiSeq	Phase_I	36418635	NM_031958	Q14DM4	Missense_Mutation	SNP	ENST00000391588.1	37	CCDS32645.1	.	.	.	.	.	.	.	.	.	.	G	12.28	1.892023	0.33442	.	.	ENSG00000212901	ENST00000391588	T	0.35236	1.32	5.3	5.3	0.74995	.	0.131964	0.34555	N	0.003867	T	0.61451	0.2348	.	.	.	0.54753	D	0.999985	D	0.89917	1.0	D	0.91635	0.999	T	0.65158	-0.6236	9	0.87932	D	0	-4.7714	14.865	0.70406	0.0:0.0:1.0:0.0	.	73	Q9BYR8	KRA31_HUMAN	L	73	ENSP00000375430:P73L	ENSP00000375430:P73L	P	-	2	0	KRTAP3-1	36418635	0.971000	0.33674	0.985000	0.45067	0.136000	0.21042	1.369000	0.34227	2.647000	0.89833	0.632000	0.83419	CCG		0.587	KRTAP3-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257699.1		
KRTAP4-1	85285	broad.mit.edu	37	17	39340710	39340710	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:39340710G>A	ENST00000398472.1	-	1	884	c.397C>T	c.(397-399)Cgt>Tgt	p.R133C				Q9BYQ7	KRA41_HUMAN	keratin associated protein 4-1	133	18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL].					keratin filament (GO:0045095)		p.R129C(1)|p.R133C(1)		kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			CAAGTTGCACGGCAGCAGGTG	0.577																																					p.R114C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C340T	17						.						94.0	102.0	99.0					17																	39340710		2164	4277	6441	36594236	SO:0001583	missense	85285	exon2			AC006070		17q21.2	2013-06-25			ENSG00000198443	ENSG00000198443		"""Keratin associated proteins"""	18907	protein-coding gene	gene with protein product			"""keratin associated protein 4-10"""	KRTAP4-10		11279113	Standard	NM_033060		Approved	KAP4.1, KAP4.10	uc002hwe.4	Q9BYQ7	OTTHUMG00000132081	ENST00000398472.1:c.397C>T	17.37:g.39340710G>A	ENSP00000381489:p.Arg133Cys	Somatic		Capture	Illumina HiSeq	Phase_I	36594236	NM_033060	A8MWS7|Q3SYF2	Missense_Mutation	SNP	ENST00000398472.1	37		.	.	.	.	.	.	.	.	.	.	.	14.93	2.683583	0.47991	.	.	ENSG00000244537;ENSG00000198443;ENSG00000198443	ENST00000458321;ENST00000398472;ENST00000334190	T	0.01484	4.84	5.33	-9.65	0.00537	.	.	.	.	.	T	0.01222	0.0040	.	.	.	0.09310	N	1	B	0.25521	0.128	B	0.25614	0.062	T	0.48833	-0.9000	8	0.62326	D	0.03	.	4.9673	0.14096	0.065:0.3404:0.2051:0.3896	.	133	Q9BYQ7	KRA41_HUMAN	C	129;133;114	ENSP00000381489:R133C	ENSP00000335483:R114C	R	-	1	0	KRTAP4-2;KRTAP4-1	36594236	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.555000	0.02170	-1.365000	0.02158	0.655000	0.94253	CGT		0.577	KRTAP4-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255108.1	NM_033060	
KRT33B	3884	broad.mit.edu	37	17	39521790	39521790	+	Missense_Mutation	SNP	G	G	A	rs370317934		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:39521790G>A	ENST00000251646.3	-	4	653	c.604C>T	c.(604-606)Cgc>Tgc	p.R202C		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	202	Coil 1B.|Rod.				aging (GO:0007568)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.R202C(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(6)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000496)				AGCTGGCAGCGCAAGGTGTTG	0.502																																					p.R202C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C604T	17						.	G	CYS/ARG	1,4379	2.1+/-5.4	0,1,2189	48.0	49.0	49.0		604	3.5	1.0	17		49	0,8600		0,0,4300	no	missense	KRT33B	NM_002279.3	180	0,1,6489	AA,AG,GG		0.0,0.0228,0.0077	probably-damaging	202/405	39521790	1,12979	2190	4300	6490	36775316	SO:0001583	missense	3884	exon4			X82634	CCDS11389.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131738	ENSG00000131738		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6451	protein-coding gene	gene with protein product	"""hard keratin type I 3II"""	602762	"""keratin, hair, acidic, 3B"""	KRTHA3B		7565656, 16831889	Standard	NM_002279		Approved	Ha-3II	uc002hwl.4	Q14525	OTTHUMG00000133429	ENST00000251646.3:c.604C>T	17.37:g.39521790G>A	ENSP00000251646:p.Arg202Cys	Somatic		Capture	Illumina HiSeq	Phase_I	36775316	NM_002279	O76010	Missense_Mutation	SNP	ENST00000251646.3	37	CCDS11389.1	.	.	.	.	.	.	.	.	.	.	g	17.24	3.339031	0.60963	2.28E-4	0.0	ENSG00000131738	ENST00000251646	D	0.89681	-2.55	4.51	3.52	0.40303	Filament (1);	0.000000	0.64402	D	0.000006	D	0.94729	0.8299	M	0.92691	3.335	0.41607	D	0.988888	D	0.76494	0.999	D	0.70016	0.967	D	0.94813	0.7980	10	0.87932	D	0	.	9.7957	0.40733	0.0:0.1625:0.6901:0.1473	.	202	Q14525	KT33B_HUMAN	C	202	ENSP00000251646:R202C	ENSP00000251646:R202C	R	-	1	0	KRT33B	36775316	0.002000	0.14202	1.000000	0.80357	0.757000	0.42996	0.840000	0.27600	1.209000	0.43321	0.650000	0.86243	CGC		0.502	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279	
KRT31	3881	broad.mit.edu	37	17	39552772	39552772	+	Missense_Mutation	SNP	C	C	T	rs565048074	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:39552772C>T	ENST00000251645.2	-	3	540	c.488G>A	c.(487-489)cGc>cAc	p.R163H		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31	163	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)	p.R163H(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	31		Breast(137;0.000496)				CAGGATCCTGCGCAGACCGTT	0.602																																					p.R163H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G488A	17						.						92.0	77.0	82.0					17																	39552772		2203	4300	6503	36806298	SO:0001583	missense	3881	exon3			X86570	CCDS11391.1	17q21.2	2014-05-20	2006-07-17	2006-07-17	ENSG00000094796	ENSG00000094796		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6448	protein-coding gene	gene with protein product	"""hard keratin type I 1"""	601077	"""keratin, hair, acidic, 1"""	KRTHA1		7578244, 16831889	Standard	NM_002277		Approved	Ha-1	uc002hwn.3	Q15323	OTTHUMG00000133423	ENST00000251645.2:c.488G>A	17.37:g.39552772C>T	ENSP00000251645:p.Arg163His	Somatic		Capture	Illumina HiSeq	Phase_I	36806298	NM_002277	Q9UE12	Missense_Mutation	SNP	ENST00000251645.2	37	CCDS11391.1	.	.	.	.	.	.	.	.	.	.	c	18.69	3.677185	0.68042	.	.	ENSG00000094796	ENST00000251645	D	0.92397	-3.03	5.11	4.14	0.48551	Filament (1);	0.000000	0.64402	D	0.000003	D	0.94345	0.8182	M	0.68952	2.095	0.39730	D	0.97159	D	0.71674	0.998	D	0.64321	0.924	D	0.94339	0.7569	10	0.49607	T	0.09	.	12.6326	0.56665	0.0:0.9204:0.0:0.0796	.	163	Q15323	K1H1_HUMAN	H	163	ENSP00000251645:R163H	ENSP00000251645:R163H	R	-	2	0	KRT31	36806298	0.983000	0.35010	0.999000	0.59377	0.893000	0.52053	2.673000	0.46858	1.274000	0.44362	0.655000	0.94253	CGC		0.602	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	NM_002277	
KRT36	8689	broad.mit.edu	37	17	39645730	39645730	+	Silent	SNP	G	G	A	rs534577749	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:39645730G>A	ENST00000328119.6	-	1	386	c.387C>T	c.(385-387)taC>taT	p.Y129Y	KRT36_ENST00000393986.2_Silent_p.Y79Y	NM_003771.4	NP_003762.1	O76013	KRT36_HUMAN	keratin 36	129	Linker 1.|Rod.				regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of epidermis (GO:0030280)	p.Y129Y(1)		breast(2)|cervix(1)|kidney(2)|large_intestine(3)|lung(8)|skin(1)	17		Breast(137;0.000286)				TCTGAAACTCGTACCACTCCT	0.572													G|||	10	0.00199681	0.0	0.0	5008	,	,		17900	0.0		0.0	False		,,,				2504	0.0102				p.Y129Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C387T	17						.						161.0	145.0	150.0					17																	39645730		2203	4300	6503	36899256	SO:0001819	synonymous_variant	8689	exon1			Y16792	CCDS11395.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000126337	ENSG00000126337		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6454	protein-coding gene	gene with protein product		604540	"""keratin, hair, acidic, 6"""	KRTHA6		9756910, 16831889	Standard	XM_005257762		Approved		uc002hwt.3	O76013	OTTHUMG00000133431	ENST00000328119.6:c.387C>T	17.37:g.39645730G>A		Somatic		Capture	Illumina HiSeq	Phase_I	36899256	NM_003771	Q86XG4	Silent	SNP	ENST00000328119.6	37	CCDS11395.1																																																																																				0.572	KRT36-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259508.1	NM_003771	
CAMKK1	84254	broad.mit.edu	37	17	3775865	3775865	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:3775865G>A	ENST00000348335.2	-	12	1255	c.1107C>T	c.(1105-1107)ccC>ccT	p.P369P	CAMKK1_ENST00000158166.5_Silent_p.P407P|CAMKK1_ENST00000381771.2_Silent_p.P407P|CAMKK1_ENST00000381769.2_Silent_p.P396P	NM_032294.2	NP_115670.1	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase kinase 1, alpha	369	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.P369P(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	11				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)		GAAACACCACGGGCTCATTCT	0.572																																					p.P369P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1107T	17						.						108.0	95.0	100.0					17																	3775865		2203	4300	6503	3722614	SO:0001819	synonymous_variant	84254	exon12			AL136576	CCDS11038.1, CCDS11039.1	17p13.3	2004-02-18			ENSG00000004660	ENSG00000004660			1469	protein-coding gene	gene with protein product		611411				11230166	Standard	NM_172207		Approved	DKFZp761M0423, CAMKKA, MGC34095	uc002fwt.3	Q8N5S9	OTTHUMG00000090725	ENST00000348335.2:c.1107C>T	17.37:g.3775865G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3722614	NM_032294	Q9BQH3	Silent	SNP	ENST00000348335.2	37	CCDS11038.1																																																																																				0.572	CAMKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207456.1	NM_032294, NM_172206, NM_172207	
KRT9	3857	broad.mit.edu	37	17	39723993	39723993	+	Silent	SNP	G	G	A	rs147473954		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:39723993G>A	ENST00000246662.4	-	7	1469	c.1404C>T	c.(1402-1404)tcC>tcT	p.S468S	KRT9_ENST00000588431.1_Silent_p.S235S	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	468	Tail.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.S468S(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				TTCCAGCTCCGGAGGATTCAC	0.502																																					p.S468S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1404T	17						.	G		0,4406		0,0,2203	69.0	68.0	68.0		1404	2.2	0.5	17	dbSNP_134	68	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	KRT9	NM_000226.3		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		468/624	39723993	4,13002	2203	4300	6503	36977519	SO:0001819	synonymous_variant	3857	exon7				CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6447	protein-coding gene	gene with protein product	"""cytokeratin 9"", ""type I cytoskeletal 9"", ""epidermolytic palmoplantar keratoderma"""	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.1404C>T	17.37:g.39723993G>A		Somatic		Capture	Illumina HiSeq	Phase_I	36977519	NM_000226	O00109|Q0IJ47|Q14665	Silent	SNP	ENST00000246662.4	37	CCDS32654.1																																																																																				0.502	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226	
ACLY	47	broad.mit.edu	37	17	40070098	40070098	+	Missense_Mutation	SNP	G	G	A	rs200879681		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:40070098G>A	ENST00000352035.2	-	2	159	c.29C>T	c.(28-30)aCg>aTg	p.T10M	ACLY_ENST00000590151.1_Missense_Mutation_p.T10M|ACLY_ENST00000537919.1_Missense_Mutation_p.T10M|ACLY_ENST00000393896.2_Missense_Mutation_p.T10M|ACLY_ENST00000353196.1_Missense_Mutation_p.T10M	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	10	ATP-grasp.				ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)	p.T10M(1)	NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				TTCTTTGCCCGTCTGCTCTGA	0.562																																					p.T10M	Colon(64;807 1396 15971 30971)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C29T	17						.	G	MET/THR,MET/THR	0,4406		0,0,2203	187.0	165.0	172.0		29,29	5.5	1.0	17		172	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	ACLY	NM_001096.2,NM_198830.1	81,81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	10/1102,10/1092	40070098	1,13005	2203	4300	6503	37323624	SO:0001583	missense	47	exon2			X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"""ATP citrate synthase"""	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.29C>T	17.37:g.40070098G>A	ENSP00000253792:p.Thr10Met	Somatic		Capture	Illumina HiSeq	Phase_I	37323624	NM_198830	B4DIM0|B4E3P0|Q13037|Q9BRL0	Missense_Mutation	SNP	ENST00000352035.2	37	CCDS11412.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.700831	0.88924	0.0	1.16E-4	ENSG00000131473	ENST00000352035;ENST00000401700;ENST00000353196;ENST00000537919;ENST00000393896	T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.81735	0.4885	M	0.69358	2.11	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	0.99;0.927;0.998;0.984;0.998	T	0.82737	-0.0309	10	0.87932	D	0	.	19.7401	0.96223	0.0:0.0:1.0:0.0	.	10;64;64;10;10	B4E3P0;B4DIM0;E7ENH9;G3XAI4;P53396	.;.;.;.;ACLY_HUMAN	M	10;64;10;10;10	ENSP00000253792:T10M;ENSP00000345398:T10M;ENSP00000445349:T10M;ENSP00000377474:T10M	ENSP00000253792:T10M	T	-	2	0	ACLY	37323624	1.000000	0.71417	0.984000	0.44739	0.772000	0.43724	9.549000	0.98106	2.735000	0.93741	0.563000	0.77884	ACG		0.562	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096	
PTRF	284119	broad.mit.edu	37	17	40556842	40556842	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:40556842C>T	ENST00000357037.5	-	2	1455	c.1036G>A	c.(1036-1038)Gcc>Acc	p.A346T		NM_012232.5	NP_036364.2			polymerase I and transcript release factor									p.A346T(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)		TCGTCGTCGGCGCCCACCTCC	0.706																																					p.A346T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1036A	17						.						41.0	37.0	38.0					17																	40556842		2201	4298	6499	37810368	SO:0001583	missense	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.1036G>A	17.37:g.40556842C>T	ENSP00000349541:p.Ala346Thr	Somatic		Capture	Illumina HiSeq	Phase_I	37810368	NM_012232		Missense_Mutation	SNP	ENST00000357037.5	37	CCDS11425.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.081641	0.36758	.	.	ENSG00000177469	ENST00000357037;ENST00000357684	T	0.59364	0.27	4.73	0.0701	0.14377	.	0.705343	0.13359	N	0.393817	T	0.34395	0.0896	N	0.08118	0	0.18873	N	0.999989	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.17471	-1.0368	10	0.32370	T	0.25	-7.0322	11.6769	0.51434	0.0:0.3503:0.5747:0.0751	.	328;346	B4DNU9;Q6NZI2	.;PTRF_HUMAN	T	346;301	ENSP00000349541:A346T	ENSP00000349541:A346T	A	-	1	0	PTRF	37810368	0.043000	0.20138	0.992000	0.48379	0.995000	0.86356	0.823000	0.27366	-0.084000	0.12595	0.557000	0.71058	GCC		0.706	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232	
PTRF	284119	broad.mit.edu	37	17	40557226	40557226	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:40557226C>T	ENST00000357037.5	-	2	1071	c.652G>A	c.(652-654)Gca>Aca	p.A218T		NM_012232.5	NP_036364.2			polymerase I and transcript release factor									p.A218T(2)		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)		ATACGCTCTGCGCGGGACTCC	0.652																																					p.A218T												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.G652A	17						.						95.0	98.0	97.0					17																	40557226		2203	4300	6503	37810752	SO:0001583	missense	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.652G>A	17.37:g.40557226C>T	ENSP00000349541:p.Ala218Thr	Somatic		Capture	Illumina HiSeq	Phase_I	37810752	NM_012232		Missense_Mutation	SNP	ENST00000357037.5	37	CCDS11425.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.923989	0.73213	.	.	ENSG00000177469	ENST00000357037;ENST00000357684	T	0.68624	-0.34	5.35	5.35	0.76521	.	0.161702	0.53938	D	0.000043	T	0.58977	0.2160	L	0.45352	1.415	0.58432	D	0.999998	P;P	0.45827	0.867;0.867	B;B	0.35931	0.214;0.214	T	0.64466	-0.6401	10	0.48119	T	0.1	-27.2661	19.0756	0.93159	0.0:1.0:0.0:0.0	.	200;218	B4DNU9;Q6NZI2	.;PTRF_HUMAN	T	218;173	ENSP00000349541:A218T	ENSP00000349541:A218T	A	-	1	0	PTRF	37810752	1.000000	0.71417	0.998000	0.56505	0.452000	0.32318	5.966000	0.70395	2.511000	0.84671	0.446000	0.29264	GCA		0.652	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232	
COASY	80347	broad.mit.edu	37	17	40717718	40717718	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:40717718C>T	ENST00000393818.2	+	8	1983	c.1527C>T	c.(1525-1527)gcC>gcT	p.A509A	COASY_ENST00000421097.2_Silent_p.A509A|MLX_ENST00000346833.4_5'Flank|COASY_ENST00000590958.1_Silent_p.A538A|MLX_ENST00000246912.4_5'Flank|COASY_ENST00000420359.1_Silent_p.A509A|COASY_ENST00000449624.1_Silent_p.A214A|MLX_ENST00000435881.2_5'Flank	NM_025233.6	NP_079509.5	Q13057	COASY_HUMAN	CoA synthase	509	DPCK.				cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|dephospho-CoA kinase activity (GO:0004140)|pantetheine-phosphate adenylyltransferase activity (GO:0004595)	p.A509A(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	21		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)		TCAGTGAAGCCGCGGCTCAAA	0.577																																					p.A509A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1527T	17						.						44.0	46.0	45.0					17																	40717718		2203	4300	6503	37971244	SO:0001819	synonymous_variant	80347	exon9			AF453478	CCDS11429.1, CCDS45685.1	17q12-q21	2010-04-30	2010-04-30			ENSG00000068120	2.7.7.3		29932	protein-coding gene	gene with protein product		609855	"""Coenzyme A synthase"""			11923312, 11980892	Standard	NM_025233		Approved	DPCK, NBP, CoASY, PPAT	uc010cyj.4	Q13057		ENST00000393818.2:c.1527C>T	17.37:g.40717718C>T		Somatic		Capture	Illumina HiSeq	Phase_I	37971244	NM_001042529	B2RA78|B4DLU0|Q6GS23|Q8NBM7|Q8NEW1|Q8WXD4|Q9NRM3	Silent	SNP	ENST00000393818.2	37	CCDS11429.1																																																																																				0.577	COASY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450409.1	NM_025233	
TUBG1	7283	broad.mit.edu	37	17	40766881	40766881	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:40766881G>A	ENST00000251413.3	+	11	1240	c.1178G>A	c.(1177-1179)cGc>cAc	p.R393H		NM_001070.4	NP_001061.2	P23258	TBG1_HUMAN	tubulin, gamma 1	393					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.R393H(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)	AGAACCTGTCGCCAGTATGAC	0.532																																					p.R393H	Colon(20;114 698 11420 22864)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1178A	17						.						129.0	132.0	131.0					17																	40766881		2203	4300	6503	38020407	SO:0001583	missense	7283	exon11			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.1178G>A	17.37:g.40766881G>A	ENSP00000251413:p.Arg393His	Somatic		Capture	Illumina HiSeq	Phase_I	38020407	NM_001070	Q53X79|Q9BW59	Missense_Mutation	SNP	ENST00000251413.3	37	CCDS11433.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.274284	0.40194	.	.	ENSG00000131462	ENST00000251413	D	0.83419	-1.72	5.02	4.05	0.47172	Tubulin/FtsZ, 2-layer sandwich domain (1);Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.74366	0.3707	L	0.35723	1.085	0.58432	D	0.999996	B	0.17852	0.024	B	0.10450	0.005	T	0.69117	-0.5230	10	0.42905	T	0.14	-13.4116	10.5502	0.45083	0.1551:0.0:0.8449:0.0	.	393	P23258	TBG1_HUMAN	H	393	ENSP00000251413:R393H	ENSP00000251413:R393H	R	+	2	0	TUBG1	38020407	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.979000	0.63806	1.124000	0.41980	0.563000	0.77884	CGC		0.532	TUBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450548.1	NM_001070	
TUBG2	27175	broad.mit.edu	37	17	40818404	40818404	+	Missense_Mutation	SNP	G	G	A	rs574597874		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:40818404G>A	ENST00000251412.7	+	10	1259	c.1060G>A	c.(1060-1062)Gcc>Acc	p.A354T	PLEKHH3_ENST00000456950.2_5'Flank	NM_016437.2	NP_057521.1	Q9NRH3	TBG2_HUMAN	tubulin, gamma 2	354					cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|gamma-tubulin complex (GO:0000930)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|pericentriolar material (GO:0000242)|spindle microtubule (GO:0005876)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)	p.A354T(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	15		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.141)		GTGGGGCCCCGCCAGCATCCA	0.657													G|||	1	0.000199681	0.0	0.0	5008	,	,		17836	0.0		0.0	False		,,,				2504	0.001				p.A354T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1060A	17						.						53.0	56.0	55.0					17																	40818404		2203	4300	6503	38071930	SO:0001583	missense	27175	exon10			AF225971	CCDS32658.1	17q21.2	2014-09-04			ENSG00000037042	ENSG00000037042		"""Tubulins"""	12419	protein-coding gene	gene with protein product		605785					Standard	NM_016437		Approved		uc010wgr.2	Q9NRH3	OTTHUMG00000180640	ENST00000251412.7:c.1060G>A	17.37:g.40818404G>A	ENSP00000251412:p.Ala354Thr	Somatic		Capture	Illumina HiSeq	Phase_I	38071930	NM_016437	A6NDI4|Q32NB2	Missense_Mutation	SNP	ENST00000251412.7	37	CCDS32658.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.279176	0.59758	.	.	ENSG00000037042	ENST00000251412	D	0.83163	-1.69	5.85	5.85	0.93711	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.82852	0.5127	M	0.66939	2.045	0.80722	D	1	P	0.35628	0.513	B	0.32805	0.153	T	0.82657	-0.0349	10	0.52906	T	0.07	-23.7697	20.1577	0.98120	0.0:0.0:1.0:0.0	.	354	Q9NRH3	TBG2_HUMAN	T	354	ENSP00000251412:A354T	ENSP00000251412:A354T	A	+	1	0	TUBG2	38071930	1.000000	0.71417	0.940000	0.37924	0.022000	0.10575	9.696000	0.98695	2.767000	0.95098	0.655000	0.94253	GCC		0.657	TUBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452326.1	NM_016437	
BECN1	8678	broad.mit.edu	37	17	40966007	40966007	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:40966007C>T	ENST00000361523.4	-	10	1132	c.1000G>A	c.(1000-1002)Gga>Aga	p.G334R	BECN1_ENST00000590099.1_Missense_Mutation_p.G334R|BECN1_ENST00000438274.3_Missense_Mutation_p.G258R	NM_003766.3	NP_003757.1	Q14457	BECN1_HUMAN	beclin 1, autophagy related	334					autophagic vacuole assembly (GO:0000045)|beta-amyloid metabolic process (GO:0050435)|cellular defense response (GO:0006968)|cellular response to aluminum ion (GO:0071275)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokinesis (GO:0000910)|defense response to virus (GO:0051607)|lysosome organization (GO:0007040)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|positive regulation of macroautophagy (GO:0016239)|regulation of catalytic activity (GO:0050790)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to vitamin E (GO:0033197)|viral process (GO:0016032)	dendrite (GO:0030425)|membrane (GO:0016020)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)		p.G334R(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	13		Breast(137;0.00104)		BRCA - Breast invasive adenocarcinoma(366;0.0745)		GAATGGTTTCCGTAAGGAACA	0.378																																					p.G334R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1000A	17						.						80.0	81.0	81.0					17																	40966007		2203	4300	6503	38219533	SO:0001583	missense	8678	exon10			AF077301	CCDS11441.1	17q21	2014-02-12	2008-01-14		ENSG00000126581	ENSG00000126581			1034	protein-coding gene	gene with protein product	"""ATG6 autophagy related 6 homolog (S. cerevisiae)"""	604378	"""beclin 1 (coiled-coil, moesin-like BCL2 interacting protein)"""			9765397	Standard	NM_003766		Approved	ATG6, VPS30	uc002ibn.2	Q14457		ENST00000361523.4:c.1000G>A	17.37:g.40966007C>T	ENSP00000355231:p.Gly334Arg	Somatic		Capture	Illumina HiSeq	Phase_I	38219533	NM_003766	B2R6N7|O75595|Q9UNA8	Missense_Mutation	SNP	ENST00000361523.4	37	CCDS11441.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.302033	0.81136	.	.	ENSG00000126581	ENST00000361523;ENST00000438274;ENST00000543382	T;T	0.68181	-0.31;-0.31	5.93	3.97	0.46021	.	0.000000	0.85682	D	0.000000	D	0.85626	0.5740	H	0.94771	3.58	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88428	0.3033	10	0.87932	D	0	.	12.7053	0.57058	0.0:0.8678:0.0:0.1322	.	258;334	E7EV84;Q14457	.;BECN1_HUMAN	R	334;258;247	ENSP00000355231:G334R;ENSP00000416173:G258R	ENSP00000355231:G334R	G	-	1	0	BECN1	38219533	1.000000	0.71417	0.999000	0.59377	0.847000	0.48162	7.754000	0.85163	0.877000	0.35895	-0.136000	0.14681	GGA		0.378	BECN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452405.1	NM_003766	
AOC2	314	broad.mit.edu	37	17	40997755	40997755	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:40997755C>T	ENST00000253799.3	+	1	1139	c.1112C>T	c.(1111-1113)cCc>cTc	p.P371L	AOC2_ENST00000452774.2_Missense_Mutation_p.P371L	NM_009590.2	NP_033720.2	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 (retina-specific)	371					amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)	p.P371L(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(14)|ovary(4)|skin(2)	30		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		GCCGATTCACCCAAGACGATG	0.537																																					p.P371L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1112T	17						.						133.0	127.0	129.0					17																	40997755		2203	4300	6503	38251281	SO:0001583	missense	314	exon1			AF081363	CCDS11443.1, CCDS45690.1	17q21	2012-07-13				ENSG00000131480	1.4.3.21		549	protein-coding gene	gene with protein product		602268				9119395, 9722954	Standard	NM_001158		Approved	RAO, DAO2	uc002ibu.3	O75106		ENST00000253799.3:c.1112C>T	17.37:g.40997755C>T	ENSP00000253799:p.Pro371Leu	Somatic		Capture	Illumina HiSeq	Phase_I	38251281	NM_001158	A5PKW2|O00120|O75105|Q4TTW5|Q9UNY0	Missense_Mutation	SNP	ENST00000253799.3	37	CCDS11443.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.686312	0.68157	.	.	ENSG00000131480	ENST00000253799;ENST00000452774	T;T	0.04502	3.61;3.61	5.59	4.63	0.57726	Copper amine oxidase, C-terminal (3);	0.057337	0.64402	N	0.000001	T	0.28200	0.0696	M	0.91717	3.235	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.27054	-1.0085	10	0.87932	D	0	-27.5842	14.4252	0.67210	0.0:0.9288:0.0:0.0712	.	371;371	O75106;O75106-2	AOC2_HUMAN;.	L	371	ENSP00000253799:P371L;ENSP00000406134:P371L	ENSP00000253799:P371L	P	+	2	0	AOC2	38251281	1.000000	0.71417	0.893000	0.35052	0.611000	0.37282	7.649000	0.83500	1.375000	0.46248	0.436000	0.28706	CCC		0.537	AOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452442.1	NM_009590, NM_001158	
DHX8	1659	broad.mit.edu	37	17	41570861	41570861	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:41570861T>C	ENST00000262415.3	+	7	984	c.912T>C	c.(910-912)ggT>ggC	p.G304G	DHX8_ENST00000540306.1_Silent_p.G304G	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	304	S1 motif. {ECO:0000255|PROSITE- ProRule:PRU00180}.				ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.G304G(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		GGCGGGAGGGTCGTGTGGCCA	0.552																																					p.G304G	NSCLC(56;1548 1661 49258 49987)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T912C	17						.						139.0	125.0	130.0					17																	41570861		2203	4300	6503	38926387	SO:0001819	synonymous_variant	1659	exon7			D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"""DEAH-boxes"""	2749	protein-coding gene	gene with protein product		600396	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"""	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.912T>C	17.37:g.41570861T>C		Somatic		Capture	Illumina HiSeq	Phase_I	38926387	NM_004941		Silent	SNP	ENST00000262415.3	37	CCDS11464.1																																																																																				0.552	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1		
ETV4	2118	broad.mit.edu	37	17	41607485	41607485	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:41607485G>A	ENST00000319349.5	-	9	1174	c.876C>T	c.(874-876)gaC>gaT	p.D292D	ETV4_ENST00000545089.1_Silent_p.D238D|ETV4_ENST00000591713.1_Silent_p.D292D|ETV4_ENST00000538265.1_Silent_p.D253D|ETV4_ENST00000393664.2_Silent_p.D292D|ETV4_ENST00000586826.1_Silent_p.D15D|ETV4_ENST00000545954.1_Silent_p.D253D	NM_001079675.2	NP_001073143.1	P43268	ETV4_HUMAN	ets variant 4	292					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|motor neuron axon guidance (GO:0008045)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)	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)	p.D292D(1)	EWSR1/ETV4(6)|CANT1/ETV4(3)|TMPRSS2/ETV4(13)|DDX5_ENST00000540698/ETV4(2)|KLK2/ETV4(2)	ovary(2)|upper_aerodigestive_tract(1)	3		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.0798)		CCATGGCCCCGTCACCTGGAG	0.647			T	"""EWSR1, TMPRSS2, DDX5, KLK2, CANT1"""	"""Ewing sarcoma, Prostate carcinoma"""																																p.D292D	Esophageal Squamous(116;1540 1611 12927 31103 34118)		Dom	yes		17	17q21	2118	"""ets variant gene 4 (E1A enhancer binding protein, E1AF)"""		"""M, E"""	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C876T	17						.						28.0	29.0	29.0					17																	41607485		2188	4275	6463	38963011	SO:0001819	synonymous_variant	2118	exon9			U18018	CCDS11465.1, CCDS58553.1, CCDS59292.1	17q21	2014-04-30	2008-09-12			ENSG00000175832			3493	protein-coding gene	gene with protein product	"""E1A enhancer binding protein"""	600711	"""ets variant gene 4 (E1A enhancer-binding protein, E1AF)"""			8530053, 1547944	Standard	NM_001986		Approved	E1A-F, E1AF, PEA3	uc002idw.3	P43268		ENST00000319349.5:c.876C>T	17.37:g.41607485G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38963011	NM_001986	A8K314|B7Z5J3|B7Z9J6|Q96AW9	Silent	SNP	ENST00000319349.5	37	CCDS11465.1																																																																																				0.647	ETV4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453489.1	NM_001986	
ZZEF1	23140	broad.mit.edu	37	17	3991983	3991983	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:3991983C>T	ENST00000381638.2	-	13	2354	c.2230G>A	c.(2230-2232)Gcc>Acc	p.A744T	ZZEF1_ENST00000574474.1_5'UTR	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	744							calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.A744T(1)		central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						AGGTCATGGGCGAGCTGCTGG	0.502																																					p.A744T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2230A	17						.						95.0	76.0	82.0					17																	3991983		2203	4300	6503	3938732	SO:0001583	missense	23140	exon13			BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.2230G>A	17.37:g.3991983C>T	ENSP00000371051:p.Ala744Thr	Somatic		Capture	Illumina HiSeq	Phase_I	3938732	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	.	.	.	.	.	.	.	.	.	.	C	13.25	2.182146	0.38511	.	.	ENSG00000074755	ENST00000381638	T	0.21734	1.99	6.01	4.02	0.46733	.	0.147900	0.64402	N	0.000008	T	0.11067	0.0270	N	0.11201	0.11	0.40554	D	0.981145	B;B	0.18968	0.032;0.019	B;B	0.21360	0.034;0.012	T	0.14364	-1.0475	10	0.18710	T	0.47	-9.0014	11.2007	0.48739	0.1283:0.8051:0.0:0.0666	.	744;744	O43149-3;O43149	.;ZZEF1_HUMAN	T	744	ENSP00000371051:A744T	ENSP00000371051:A744T	A	-	1	0	ZZEF1	3938732	0.998000	0.40836	0.984000	0.44739	0.995000	0.86356	3.303000	0.51858	0.868000	0.35678	0.650000	0.86243	GCC		0.502	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
MPP2	4355	broad.mit.edu	37	17	41955335	41955335	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:41955335C>T	ENST00000461854.1	-	14	1656	c.1571G>A	c.(1570-1572)cGg>cAg	p.R524Q	MPP2_ENST00000520305.1_Missense_Mutation_p.R361Q|MPP2_ENST00000377184.3_Missense_Mutation_p.R517Q|MPP2_ENST00000536246.1_Missense_Mutation_p.R489Q|MPP2_ENST00000518766.1_Missense_Mutation_p.R545Q|MPP2_ENST00000523501.1_Missense_Mutation_p.R489Q|MPP2_ENST00000269095.4_Missense_Mutation_p.R500Q			Q14168	MPP2_HUMAN	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	524	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)	p.R500Q(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(4)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)		CTCCACTGTCCGTCTCAGGTC	0.632																																					p.R500Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1499A	17						.						57.0	45.0	49.0					17																	41955335		2203	4300	6503	39310861	SO:0001583	missense	4355	exon13				CCDS11471.1, CCDS62206.1, CCDS62207.1, CCDS62208.1, CCDS62209.1, CCDS62210.1	17q12-q21	2008-07-18			ENSG00000108852	ENSG00000108852			7220	protein-coding gene	gene with protein product	"""MAGUK p55 subfamily member 2"", ""discs large, homolog 2"""	600723		DLG2		7590743	Standard	NM_001278370		Approved	DKFZp761D0712	uc002ieo.1	Q14168	OTTHUMG00000133840	ENST00000461854.1:c.1571G>A	17.37:g.41955335C>T	ENSP00000428286:p.Arg524Gln	Somatic		Capture	Illumina HiSeq	Phase_I	39310861	NM_005374	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000461854.1	37		.	.	.	.	.	.	.	.	.	.	c	18.49	3.635662	0.67130	.	.	ENSG00000108852	ENST00000377184;ENST00000269095;ENST00000461854;ENST00000520305;ENST00000523501;ENST00000536246;ENST00000518766	T;T;T;T;T;T;T	0.16743	2.32;2.32;2.32;2.32;2.32;2.32;2.32	5.21	4.24	0.50183	.	.	.	.	.	T	0.25457	0.0619	L	0.49699	1.58	0.51767	D	0.999937	D;D	0.57257	0.979;0.974	P;P	0.53006	0.715;0.453	T	0.01087	-1.1456	9	0.48119	T	0.1	.	11.3608	0.49642	0.0:0.9121:0.0:0.0879	.	545;517	E7EV80;Q14168-3	.;.	Q	517;500;524;361;489;489;545	ENSP00000366389:R517Q;ENSP00000269095:R500Q;ENSP00000428286:R524Q;ENSP00000428136:R361Q;ENSP00000430540:R489Q;ENSP00000438012:R489Q;ENSP00000428182:R545Q	ENSP00000269095:R500Q	R	-	2	0	MPP2	39310861	0.998000	0.40836	0.951000	0.38953	0.952000	0.60782	1.243000	0.32767	1.206000	0.43276	0.555000	0.69702	CGG		0.632	MPP2-003	KNOWN	non_canonical_polymorphism|basic	protein_coding	protein_coding	OTTHUMT00000258388.2	NM_005374	
SLC4A1	6521	broad.mit.edu	37	17	42334882	42334882	+	Missense_Mutation	SNP	C	C	T	rs28931584		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:42334882C>T	ENST00000262418.6	-	13	1617	c.1462G>A	c.(1462-1464)Gtg>Atg	p.V488M	SLC4A1_ENST00000471005.1_5'Flank|AC003043.1_ENST00000597382.1_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	488	Membrane (anion exchange).		V -> M (in SPH4; Coimbra; also in AR- dRTA; dbSNP:rs28931584). {ECO:0000269|PubMed:10942416, ECO:0000269|PubMed:9207478}.		anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.V488M(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		ACGCGGCCCACGATGTACTCT	0.597																																					p.V488M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1462A	17	GRCh37	CM971385	SLC4A1	M	rs28931584	.						102.0	86.0	91.0					17																	42334882		2203	4300	6503	39690408	SO:0001583	missense	6521	exon13				CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	11027	protein-coding gene	gene with protein product	"""Froese blood group"", ""Swann blood group"", ""Wright blood group"""	109270	"""Waldner blood group"", ""erythrocyte membrane protein band 3"", ""Diego blood group"", ""solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)"", ""solute carrier family 4 (anion exchanger), member 1"""	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.1462G>A	17.37:g.42334882C>T	ENSP00000262418:p.Val488Met	Somatic		Capture	Illumina HiSeq	Phase_I	39690408	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	c	17.60	3.428750	0.62844	.	.	ENSG00000004939	ENST00000262418	T	0.79454	-1.27	5.57	5.57	0.84162	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.89945	0.6862	M	0.87038	2.855	0.58432	A	0.999999	D;D	0.89917	1.0;0.999	D;D	0.81914	0.995;0.915	D	0.90860	0.4738	9	0.62326	D	0.03	.	19.1573	0.93516	0.0:1.0:0.0:0.0	rs28931584	488;488	E2RVJ0;P02730	.;B3AT_HUMAN	M	488	ENSP00000262418:V488M	ENSP00000262418:V488M	V	-	1	0	SLC4A1	39690408	0.952000	0.32445	1.000000	0.80357	0.090000	0.18270	2.173000	0.42472	2.619000	0.88677	0.561000	0.74099	GTG		0.597	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342	
ANKFY1	51479	broad.mit.edu	37	17	4077311	4077311	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:4077311C>T	ENST00000341657.4	-	20	2851	c.2816G>A	c.(2815-2817)cGc>cAc	p.R939H	ANKFY1_ENST00000574367.1_Missense_Mutation_p.R940H|ANKFY1_ENST00000570535.1_Missense_Mutation_p.R981H|CYB5D2_ENST00000573984.1_Intron	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	939					endosomal vesicle fusion (GO:0034058)|endosome localization (GO:0032439)|Golgi to lysosome transport (GO:0090160)|positive regulation of pinocytosis (GO:0048549)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|macropinosome (GO:0044354)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol phosphate binding (GO:1901981)|Rab GTPase binding (GO:0017137)	p.R940H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|liver(1)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32						GGCAGTCTGGCGATGCTTGGT	0.522																																					p.R940H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2819A	17						.						117.0	124.0	122.0					17																	4077311		2137	4247	6384	4024060	SO:0001583	missense	51479	exon20			AB033081	CCDS42236.1, CCDS58502.1	17p13.3	2013-01-10			ENSG00000185722	ENSG00000185722		"""Zinc fingers, FYVE domain containing"", ""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	20763	protein-coding gene	gene with protein product		607927				10940552, 17273843	Standard	NM_016376		Approved	ANKHZN, KIAA1255, ZFYVE14, BTBD23	uc002fxn.3	Q9P2R3	OTTHUMG00000177727	ENST00000341657.4:c.2816G>A	17.37:g.4077311C>T	ENSP00000343362:p.Arg939His	Somatic		Capture	Illumina HiSeq	Phase_I	4024060	NM_016376	A8KA65|Q5RKV4|Q9ULG5	Missense_Mutation	SNP	ENST00000341657.4	37		.	.	.	.	.	.	.	.	.	.	C	33	5.287618	0.95517	.	.	ENSG00000185722	ENST00000341657;ENST00000535427	.	.	.	5.55	5.55	0.83447	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.66237	0.2769	N	0.21508	0.67	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;0.999;0.999	D;P;P;P	0.83275	0.996;0.903;0.843;0.843	T	0.70099	-0.4965	9	0.72032	D	0.01	-18.1505	18.486	0.90830	0.0:1.0:0.0:0.0	.	881;939;940;981	F5H754;Q9P2R3;Q9P2R3-2;Q9P2R3-4	.;ANFY1_HUMAN;.;.	H	940;881	.	ENSP00000343362:R940H	R	-	2	0	ANKFY1	4024060	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.786000	0.85741	2.608000	0.88229	0.462000	0.41574	CGC		0.522	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376	
FZD2	2535	broad.mit.edu	37	17	42636401	42636401	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:42636401G>A	ENST00000315323.3	+	1	1477	c.1345G>A	c.(1345-1347)Ggc>Agc	p.G449S		NM_001466.3	NP_001457.1	Q14332	FZD2_HUMAN	frizzled class receptor 2	449					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cell-cell signaling (GO:0007267)|cochlea morphogenesis (GO:0090103)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|inner ear receptor cell development (GO:0060119)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of cGMP metabolic process (GO:0030825)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|sensory perception of smell (GO:0007608)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.G449S(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(8)	33		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		GAAGCACGACGGCACCAAGAC	0.607																																					p.G449S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1345A	17						.						106.0	91.0	96.0					17																	42636401		2203	4300	6503	39991927	SO:0001583	missense	2535	exon1			L37882	CCDS11484.1	17q21.1	2014-01-29	2014-01-29			ENSG00000180340		"""GPCR / Class F : Frizzled receptors"""	4040	protein-coding gene	gene with protein product		600667	"""frizzled (Drosophila) homolog 2"", ""frizzled homolog 2 (Drosophila)"", ""frizzled 2, seven transmembrane spanning receptor"", ""frizzled family receptor 2"""			7558010, 9813155	Standard	NM_001466		Approved		uc002igx.2	Q14332		ENST00000315323.3:c.1345G>A	17.37:g.42636401G>A	ENSP00000323901:p.Gly449Ser	Somatic		Capture	Illumina HiSeq	Phase_I	39991927	NM_001466	Q0VG82	Missense_Mutation	SNP	ENST00000315323.3	37	CCDS11484.1	.	.	.	.	.	.	.	.	.	.	g	32	5.135087	0.94517	.	.	ENSG00000180340	ENST00000541149;ENST00000315323	D	0.83075	-1.68	5.24	5.24	0.73138	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	D	0.91523	0.7323	M	0.92691	3.335	0.80722	D	1	D	0.60575	0.988	P	0.54238	0.746	D	0.93669	0.6988	10	0.87932	D	0	.	18.433	0.90633	0.0:0.0:1.0:0.0	.	449	Q14332	FZD2_HUMAN	S	525;449	ENSP00000323901:G449S	ENSP00000323901:G449S	G	+	1	0	FZD2	39991927	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.857000	0.99534	2.436000	0.82500	0.561000	0.74099	GGC		0.607	FZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457806.1	NM_001466	
FMNL1	752	broad.mit.edu	37	17	43319001	43319001	+	Splice_Site	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:43319001G>T	ENST00000331495.3	+	14	1921	c.1585G>T	c.(1585-1587)Gat>Tat	p.D529Y	CTD-2020K17.3_ENST00000587534.1_RNA|FMNL1_ENST00000328118.3_Splice_Site_p.D529Y|FMNL1_ENST00000587489.1_Splice_Site_p.D107Y|CTD-2020K17.3_ENST00000393507.2_RNA	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	529	Pro-rich.				actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)	p.D529Y(1)		biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						CCCCAGCCCAGGTGCGCAGGA	0.701																																					p.D529Y	GBM(164;1247 1997 8702 11086 51972)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1585T	17						.						4.0	4.0	4.0					17																	43319001		1629	3190	4819	40674784	SO:0001630	splice_region_variant	752	exon14			AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"""formin-like"""	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.1585+1G>T	17.37:g.43319001G>T		Somatic		Capture	Illumina HiSeq	Phase_I	40674784	NM_005892	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Missense_Mutation	SNP	ENST00000331495.3	37	CCDS11497.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.153837	0.57259	.	.	ENSG00000184922	ENST00000328118;ENST00000331495;ENST00000539884	T;T	0.79554	-1.28;-1.28	4.26	1.93	0.25924	.	6.331140	0.01069	U	0.004800	T	0.67401	0.2889	N	0.08118	0	0.33274	D	0.56141	B	0.02656	0.0	B	0.01281	0.0	T	0.61860	-0.6976	10	0.59425	D	0.04	.	9.5525	0.39319	0.0:0.0:0.5912:0.4088	.	529	O95466	FMNL_HUMAN	Y	529;529;247	ENSP00000327442:D529Y;ENSP00000329219:D529Y	ENSP00000327442:D529Y	D	+	1	0	FMNL1	40674784	0.998000	0.40836	1.000000	0.80357	0.374000	0.29953	2.446000	0.44908	1.918000	0.55548	0.407000	0.27541	GAT		0.701	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892	Missense_Mutation
SPATA32	124783	broad.mit.edu	37	17	43332977	43332977	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:43332977G>A	ENST00000331780.4	-	4	667	c.572C>T	c.(571-573)cCg>cTg	p.P191L	MAP3K14-AS1_ENST00000588698.1_RNA|MAP3K14-AS1_ENST00000585346.1_RNA|MAP3K14-AS1_ENST00000591263.1_RNA|SPATA32_ENST00000543122.1_Missense_Mutation_p.P170L|MAP3K14-AS1_ENST00000588160.1_RNA|MAP3K14-AS1_ENST00000588504.1_RNA|MAP3K14-AS1_ENST00000590100.1_RNA|MAP3K14-AS1_ENST00000592422.1_RNA	NM_152343.2	NP_689556.2	Q96LK8	SPT32_HUMAN	spermatogenesis associated 32	191					spermatogenesis (GO:0007283)	perinuclear region of cytoplasm (GO:0048471)		p.P191L(1)									CTCCCGGAGCGGGGATCTGAT	0.632																																					p.P191L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C572T	17						.						81.0	69.0	73.0					17																	43332977		2203	4300	6503	40688760	SO:0001583	missense	124783	exon4			AK058143	CCDS32669.1	17q21.31	2013-10-11	2012-10-08	2012-10-08	ENSG00000184361	ENSG00000184361			26349	protein-coding gene	gene with protein product	"""acrosome expressed 2"""		"""chromosome 17 open reading frame 46"", ""testis expressed 34"""	C17orf46, TEX34		18621766	Standard	NM_152343		Approved	FLJ25414, AEP2, VAD1.2	uc002iis.1	Q96LK8	OTTHUMG00000180363	ENST00000331780.4:c.572C>T	17.37:g.43332977G>A	ENSP00000331532:p.Pro191Leu	Somatic		Capture	Illumina HiSeq	Phase_I	40688760	NM_152343	Q7Z4U1|Q8N6V6	Missense_Mutation	SNP	ENST00000331780.4	37	CCDS32669.1	.	.	.	.	.	.	.	.	.	.	G	7.721	0.697152	0.15106	.	.	ENSG00000184361	ENST00000331780;ENST00000543122	T;T	0.39406	1.08;1.08	4.6	-9.2	0.00682	.	2.328530	0.02045	N	0.049608	T	0.19765	0.0475	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.12578	-1.0542	10	0.38643	T	0.18	.	1.8941	0.03254	0.1955:0.3669:0.2073:0.2303	.	191	Q96LK8	CQ046_HUMAN	L	191;170	ENSP00000331532:P191L;ENSP00000442724:P170L	ENSP00000331532:P191L	P	-	2	0	C17orf46	40688760	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.418000	0.00237	-2.894000	0.00314	-2.716000	0.00133	CCG		0.632	SPATA32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450946.1	NM_152343	
SPATA32	124783	broad.mit.edu	37	17	43333057	43333057	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:43333057G>T	ENST00000331780.4	-	4	587	c.492C>A	c.(490-492)atC>atA	p.I164I	MAP3K14-AS1_ENST00000588698.1_RNA|MAP3K14-AS1_ENST00000585346.1_RNA|MAP3K14-AS1_ENST00000591263.1_RNA|SPATA32_ENST00000543122.1_Silent_p.I143I|MAP3K14-AS1_ENST00000588160.1_RNA|MAP3K14-AS1_ENST00000588504.1_RNA|MAP3K14-AS1_ENST00000590100.1_RNA|MAP3K14-AS1_ENST00000592422.1_RNA	NM_152343.2	NP_689556.2	Q96LK8	SPT32_HUMAN	spermatogenesis associated 32	164					spermatogenesis (GO:0007283)	perinuclear region of cytoplasm (GO:0048471)		p.I164I(1)									CTGAGGCCTGGATGAGCTTGT	0.612																																					p.I164I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C492A	17						.						103.0	86.0	92.0					17																	43333057		2203	4300	6503	40688840	SO:0001819	synonymous_variant	124783	exon4			AK058143	CCDS32669.1	17q21.31	2013-10-11	2012-10-08	2012-10-08	ENSG00000184361	ENSG00000184361			26349	protein-coding gene	gene with protein product	"""acrosome expressed 2"""		"""chromosome 17 open reading frame 46"", ""testis expressed 34"""	C17orf46, TEX34		18621766	Standard	NM_152343		Approved	FLJ25414, AEP2, VAD1.2	uc002iis.1	Q96LK8	OTTHUMG00000180363	ENST00000331780.4:c.492C>A	17.37:g.43333057G>T		Somatic		Capture	Illumina HiSeq	Phase_I	40688840	NM_152343	Q7Z4U1|Q8N6V6	Silent	SNP	ENST00000331780.4	37	CCDS32669.1																																																																																				0.612	SPATA32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450946.1	NM_152343	
GOSR2	9570	broad.mit.edu	37	17	45012621	45012621	+	Intron	SNP	C	C	T	rs186325723		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:45012621C>T	ENST00000393456.2	+	5	534				GOSR2_ENST00000415811.2_Missense_Mutation_p.T188M|RP11-156P1.2_ENST00000571841.1_Intron|GOSR2_ENST00000439730.2_Intron|GOSR2_ENST00000576910.2_Intron|GOSR2_ENST00000225567.4_Intron	NM_004287.3	NP_004278.2	O14653	GOSR2_HUMAN	golgi SNAP receptor complex member 2						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)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)	p.T188M(1)		kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|skin(1)	7			BRCA - Breast invasive adenocarcinoma(9;0.102)			ATTTTGATTACGTGTCCTCAA	0.438													C|||	1	0.000199681	0.0	0.0	5008	,	,		21914	0.001		0.0	False		,,,				2504	0.0				p.T188M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C563T	17						.						51.0	55.0	54.0					17																	45012621		1321	2308	3629	42367620	SO:0001627	intron_variant	9570	exon5			AF007548	CCDS11507.1, CCDS42355.1, CCDS45719.1	17q21	2006-02-10				ENSG00000108433			4431	protein-coding gene	gene with protein product		604027				9349823, 10198168	Standard	XM_005257843		Approved	GS27, Bos1	uc002ikz.3	O14653		ENST00000393456.2:c.477+86C>T	17.37:g.45012621C>T		Somatic		Capture	Illumina HiSeq	Phase_I	42367620	NM_001012511	D3DXJ5|D3DXJ6|Q8N4B8|Q96DA5|Q9BZZ4	Missense_Mutation	SNP	ENST00000393456.2	37	CCDS42355.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	2.944	-0.218274	0.06101	.	.	ENSG00000108433	ENST00000415811	T	0.64260	-0.09	3.62	-5.15	0.02866	.	.	.	.	.	T	0.42131	0.1189	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.26052	-1.0114	7	.	.	.	.	11.9652	0.53031	0.0:0.2772:0.0:0.7228	.	188	Q8N4B8	.	M	188	ENSP00000394559:T188M	.	T	+	2	0	GOSR2	42367620	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.311000	0.02723	-1.198000	0.02669	-0.736000	0.03550	ACG		0.438	GOSR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440438.1		
NPEPPS	9520	broad.mit.edu	37	17	45623285	45623285	+	Missense_Mutation	SNP	C	C	T	rs369570255	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:45623285C>T	ENST00000322157.4	+	2	503	c.266C>T	c.(265-267)gCg>gTg	p.A89V	NPEPPS_ENST00000530173.1_Missense_Mutation_p.A85V|NPEPPS_ENST00000525037.1_3'UTR|NPEPPS_ENST00000544660.1_Missense_Mutation_p.A45V	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	89					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.A89V(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						GTGAGGCAGGCGACTAATCAG	0.383													C|||	4	0.000798722	0.003	0.0	5008	,	,		27199	0.0		0.0	False		,,,				2504	0.0				p.A89V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C266T	17						.	C	VAL/ALA	26,3552		0,26,1763	17.0	14.0	15.0		266	4.4	1.0	17		15	0,8062		0,0,4031	no	missense	NPEPPS	NM_006310.3	64	0,26,5794	TT,TC,CC		0.0,0.7267,0.2234	possibly-damaging	89/920	45623285	26,11614	1789	4031	5820	42978284	SO:0001583	missense	9520	exon2			Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"""puromycin-sensitive aminopeptidase"", ""metalloproteinase MP100"""	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.266C>T	17.37:g.45623285C>T	ENSP00000320324:p.Ala89Val	Somatic		Capture	Illumina HiSeq	Phase_I	42978284	NM_006310	B7Z463|Q6P145|Q9NP16|Q9UEM2	Missense_Mutation	SNP	ENST00000322157.4	37	CCDS45721.1	.	.	.	.	.	.	.	.	.	.	C	16.40	3.111621	0.56398	0.007267	0.0	ENSG00000141279	ENST00000525007;ENST00000530173;ENST00000322157;ENST00000539572;ENST00000544660	T;T;T;T	0.04706	3.57;3.57;3.57;3.57	4.37	4.37	0.52481	Peptidase M1, membrane alanine aminopeptidase, N-terminal (2);	0.054505	0.64402	D	0.000001	T	0.06142	0.0159	L	0.53561	1.675	0.58432	D	0.999997	P;P;P	0.50943	0.94;0.897;0.897	P;B;P	0.45794	0.453;0.301;0.493	T	0.14727	-1.0462	10	0.45353	T	0.12	.	15.8614	0.79026	0.0:1.0:0.0:0.0	.	89;85;89	A6NEC2;E9PLK3;P55786	PSAL_HUMAN;.;PSA_HUMAN	V	76;85;89;76;45	ENSP00000437019:A76V;ENSP00000433287:A85V;ENSP00000320324:A89V;ENSP00000442461:A45V	ENSP00000320324:A89V	A	+	2	0	NPEPPS	42978284	1.000000	0.71417	0.992000	0.48379	0.452000	0.32318	4.571000	0.60879	2.236000	0.73375	0.555000	0.69702	GCG		0.383	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310	
NPEPPS	9520	broad.mit.edu	37	17	45695737	45695737	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:45695737C>T	ENST00000322157.4	+	20	2554	c.2317C>T	c.(2317-2319)Caa>Taa	p.Q773*	RP11-580I16.2_ENST00000582389.1_RNA|RP11-580I16.2_ENST00000582066.1_RNA|NPEPPS_ENST00000530173.1_Nonsense_Mutation_p.Q769*|NPEPPS_ENST00000544660.1_Nonsense_Mutation_p.Q693*	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	773					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.Q773*(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						AGCAGATATGCAAGAAGAGAA	0.398																																					p.Q773X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2317T	17						.						90.0	87.0	88.0					17																	45695737		1827	4091	5918	43050736	SO:0001587	stop_gained	9520	exon20			Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"""puromycin-sensitive aminopeptidase"", ""metalloproteinase MP100"""	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.2317C>T	17.37:g.45695737C>T	ENSP00000320324:p.Gln773*	Somatic		Capture	Illumina HiSeq	Phase_I	43050736	NM_006310	B7Z463|Q6P145|Q9NP16|Q9UEM2	Nonsense_Mutation	SNP	ENST00000322157.4	37	CCDS45721.1	.	.	.	.	.	.	.	.	.	.	C	40	8.160291	0.98683	.	.	ENSG00000141279	ENST00000530173;ENST00000322157;ENST00000544660;ENST00000528565	.	.	.	5.86	5.86	0.93980	.	0.101366	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	19.7774	0.96400	0.0:1.0:0.0:0.0	.	.	.	.	X	769;773;693;8	.	ENSP00000320324:Q773X	Q	+	1	0	NPEPPS	43050736	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.796000	0.85898	2.771000	0.95319	0.650000	0.86243	CAA		0.398	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310	
SP6	80320	broad.mit.edu	37	17	45925741	45925741	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:45925741C>T	ENST00000536300.1	-	2	386	c.55G>A	c.(55-57)Gcc>Acc	p.A19T	SP6_ENST00000342234.2_Missense_Mutation_p.A19T	NM_001258248.1	NP_001245177.1	Q3SY56	SP6_HUMAN	Sp6 transcription factor	19					positive regulation of cell proliferation (GO:0008284)|regulation of odontogenesis (GO:0042481)|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.A19T(1)		large_intestine(1)|lung(5)|prostate(1)|skin(1)	8						GGCGGGGAGGCGTGCGGCGCT	0.711																																					p.A19T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G55A	17						.						6.0	7.0	7.0					17																	45925741		2140	4201	6341	43280740	SO:0001583	missense	80320	exon2				CCDS11520.1	17q21.32	2013-01-08			ENSG00000189120	ENSG00000189120		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	14530	protein-coding gene	gene with protein product	"""epiprofin"""	608613				11087666, 14551215	Standard	NM_001258248		Approved	KLF14, Epfn	uc002img.2	Q3SY56	OTTHUMG00000132067	ENST00000536300.1:c.55G>A	17.37:g.45925741C>T	ENSP00000438209:p.Ala19Thr	Somatic		Capture	Illumina HiSeq	Phase_I	43280740	NM_199262	B3KXS4	Missense_Mutation	SNP	ENST00000536300.1	37	CCDS11520.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.563545	0.45694	.	.	ENSG00000189120	ENST00000342234;ENST00000536300	T;T	0.08546	3.08;3.08	4.29	3.3	0.37823	.	0.374079	0.19281	N	0.118149	T	0.03178	0.0093	N	0.08118	0	0.28656	N	0.906416	B	0.34372	0.451	B	0.12837	0.008	T	0.37384	-0.9708	10	0.10902	T	0.67	.	11.1592	0.48505	0.3299:0.6701:0.0:0.0	.	19	Q3SY56	SP6_HUMAN	T	19	ENSP00000340799:A19T;ENSP00000438209:A19T	ENSP00000340799:A19T	A	-	1	0	SP6	43280740	0.904000	0.30761	1.000000	0.80357	0.980000	0.70556	0.145000	0.16157	0.979000	0.38497	0.462000	0.41574	GCC		0.711	SP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441395.1	NM_199262	
NFE2L1	4779	broad.mit.edu	37	17	46134846	46134846	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:46134846G>A	ENST00000362042.3	+	5	1570	c.954G>A	c.(952-954)atG>atA	p.M318I	NFE2L1_ENST00000583378.1_Missense_Mutation_p.M119I|NFE2L1_ENST00000357480.5_Missense_Mutation_p.M288I|NFE2L1_ENST00000585291.1_Missense_Mutation_p.M288I|NFE2L1_ENST00000361665.3_Missense_Mutation_p.M307I|RP5-890E16.4_ENST00000583349.1_RNA|NFE2L1_ENST00000536222.1_Missense_Mutation_p.M162I|NFE2L1_ENST00000582155.1_Missense_Mutation_p.M130I	NM_003204.2	NP_003195.1	Q14494	NF2L1_HUMAN	nuclear factor, erythroid 2-like 1	318					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.M318I(1)		cervix(1)|endometrium(3)|kidney(9)|large_intestine(7)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						AAGATCTCATGTCCATCATGG	0.483																																					p.M318I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G954A	17						.						121.0	101.0	108.0					17																	46134846		2203	4300	6503	43489845	SO:0001583	missense	4779	exon5			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.954G>A	17.37:g.46134846G>A	ENSP00000354855:p.Met318Ile	Somatic		Capture	Illumina HiSeq	Phase_I	43489845	NM_003204	D3DTU3|D3DTU5|Q12877|Q96FN6	Missense_Mutation	SNP	ENST00000362042.3	37	CCDS11524.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.887069	0.52014	.	.	ENSG00000082641	ENST00000362042;ENST00000361665;ENST00000357480;ENST00000536222	T;T	0.19394	2.46;2.15	5.64	5.64	0.86602	.	0.073073	0.85682	D	0.000000	T	0.43743	0.1261	L	0.59436	1.845	0.80722	D	1	D;D;D;D	0.59767	0.986;0.969;0.982;0.977	D;D;D;P	0.71656	0.974;0.914;0.961;0.883	T	0.02829	-1.1105	10	0.33940	T	0.23	-0.7743	18.8473	0.92212	0.0:0.0:1.0:0.0	.	162;130;288;318	F5H1B7;B4DYE1;Q14494-2;Q14494	.;.;.;NF2L1_HUMAN	I	337;318;288;162	ENSP00000350072:M288I;ENSP00000445811:M162I	ENSP00000350072:M288I	M	+	3	0	NFE2L1	43489845	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.165000	0.94761	2.820000	0.97059	0.650000	0.86243	ATG		0.483	NFE2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443019.1	NM_003204	
HOXB1	3211	broad.mit.edu	37	17	46608006	46608006	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:46608006G>A	ENST00000239174.6	-	1	353	c.261C>T	c.(259-261)gcC>gcT	p.A87A	HOXB1_ENST00000577092.1_Silent_p.A87A	NM_002144.3	NP_002135.2	P14653	HXB1_HUMAN	homeobox B1	87					anatomical structure formation involved in morphogenesis (GO:0048646)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|multicellular organismal development (GO:0007275)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)	p.A87A(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GGCTGCAGGCGGCAGGAGCAT	0.657																																					p.A87A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C261T	17						.						46.0	52.0	50.0					17																	46608006		2203	4298	6501	43963005	SO:0001819	synonymous_variant	3211	exon1				CCDS32675.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120094	ENSG00000120094		"""Homeoboxes / ANTP class : HOXL subclass"""	5111	protein-coding gene	gene with protein product		142968	"""homeo box B1"""	HOX2, HOX2I		1973146, 1358459	Standard	NM_002144		Approved		uc002ink.1	P14653	OTTHUMG00000159929	ENST00000239174.6:c.261C>T	17.37:g.46608006G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43963005	NM_002144	Q4VB03	Silent	SNP	ENST00000239174.6	37	CCDS32675.1																																																																																				0.657	HOXB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358383.3		
SPOP	8405	broad.mit.edu	37	17	47679313	47679313	+	Silent	SNP	G	G	A	rs146116174		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:47679313G>A	ENST00000393328.2	-	10	1259	c.894C>T	c.(892-894)tcC>tcT	p.S298S	SPOP_ENST00000393331.3_Silent_p.S298S|SPOP_ENST00000503676.1_Silent_p.S298S|SPOP_ENST00000504102.1_Silent_p.S298S|SPOP_ENST00000347630.2_Silent_p.S298S	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	298	Important for homodimerization.				glucose homeostasis (GO:0042593)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	Cul3-RING ubiquitin ligase complex (GO:0031463)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)	p.S298S(1)		endometrium(18)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(3)|prostate(33)	63						CGTTCTCCACGGACAGGTTAC	0.493										Prostate(2;0.17)																											p.S298S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C894T	17						.	G	,,,,,	1,4405	2.1+/-5.4	0,1,2202	138.0	127.0	131.0		894,894,894,894,894,894	-4.6	0.9	17	dbSNP_134	131	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPOP	NM_001007226.1,NM_001007227.1,NM_001007228.1,NM_001007229.1,NM_001007230.1,NM_003563.3	,,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,,	298/375,298/375,298/375,298/375,298/375,298/375	47679313	1,13005	2203	4300	6503	45034312	SO:0001819	synonymous_variant	8405	exon10			AJ000644	CCDS11551.1	17q21.33	2013-01-09			ENSG00000121067	ENSG00000121067		"""BTB/POZ domain containing"""	11254	protein-coding gene	gene with protein product		602650				9414087	Standard	NM_001007227		Approved	TEF2, BTBD32	uc002ipg.3	O43791	OTTHUMG00000161496	ENST00000393328.2:c.894C>T	17.37:g.47679313G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45034312	NM_001007229	B2R6S3|D3DTW7|Q53HJ1	Silent	SNP	ENST00000393328.2	37	CCDS11551.1																																																																																				0.493	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563	
ITGA3	3675	broad.mit.edu	37	17	48151822	48151822	+	Missense_Mutation	SNP	G	G	A	rs140792604		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:48151822G>A	ENST00000320031.8	+	10	1723	c.1393G>A	c.(1393-1395)Gtc>Atc	p.V465I	ITGA3_ENST00000544892.1_Missense_Mutation_p.V240I|ITGA3_ENST00000007722.7_Missense_Mutation_p.V465I	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	465					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)	p.V465I(1)		endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						GGCCCGGCCCGTCATCAACAT	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		16578	0.001		0.0	False		,,,				2504	0.0				p.V465I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1393A	17						.	G	ILE/VAL,ILE/VAL	0,4406		0,0,2203	76.0	66.0	69.0		1393,1393	3.6	0.8	17	dbSNP_134	69	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ITGA3	NM_002204.2,NM_005501.2	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	465/1052,465/1067	48151822	1,13005	2203	4300	6503	45506821	SO:0001583	missense	3675	exon10			M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"""CD molecules"", ""Integrins"""	6139	protein-coding gene	gene with protein product		605025	"""antigen identified by monoclonal antibody J143"""	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.1393G>A	17.37:g.48151822G>A	ENSP00000315190:p.Val465Ile	Somatic		Capture	Illumina HiSeq	Phase_I	45506821	NM_002204	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Missense_Mutation	SNP	ENST00000320031.8	37	CCDS11558.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	18.01	3.526803	0.64860	0.0	1.16E-4	ENSG00000005884	ENST00000544892;ENST00000007722;ENST00000538917;ENST00000320031	T;T;T	0.73363	-0.74;0.42;0.42	5.6	3.64	0.41730	Integrin alpha-2 (1);	0.184196	0.46758	N	0.000270	D	0.83399	0.5246	M	0.78801	2.425	0.31775	N	0.631572	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.82536	-0.0408	10	0.32370	T	0.25	.	9.6489	0.39886	0.1632:0.0:0.8368:0.0	.	465;465	P26006-1;P26006	.;ITA3_HUMAN	I	240;465;451;465	ENSP00000446133:V240I;ENSP00000007722:V465I;ENSP00000315190:V465I	ENSP00000007722:V465I	V	+	1	0	ITGA3	45506821	1.000000	0.71417	0.824000	0.32777	0.742000	0.42306	4.198000	0.58419	0.743000	0.32719	-0.251000	0.11542	GTC		0.612	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501	
SAMD14	201191	broad.mit.edu	37	17	48193258	48193258	+	Missense_Mutation	SNP	G	G	A	rs369339604		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:48193258G>A	ENST00000330175.4	-	6	915	c.598C>T	c.(598-600)Cgc>Tgc	p.R200C	SAMD14_ENST00000503734.1_5'Flank|SAMD14_ENST00000503131.1_Missense_Mutation_p.R200C	NM_001257359.1	NP_001244288.1	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	200								p.R200C(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	15						GATGCTCGGCGCAGGGTGACC	0.677																																					p.R200C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C598T	17						.	G	CYS/ARG	0,4404		0,0,2202	25.0	24.0	25.0		598	5.4	1.0	17		25	1,8599	1.2+/-3.3	0,1,4299	no	missense	SAMD14	NM_174920.2	180	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	200/446	48193258	1,13003	2202	4300	6502	45548257	SO:0001583	missense	201191	exon6				CCDS11560.1, CCDS58562.1	17q21.33	2013-01-10				ENSG00000167100		"""Sterile alpha motif (SAM) domain containing"""	27312	protein-coding gene	gene with protein product						8619474	Standard	NM_174920		Approved	FLJ36890	uc002iqg.4	Q8IZD0		ENST00000330175.4:c.598C>T	17.37:g.48193258G>A	ENSP00000329144:p.Arg200Cys	Somatic		Capture	Illumina HiSeq	Phase_I	45548257	NM_174920	A5D8V1|Q8N2X0	Missense_Mutation	SNP	ENST00000330175.4	37	CCDS58562.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.757738	0.69648	0.0	1.16E-4	ENSG00000167100	ENST00000330175;ENST00000285206;ENST00000503131	.	.	.	5.41	5.41	0.78517	.	0.093131	0.45361	D	0.000375	T	0.75162	0.3812	M	0.63843	1.955	0.51233	D	0.999913	D;D	0.89917	0.999;1.0	P;D	0.85130	0.801;0.997	T	0.77175	-0.2684	9	0.87932	D	0	-19.1786	11.7776	0.51995	0.0:0.0:0.8245:0.1755	.	200;200	Q8IZD0;Q8IZD0-2	SAM14_HUMAN;.	C	200;212;200	.	ENSP00000285206:R212C	R	-	1	0	SAMD14	45548257	0.998000	0.40836	1.000000	0.80357	0.939000	0.58152	2.593000	0.46180	2.533000	0.85409	0.313000	0.20887	CGC		0.677	SAMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366661.1	NM_174920	
MED11	400569	broad.mit.edu	37	17	4638400	4638400	+	IGR	SNP	C	C	T	rs138114709	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:4638400C>T	ENST00000293777.5	+	0	833				RP11-314A20.5_ENST00000570493.2_RNA|CXCL16_ENST00000574412.1_Silent_p.P254P|CXCL16_ENST00000293778.6_Silent_p.P254P|CXCL16_ENST00000576153.1_5'UTR	NM_001001683.2	NP_001001683.1	Q9P086	MED11_HUMAN	mediator complex subunit 11							mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.P254P(2)		lung(2)|ovary(2)	4						GAGAGGACTGCGGTGACTGCC	0.602													C|||	3	0.000599042	0.0	0.0	5008	,	,		18627	0.0		0.0	False		,,,				2504	0.0031				p.P254P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G762A	17						.	C	,	0,4406		0,0,2203	51.0	47.0	49.0		762,762	0.9	0.0	17	dbSNP_134	49	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous,coding-synonymous	CXCL16	NM_001100812.1,NM_022059.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	254/274,254/274	4638400	1,13005	2203	4300	6503	4585149	SO:0001628	intergenic_variant	58191	exon4			AF161414	CCDS32533.1	17p13.2	2007-07-30	2007-07-30			ENSG00000161920			32687	protein-coding gene	gene with protein product		612383	"""mediator of RNA polymerase II transcription, subunit 11 homolog (S. cerevisiae)"""			15175163, 12584197	Standard	NM_001001683		Approved	HSPC296, MGC88387	uc002fyp.3	Q9P086			17.37:g.4638400C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4585149	NM_001100812	Q6NS89	Silent	SNP	ENST00000293777.5	37	CCDS32533.1																																																																																				0.602	MED11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439574.1	NM_001001683	
COL1A1	1277	broad.mit.edu	37	17	48268238	48268238	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:48268238G>A	ENST00000225964.5	-	33	2401	c.2283C>T	c.(2281-2283)ggC>ggT	p.G761G		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	761	Triple-helical region.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)	p.G761G(3)	COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	GACCACGGACGCCATCTTTGC	0.587			T	"""PDGFB, USP6"""	"""dermatofibrosarcoma protuberans, aneurysmal bone cyst """		Osteogenesis imperfecta																														p.G761G			Dom	yes		17	17q21.31-q22	1277	"""collagen, type I, alpha 1"""	yes	M	.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C2283T	17						.						119.0	93.0	102.0					17																	48268238		2203	4300	6503	45623237	SO:0001819	synonymous_variant	1277	exon33			Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"""Collagens"""	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.2283C>T	17.37:g.48268238G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45623237	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Silent	SNP	ENST00000225964.5	37	CCDS11561.1																																																																																				0.587	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2		
RSAD1	55316	broad.mit.edu	37	17	48560824	48560824	+	Missense_Mutation	SNP	G	G	A	rs375119650		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:48560824G>A	ENST00000258955.2	+	6	1113	c.1028G>A	c.(1027-1029)cGt>cAt	p.R343H		NM_018346.1	NP_060816.1	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing 1	343					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.R343H(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)			ACCCGGAAGCGTGTCCCCCTG	0.597																																					p.R343H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1028A	17						.	G	HIS/ARG	0,4406		0,0,2203	41.0	44.0	43.0		1028	4.2	0.7	17		43	1,8599	1.2+/-3.3	0,1,4299	no	missense	RSAD1	NM_018346.1	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	343/443	48560824	1,13005	2203	4300	6503	45915823	SO:0001583	missense	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.1028G>A	17.37:g.48560824G>A	ENSP00000258955:p.Arg343His	Somatic		Capture	Illumina HiSeq	Phase_I	45915823	NM_018346	B4DMW0|Q53HV8|Q86VC4|Q9BRY7|Q9NUS7	Missense_Mutation	SNP	ENST00000258955.2	37	CCDS11569.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.429006	0.43122	0.0	1.16E-4	ENSG00000136444	ENST00000258955	T	0.22743	1.94	5.19	4.21	0.49690	HemN, C-terminal (1);	0.225717	0.37761	N	0.001952	T	0.15003	0.0362	L	0.33189	0.99	0.28581	N	0.910144	P	0.51653	0.947	B	0.42188	0.379	T	0.09997	-1.0649	10	0.52906	T	0.07	-8.0984	6.2368	0.20768	0.1574:0.0:0.6926:0.15	.	343	Q9HA92	RSAD1_HUMAN	H	343	ENSP00000258955:R343H	ENSP00000258955:R343H	R	+	2	0	RSAD1	45915823	1.000000	0.71417	0.705000	0.30386	0.126000	0.20510	4.445000	0.60007	1.319000	0.45190	0.655000	0.94253	CGT		0.597	RSAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367413.1	NM_018346	
EPN3	55040	broad.mit.edu	37	17	48618667	48618667	+	Missense_Mutation	SNP	C	C	T	rs539835428	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:48618667C>T	ENST00000268933.3	+	8	1906	c.1327C>T	c.(1327-1329)Ccc>Tcc	p.P443S	RP11-94C24.8_ENST00000513017.1_RNA|EPN3_ENST00000541226.1_3'UTR|EPN3_ENST00000537145.1_Missense_Mutation_p.P471S	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	443						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.P443S(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)			GCAGGCCCTGCCCTCTGGGAA	0.632																																					p.P443S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1327T	17						.						112.0	120.0	117.0					17																	48618667		2203	4300	6503	45973666	SO:0001583	missense	55040	exon8			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.1327C>T	17.37:g.48618667C>T	ENSP00000268933:p.Pro443Ser	Somatic		Capture	Illumina HiSeq	Phase_I	45973666	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Missense_Mutation	SNP	ENST00000268933.3	37	CCDS11570.1	.	.	.	.	.	.	.	.	.	.	C	2.937	-0.219828	0.06061	.	.	ENSG00000049283	ENST00000268933;ENST00000442715;ENST00000537145	T;T	0.38722	1.12;1.12	4.76	2.73	0.32206	.	5.207350	0.01243	N	0.008678	T	0.29288	0.0729	L	0.36672	1.1	0.80722	D	1	B;B;B	0.25667	0.1;0.131;0.001	B;B;B	0.16289	0.009;0.015;0.007	T	0.48115	-0.9063	10	0.02654	T	1	-15.1905	4.7627	0.13116	0.0:0.4562:0.3246:0.2192	.	471;471;443	B4DK18;F6QWW5;Q9H201	.;.;EPN3_HUMAN	S	443;471;471	ENSP00000268933:P443S;ENSP00000439512:P471S	ENSP00000268933:P443S	P	+	1	0	EPN3	45973666	0.017000	0.18338	0.517000	0.27799	0.008000	0.06430	-0.024000	0.12435	0.593000	0.29745	-0.291000	0.09656	CCC		0.632	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957	
CACNA1G	8913	broad.mit.edu	37	17	48694872	48694872	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:48694872G>A	ENST00000359106.5	+	29	5095	c.5095G>A	c.(5095-5097)Gcc>Acc	p.A1699T	CACNA1G_ENST00000515765.1_Missense_Mutation_p.A1688T|CACNA1G_ENST00000514079.1_Missense_Mutation_p.A1706T|CACNA1G_ENST00000502264.1_Missense_Mutation_p.A1676T|CACNA1G_ENST00000442258.2_Missense_Mutation_p.A1658T|CACNA1G_ENST00000514717.1_Missense_Mutation_p.A1642T|CACNA1G_ENST00000515165.1_Missense_Mutation_p.A1699T|CACNA1G_ENST00000510366.1_Missense_Mutation_p.A1647T|CACNA1G_ENST00000507336.1_Missense_Mutation_p.A1688T|CACNA1G_ENST00000514181.1_Missense_Mutation_p.A1681T|CACNA1G_ENST00000513964.1_Missense_Mutation_p.A1654T|CACNA1G_ENST00000512389.1_Missense_Mutation_p.A1688T|CACNA1G_ENST00000352832.5_Missense_Mutation_p.A1665T|CACNA1G_ENST00000515411.1_Missense_Mutation_p.A1681T|CACNA1G_ENST00000507896.1_Missense_Mutation_p.A1688T|CACNA1G_ENST00000505165.1_Missense_Mutation_p.A1699T|CACNA1G_ENST00000507510.2_Missense_Mutation_p.A1699T|CACNA1G_ENST00000507609.1_Missense_Mutation_p.A1699T|CACNA1G_ENST00000513689.2_Missense_Mutation_p.A1654T|CACNA1G_ENST00000503485.1_Missense_Mutation_p.A1665T|CACNA1G_ENST00000510115.1_Missense_Mutation_p.A1665T|CACNA1G_ENST00000358244.5_Missense_Mutation_p.A1665T|CACNA1G_ENST00000429973.2_Missense_Mutation_p.A1681T|CACNA1G_ENST00000360761.4_Missense_Mutation_p.A1676T|CACNA1G_ENST00000354983.4_Missense_Mutation_p.A1665T	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1699					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.A1699T(1)|p.A1665T(1)		breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CGAGGTCAACGCCTCGCTGCC	0.617																																					p.A1676T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G5026A	17						.						71.0	73.0	72.0					17																	48694872		2172	4268	6440	46049871	SO:0001583	missense	8913	exon28			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.5095G>A	17.37:g.48694872G>A	ENSP00000352011:p.Ala1699Thr	Somatic		Capture	Illumina HiSeq	Phase_I	46049871	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	5.532979	0.96446	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;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	0.98400	-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91;-4.91	5.02	5.02	0.67125	Ion transport (1);	0.000000	0.64402	D	0.000001	D	0.97870	0.9300	N	0.20986	0.625	0.80722	D	1	B;D;P;P;P;P;P;D;P;D;D;D;P;D;P;P;D;D;D;D;P;B;D;D;D	0.89917	0.176;0.997;0.897;0.831;0.942;0.941;0.9;0.988;0.9;1.0;0.997;0.962;0.764;1.0;0.9;0.635;0.994;0.984;0.994;0.995;0.613;0.432;0.977;0.997;1.0	B;D;P;P;P;P;P;P;P;D;P;P;P;D;P;B;P;P;D;D;B;B;P;D;D	0.97110	0.205;0.964;0.685;0.697;0.828;0.685;0.51;0.884;0.51;0.987;0.907;0.754;0.575;1.0;0.51;0.311;0.884;0.772;0.928;0.947;0.326;0.242;0.853;0.952;0.999	D	0.99804	1.1037	10	0.54805	T	0.06	.	18.3653	0.90389	0.0:0.0:1.0:0.0	.	1642;1654;1647;1681;1654;1681;1706;1665;1699;1688;1699;1676;1688;1688;1681;1688;1699;1676;1699;1665;1658;1665;1676;1699;1665	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	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.	T	1676;1665;1665;1658;1676;1688;1654;1642;1647;1665;1699;1688;1654;1699;1665;1699;1681;1688;1706;1665;1699;1681;1681;1699;1688	ENSP00000353990:A1676T;ENSP00000339302:A1665T;ENSP00000347078:A1665T;ENSP00000409759:A1658T;ENSP00000425522:A1676T;ENSP00000426261:A1688T;ENSP00000425451:A1654T;ENSP00000422407:A1642T;ENSP00000426814:A1647T;ENSP00000427238:A1665T;ENSP00000423112:A1699T;ENSP00000420918:A1688T;ENSP00000426172:A1654T;ENSP00000423045:A1699T;ENSP00000427173:A1665T;ENSP00000426098:A1699T;ENSP00000425698:A1681T;ENSP00000426232:A1688T;ENSP00000423317:A1706T;ENSP00000350979:A1665T;ENSP00000352011:A1699T;ENSP00000414388:A1681T;ENSP00000423155:A1681T;ENSP00000422268:A1699T;ENSP00000421518:A1688T	ENSP00000339302:A1665T	A	+	1	0	CACNA1G	46049871	1.000000	0.71417	0.963000	0.40424	0.885000	0.51271	9.869000	0.99810	2.348000	0.79779	0.655000	0.94253	GCC		0.617	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
CHRNE	1145	broad.mit.edu	37	17	4802129	4802129	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:4802129C>T	ENST00000293780.4	-	12	1394	c.1384G>A	c.(1384-1386)Gct>Act	p.A462T	C17orf107_ENST00000521575.1_5'Flank|CHRNE_ENST00000575637.1_5'Flank|C17orf107_ENST00000381365.3_5'Flank	NM_000080.3	NP_000071.1	Q04844	ACHE_HUMAN	cholinergic receptor, nicotinic, epsilon (muscle)	462					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|cation transmembrane transporter activity (GO:0008324)	p.A462T(1)		central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)	12					Galantamine(DB00674)	AGCACCAGAGCGGCCCAGAAG	0.607																																					p.A462T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1384A	17						.						60.0	42.0	48.0					17																	4802129		2199	4297	6496	4742908	SO:0001583	missense	1145	exon12			X66403	CCDS11058.1	17p13.2	2012-02-11	2012-02-07		ENSG00000108556	ENSG00000108556		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1966	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, epsilon (muscle)"""	100725	"""cholinergic receptor, nicotinic, epsilon"""			7688301	Standard	NM_000080		Approved	ACHRE	uc002fzk.1	Q04844	OTTHUMG00000090778	ENST00000293780.4:c.1384G>A	17.37:g.4802129C>T	ENSP00000293780:p.Ala462Thr	Somatic		Capture	Illumina HiSeq	Phase_I	4742908	NM_000080	D3DTK6	Missense_Mutation	SNP	ENST00000293780.4	37	CCDS11058.1	.	.	.	.	.	.	.	.	.	.	C	32	5.112324	0.94339	.	.	ENSG00000108556	ENST00000293780	D	0.84298	-1.83	4.91	4.91	0.64330	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.90930	0.7149	M	0.65975	2.015	0.58432	D	0.999995	D	0.89917	1.0	D	0.91635	0.999	D	0.90114	0.4194	10	0.40728	T	0.16	.	15.6431	0.77025	0.0:1.0:0.0:0.0	.	462	Q04844	ACHE_HUMAN	T	462	ENSP00000293780:A462T	ENSP00000293780:A462T	A	-	1	0	CHRNE	4742908	1.000000	0.71417	0.101000	0.21167	0.938000	0.57974	4.764000	0.62264	2.549000	0.85964	0.655000	0.94253	GCT		0.607	CHRNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207560.3		
ENO3	2027	broad.mit.edu	37	17	4859401	4859401	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:4859401G>A	ENST00000323997.6	+	9	1162	c.1030G>A	c.(1030-1032)Gtc>Atc	p.V344I	ENO3_ENST00000518175.1_Missense_Mutation_p.V344I|ENO3_ENST00000519584.1_Missense_Mutation_p.V301I	NM_001976.4|NM_053013.3	NP_001967.3|NP_443739.3	P13929	ENOB_HUMAN	enolase 3 (beta, muscle)	344					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to drug (GO:0042493)|skeletal muscle tissue regeneration (GO:0043403)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|phosphopyruvate hydratase complex (GO:0000015)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)	p.V344I(1)		cervix(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)	15						GCTGCTGAAGGTCAACCAGAT	0.592																																					p.V344I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1030A	17						.						97.0	76.0	83.0					17																	4859401		2203	4300	6503	4800125	SO:0001583	missense	2027	exon9			X16504	CCDS11062.1, CCDS54070.1	17p13.2	2013-09-19	2004-11-22		ENSG00000108515	ENSG00000108515	4.2.1.11		3354	protein-coding gene	gene with protein product		131370	"""enolase 3, (beta, muscle)"""				Standard	NM_001976		Approved		uc002gab.4	P13929	OTTHUMG00000099394	ENST00000323997.6:c.1030G>A	17.37:g.4859401G>A	ENSP00000324105:p.Val344Ile	Somatic		Capture	Illumina HiSeq	Phase_I	4800125	NM_053013	B4DUI6|B4DUM6|D3DTL2|E7ENK8|Q96AE2	Missense_Mutation	SNP	ENST00000323997.6	37	CCDS11062.1	.	.	.	.	.	.	.	.	.	.	G	33	5.198828	0.94997	.	.	ENSG00000108515	ENST00000323997;ENST00000519584;ENST00000518175	T;T;T	0.56776	0.44;0.44;0.44	5.53	5.53	0.82687	Enolase, conserved site (1);Enolase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.74374	0.3708	M	0.87180	2.865	0.80722	D	1	P;P;P	0.49862	0.866;0.929;0.866	P;P;P	0.59643	0.861;0.839;0.861	T	0.78961	-0.1997	10	0.87932	D	0	-0.6928	17.0153	0.86416	0.0:0.0:1.0:0.0	.	344;301;344	P13929;P13929-3;D3DTL2	ENOB_HUMAN;.;.	I	344;301;344	ENSP00000324105:V344I;ENSP00000430636:V301I;ENSP00000431087:V344I	ENSP00000324105:V344I	V	+	1	0	ENO3	4800125	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	9.869000	0.99810	2.620000	0.88729	0.460000	0.39030	GTC		0.592	ENO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216851.2		
CAMTA2	23125	broad.mit.edu	37	17	4876070	4876070	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:4876070C>A	ENST00000348066.3	-	15	2620	c.2497G>T	c.(2497-2499)Gac>Tac	p.D833Y	CAMTA2_ENST00000572543.1_Missense_Mutation_p.D838Y|CAMTA2_ENST00000414043.3_Missense_Mutation_p.D856Y|CAMTA2_ENST00000358183.4_Missense_Mutation_p.D833Y|RP5-1050D4.2_ENST00000430920.1_RNA|CAMTA2_ENST00000361571.5_Missense_Mutation_p.D832Y|CAMTA2_ENST00000381311.5_Missense_Mutation_p.D835Y	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	833					cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)	p.D833Y(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						TCACCAGTGTCTGGGCTGGAG	0.592																																					p.D833Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2497T	17						.						65.0	79.0	74.0					17																	4876070		2195	4290	6485	4816794	SO:0001583	missense	23125	exon15			AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.2497G>T	17.37:g.4876070C>A	ENSP00000321813:p.Asp833Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	4816794	NM_015099	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	37	CCDS11063.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.330738	0.81690	.	.	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.34472	2.58;1.59;1.36;1.59;1.37	4.85	4.85	0.62838	.	0.070701	0.56097	D	0.000036	T	0.44912	0.1316	N	0.24115	0.695	0.50632	D	0.999883	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.997;0.997;0.998;0.996;0.997	T	0.38972	-0.9636	10	0.51188	T	0.08	-19.8324	13.3308	0.60485	0.0:1.0:0.0:0.0	.	809;856;835;833;832	B7ZM30;E7EWU5;O94983-3;O94983;O94983-4	.;.;.;CMTA2_HUMAN;.	Y	856;835;832;833;833	ENSP00000412886:D856Y;ENSP00000370712:D835Y;ENSP00000354828:D832Y;ENSP00000350910:D833Y;ENSP00000321813:D833Y	ENSP00000321813:D833Y	D	-	1	0	CAMTA2	4816794	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	4.504000	0.60414	2.528000	0.85240	0.655000	0.94253	GAC		0.592	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099	
KIF1C	10749	broad.mit.edu	37	17	4923886	4923886	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:4923886C>T	ENST00000320785.5	+	20	2207	c.1850C>T	c.(1849-1851)cCg>cTg	p.P617L	KIF1C_ENST00000573815.1_3'UTR|AC109333.10_ENST00000438266.1_RNA	NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	617					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.P617L(1)		NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						CCCCCAGGACCGCCCTCTGAG	0.592																																					p.P617L	Melanoma(96;1023 1447 10250 19259 33730)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1850T	17						.						47.0	50.0	49.0					17																	4923886		2203	4299	6502	4864610	SO:0001583	missense	10749	exon20			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.1850C>T	17.37:g.4923886C>T	ENSP00000320821:p.Pro617Leu	Somatic		Capture	Illumina HiSeq	Phase_I	4864610	NM_006612	D3DTL6|O75186|Q5U618	Missense_Mutation	SNP	ENST00000320785.5	37	CCDS11065.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.702821	0.68501	.	.	ENSG00000129250	ENST00000320785	T	0.72505	-0.66	5.68	5.68	0.88126	.	.	.	.	.	T	0.50548	0.1622	N	0.14661	0.345	0.80722	D	1	D	0.53619	0.961	B	0.35114	0.196	T	0.54351	-0.8307	9	0.24483	T	0.36	.	17.2982	0.87174	0.0:1.0:0.0:0.0	.	617	O43896	KIF1C_HUMAN	L	617	ENSP00000320821:P617L	ENSP00000320821:P617L	P	+	2	0	KIF1C	4864610	0.049000	0.20398	0.921000	0.36526	0.953000	0.61014	1.742000	0.38248	2.683000	0.91414	0.655000	0.94253	CCG		0.592	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1		
KIF1C	10749	broad.mit.edu	37	17	4925926	4925926	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:4925926G>A	ENST00000320785.5	+	22	2907	c.2550G>A	c.(2548-2550)caG>caA	p.Q850Q	AC109333.10_ENST00000438266.1_RNA	NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	850					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.Q850Q(1)		NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						TGAAGCTGCAGAACAGCAGCA	0.677																																					p.Q850Q	Melanoma(96;1023 1447 10250 19259 33730)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2550A	17						.						29.0	30.0	30.0					17																	4925926		2201	4300	6501	4866650	SO:0001819	synonymous_variant	10749	exon22			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.2550G>A	17.37:g.4925926G>A		Somatic		Capture	Illumina HiSeq	Phase_I	4866650	NM_006612	D3DTL6|O75186|Q5U618	Silent	SNP	ENST00000320785.5	37	CCDS11065.1																																																																																				0.677	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1		
SPAG9	9043	broad.mit.edu	37	17	49048172	49048172	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:49048172G>A	ENST00000262013.7	-	29	3954	c.3746C>T	c.(3745-3747)aCg>aTg	p.T1249M	SPAG9_ENST00000510283.1_Missense_Mutation_p.T1105M|SPAG9_ENST00000505279.1_Missense_Mutation_p.T1239M|SPAG9_ENST00000357122.4_Missense_Mutation_p.T1235M	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	1249					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)		p.T1235M(1)		NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			TTTGTCACCCGTCAGATCCGT	0.488																																					p.T1235M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3704T	17						.						134.0	109.0	118.0					17																	49048172		2203	4300	6503	46403171	SO:0001583	missense	9043	exon28			AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"""sperm surface protein"", ""JNK/SAPK-associated protein"", ""JNK interacting protein"", ""sperm specific protein"", ""c-Jun NH2-terminal kinase-associated leucine zipper protein"", ""Max-binding protein"", ""JNK-associated leucine-zipper protein"", ""HLC-4 protein"", ""lung cancer oncogene 4"", ""proliferation-inducing gene 6"", ""cancer/testis antigen 89"""	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.3746C>T	17.37:g.49048172G>A	ENSP00000262013:p.Thr1249Met	Somatic		Capture	Illumina HiSeq	Phase_I	46403171	NM_003971	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	37	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.640093	0.29157	.	.	ENSG00000008294	ENST00000262013;ENST00000376407;ENST00000357804;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445	T;T;T;T	0.24538	1.85;1.85;1.86;1.86	5.01	3.04	0.35103	.	0.376195	0.31685	N	0.007238	T	0.18635	0.0447	L	0.27053	0.805	0.19300	N	0.999976	P;B;P;P	0.40553	0.465;0.335;0.721;0.592	B;B;B;B	0.40901	0.299;0.157;0.343;0.343	T	0.06734	-1.0810	10	0.51188	T	0.08	0.0471	9.5269	0.39169	0.2254:0.0:0.7746:0.0	.	1239;1249;1235;1105	O60271-2;O60271;O60271-4;E7ENU2	.;JIP4_HUMAN;.;.	M	1249;1006;996;1105;1239;1235;847	ENSP00000262013:T1249M;ENSP00000423165:T1105M;ENSP00000426900:T1239M;ENSP00000349636:T1235M	ENSP00000262013:T1249M	T	-	2	0	SPAG9	46403171	0.148000	0.22702	0.110000	0.21437	0.548000	0.35241	2.394000	0.44450	0.716000	0.32124	0.655000	0.94253	ACG		0.488	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971	
ANKFN1	162282	broad.mit.edu	37	17	54431392	54431392	+	Nonsense_Mutation	SNP	C	C	T	rs376046142		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:54431392C>T	ENST00000318698.2	+	5	630	c.595C>T	c.(595-597)Cga>Tga	p.R199*	ANKFN1_ENST00000566473.2_Nonsense_Mutation_p.R199*	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	199								p.R199*(1)		NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						GACAGGGGCCCGAGAAAGTCC	0.468																																					p.R199X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C595T	17						.	C	stop/ARG	0,4406		0,0,2203	87.0	75.0	79.0		595	-3.7	0.1	17		79	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	ANKFN1	NM_153228.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		199/764	54431392	1,13005	2203	4300	6503	51786391	SO:0001587	stop_gained	162282	exon5			AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"""Ankyrin repeat domain containing"", ""Fibronectin type III domain containing"""	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.595C>T	17.37:g.54431392C>T	ENSP00000321627:p.Arg199*	Somatic		Capture	Illumina HiSeq	Phase_I	51786391	NM_153228		Nonsense_Mutation	SNP	ENST00000318698.2	37	CCDS32686.1	.	.	.	.	.	.	.	.	.	.	C	17.14	3.312160	0.60414	0.0	1.16E-4	ENSG00000153930	ENST00000318698	.	.	.	5.22	-3.69	0.04450	.	0.207594	0.49305	D	0.000154	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-0.162	18.7918	0.91976	0.8519:0.1481:0.0:0.0	.	.	.	.	X	199	.	ENSP00000321627:R199X	R	+	1	2	ANKFN1	51786391	1.000000	0.71417	0.086000	0.20670	0.958000	0.62258	2.517000	0.45529	-0.377000	0.07930	0.655000	0.94253	CGA		0.468	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228	
SCPEP1	59342	broad.mit.edu	37	17	55079447	55079447	+	Missense_Mutation	SNP	G	G	A	rs377343195		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:55079447G>A	ENST00000262288.3	+	12	1256	c.1201G>A	c.(1201-1203)Gcc>Acc	p.A401T	AC007114.1_ENST00000580911.1_RNA	NM_021626.2	NP_067639.1	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1	401					negative regulation of blood pressure (GO:0045776)|positive regulation of vasodilation (GO:0045909)|retinoic acid metabolic process (GO:0042573)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)	p.A401T(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	14	Breast(9;2.86e-08)					GAAGTGGAAGGCCCTGTACAG	0.483																																					p.A401T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1201A	17						.	G	THR/ALA	0,4406		0,0,2203	130.0	120.0	123.0		1201	0.9	0.9	17		123	1,8599	1.2+/-3.3	0,1,4299	no	missense	SCPEP1	NM_021626.2	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	401/453	55079447	1,13005	2203	4300	6503	52434446	SO:0001583	missense	59342	exon12			AF282618	CCDS11593.1	17q22	2012-09-20			ENSG00000121064	ENSG00000121064			29507	protein-coding gene	gene with protein product	"""retinoid inducible serine carboxypeptidase"""					11447226, 12975309	Standard	NM_021626		Approved	RISC	uc002iuv.4	Q9HB40	OTTHUMG00000178129	ENST00000262288.3:c.1201G>A	17.37:g.55079447G>A	ENSP00000262288:p.Ala401Thr	Somatic		Capture	Illumina HiSeq	Phase_I	52434446	NM_021626	Q96A94|Q9H3F0	Missense_Mutation	SNP	ENST00000262288.3	37	CCDS11593.1	.	.	.	.	.	.	.	.	.	.	G	18.80	3.701366	0.68501	0.0	1.16E-4	ENSG00000121064	ENST00000262288	T	0.43294	0.95	5.56	0.94	0.19513	.	0.302155	0.34853	N	0.003635	T	0.45074	0.1324	L	0.50919	1.6	0.46749	D	0.99918	P	0.39044	0.656	B	0.43701	0.428	T	0.56038	-0.8045	10	0.56958	D	0.05	-6.6229	18.2999	0.90160	0.0:0.3817:0.6183:0.0	.	401	Q9HB40	RISC_HUMAN	T	401	ENSP00000262288:A401T	ENSP00000262288:A401T	A	+	1	0	SCPEP1	52434446	1.000000	0.71417	0.854000	0.33618	0.758000	0.43043	1.055000	0.30467	0.367000	0.24454	0.655000	0.94253	GCC		0.483	SCPEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440622.1	NM_021626	
NLRP1	22861	broad.mit.edu	37	17	5433982	5433982	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:5433982C>T	ENST00000572272.1	-	12	3338	c.3339G>A	c.(3337-3339)acG>acA	p.T1113T	NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000262467.5_Silent_p.T1117T|NLRP1_ENST00000269280.4_Silent_p.T1113T|NLRP1_ENST00000577119.1_Silent_p.T1083T|NLRP1_ENST00000345221.3_Silent_p.T1113T|NLRP1_ENST00000354411.3_Silent_p.T1083T			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	1113					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)	p.T1113T(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				AGCAGAGACCCGTGTTGGGCC	0.557																																					p.T1083T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3249A	17						.						73.0	69.0	70.0					17																	5433982		2203	4300	6503	5374706	SO:0001819	synonymous_variant	22861	exon11			AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.3339G>A	17.37:g.5433982C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5374706	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Silent	SNP	ENST00000572272.1	37	CCDS42246.1																																																																																				0.557	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
BZRAP1	9256	broad.mit.edu	37	17	56388371	56388371	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:56388371G>C	ENST00000343736.4	-	19	3448	c.3285C>G	c.(3283-3285)agC>agG	p.S1095R	BZRAP1_ENST00000355701.3_Missense_Mutation_p.S1095R|BZRAP1_ENST00000268893.6_Missense_Mutation_p.S1035R			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1095	Pro-rich.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)	p.S1095R(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)					TGGCCTCTGGGCTTGGGTGCG	0.701																																					p.S1095R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3285G	17						.						15.0	20.0	18.0					17																	56388371		2194	4290	6484	53743370	SO:0001583	missense	9256	exon19			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.3285C>G	17.37:g.56388371G>C	ENSP00000345824:p.Ser1095Arg	Somatic		Capture	Illumina HiSeq	Phase_I	53743370	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	G	9.991	1.230818	0.22542	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.34072	1.38;1.38;1.38	5.79	4.81	0.61882	.	0.607850	0.18678	N	0.134258	T	0.33411	0.0862	L	0.36672	1.1	0.28157	N	0.929167	B;P;B	0.45212	0.412;0.853;0.203	B;P;B	0.46850	0.133;0.529;0.163	T	0.08973	-1.0696	10	0.14252	T	0.57	.	12.3532	0.55161	0.0:0.0:0.8317:0.1683	.	1095;1035;1095	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	R	1095;1095;1035	ENSP00000347929:S1095R;ENSP00000345824:S1095R;ENSP00000268893:S1035R	ENSP00000268893:S1035R	S	-	3	2	BZRAP1	53743370	0.081000	0.21417	0.678000	0.29963	0.700000	0.40528	0.759000	0.26461	1.433000	0.47394	0.655000	0.94253	AGC		0.701	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
SUPT4H1	6827	broad.mit.edu	37	17	56424937	56424937	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:56424937G>A	ENST00000225504.3	-	3	251	c.185C>T	c.(184-186)gCg>gTg	p.A62V	BZRAP1-AS1_ENST00000579527.1_RNA|BZRAP1-AS1_ENST00000582348.1_RNA|BZRAP1-AS1_ENST00000583841.1_RNA|BZRAP1-AS1_ENST00000580633.1_RNA|BZRAP1-AS1_ENST00000578334.1_RNA|BZRAP1-AS1_ENST00000583826.1_RNA|SUPT4H1_ENST00000577396.1_Missense_Mutation_p.A21V|BZRAP1-AS1_ENST00000580022.1_RNA|BZRAP1-AS1_ENST00000585236.1_RNA|BZRAP1-AS1_ENST00000579859.1_RNA|SUPT4H1_ENST00000580947.1_Missense_Mutation_p.A62V|SUPT4H1_ENST00000581540.1_Missense_Mutation_p.A53V|BZRAP1-AS1_ENST00000578025.1_RNA|BZRAP1-AS1_ENST00000580515.1_RNA	NM_003168.1	NP_003159.1	P63272	SPT4H_HUMAN	suppressor of Ty 4 homolog 1 (S. cerevisiae)	62					chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.A62V(1)		large_intestine(2)|skin(2)	4	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ACTCATCATCGCAATGATTCT	0.502																																					p.A62V	NSCLC(25;723 896 19867 29219 40028)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C185T	17						.						80.0	65.0	70.0					17																	56424937		2203	4300	6503	53779936	SO:0001583	missense	6827	exon3			U38817	CCDS11606.1	17q22	2014-06-23	2001-11-28		ENSG00000213246	ENSG00000213246			11467	protein-coding gene	gene with protein product		603555	"""suppressor of Ty (S.cerevisiae) 4 homolog 1"""	SUPT4H		8786137	Standard	NM_003168		Approved	SPT4H	uc002iwe.2	P63272	OTTHUMG00000178926	ENST00000225504.3:c.185C>T	17.37:g.56424937G>A	ENSP00000225504:p.Ala62Val	Somatic		Capture	Illumina HiSeq	Phase_I	53779936	NM_003168	B2R4X8|D3DTZ4|Q16550|Q62387|Q6ZP89	Missense_Mutation	SNP	ENST00000225504.3	37	CCDS11606.1	.	.	.	.	.	.	.	.	.	.	G	32	5.139804	0.94560	.	.	ENSG00000213246	ENST00000225504	.	.	.	5.45	5.45	0.79879	Spt4/RpoE2 zinc finger (1);	0.065703	0.64402	U	0.000012	T	0.73225	0.3560	M	0.82716	2.605	0.80722	D	1	D	0.69078	0.997	P	0.50934	0.654	T	0.78612	-0.2136	9	0.87932	D	0	-11.844	15.1272	0.72493	0.0:0.0:1.0:0.0	.	62	P63272	SPT4H_HUMAN	V	62	.	ENSP00000225504:A62V	A	-	2	0	SUPT4H1	53779936	1.000000	0.71417	0.983000	0.44433	0.985000	0.73830	8.597000	0.90847	2.722000	0.93159	0.462000	0.41574	GCG		0.502	SUPT4H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444000.1	NM_003168	
MTMR4	9110	broad.mit.edu	37	17	56569120	56569120	+	Silent	SNP	G	G	A	rs141228725		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:56569120G>A	ENST00000323456.5	-	19	3616	c.3492C>T	c.(3490-3492)ctC>ctT	p.L1164L	MTMR4_ENST00000579925.1_Silent_p.L1107L	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	1164					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)	p.L1164L(1)		breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGTTACAGACGAGAACTGGGT	0.473													G|||	1	0.000199681	0.0	0.0	5008	,	,		19779	0.0		0.0	False		,,,				2504	0.001				p.L1164L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3492T	17						.	G		1,4405	2.1+/-5.4	0,1,2202	111.0	97.0	102.0		3492	0.1	1.0	17	dbSNP_134	102	0,8600		0,0,4300	no	coding-synonymous	MTMR4	NM_004687.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1164/1196	56569120	1,13005	2203	4300	6503	53924119	SO:0001819	synonymous_variant	9110	exon19			AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.3492C>T	17.37:g.56569120G>A		Somatic		Capture	Illumina HiSeq	Phase_I	53924119	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Silent	SNP	ENST00000323456.5	37	CCDS11608.1																																																																																				0.473	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687	
TEX14	56155	broad.mit.edu	37	17	56650660	56650660	+	Silent	SNP	C	C	T	rs55768547	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:56650660C>T	ENST00000240361.8	-	24	3616	c.3531G>A	c.(3529-3531)acG>acA	p.T1177T	TEX14_ENST00000389934.3_Silent_p.T1171T|TEX14_ENST00000349033.5_Silent_p.T1131T			Q8IWB6	TEX14_HUMAN	testis expressed 14	1177					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.T1177T(1)|p.T1131T(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)					CTTGAATATCCGTCAATGATC	0.353													C|||	3	0.000599042	0.0	0.0	5008	,	,		19588	0.0		0.003	False		,,,				2504	0.0				p.T1171T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G3513A	17						.	C	,,	1,4405	2.1+/-5.4	0,1,2202	201.0	197.0	199.0		3531,3393,3513	2.0	1.0	17	dbSNP_129	199	21,8579	16.0+/-53.3	0,21,4279	no	coding-synonymous,coding-synonymous,coding-synonymous	TEX14	NM_001201457.1,NM_031272.4,NM_198393.3	,,	0,22,6481	TT,TC,CC		0.2442,0.0227,0.1692	,,	1177/1498,1131/1452,1171/1492	56650660	22,12984	2203	4300	6503	54005659	SO:0001819	synonymous_variant	56155	exon24			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.3531G>A	17.37:g.56650660C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54005659	NM_198393	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Silent	SNP	ENST00000240361.8	37	CCDS56042.1																																																																																				0.353	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
TRIM37	4591	broad.mit.edu	37	17	57165733	57165733	+	Missense_Mutation	SNP	C	C	T	rs201317687		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:57165733C>T	ENST00000262294.7	-	4	459	c.200G>A	c.(199-201)cGt>cAt	p.R67H	TRIM37_ENST00000393066.3_Missense_Mutation_p.R67H|TRIM37_ENST00000393065.2_Missense_Mutation_p.R33H|TRIM37_ENST00000376149.3_5'UTR|TRIM37_ENST00000584889.1_Missense_Mutation_p.R67H	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	67					aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|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.R67H(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					TTCTGCCCAACGACAATTTAC	0.363									Mulibrey Nanism																												p.R67H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G200A	17						.						139.0	114.0	122.0					17																	57165733		2203	4300	6503	54520515	SO:0001583	missense	4591	exon4	Familial Cancer Database	Perheentupa syndrome	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	7523	protein-coding gene	gene with protein product	"""RING-B-box-coiled-coil protein"""	605073	"""tripartite motif-containing 37"""	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.200G>A	17.37:g.57165733C>T	ENSP00000262294:p.Arg67His	Somatic		Capture	Illumina HiSeq	Phase_I	54520515	NM_001005207	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000262294.7	37	CCDS32694.1	.	.	.	.	.	.	.	.	.	.	C	36	5.664264	0.96745	.	.	ENSG00000108395	ENST00000393066;ENST00000262294;ENST00000393065	T;T;T	0.17370	2.28;2.28;2.28	5.2	5.2	0.72013	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.33644	0.0870	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.982	T	0.07501	-1.0769	10	0.72032	D	0.01	-16.8696	18.3457	0.90321	0.0:1.0:0.0:0.0	.	33;67	F8WEE6;O94972	.;TRI37_HUMAN	H	67;67;33	ENSP00000376785:R67H;ENSP00000262294:R67H;ENSP00000376784:R33H	ENSP00000262294:R67H	R	-	2	0	TRIM37	54520515	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.647000	0.83462	2.445000	0.82738	0.650000	0.86243	CGT		0.363	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294	
DHX40	79665	broad.mit.edu	37	17	57684508	57684508	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:57684508G>A	ENST00000251241.4	+	18	2462	c.2315G>A	c.(2314-2316)aGt>aAt	p.S772N	DHX40_ENST00000451169.2_Missense_Mutation_p.S724N|DHX40_ENST00000425628.3_Missense_Mutation_p.S695N	NM_024612.4	NP_078888.4	Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40	772							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)	p.S772N(1)		endometrium(7)|large_intestine(6)|lung(6)|prostate(1)	20	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					CAGGACCACAGTGACACACGA	0.458																																					p.S772N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2315A	17						.						149.0	146.0	147.0					17																	57684508		2203	4300	6503	55039290	SO:0001583	missense	79665	exon18			AF260270	CCDS11617.1, CCDS54150.1	17q22	2014-01-28	2003-06-13	2003-06-20		ENSG00000108406		"""DEAH-boxes"""	18018	protein-coding gene	gene with protein product		607570	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 40 (RNA helicase)"""	DDX40			Standard	NM_024612		Approved	ARG147, PAD, FLJ22060	uc002ixn.2	Q8IX18		ENST00000251241.4:c.2315G>A	17.37:g.57684508G>A	ENSP00000251241:p.Ser772Asn	Somatic		Capture	Illumina HiSeq	Phase_I	55039290	NM_024612	B3KTJ5|C9JR60|Q5JPH4|Q8TC86|Q8WY53|Q9BXM1|Q9H6M9	Missense_Mutation	SNP	ENST00000251241.4	37	CCDS11617.1	.	.	.	.	.	.	.	.	.	.	G	13.06	2.125789	0.37533	.	.	ENSG00000108406	ENST00000251241;ENST00000538926;ENST00000451169	T;T	0.03982	4.1;3.74	5.88	3.83	0.44106	.	0.414132	0.27366	N	0.019682	T	0.02929	0.0087	N	0.08118	0	0.31746	N	0.63525	B;B	0.32160	0.358;0.244	B;B	0.30572	0.117;0.055	T	0.13926	-1.0491	10	0.59425	D	0.04	.	11.1196	0.48281	0.0:0.1442:0.7225:0.1333	.	695;772	F5H625;Q8IX18	.;DHX40_HUMAN	N	772;695;724	ENSP00000251241:S772N;ENSP00000396039:S724N	ENSP00000251241:S772N	S	+	2	0	DHX40	55039290	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	1.402000	0.34600	2.797000	0.96272	0.561000	0.74099	AGT		0.458	DHX40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446095.1	NM_024612	
VMP1	81671	broad.mit.edu	37	17	57915717	57915717	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:57915717C>T	ENST00000262291.4	+	11	1346	c.1036C>T	c.(1036-1038)Cgg>Tgg	p.R346W	VMP1_ENST00000536180.1_Missense_Mutation_p.R249W|VMP1_ENST00000537567.1_Missense_Mutation_p.R212W|VMP1_ENST00000539763.1_Missense_Mutation_p.R154W|VMP1_ENST00000588617.1_3'UTR|MIR21_ENST00000362134.1_RNA|VMP1_ENST00000545362.1_Missense_Mutation_p.R290W	NM_030938.3	NP_112200.2	Q96GC9	VMP1_HUMAN	vacuole membrane protein 1	346					autophagy (GO:0006914)|cell junction assembly (GO:0034329)|embryo implantation (GO:0007566)|regulation of autophagy (GO:0010506)|single organismal cell-cell adhesion (GO:0016337)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|pre-autophagosomal structure (GO:0000407)		p.R346W(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|skin(2)	16						GGAGGCTCAACGGCAGAAGCT	0.502																																					p.R346W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1036T	17						.						90.0	84.0	86.0					17																	57915717		2203	4300	6503	55270499	SO:0001583	missense	81671	exon11				CCDS11619.1	17q23.1	2014-05-20	2011-03-02	2011-03-02	ENSG00000062716	ENSG00000062716			29559	protein-coding gene	gene with protein product	"""ectopic P-granules autophagy protein 3 homolog (C. elegans)"", ""transport and golgi organization 5 homolog (Drosophila)"""	611753	"""transmembrane protein 49"""	TMEM49		11230166, 11785947	Standard	NM_030938		Approved	EPG3, TANGO5	uc002ixu.4	Q96GC9	OTTHUMG00000179882	ENST00000262291.4:c.1036C>T	17.37:g.57915717C>T	ENSP00000262291:p.Arg346Trp	Somatic		Capture	Illumina HiSeq	Phase_I	55270499	NM_030938	B4DVV9|Q9H0P4|Q9P089	Missense_Mutation	SNP	ENST00000262291.4	37	CCDS11619.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.512058	0.85389	.	.	ENSG00000062716	ENST00000262291;ENST00000537567;ENST00000539763;ENST00000536180;ENST00000545362	.	.	.	5.95	5.95	0.96441	.	0.049123	0.85682	D	0.000000	T	0.76471	0.3992	M	0.78456	2.415	0.80722	D	1	D;D;D;D	0.67145	0.992;0.987;0.996;0.994	P;P;P;P	0.57846	0.761;0.629;0.721;0.828	T	0.79006	-0.1979	9	0.87932	D	0	-10.0857	16.0297	0.80570	0.1422:0.8578:0.0:0.0	.	212;249;290;346	B4DED7;B4DGZ7;F5H2J3;Q96GC9	.;.;.;VMP1_HUMAN	W	346;212;154;249;290	.	ENSP00000262291:R346W	R	+	1	2	VMP1	55270499	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.010000	0.57117	2.827000	0.97445	0.650000	0.86243	CGG		0.502	VMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448793.1	NM_030938	
TBX4	9496	broad.mit.edu	37	17	59560792	59560792	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:59560792A>G	ENST00000240335.1	+	8	1598	c.1553A>G	c.(1552-1554)tAc>tGc	p.Y518C	TBX4_ENST00000393853.4_Missense_Mutation_p.Y519C	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	518					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Y518C(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						GAGTTTCTCTACTCTCAAACC	0.562																																					p.Y518C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1553G	17						.						87.0	84.0	85.0					17																	59560792		2203	4300	6503	56915574	SO:0001583	missense	9496	exon8			AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"""T-boxes"""	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.1553A>G	17.37:g.59560792A>G	ENSP00000240335:p.Tyr518Cys	Somatic		Capture	Illumina HiSeq	Phase_I	56915574	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Missense_Mutation	SNP	ENST00000240335.1	37	CCDS11629.1	.	.	.	.	.	.	.	.	.	.	A	17.62	3.434219	0.62955	.	.	ENSG00000121075	ENST00000393853;ENST00000240335	D;D	0.87729	-2.29;-2.29	5.14	5.14	0.70334	.	1.619260	0.02915	N	0.137263	D	0.93782	0.8012	M	0.66939	2.045	0.44104	D	0.996878	D;D	0.89917	1.0;0.994	D;P	0.81914	0.995;0.57	T	0.82232	-0.0559	9	.	.	.	.	14.127	0.65228	1.0:0.0:0.0:0.0	.	519;518	A5PKU7;P57082	.;TBX4_HUMAN	C	519;518	ENSP00000377435:Y519C;ENSP00000240335:Y518C	.	Y	+	2	0	TBX4	56915574	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.254000	0.65457	1.933000	0.56026	0.533000	0.62120	TAC		0.562	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488	
MED13	9969	broad.mit.edu	37	17	60038435	60038435	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:60038435C>T	ENST00000397786.2	-	23	5349	c.5273G>A	c.(5272-5274)cGa>cAa	p.R1758Q		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1758					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	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 coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.R1758Q(1)		breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TGCATAAAGTCGAATACACTC	0.318																																					p.R1758Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5273A	17						.						80.0	69.0	72.0					17																	60038435		1811	4064	5875	57393217	SO:0001583	missense	9969	exon23			AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.5273G>A	17.37:g.60038435C>T	ENSP00000380888:p.Arg1758Gln	Somatic		Capture	Illumina HiSeq	Phase_I	57393217	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	C	14.51	2.558396	0.45590	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	D	0.84516	-1.86	5.16	4.19	0.49359	.	0.184796	0.48767	D	0.000165	T	0.70640	0.3247	N	0.17631	0.505	0.58432	D	0.999999	P	0.45126	0.851	B	0.40864	0.342	T	0.69569	-0.5110	10	0.06236	T	0.91	-33.274	10.2749	0.43504	0.0:0.7891:0.1372:0.0737	.	1758	Q9UHV7	MED13_HUMAN	Q	1758;1757	ENSP00000380888:R1758Q	ENSP00000262436:R1757Q	R	-	2	0	MED13	57393217	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.614000	0.61183	1.187000	0.43000	-0.133000	0.14855	CGA		0.318	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
MARCH10	162333	broad.mit.edu	37	17	60865911	60865911	+	Missense_Mutation	SNP	C	C	T	rs200380804		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:60865911C>T	ENST00000311269.5	-	3	414	c.140G>A	c.(139-141)cGc>cAc	p.R47H	MARCH10_ENST00000456609.2_Missense_Mutation_p.R47H|MARCH10_ENST00000544856.2_Missense_Mutation_p.R47H|MARCH10_ENST00000583600.1_Missense_Mutation_p.R47H	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	47					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R47H(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						AAACTGATCGCGTTTCTTCTC	0.443													C|||	1	0.000199681	0.0	0.0	5008	,	,		17740	0.001		0.0	False		,,,				2504	0.0				p.R47H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G140A	17						.						142.0	121.0	128.0					17																	60865911		2203	4300	6503	58219643	SO:0001583	missense	162333	exon3			AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"""RING-type (C3HC4) zinc fingers"", ""MARCH membrane-associated ring fingers"""	26655	protein-coding gene	gene with protein product		613337	"""ring finger protein 190"", ""membrane-associated ring finger (C3HC4) 10"""	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.140G>A	17.37:g.60865911C>T	ENSP00000311496:p.Arg47His	Somatic		Capture	Illumina HiSeq	Phase_I	58219643	NM_001100875	D3DU09|Q8IYS7|Q8N7Z7	Missense_Mutation	SNP	ENST00000311269.5	37	CCDS11635.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	10.32	1.317598	0.23994	.	.	ENSG00000173838	ENST00000456609;ENST00000311269;ENST00000544856	T;T;T	0.23552	1.9;1.9;1.9	5.2	-1.32	0.09201	.	0.488505	0.14673	N	0.305231	T	0.37293	0.0998	M	0.63428	1.95	0.20074	N	0.999937	D;D;D	0.76494	0.998;0.999;0.998	P;D;P	0.64687	0.849;0.928;0.849	T	0.20009	-1.0288	10	0.87932	D	0	-0.8947	4.7806	0.13201	0.0:0.3254:0.1611:0.5135	.	47;47;47	B3KVK0;G3V1Q5;Q8NA82	.;.;MARHA_HUMAN	H	47	ENSP00000416177:R47H;ENSP00000311496:R47H;ENSP00000443746:R47H	ENSP00000311496:R47H	R	-	2	0	MARCH10	58219643	0.770000	0.28543	0.035000	0.18076	0.653000	0.38743	-0.075000	0.11431	-0.580000	0.05944	0.561000	0.74099	CGC		0.443	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598	
GEMIN4	50628	broad.mit.edu	37	17	649336	649336	+	Silent	SNP	G	G	A	rs370625526		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:649336G>A	ENST00000319004.5	-	2	2065	c.1947C>T	c.(1945-1947)gaC>gaT	p.D649D	GEMIN4_ENST00000576778.1_Silent_p.D638D	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	649					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)		p.D649D(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TCAGCACCTCGTCTGGCTCAA	0.493																																					p.D649D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1947T	17						.	G		3,3803		0,3,1900	63.0	66.0	65.0		1947	-4.2	1.0	17		65	0,8244		0,0,4122	no	coding-synonymous	GEMIN4	NM_015721.2		0,3,6022	AA,AG,GG		0.0,0.0788,0.0249		649/1059	649336	3,12047	1903	4122	6025	596086	SO:0001819	synonymous_variant	50628	exon2			AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.1947C>T	17.37:g.649336G>A		Somatic		Capture	Illumina HiSeq	Phase_I	596086	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																				0.493	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
WSCD1	23302	broad.mit.edu	37	17	6021508	6021508	+	Splice_Site	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:6021508G>T	ENST00000574946.1	+	8	1765	c.1375G>T	c.(1375-1377)Gag>Tag	p.E459*	WSCD1_ENST00000574232.1_Splice_Site_p.E459*|WSCD1_ENST00000317744.5_Splice_Site_p.E459*|WSCD1_ENST00000539421.1_Splice_Site_p.E459*|WSCD1_ENST00000573634.1_Splice_Site_p.E343*			Q658N2	WSCD1_HUMAN	WSC domain containing 1	459						integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)	p.E459*(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						GAAGAGCAAAGGTAATCAAGG	0.537																																					p.E459X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1375T	17						.						31.0	32.0	32.0					17																	6021508		2203	4300	6503	5962232	SO:0001630	splice_region_variant	23302	exon8				CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.1375+1G>T	17.37:g.6021508G>T		Somatic		Capture	Illumina HiSeq	Phase_I	5962232	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Nonsense_Mutation	SNP	ENST00000574946.1	37	CCDS32538.1	.	.	.	.	.	.	.	.	.	.	G	38	6.652507	0.97734	.	.	ENSG00000179314	ENST00000317744;ENST00000539421	.	.	.	5.47	5.47	0.80525	.	0.049427	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-31.8585	16.8089	0.85713	0.0:0.0:1.0:0.0	.	.	.	.	X	459	.	ENSP00000323087:E459X	E	+	1	0	WSCD1	5962232	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	9.464000	0.97655	2.583000	0.87209	0.655000	0.94253	GAG		0.537	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253	Nonsense_Mutation
FTSJ3	117246	broad.mit.edu	37	17	61901274	61901274	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:61901274C>T	ENST00000427159.2	-	13	1838	c.1193G>A	c.(1192-1194)cGg>cAg	p.R398Q		NM_017647.3	NP_060117.3			FtsJ homolog 3 (E. coli)									p.R398Q(1)		breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CACACGCTCCCGCTGCTTTCT	0.562																																					p.R398Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1193A	17						.						113.0	97.0	102.0					17																	61901274		2203	4300	6503	59255006	SO:0001583	missense	117246	exon13			AF327355	CCDS11644.1	17q23.3	2014-09-11			ENSG00000108592	ENSG00000108592			17136	protein-coding gene	gene with protein product	"""SPB1 RNA methyltransferase homolog (S. cerevisiae)"""						Standard	NM_017647		Approved	SPB1	uc002jca.3	Q8IY81	OTTHUMG00000179012	ENST00000427159.2:c.1193G>A	17.37:g.61901274C>T	ENSP00000396673:p.Arg398Gln	Somatic		Capture	Illumina HiSeq	Phase_I	59255006	NM_017647		Missense_Mutation	SNP	ENST00000427159.2	37	CCDS11644.1	.	.	.	.	.	.	.	.	.	.	C	34	5.306585	0.95629	.	.	ENSG00000108592	ENST00000427159	T	0.31769	1.48	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.49167	0.1541	L	0.55481	1.735	0.48696	D	0.999699	D	0.89917	1.0	D	0.87578	0.998	T	0.13495	-1.0507	10	0.13470	T	0.59	-15.4018	17.2626	0.87075	0.0:1.0:0.0:0.0	.	398	Q8IY81	RRMJ3_HUMAN	Q	398	ENSP00000396673:R398Q	ENSP00000396673:R398Q	R	-	2	0	FTSJ3	59255006	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.516000	0.67055	2.941000	0.99782	0.655000	0.94253	CGG		0.562	FTSJ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444386.1		
LRRC37A3	374819	broad.mit.edu	37	17	62855863	62855863	+	Silent	SNP	C	C	T	rs369882842		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:62855863C>T	ENST00000584306.1	-	11	4931	c.4401G>A	c.(4399-4401)tcG>tcA	p.S1467S	LRRC37A3_ENST00000400877.3_Silent_p.S505S|LRRC37A3_ENST00000319651.5_Silent_p.S1467S|LRRC37A3_ENST00000339474.5_Silent_p.S585S|LRRC37A3_ENST00000334962.5_Silent_p.S444S	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1467						integral component of membrane (GO:0016021)		p.S1467S(2)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CACCTGGGGACGAGAGCAATG	0.488													-|||	1	0.000199681	0.0	0.0	5008	,	,		19098	0.001		0.0	False		,,,				2504	0.0				p.S1467S												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.G4401A	17						.	C		1,4405		0,1,2202	136.0	142.0	140.0		4401	-1.7	0.0	17		140	2,8594		0,2,4296	no	coding-synonymous	LRRC37A3	NM_199340.2		0,3,6498	TT,TC,CC		0.0233,0.0227,0.0231		1467/1635	62855863	3,12999	2203	4298	6501	60286325	SO:0001819	synonymous_variant	374819	exon11			AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.4401G>A	17.37:g.62855863C>T		Somatic		Capture	Illumina HiSeq	Phase_I	60286325	NM_199340	Q49A01|Q49A80|Q8NB33	Silent	SNP	ENST00000584306.1	37	CCDS32708.1																																																																																				0.488	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340	
PITPNM3	83394	broad.mit.edu	37	17	6373678	6373678	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:6373678G>A	ENST00000262483.8	-	13	1762	c.1675C>T	c.(1675-1677)Cct>Tct	p.P559S	PITPNM3_ENST00000421306.3_Missense_Mutation_p.P523S|PITPNM3_ENST00000576664.1_5'UTR	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	559	DDHD. {ECO:0000255|PROSITE- ProRule:PRU00378}.				phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)	p.P559S(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		AGGACATCAGGGCAGTACAGG	0.637																																					p.P559S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1675T	17						.						165.0	114.0	132.0					17																	6373678		2203	4300	6503	6314402	SO:0001583	missense	83394	exon13			AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"""GPCR / Class A : Chemokine receptors : Atypical"""	21043	protein-coding gene	gene with protein product	"""atypical chemokine receptor 6"""	608921	"""cone rod dystrophy 5"""	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.1675C>T	17.37:g.6373678G>A	ENSP00000262483:p.Pro559Ser	Somatic		Capture	Illumina HiSeq	Phase_I	6314402	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Missense_Mutation	SNP	ENST00000262483.8	37	CCDS11076.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.911790	0.92178	.	.	ENSG00000091622	ENST00000262483;ENST00000421306	T;T	0.51574	0.7;0.7	4.65	4.65	0.58169	DDHD (2);	0.161098	0.56097	D	0.000029	T	0.69949	0.3168	M	0.81682	2.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.74699	-0.3577	10	0.87932	D	0	-23.2209	15.4169	0.74977	0.0:0.0:1.0:0.0	.	523;559	F8WEW5;Q9BZ71	.;PITM3_HUMAN	S	559;523	ENSP00000262483:P559S;ENSP00000407882:P523S	ENSP00000262483:P559S	P	-	1	0	PITPNM3	6314402	1.000000	0.71417	0.999000	0.59377	0.935000	0.57460	9.657000	0.98554	2.576000	0.86940	0.563000	0.77884	CCT		0.637	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220	
PRKCA	5578	broad.mit.edu	37	17	64784984	64784984	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:64784984C>T	ENST00000413366.3	+	16	1767	c.1741C>T	c.(1741-1743)Ctg>Ttg	p.L581L	MIR634_ENST00000385208.1_RNA	NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	581	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|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 inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)	p.L581L(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	AGCCAAGCGGCTGGGCTGTGG	0.547																																					p.L581L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1741T	17						.						78.0	81.0	80.0					17																	64784984		2203	4300	6503	62215446	SO:0001819	synonymous_variant	5578	exon16				CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA			Standard	NM_002737		Approved		uc002jfp.1	P17252		ENST00000413366.3:c.1741C>T	17.37:g.64784984C>T		Somatic		Capture	Illumina HiSeq	Phase_I	62215446	NM_002737	B5BU22|Q15137|Q32M72|Q96RE4	Silent	SNP	ENST00000413366.3	37	CCDS11664.1																																																																																				0.547	PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446976.1		
NOL11	25926	broad.mit.edu	37	17	65720242	65720242	+	Missense_Mutation	SNP	C	C	G	rs377003215		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:65720242C>G	ENST00000253247.4	+	6	712	c.597C>G	c.(595-597)gaC>gaG	p.D199E	NOL11_ENST00000535137.1_Missense_Mutation_p.D17E	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	199					maturation of SSU-rRNA (GO:0030490)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)	p.D199E(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	11	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			TTGGACAAGACGAAAACTCTG	0.303																																					p.D199E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C597G	17						.						90.0	91.0	90.0					17																	65720242		2203	4299	6502	63150704	SO:0001583	missense	25926	exon6			AK023702	CCDS11671.1	17q24.2	2005-08-08							24557	protein-coding gene	gene with protein product		615366				12477932	Standard	NM_015462		Approved	DKFZP586L0724	uc002jgd.1	Q9H8H0		ENST00000253247.4:c.597C>G	17.37:g.65720242C>G	ENSP00000253247:p.Asp199Glu	Somatic		Capture	Illumina HiSeq	Phase_I	63150704	NM_015462	B7Z5V9|Q7L5S1|Q9UG18	Missense_Mutation	SNP	ENST00000253247.4	37	CCDS11671.1	.	.	.	.	.	.	.	.	.	.	C	1.426	-0.571665	0.03882	.	.	ENSG00000130935	ENST00000253247;ENST00000535137	T	0.21361	2.01	3.45	1.12	0.20585	.	0.367329	0.28109	N	0.016566	T	0.05640	0.0148	N	0.02960	-0.455	0.22684	N	0.998856	B	0.02656	0.0	B	0.04013	0.001	T	0.40232	-0.9574	10	0.02654	T	1	-13.6533	5.0798	0.14651	0.633:0.1833:0.0:0.1838	.	199	Q9H8H0	NOL11_HUMAN	E	199;17	ENSP00000253247:D199E	ENSP00000253247:D199E	D	+	3	2	NOL11	63150704	0.991000	0.36638	0.993000	0.49108	0.086000	0.17979	0.294000	0.19047	0.211000	0.20683	-1.783000	0.00646	GAC		0.303	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462	
BPTF	2186	broad.mit.edu	37	17	65908497	65908497	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:65908497T>C	ENST00000321892.4	+	13	4936	c.4875T>C	c.(4873-4875)gaT>gaC	p.D1625D	BPTF_ENST00000306378.6_Silent_p.D1499D|BPTF_ENST00000424123.3_Silent_p.D1486D|BPTF_ENST00000335221.5_Silent_p.D1625D			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1625					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.D1625D(1)|p.D1499D(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			ACTACCGAGATAGCCTTGAGA	0.428																																					p.D1499D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T4497C	17						.						74.0	69.0	71.0					17																	65908497		2203	4300	6503	63338959	SO:0001819	synonymous_variant	2186	exon11			AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.4875T>C	17.37:g.65908497T>C		Somatic		Capture	Illumina HiSeq	Phase_I	63338959	NM_182641	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	37																																																																																					0.428	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
BPTF	2186	broad.mit.edu	37	17	65941738	65941738	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:65941738T>C	ENST00000321892.4	+	23	7353	c.7292T>C	c.(7291-7293)gTt>gCt	p.V2431A	BPTF_ENST00000306378.6_Missense_Mutation_p.V2305A|BPTF_ENST00000424123.3_Missense_Mutation_p.V2292A|BPTF_ENST00000335221.5_Missense_Mutation_p.V2431A			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2431					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.V2305A(1)|p.V2431A(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			CAAACAACTGTTTCATCCCAT	0.557																																					p.V2305A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T6914C	17						.						133.0	119.0	124.0					17																	65941738		2203	4300	6503	63372200	SO:0001583	missense	2186	exon21			AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.7292T>C	17.37:g.65941738T>C	ENSP00000315454:p.Val2431Ala	Somatic		Capture	Illumina HiSeq	Phase_I	63372200	NM_182641	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.487|0.487	-0.877062|-0.877062	0.02550|0.02550	.|.	.|.	ENSG00000171634|ENSG00000171634	ENST00000424123|ENST00000306378;ENST00000335221;ENST00000321892	.|T;T;T	.|0.61274	.|0.15;0.12;0.16	5.76|5.76	0.414|0.414	0.16406|0.16406	.|.	.|.	.|.	.|.	.|.	T|T	0.44623|0.44623	0.1302|0.1302	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.06786	.|0.0;0.001;0.001	.|B;B;B	.|0.04013	.|0.0;0.001;0.001	T|T	0.29212|0.29212	-1.0019|-1.0019	6|9	0.27082|0.20519	T|T	0.32|0.43	-11.001|-11.001	10.6683|10.6683	0.45743|0.45743	0.0:0.4218:0.0:0.5782|0.0:0.4218:0.0:0.5782	.|.	.|109;2305;2431	.|B4DJV8;Q12830-2;Q12830-4	.|.;.;.	L|A	103|2305;2431;2431	.|ENSP00000307208:V2305A;ENSP00000334351:V2431A;ENSP00000315454:V2431A	ENSP00000388405:F103L|ENSP00000307208:V2305A	F|V	+|+	1|2	0|0	BPTF|BPTF	63372200|63372200	0.000000|0.000000	0.05858|0.05858	0.047000|0.047000	0.18901|0.18901	0.092000|0.092000	0.18411|0.18411	-0.262000|-0.262000	0.08682|0.08682	0.093000|0.093000	0.17368|0.17368	-0.263000|-0.263000	0.10527|0.10527	TTT|GTT		0.557	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
FAM20A	54757	broad.mit.edu	37	17	66539855	66539855	+	Nonsense_Mutation	SNP	G	G	A	rs367720325		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:66539855G>A	ENST00000592554.1	-	5	1449	c.727C>T	c.(727-729)Cga>Tga	p.R243*	AC079210.1_ENST00000600820.1_Silent_p.S38S|PRKAR1A_ENST00000588188.2_Intron|FAM20A_ENST00000226094.5_5'UTR	NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	243					calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)		p.R243*(1)		cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					TCCTCATCTCGCTGCTGTCTG	0.527																																					p.R243X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C727T	17						.	G	stop/ARG	0,4406		0,0,2203	148.0	131.0	137.0		727	5.4	1.0	17		137	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	FAM20A	NM_017565.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		243/542	66539855	1,13005	2203	4300	6503	64051450	SO:0001587	stop_gained	54757	exon5			AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.727C>T	17.37:g.66539855G>A	ENSP00000468308:p.Arg243*	Somatic		Capture	Illumina HiSeq	Phase_I	64051450	NM_017565	B2RN47|B2RN49|Q9UF95	Nonsense_Mutation	SNP	ENST00000592554.1	37	CCDS11679.1	.	.	.	.	.	.	.	.	.	.	G	39	7.358934	0.98235	0.0	1.16E-4	ENSG00000108950	ENST00000226094	.	.	.	5.36	5.36	0.76844	.	0.123300	0.53938	D	0.000052	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.1215	19.0448	0.93015	0.0:0.0:1.0:0.0	.	.	.	.	X	243	.	ENSP00000226094:R243X	R	-	1	2	FAM20A	64051450	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	3.884000	0.56175	2.680000	0.91292	0.561000	0.74099	CGA		0.527	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565	
ABCA9	10350	broad.mit.edu	37	17	66986992	66986992	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:66986992G>A	ENST00000340001.4	-	29	4034	c.3823C>T	c.(3823-3825)Cga>Tga	p.R1275*	ABCA9_ENST00000453985.2_Nonsense_Mutation_p.R1237*|ABCA9_ENST00000482072.1_5'Flank|ABCA9_ENST00000370732.2_Nonsense_Mutation_p.R1275*	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	1275					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R1275*(1)		NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					TCAAAGTCTCGCACAGCCATA	0.383																																					p.R1275X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C3823T	17						.						189.0	161.0	170.0					17																	66986992		2203	4300	6503	64498587	SO:0001587	stop_gained	10350	exon29			AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"""ATP binding cassette transporters / subfamily A"""	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.3823C>T	17.37:g.66986992G>A	ENSP00000342216:p.Arg1275*	Somatic		Capture	Illumina HiSeq	Phase_I	64498587	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Nonsense_Mutation	SNP	ENST00000340001.4	37	CCDS11681.1	.	.	.	.	.	.	.	.	.	.	G	39	7.699769	0.98441	.	.	ENSG00000154258	ENST00000340001;ENST00000453985;ENST00000370732	.	.	.	5.4	-2.75	0.05914	.	0.821731	0.10245	N	0.697887	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	.	3.9128	0.09210	0.1558:0.186:0.4925:0.1656	.	.	.	.	X	1275;1220;1275	.	ENSP00000342216:R1275X	R	-	1	2	ABCA9	64498587	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.016000	0.12613	-0.563000	0.06078	-2.730000	0.00130	CGA		0.383	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386	
SLC13A5	284111	broad.mit.edu	37	17	6616580	6616580	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:6616580G>A	ENST00000433363.2	-	1	306	c.73C>T	c.(73-75)Ctg>Ttg	p.L25L	SLC13A5_ENST00000573648.1_Silent_p.L25L|SLC13A5_ENST00000293800.6_Silent_p.L25L|SLC13A5_ENST00000381074.4_Silent_p.L25L	NM_001284510.1|NM_177550.3	NP_001271439.1|NP_808218.1	Q86YT5	S13A5_HUMAN	solute carrier family 13 (sodium-dependent citrate transporter), member 5	25					transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	citrate transmembrane transporter activity (GO:0015137)|sodium:dicarboxylate symporter activity (GO:0017153)|succinate transmembrane transporter activity (GO:0015141)	p.L25L(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|prostate(5)|skin(3)|urinary_tract(1)	26						ACGAGTGGCAGCAGCAGGAGC	0.642																																					p.L25L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C73T	17						.						75.0	62.0	66.0					17																	6616580		2203	4299	6502	6557304	SO:0001819	synonymous_variant	284111	exon1			AJ489980	CCDS11079.1, CCDS45593.1, CCDS67136.1, CCDS67137.1	17p13.1	2013-05-22			ENSG00000141485	ENSG00000141485		"""Solute carriers"""	23089	protein-coding gene	gene with protein product		608305				12445824	Standard	NM_001284510		Approved	NACT	uc002gdj.3	Q86YT5	OTTHUMG00000102052	ENST00000433363.2:c.73C>T	17.37:g.6616580G>A		Somatic		Capture	Illumina HiSeq	Phase_I	6557304	NM_001143838	B3KXR0|B7Z4P2|B7ZLB4|F8W7N2|Q6ZMG1	Silent	SNP	ENST00000433363.2	37	CCDS11079.1																																																																																				0.642	SLC13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219853.2	NM_177550	
ABCA5	23461	broad.mit.edu	37	17	67309336	67309336	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:67309336A>G	ENST00000392676.3	-	3	268	c.204T>C	c.(202-204)ccT>ccC	p.P68P	ABCA5_ENST00000588877.1_Silent_p.P68P|ABCA5_ENST00000392677.2_Silent_p.P68P			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	68					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.P68P(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)	ACTTGTCCATAGGATTGAGTT	0.303																																					p.P68P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T204C	17						.						83.0	88.0	87.0					17																	67309336		2202	4297	6499	64820931	SO:0001819	synonymous_variant	23461	exon3			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.204T>C	17.37:g.67309336A>G		Somatic		Capture	Illumina HiSeq	Phase_I	64820931	NM_172232	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Silent	SNP	ENST00000392676.3	37	CCDS11685.1																																																																																				0.303	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	
COG1	9382	broad.mit.edu	37	17	71197560	71197560	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:71197560C>A	ENST00000299886.4	+	7	1674	c.1594C>A	c.(1594-1596)Ctc>Atc	p.L532I		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	532					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)		p.L532I(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			ACTAGATGACCTCCTGGCTTA	0.527																																					p.L532I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1594A	17						.						127.0	127.0	127.0					17																	71197560		2203	4300	6503	68709155	SO:0001583	missense	9382	exon7				CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"""Components of oligomeric golgi complex"""	6545	protein-coding gene	gene with protein product		606973	"""low density lipoprotein receptor defect B complementing"""	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.1594C>A	17.37:g.71197560C>A	ENSP00000299886:p.Leu532Ile	Somatic		Capture	Illumina HiSeq	Phase_I	68709155	NM_018714	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	37	CCDS11692.1	.	.	.	.	.	.	.	.	.	.	C	12.41	1.928815	0.34002	.	.	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.28255	1.62;1.62	5.53	2.4	0.29515	.	0.121064	0.56097	N	0.000023	T	0.41050	0.1142	M	0.72894	2.215	0.58432	D	0.999999	D;D;D	0.69078	0.997;0.987;0.997	P;B;P	0.56960	0.81;0.446;0.81	T	0.16660	-1.0395	10	0.30078	T	0.28	-21.8326	6.3133	0.21176	0.2418:0.5768:0.1168:0.0646	.	532;532;532	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	I	532	ENSP00000400111:L532I;ENSP00000299886:L532I	ENSP00000299886:L532I	L	+	1	0	COG1	68709155	1.000000	0.71417	0.998000	0.56505	0.764000	0.43329	2.977000	0.49297	0.279000	0.22186	-0.152000	0.13540	CTC		0.527	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1		
SDK2	54549	broad.mit.edu	37	17	71382033	71382033	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:71382033G>T	ENST00000392650.3	-	32	4522	c.4522C>A	c.(4522-4524)Ctc>Atc	p.L1508I	SDK2_ENST00000388726.3_Missense_Mutation_p.L1508I	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1508	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.L1508I(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						GTCACGGAGAGGATGGTGGGT	0.622																																					p.L1508I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4522A	17						.						79.0	72.0	74.0					17																	71382033		2203	4300	6503	68893628	SO:0001583	missense	54549	exon32			AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.4522C>A	17.37:g.71382033G>T	ENSP00000376421:p.Leu1508Ile	Somatic		Capture	Illumina HiSeq	Phase_I	68893628	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.340427	0.41498	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893	T;T;T	0.63913	-0.07;-0.07;-0.07	4.57	1.38	0.22167	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.140488	0.49305	N	0.000151	T	0.48572	0.1507	L	0.46157	1.445	0.42037	D	0.991052	B;B;B	0.16802	0.019;0.001;0.001	B;B;B	0.23419	0.046;0.026;0.028	T	0.30179	-0.9987	10	0.40728	T	0.16	.	3.9481	0.09356	0.0838:0.1651:0.5108:0.2403	.	1508;1508;1508	Q58EX2-2;Q58EX2;Q58EX2-3	.;SDK2_HUMAN;.	I	1132;1508;1508;684;1508	ENSP00000376421:L1508I;ENSP00000373378:L1508I;ENSP00000407098:L684I	ENSP00000324967:L1508I	L	-	1	0	SDK2	68893628	1.000000	0.71417	0.806000	0.32338	0.939000	0.58152	1.362000	0.34148	0.080000	0.16959	0.655000	0.94253	CTC		0.622	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
SDK2	54549	broad.mit.edu	37	17	71418481	71418481	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:71418481G>A	ENST00000392650.3	-	15	1990	c.1990C>T	c.(1990-1992)Cgt>Tgt	p.R664C	SDK2_ENST00000388726.3_Missense_Mutation_p.R664C	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	664	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.R664C(1)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						GCACAAAGACGGAACTGGTAG	0.607																																					p.R664C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1990T	17						.						155.0	125.0	135.0					17																	71418481		2203	4300	6503	68930076	SO:0001583	missense	54549	exon15			AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.1990C>T	17.37:g.71418481G>A	ENSP00000376421:p.Arg664Cys	Somatic		Capture	Illumina HiSeq	Phase_I	68930076	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.918756	0.92249	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000316893	T;T	0.60920	0.15;0.15	5.12	5.12	0.69794	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.86393	0.5922	H	0.98833	4.345	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92293	0.5843	10	0.87932	D	0	.	18.1572	0.89696	0.0:0.0:1.0:0.0	.	664;664	Q58EX2-2;Q58EX2	.;SDK2_HUMAN	C	288;664;664;664	ENSP00000376421:R664C;ENSP00000373378:R664C	ENSP00000324967:R664C	R	-	1	0	SDK2	68930076	1.000000	0.71417	0.997000	0.53966	0.962000	0.63368	5.256000	0.65468	2.373000	0.80994	0.462000	0.41574	CGT		0.607	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
TTYH2	94015	broad.mit.edu	37	17	72256286	72256286	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:72256286G>A	ENST00000269346.4	+	14	1617	c.1543G>A	c.(1543-1545)Gcc>Acc	p.A515T	CTD-2514K5.4_ENST00000583018.1_RNA|TTYH2_ENST00000529107.1_Missense_Mutation_p.A494T|TTYH2_ENST00000441391.2_Missense_Mutation_p.A194T	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	515						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.A515T(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						CAGCATGAGAGCCACCTACCT	0.567																																					p.A515T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1543A	17						.						171.0	156.0	161.0					17																	72256286		2203	4300	6503	69767881	SO:0001583	missense	94015	exon14				CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"""tweety (Drosophila) homolog 2"", ""tweety homolog 2 (Drosophila)"""			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.1543G>A	17.37:g.72256286G>A	ENSP00000269346:p.Ala515Thr	Somatic		Capture	Illumina HiSeq	Phase_I	69767881	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.709716	0.48517	.	.	ENSG00000141540	ENST00000269346;ENST00000529107;ENST00000441391	T;T;T	0.53206	0.63;0.63;0.63	4.55	3.57	0.40892	.	0.060960	0.64402	D	0.000005	T	0.33000	0.0848	L	0.29908	0.895	0.42632	D	0.993383	B;B	0.22746	0.031;0.074	B;B	0.17979	0.02;0.014	T	0.11567	-1.0582	10	0.35671	T	0.21	-20.6877	9.5369	0.39229	0.0:0.1543:0.6864:0.1592	.	494;515	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	T	515;494;194	ENSP00000269346:A515T;ENSP00000433089:A494T;ENSP00000394576:A194T	ENSP00000269346:A515T	A	+	1	0	TTYH2	69767881	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.064000	0.57506	1.110000	0.41699	0.650000	0.86243	GCC		0.567	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
DNAI2	64446	broad.mit.edu	37	17	72301382	72301382	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:72301382G>A	ENST00000311014.6	+	9	1079	c.1012G>A	c.(1012-1014)Gag>Aag	p.E338K	DNAI2_ENST00000446837.2_Missense_Mutation_p.E338K|DNAI2_ENST00000579490.1_Missense_Mutation_p.E395K|AC103809.1_ENST00000516976.1_RNA|RP11-647F2.2_ENST00000585167.1_RNA|DNAI2_ENST00000307504.5_Missense_Mutation_p.E195K|DNAI2_ENST00000582036.1_Missense_Mutation_p.E338K			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	338					cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)	p.E338K(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GGTGGGGACCGAGCAGGGCAT	0.582									Kartagener syndrome																												p.E338K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1012A	17						.						82.0	66.0	72.0					17																	72301382		2203	4300	6503	69812977	SO:0001583	missense	64446	exon9	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595		"""Axonemal dyneins"", ""WD repeat domain containing"""	18744	protein-coding gene	gene with protein product	"""dynein intermediate chain 2"""	605483	"""dynein, axonemal, intermediate polypeptide 2"""			11153919, 21953912	Standard	NM_023036		Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.1012G>A	17.37:g.72301382G>A	ENSP00000308312:p.Glu338Lys	Somatic		Capture	Illumina HiSeq	Phase_I	69812977	NM_023036	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Missense_Mutation	SNP	ENST00000311014.6	37	CCDS11697.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.749362	0.89753	.	.	ENSG00000171595	ENST00000311014;ENST00000307504;ENST00000446837	T;T;T	0.16597	2.33;2.33;2.33	5.06	5.06	0.68205	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	0.53867	0.1823	M	0.94101	3.495	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	T	0.68462	-0.5402	10	0.87932	D	0	-37.93	18.5131	0.90925	0.0:0.0:1.0:0.0	.	338	Q9GZS0	DNAI2_HUMAN	K	338;195;338	ENSP00000308312:E338K;ENSP00000302929:E195K;ENSP00000400252:E338K	ENSP00000302929:E195K	E	+	1	0	DNAI2	69812977	1.000000	0.71417	0.932000	0.37286	0.437000	0.31866	9.417000	0.97391	2.373000	0.80994	0.556000	0.70494	GAG		0.582	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036	
KIF19	124602	broad.mit.edu	37	17	72349364	72349364	+	Missense_Mutation	SNP	C	C	G	rs556088065		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:72349364C>G	ENST00000389916.4	+	16	2282	c.2144C>G	c.(2143-2145)aCt>aGt	p.T715S	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	715					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)	p.T715S(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						AAGGCTGGTACTGGGGCCTGG	0.627																																					p.T715S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2144G	17						.						33.0	38.0	36.0					17																	72349364		2057	4198	6255	69860959	SO:0001583	missense	124602	exon16			AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2144C>G	17.37:g.72349364C>G	ENSP00000374566:p.Thr715Ser	Somatic		Capture	Illumina HiSeq	Phase_I	69860959	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	37	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	C	7.090	0.572043	0.13623	.	.	ENSG00000196169	ENST00000389916	T	0.69175	-0.38	5.14	5.14	0.70334	.	.	.	.	.	T	0.46502	0.1396	N	0.03608	-0.345	0.22926	N	0.998553	B	0.02656	0.0	B	0.01281	0.0	T	0.37934	-0.9684	9	0.41790	T	0.15	.	15.5858	0.76482	0.0:1.0:0.0:0.0	.	715	Q2TAC6	KIF19_HUMAN	S	715	ENSP00000374566:T715S	ENSP00000374566:T715S	T	+	2	0	KIF19	69860959	0.569000	0.26643	0.110000	0.21437	0.017000	0.09413	4.391000	0.59652	2.394000	0.81467	0.456000	0.33151	ACT		0.627	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
CD300LF	146722	broad.mit.edu	37	17	72691965	72691965	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:72691965C>T	ENST00000326165.6	-	6	727	c.616G>A	c.(616-618)Gca>Aca	p.A206T	CD300LF_ENST00000464910.1_Missense_Mutation_p.A209T|CD300LF_ENST00000343125.4_Missense_Mutation_p.C171Y|CD300LF_ENST00000301573.9_Missense_Mutation_p.C221Y|RAB37_ENST00000340415.3_Intron|CD300LF_ENST00000583937.1_Missense_Mutation_p.A221T|RAB37_ENST00000402449.4_Intron|CD300LF_ENST00000469092.1_Missense_Mutation_p.C171Y|CD300LF_ENST00000361254.4_Missense_Mutation_p.C216Y|CD300LF_ENST00000581500.1_Missense_Mutation_p.C216Y	NM_139018.3	NP_620587.2	Q8TDQ1	CLM1_HUMAN	CD300 molecule-like family member f	206					immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A206T(2)		endometrium(2)|large_intestine(1)|lung(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						GTCAGGTCTGCATAGCAGAGG	0.587																																					p.A206T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G616A	17						.						74.0	64.0	68.0					17																	72691965		2203	4300	6503	70203560	SO:0001583	missense	146722	exon6			BC028199	CCDS11704.1, CCDS74148.1, CCDS74149.1, CCDS74150.1, CCDS74151.1, CCDS74152.1	17q25.2	2013-01-11	2006-03-29		ENSG00000186074	ENSG00000186074		"""Immunoglobulin superfamily / V-set domain containing"""	29883	protein-coding gene	gene with protein product		609807	"""CD300 antigen like family member F"""			12975309	Standard	NM_139018		Approved	IREM1, NKIR, IGSF13, CD300f, CLM1	uc002jlg.3	Q8TDQ1	OTTHUMG00000067609	ENST00000326165.6:c.616G>A	17.37:g.72691965C>T	ENSP00000327075:p.Ala206Thr	Somatic		Capture	Illumina HiSeq	Phase_I	70203560	NM_139018	B2RCL2|C9JDN3|Q3Y6P0|Q6UX24|Q7Z6A6|Q7Z7I4|Q7Z7I5|Q8N6D0|Q8NAF5	Missense_Mutation	SNP	ENST00000326165.6	37	CCDS11704.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.84|10.84	1.463580|1.463580	0.26248|0.26248	.|.	.|.	ENSG00000186074|ENSG00000186074	ENST00000326165|ENST00000301573;ENST00000361254;ENST00000343125	T|T;T;T	0.55234|0.06849	0.53|3.25;3.3;3.32	4.54|4.54	2.56|2.56	0.30785|0.30785	.|.	0.348186|.	0.20765|.	N|.	0.086096|.	T|T	0.21550|0.21550	0.0519|0.0519	M|M	0.77820|0.77820	2.39|2.39	0.09310|0.09310	N|N	1|1	D;D;D|D;D;D	0.56521|0.62365	0.959;0.959;0.976|0.982;0.964;0.991	P;P;P|P;P;P	0.56398|0.60068	0.556;0.556;0.797|0.778;0.778;0.868	T|T	0.05022|0.05022	-1.0911|-1.0911	10|9	0.59425|0.45353	D|T	0.04|0.12	.|.	6.7871|6.7871	0.23679|0.23679	0.0:0.7902:0.0:0.2098|0.0:0.7902:0.0:0.2098	.|.	221;206;209|216;171;221	E7EME0;Q8TDQ1;Q8TDQ1-6|Q8TDQ1-2;Q8TDQ1-4;Q8TDQ1-5	.;CLM1_HUMAN;.|.;.;.	T|Y	206|221;216;171	ENSP00000327075:A206T|ENSP00000301573:C221Y;ENSP00000355294:C216Y;ENSP00000343751:C171Y	ENSP00000327075:A206T|ENSP00000301573:C221Y	A|C	-|-	1|2	0|0	CD300LF|CD300LF	70203560|70203560	0.224000|0.224000	0.23674|0.23674	0.011000|0.011000	0.14972|0.14972	0.240000|0.240000	0.25518|0.25518	0.961000|0.961000	0.29267|0.29267	0.656000|0.656000	0.30886|0.30886	0.655000|0.655000	0.94253|0.94253	GCA|TGC		0.587	CD300LF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000145085.1	NM_139018	
SLC9A3R1	9368	broad.mit.edu	37	17	72764669	72764669	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:72764669C>T	ENST00000262613.5	+	6	1146	c.951C>T	c.(949-951)tcC>tcT	p.S317S	SLC9A3R1_ENST00000413388.2_Silent_p.S161S	NM_004252.4	NP_004243.1	O14745	NHRF1_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 regulator 1	317					actin cytoskeleton organization (GO:0030036)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|bile acid secretion (GO:0032782)|cellular phosphate ion homeostasis (GO:0030643)|cellular protein localization (GO:0034613)|glutathione transport (GO:0034635)|microvillus assembly (GO:0030033)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of sodium:proton antiporter activity (GO:0032416)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|protein complex assembly (GO:0006461)|regulation of excretion (GO:0044062)|regulation of protein kinase activity (GO:0045859)|regulation of sodium:proton antiporter activity (GO:0032415)|renal absorption (GO:0070293)|renal phosphate ion absorption (GO:0097291)|renal sodium ion transport (GO:0003096)|Wnt signaling pathway (GO:0016055)	actin cytoskeleton (GO:0015629)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell periphery (GO:0071944)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|membrane raft (GO:0045121)|microvillus (GO:0005902)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)|vesicle (GO:0031982)	beta-2 adrenergic receptor binding (GO:0031698)|beta-catenin binding (GO:0008013)|chloride channel regulator activity (GO:0017081)|growth factor receptor binding (GO:0070851)|PDZ domain binding (GO:0030165)|phosphatase binding (GO:0019902)|protein self-association (GO:0043621)|receptor binding (GO:0005102)	p.S317S(1)		large_intestine(4)	4						CCTCCTCCTCCGACCCCATCC	0.587																																					p.S317S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C951T	17						.						164.0	171.0	168.0					17																	72764669		2203	4300	6503	70276264	SO:0001819	synonymous_variant	9368	exon6			AF015926	CCDS11705.1	17q25.1	2014-09-04	2012-03-22		ENSG00000109062	ENSG00000109062			11075	protein-coding gene	gene with protein product		604990	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory factor 1"", ""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulator 1"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1"""			9314537, 9430655	Standard	NM_004252		Approved	NHERF, EBP50	uc002jlo.4	O14745	OTTHUMG00000178863	ENST00000262613.5:c.951C>T	17.37:g.72764669C>T		Somatic		Capture	Illumina HiSeq	Phase_I	70276264	NM_004252	B3KY21|O43552|Q86WQ5	Silent	SNP	ENST00000262613.5	37	CCDS11705.1	.	.	.	.	.	.	.	.	.	.	C	10.19	1.282003	0.23392	.	.	ENSG00000109062	ENST00000413388	.	.	.	4.89	-5.62	0.02481	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.4195	14.6566	0.68838	0.0:0.6681:0.0:0.3319	.	.	.	.	X	205	.	ENSP00000398782:R205X	R	+	1	2	SLC9A3R1	70276264	0.000000	0.05858	0.953000	0.39169	0.981000	0.71138	-4.758000	0.00189	-1.085000	0.03088	-0.423000	0.05987	CGA		0.587	SLC9A3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443671.1		
GRIN2C	2905	broad.mit.edu	37	17	72851140	72851140	+	Missense_Mutation	SNP	G	G	A	rs370446235		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:72851140G>A	ENST00000293190.5	-	2	238	c.92C>T	c.(91-93)aCg>aTg	p.T31M	GRIN2C_ENST00000578159.1_Intron|GRIN2C_ENST00000347612.4_Missense_Mutation_p.T31M	NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	31					directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|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)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)	p.T31M(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CACAGCCACCGTCATGCCCTG	0.716																																					p.T31M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C92T	17						.	G	MET/THR	1,4395		0,1,2197	19.0	23.0	22.0		92	4.5	1.0	17		22	0,8592		0,0,4296	no	missense	GRIN2C	NM_000835.3	81	0,1,6493	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	31/1234	72851140	1,12987	2198	4296	6494	70362735	SO:0001583	missense	2905	exon2				CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.92C>T	17.37:g.72851140G>A	ENSP00000293190:p.Thr31Met	Somatic		Capture	Illumina HiSeq	Phase_I	70362735	NM_000835	B2RTT1	Missense_Mutation	SNP	ENST00000293190.5	37	CCDS32724.1	.	.	.	.	.	.	.	.	.	.	G	10.31	1.314724	0.23908	2.27E-4	0.0	ENSG00000161509	ENST00000293190;ENST00000347612	T	0.11712	2.75	4.49	4.49	0.54785	.	0.134016	0.48286	D	0.000187	T	0.21145	0.0509	L	0.57536	1.79	0.36409	D	0.86361	P;D;D	0.71674	0.621;0.998;0.998	B;P;P	0.56216	0.075;0.794;0.731	T	0.06954	-1.0798	10	0.87932	D	0	.	10.513	0.44872	0.0:0.0:0.6613:0.3387	.	31;65;31	Q6PCC5;Q8IW23;Q14957	.;.;NMDE3_HUMAN	M	31;65	ENSP00000293190:T31M	ENSP00000293190:T31M	T	-	2	0	GRIN2C	70362735	1.000000	0.71417	0.977000	0.42913	0.474000	0.32979	3.545000	0.53648	2.320000	0.78422	0.557000	0.71058	ACG		0.716	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1		
OTOP3	347741	broad.mit.edu	37	17	72937587	72937587	+	Missense_Mutation	SNP	C	C	T	rs538596544		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:72937587C>T	ENST00000328801.4	+	2	173	c.173C>T	c.(172-174)gCg>gTg	p.A58V		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	58						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)	p.A58V(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_lung(278;0.151)|Lung NSC(278;0.185)					GAGGAGAGAGCGGCCGCCACC	0.657													C|||	1	0.000199681	0.0008	0.0	5008	,	,		13661	0.0		0.0	False		,,,				2504	0.0				p.A58V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C173T	17						.						18.0	23.0	21.0					17																	72937587		2202	4287	6489	70449182	SO:0001583	missense	347741	exon2			BK000568	CCDS11709.1	17q25	2004-01-19				ENSG00000182938			19658	protein-coding gene	gene with protein product		607828				12651873	Standard	NM_178233		Approved		uc010wrr.3	Q7RTS5		ENST00000328801.4:c.173C>T	17.37:g.72937587C>T	ENSP00000328090:p.Ala58Val	Somatic		Capture	Illumina HiSeq	Phase_I	70449182	NM_178233		Missense_Mutation	SNP	ENST00000328801.4	37	CCDS11709.1	.	.	.	.	.	.	.	.	.	.	C	10.71	1.427017	0.25726	.	.	ENSG00000182938	ENST00000328801	T	0.08896	3.04	4.86	0.495	0.16890	.	1.082470	0.07169	N	0.851969	T	0.03739	0.0106	N	0.08118	0	0.09310	N	1	B	0.24426	0.103	B	0.14578	0.011	T	0.43940	-0.9360	10	0.33141	T	0.24	-8.6042	2.1114	0.03703	0.2377:0.138:0.4925:0.1317	.	58	Q7RTS5	OTOP3_HUMAN	V	58	ENSP00000328090:A58V	ENSP00000328090:A58V	A	+	2	0	OTOP3	70449182	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.032000	0.12266	-0.116000	0.11893	-1.520000	0.00934	GCG		0.657	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233	
PHF23	79142	broad.mit.edu	37	17	7139699	7139699	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:7139699G>A	ENST00000320316.3	-	4	773	c.547C>T	c.(547-549)Cga>Tga	p.R183*	PHF23_ENST00000570753.1_5'Flank|PHF23_ENST00000454255.2_Nonsense_Mutation_p.R179*|PHF23_ENST00000576955.1_Nonsense_Mutation_p.R53*|PHF23_ENST00000571362.1_Nonsense_Mutation_p.R116*|DVL2_ENST00000005340.5_5'Flank|DVL2_ENST00000575458.1_5'Flank	NM_001284518.1|NM_024297.2	NP_001271447.1|NP_077273.2	Q9BUL5	PHF23_HUMAN	PHD finger protein 23	183							zinc ion binding (GO:0008270)	p.R183*(1)		breast(4)|kidney(2)|large_intestine(6)|lung(3)	15						CGGTTCTTTCGGTCCTTCTTT	0.622																																					p.R183X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C547T	17						.						51.0	58.0	56.0					17																	7139699		1869	4088	5957	7080423	SO:0001587	stop_gained	79142	exon4			AK122791	CCDS42250.1, CCDS67143.1, CCDS67144.1	17p13.1	2014-08-13			ENSG00000040633	ENSG00000040633		"""Zinc fingers, PHD-type"""	28428	protein-coding gene	gene with protein product		612910					Standard	NM_024297		Approved	MGC2941, FLJ16355	uc002gfa.3	Q9BUL5	OTTHUMG00000177972	ENST00000320316.3:c.547C>T	17.37:g.7139699G>A	ENSP00000322579:p.Arg183*	Somatic		Capture	Illumina HiSeq	Phase_I	7080423	NM_024297	A1DZ74|B3KVH8|B4DLK6|D3DTN4|Q8IZK0|Q96HG7|Q9H5X0	Nonsense_Mutation	SNP	ENST00000320316.3	37	CCDS42250.1	.	.	.	.	.	.	.	.	.	.	G	18.23	3.577527	0.65878	.	.	ENSG00000040633	ENST00000320316;ENST00000454255	.	.	.	4.92	4.92	0.64577	.	0.084309	0.47852	D	0.000207	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.437	13.4841	0.61355	0.0:0.0:1.0:0.0	.	.	.	.	X	183;179	.	ENSP00000322579:R183X	R	-	1	2	PHF23	7080423	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.828000	0.48120	2.539000	0.85634	0.563000	0.77884	CGA		0.622	PHF23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440047.1	NM_024297	
NUP85	79902	broad.mit.edu	37	17	73227439	73227439	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:73227439G>A	ENST00000245544.4	+	12	1170	c.1099G>A	c.(1099-1101)Gcc>Acc	p.A367T	NUP85_ENST00000540768.1_5'UTR|NUP85_ENST00000579324.1_Missense_Mutation_p.A255T|NUP85_ENST00000447371.2_Missense_Mutation_p.A199T|NUP85_ENST00000579298.1_Missense_Mutation_p.A322T|NUP85_ENST00000541827.1_Missense_Mutation_p.A321T	NM_024844.3	NP_079120.1	Q9BW27	NUP85_HUMAN	nucleoporin 85kDa	367					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|lamellipodium assembly (GO:0030032)|macrophage chemotaxis (GO:0048246)|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)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)		p.A367T(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	16	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			CTGCAGCATCGCCCTGAGCAA	0.592																																					p.A367T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1099A	17						.						154.0	147.0	149.0					17																	73227439		2203	4300	6503	70739034	SO:0001583	missense	79902	exon12			AF514995	CCDS32730.1	17q25	2006-11-29	2005-11-03	2005-11-03		ENSG00000125450			8734	protein-coding gene	gene with protein product		170285				8124707	Standard	XM_005257690		Approved	NUP75, FLJ12549	uc002jng.1	Q9BW27		ENST00000245544.4:c.1099G>A	17.37:g.73227439G>A	ENSP00000245544:p.Ala367Thr	Somatic		Capture	Illumina HiSeq	Phase_I	70739034	NM_024844	B4DMQ3|B4DPW1|Q8NDI4|Q9H9U1	Missense_Mutation	SNP	ENST00000245544.4	37	CCDS32730.1	.	.	.	.	.	.	.	.	.	.	G	14.51	2.556005	0.45487	.	.	ENSG00000125450	ENST00000245544;ENST00000541827;ENST00000447371	.	.	.	5.83	4.86	0.63082	.	0.090887	0.85682	D	0.000000	T	0.57154	0.2034	M	0.63428	1.95	0.52099	D	0.999942	B;B	0.25105	0.056;0.118	B;B	0.25506	0.061;0.056	T	0.53968	-0.8363	9	0.09084	T	0.74	-7.8992	14.9046	0.70709	0.0684:0.0:0.9315:0.0	.	321;367	B4DMQ3;Q9BW27	.;NUP85_HUMAN	T	367;321;199	.	ENSP00000245544:A367T	A	+	1	0	NUP85	70739034	1.000000	0.71417	0.966000	0.40874	0.792000	0.44763	9.193000	0.94954	1.480000	0.48289	0.561000	0.74099	GCC		0.592	NUP85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446619.1	NM_024844	
RECQL5	9400	broad.mit.edu	37	17	73657074	73657074	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:73657074G>A	ENST00000317905.5	-	6	1106	c.947C>T	c.(946-948)aCc>aTc	p.T316I	RECQL5_ENST00000584999.1_Missense_Mutation_p.T316I|RECQL5_ENST00000423245.2_Missense_Mutation_p.T289I|RECQL5_ENST00000340830.5_Missense_Mutation_p.T316I|RECQL5_ENST00000420326.2_Missense_Mutation_p.T316I	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	316	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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.T289I(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)			AAAACTAATGGTTGCAACAAT	0.542								Other identified genes with known or suspected DNA repair function																													p.T316I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C947T	17						.						202.0	160.0	174.0					17																	73657074		2203	4300	6503	71168669	SO:0001583	missense	9400	exon6			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.947C>T	17.37:g.73657074G>A	ENSP00000317636:p.Thr316Ile	Somatic		Capture	Illumina HiSeq	Phase_I	71168669	NM_001003715	Q9H0B1|Q9P1W7|Q9UNC8	Missense_Mutation	SNP	ENST00000317905.5	37	CCDS42380.1	.	.	.	.	.	.	.	.	.	.	G	16.26	3.073736	0.55646	.	.	ENSG00000108469	ENST00000423245;ENST00000317905;ENST00000420326;ENST00000340830	T;T;T	0.12465	2.68;2.68;2.68	5.6	5.6	0.85130	Helicase, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.62270	0.2414	H	0.99740	4.74	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	0.81106	-0.1083	10	0.87932	D	0	-22.7133	19.6143	0.95626	0.0:0.0:1.0:0.0	.	316;289;316	O94762;Q6P4G0;O94762-3	RECQ5_HUMAN;.;.	I	316	ENSP00000317636:T316I;ENSP00000414933:T316I;ENSP00000341983:T316I	ENSP00000317636:T316I	T	-	2	0	RECQL5	71168669	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.640000	0.89533	0.561000	0.74099	ACC		0.542	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259	
UNK	85451	broad.mit.edu	37	17	73809228	73809228	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:73809228G>A	ENST00000589666.1	+	5	802	c.692G>A	c.(691-693)gGc>gAc	p.G231D	UNK_ENST00000293218.3_Missense_Mutation_p.G307D	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	231							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.G231D(1)		cervix(3)|endometrium(8)|kidney(2)|large_intestine(5)|lung(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	25			all cancers(21;2.61e-06)|Epithelial(20;7.39e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGCCGCCAAGGCTATGCCTGT	0.647																																					p.G307D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G920A	17						.						22.0	27.0	26.0					17																	73809228		1880	4102	5982	71320823	SO:0001583	missense	85451	exon6			AB051540	CCDS45778.1, CCDS45778.2	17q25.3	2013-10-17	2013-10-17	2007-02-06		ENSG00000132478		"""Zinc fingers, CCCH-type domain containing"""	29369	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 5"", ""zinc finger CCCH-type containing 5"", ""unkempt homolog (Drosophila)"""	ZC3HDC5, ZC3H5		11214970	Standard	NM_001080419		Approved	KIAA1753	uc021udd.2	Q9C0B0		ENST00000589666.1:c.692G>A	17.37:g.73809228G>A	ENSP00000464893:p.Gly231Asp	Somatic		Capture	Illumina HiSeq	Phase_I	71320823	NM_001080419		Missense_Mutation	SNP	ENST00000589666.1	37	CCDS45778.2	.	.	.	.	.	.	.	.	.	.	G	33	5.202421	0.94997	.	.	ENSG00000132478	ENST00000293218	.	.	.	4.84	4.84	0.62591	Zinc finger, CCCH-type (2);	0.000000	0.85682	D	0.000000	D	0.84188	0.5417	M	0.87758	2.905	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.85907	0.1438	9	0.49607	T	0.09	-8.5739	18.1613	0.89708	0.0:0.0:1.0:0.0	.	231	Q9C0B0	UNK_HUMAN	D	307	.	ENSP00000293218:G307D	G	+	2	0	UNK	71320823	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.487000	0.97945	2.523000	0.85059	0.655000	0.94253	GGC		0.647	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419	
EVPL	2125	broad.mit.edu	37	17	74004698	74004698	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:74004698G>T	ENST00000301607.3	-	22	4841	c.4588C>A	c.(4588-4590)Cgc>Agc	p.R1530S	EVPL_ENST00000586740.1_Missense_Mutation_p.R1552S|TEN1-CDK3_ENST00000567351.1_RNA	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1530	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.R1530S(1)		breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						TCCAGGACGCGGTCCTTCTGC	0.647																																					p.R1530S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4588A	17						.						123.0	92.0	103.0					17																	74004698		2203	4300	6503	71516293	SO:0001583	missense	2125	exon22			U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.4588C>A	17.37:g.74004698G>T	ENSP00000301607:p.Arg1530Ser	Somatic		Capture	Illumina HiSeq	Phase_I	71516293	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	G	9.375	1.071470	0.20147	.	.	ENSG00000167880	ENST00000301607	T	0.48201	0.82	4.88	4.88	0.63580	.	0.556836	0.18948	N	0.126758	T	0.35508	0.0934	L	0.44542	1.39	0.30608	N	0.759848	B;B	0.28998	0.23;0.116	B;B	0.25987	0.065;0.048	T	0.27020	-1.0086	10	0.08599	T	0.76	-9.3965	11.4544	0.50171	0.0:0.0:0.6872:0.3128	.	1552;1530	B7ZLH8;Q92817	.;EVPL_HUMAN	S	1530	ENSP00000301607:R1530S	ENSP00000301607:R1530S	R	-	1	0	EVPL	71516293	1.000000	0.71417	0.932000	0.37286	0.773000	0.43773	4.984000	0.63838	2.262000	0.75019	0.561000	0.74099	CGC		0.647	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
EVPL	2125	broad.mit.edu	37	17	74005452	74005452	+	Silent	SNP	G	G	A	rs138831181		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:74005452G>A	ENST00000301607.3	-	22	4087	c.3834C>T	c.(3832-3834)aaC>aaT	p.N1278N	EVPL_ENST00000586740.1_Silent_p.N1300N	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1278	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.N1278N(1)		breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						TGACGAGCTCGTTGAGCTGAG	0.662																																					p.N1278N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3834T	17						.	G		1,4405	2.1+/-5.4	0,1,2202	78.0	71.0	73.0		3834	-8.0	0.8	17	dbSNP_134	73	0,8600		0,0,4300	no	coding-synonymous	EVPL	NM_001988.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1278/2034	74005452	1,13005	2203	4300	6503	71517047	SO:0001819	synonymous_variant	2125	exon22			U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.3834C>T	17.37:g.74005452G>A		Somatic		Capture	Illumina HiSeq	Phase_I	71517047	NM_001988	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																				0.662	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
NEURL4	84461	broad.mit.edu	37	17	7221198	7221198	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:7221198G>A	ENST00000399464.2	-	26	4129	c.4114C>T	c.(4114-4116)Cgg>Tgg	p.R1372W	GPS2_ENST00000391950.3_5'Flank|NEURL4_ENST00000574120.1_5'UTR|NEURL4_ENST00000570460.1_Missense_Mutation_p.R1348W|GPS2_ENST00000380728.2_5'Flank|NEURL4_ENST00000315614.7_Missense_Mutation_p.R1370W|RP11-542C16.2_ENST00000575474.1_Silent_p.A185A|GPS2_ENST00000389167.5_5'Flank	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	1372						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R1370W(1)|p.R1372W(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CGCAGCTTCCGGCAAGACTCA	0.587																																					p.R1372W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C4114T	17						.						56.0	61.0	59.0					17																	7221198		2104	4230	6334	7161922	SO:0001583	missense	84461	exon26				CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"""neuralized homolog 4 (Drosophila)"""			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.4114C>T	17.37:g.7221198G>A	ENSP00000382390:p.Arg1372Trp	Somatic		Capture	Illumina HiSeq	Phase_I	7161922	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	ENST00000399464.2	37	CCDS42251.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.989009	0.53934	.	.	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.30714	1.52;1.52	5.05	5.05	0.67936	.	0.148983	0.47093	D	0.000250	T	0.31040	0.0784	L	0.29908	0.895	0.36507	D	0.86936	D;D	0.60575	0.988;0.98	P;B	0.47705	0.555;0.353	T	0.18366	-1.0339	10	0.38643	T	0.18	-10.2041	17.3361	0.87281	0.0:0.0:1.0:0.0	.	1370;1372	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	W	1370;1372	ENSP00000319826:R1370W;ENSP00000382390:R1372W	ENSP00000319826:R1370W	R	-	1	2	NEURL4	7161922	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.482000	0.60257	2.626000	0.88956	0.455000	0.32223	CGG		0.587	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442	
NEURL4	84461	broad.mit.edu	37	17	7230150	7230150	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:7230150G>A	ENST00000399464.2	-	4	987	c.972C>T	c.(970-972)tgC>tgT	p.C324C	NEURL4_ENST00000570460.1_Silent_p.C302C|NEURL4_ENST00000315614.7_Silent_p.C324C	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	324	NHR 2. {ECO:0000255|PROSITE- ProRule:PRU00400}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.C324C(2)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TGAGGGTCCCGCACTTTTCAT	0.577																																					p.C324C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C972T	17						.						60.0	63.0	62.0					17																	7230150		1960	4130	6090	7170874	SO:0001819	synonymous_variant	84461	exon4				CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"""neuralized homolog 4 (Drosophila)"""			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.972C>T	17.37:g.7230150G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7170874	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Silent	SNP	ENST00000399464.2	37	CCDS42251.1																																																																																				0.577	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442	
EXOC7	23265	broad.mit.edu	37	17	74083754	74083754	+	Silent	SNP	G	G	A	rs530110887	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:74083754G>A	ENST00000335146.7	-	13	1616	c.1563C>T	c.(1561-1563)ggC>ggT	p.G521G	EXOC7_ENST00000411744.2_Silent_p.G462G|EXOC7_ENST00000607838.1_Silent_p.G493G|EXOC7_ENST00000467929.2_Silent_p.G429G|EXOC7_ENST00000589210.1_Silent_p.G470G|EXOC7_ENST00000332065.5_Silent_p.G439G|EXOC7_ENST00000405575.4_Silent_p.G493G			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	521					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)		p.G470G(1)		NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			CCAGCATGGCGCCTGCCGTCT	0.647													g|||	2	0.000399361	0.0	0.0	5008	,	,		18836	0.0		0.0	False		,,,				2504	0.002				p.G493G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1479T	17						.						48.0	42.0	44.0					17																	74083754		2020	3953	5973	71595349	SO:0001819	synonymous_variant	23265	exon13			BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.1563C>T	17.37:g.74083754G>A		Somatic		Capture	Illumina HiSeq	Phase_I	71595349	NM_001145299	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Silent	SNP	ENST00000335146.7	37	CCDS45782.1																																																																																				0.647	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219	
QRICH2	84074	broad.mit.edu	37	17	74289938	74289938	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:74289938G>A	ENST00000262765.5	-	4	551	c.372C>T	c.(370-372)ggC>ggT	p.G124G		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	124								p.G124G(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						GGTGTGCTGTGCCACCAGATC	0.587																																					p.G124G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C372T	17						.						73.0	72.0	72.0					17																	74289938		2203	4300	6503	71801533	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.372C>T	17.37:g.74289938G>A		Somatic		Capture	Illumina HiSeq	Phase_I	71801533	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																				0.587	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
RHBDF2	79651	broad.mit.edu	37	17	74468017	74468017	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:74468017G>T	ENST00000313080.4	-	19	2542	c.2269C>A	c.(2269-2271)Ctc>Atc	p.L757I	RHBDF2_ENST00000389760.4_Missense_Mutation_p.L728I|RHBDF2_ENST00000591885.1_Missense_Mutation_p.L728I	NM_024599.5	NP_078875.4	Q6PJF5	RHDF2_HUMAN	rhomboid 5 homolog 2 (Drosophila)	757					negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)	p.L757I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(4)|skin(1)	27						AACAGGAAGAGCACGATGGCC	0.627																																					p.L757I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2269A	17						.						107.0	74.0	85.0					17																	74468017		2196	4286	6482	71979612	SO:0001583	missense	79651	exon19			BC016034	CCDS32743.1, CCDS32744.1	17q25.3	2014-09-17	2006-02-22	2006-02-22		ENSG00000129667			20788	protein-coding gene	gene with protein product		614404	"""rhomboid, veinlet-like 6 (Drosophila)"", ""tylosis with oesophageal cancer"""	RHBDL6, TOC		12838346, 22265016	Standard	NM_024599		Approved	FLJ22341, RHBDL5, TOCG	uc002jrq.2	Q6PJF5		ENST00000313080.4:c.2269C>A	17.37:g.74468017G>T	ENSP00000322775:p.Leu757Ile	Somatic		Capture	Illumina HiSeq	Phase_I	71979612	NM_024599	A6NEM3|A8K801|Q5U607|Q5YGQ8|Q9H6E9	Missense_Mutation	SNP	ENST00000313080.4	37	CCDS32743.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.274825	0.23307	.	.	ENSG00000129667	ENST00000313080;ENST00000389760	T;T	0.12465	2.68;2.68	4.52	3.24	0.37175	Peptidase S54, rhomboid domain (1);	0.151725	0.44688	D	0.000433	T	0.10852	0.0265	L	0.28504	0.86	0.50313	D	0.999864	B;B	0.16802	0.01;0.019	B;B	0.25759	0.063;0.012	T	0.12319	-1.0552	10	0.29301	T	0.29	-34.449	11.341	0.49533	0.1514:0.0:0.8486:0.0	.	757;728	Q6PJF5;Q6PJF5-2	RHDF2_HUMAN;.	I	757;728	ENSP00000322775:L757I;ENSP00000374410:L728I	ENSP00000322775:L757I	L	-	1	0	RHBDF2	71979612	1.000000	0.71417	1.000000	0.80357	0.469000	0.32828	2.570000	0.45981	1.154000	0.42482	0.467000	0.42956	CTC		0.627	RHBDF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450134.1	NM_024599	
NLGN2	57555	broad.mit.edu	37	17	7315507	7315507	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:7315507G>A	ENST00000302926.2	+	2	562	c.489G>A	c.(487-489)acG>acA	p.T163T	NLGN2_ENST00000575301.1_Silent_p.T163T	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	163					cell-cell junction maintenance (GO:0045217)|gephyrin clustering (GO:0097116)|locomotory exploration behavior (GO:0035641)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|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)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|sensory perception of pain (GO:0019233)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)	p.T163T(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|prostate(2)|skin(3)	22		Prostate(122;0.157)				ACGAGGCGACGCTCAATCCGC	0.512																																					p.T163T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G489A	17						.						75.0	73.0	74.0					17																	7315507		2203	4300	6503	7256231	SO:0001819	synonymous_variant	57555	exon2			AB037787	CCDS11103.1	17p13.2	2008-07-18			ENSG00000169992	ENSG00000169992			14290	protein-coding gene	gene with protein product		606479				10767552, 10819331	Standard	NM_020795		Approved	KIAA1366	uc002ggt.1	Q8NFZ4	OTTHUMG00000108138	ENST00000302926.2:c.489G>A	17.37:g.7315507G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7256231	NM_020795	Q9P2I1	Silent	SNP	ENST00000302926.2	37	CCDS11103.1																																																																																				0.512	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795	
SLC35G6	643664	broad.mit.edu	37	17	7385797	7385797	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:7385797G>A	ENST00000412468.2	+	2	609	c.494G>A	c.(493-495)aGc>aAc	p.S165N	POLR2A_ENST00000572844.1_5'Flank|ZBTB4_ENST00000311403.4_Intron|ZBTB4_ENST00000380599.4_5'Flank|POLR2A_ENST00000322644.6_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	165	EamA 1.					integral component of membrane (GO:0016021)		p.S165N(1)									CTGTTGGGCAGCATCCTAGGA	0.587																																					p.S165N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G494A	17						.						185.0	178.0	180.0					17																	7385797		2203	4300	6503	7326521	SO:0001583	missense	643664	exon2				CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.494G>A	17.37:g.7385797G>A	ENSP00000396523:p.Ser165Asn	Somatic		Capture	Illumina HiSeq	Phase_I	7326521	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.857778	0.71834	.	.	ENSG00000181222	ENST00000412468	T	0.69685	-0.42	3.93	3.93	0.45458	.	.	.	.	.	T	0.64416	0.2596	L	0.36672	1.1	0.44539	D	0.997496	B	0.32324	0.364	B	0.43225	0.412	T	0.65446	-0.6166	9	0.42905	T	0.14	-3.7175	13.7333	0.62802	0.0:0.0:1.0:0.0	.	165	P0C7Q6	S35G6_HUMAN	N	165	ENSP00000396523:S165N	ENSP00000396523:S165N	S	+	2	0	SLC35G6	7326521	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	4.214000	0.58527	2.144000	0.66660	0.563000	0.77884	AGC		0.587	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
POLR2A	5430	broad.mit.edu	37	17	7415801	7415801	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:7415801G>T	ENST00000322644.6	+	27	4897	c.4498G>T	c.(4498-4500)Ggc>Tgc	p.G1500C		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1500					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)	p.G1500C(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				TGCAGCCACCGGCATGTTCTT	0.607																																					p.G1500C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4498T	17						.						55.0	47.0	50.0					17																	7415801		2203	4300	6503	7356525	SO:0001583	missense	5430	exon27					17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.4498G>T	17.37:g.7415801G>T	ENSP00000314949:p.Gly1500Cys	Somatic		Capture	Illumina HiSeq	Phase_I	7356525	NM_000937	A6NN93|B9EH88|Q6NX41	Missense_Mutation	SNP	ENST00000322644.6	37	CCDS32548.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.494545	0.85069	.	.	ENSG00000181222	ENST00000535204;ENST00000545644;ENST00000322644	T	0.72725	-0.68	4.48	4.48	0.54585	.	0.000000	0.64402	D	0.000001	T	0.81583	0.4853	M	0.72118	2.19	0.80722	D	1	D	0.76494	0.999	D	0.63192	0.912	D	0.83975	0.0329	10	0.62326	D	0.03	-13.5618	16.1463	0.81575	0.0:0.0:1.0:0.0	.	1500	P24928	RPB1_HUMAN	C	1456;399;1500	ENSP00000314949:G1500C	ENSP00000314949:G1500C	G	+	1	0	SLC35G6	7356525	1.000000	0.71417	0.997000	0.53966	0.945000	0.59286	8.648000	0.91062	2.331000	0.79229	0.456000	0.33151	GGC		0.607	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
FXR2	9513	broad.mit.edu	37	17	7504780	7504780	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:7504780G>A	ENST00000250113.7	-	7	941	c.607C>T	c.(607-609)Cgc>Tgc	p.R203C		NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	203						cytoplasm (GO:0005737)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.?(1)|p.R203C(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		AGTTTGGTGCGCAGGCTTCGG	0.493																																					p.R203C												.	.	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.C607T	17						.						222.0	221.0	221.0					17																	7504780		1988	4178	6166	7445505	SO:0001583	missense	9513	exon7			U31501	CCDS45604.1	17p13.3	2014-09-17				ENSG00000129245			4024	protein-coding gene	gene with protein product		605339		FMR1L2		7489725, 9259278	Standard	NM_004860		Approved		uc002gia.2	P51116		ENST00000250113.7:c.607C>T	17.37:g.7504780G>A	ENSP00000250113:p.Arg203Cys	Somatic		Capture	Illumina HiSeq	Phase_I	7445505	NM_004860	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Missense_Mutation	SNP	ENST00000250113.7	37	CCDS45604.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.998588	0.93227	.	.	ENSG00000129245	ENST00000250113	T	0.48201	0.82	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.64294	0.2585	L	0.55990	1.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.69142	0.943;0.962	T	0.66452	-0.5920	10	0.87932	D	0	2.7472	16.7517	0.85488	0.0:0.0:1.0:0.0	.	203;203	Q86V09;P51116	.;FXR2_HUMAN	C	203	ENSP00000250113:R203C	ENSP00000250113:R203C	R	-	1	0	FXR2	7445505	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	6.410000	0.73294	2.546000	0.85860	0.643000	0.83706	CGC		0.493	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1		
MFSD11	79157	broad.mit.edu	37	17	74774409	74774409	+	Missense_Mutation	SNP	G	G	A	rs151239652		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:74774409G>A	ENST00000588460.1	+	13	3367	c.1325G>A	c.(1324-1326)cGc>cAc	p.R442H	MFSD11_ENST00000586622.1_Missense_Mutation_p.R442H|MFSD11_ENST00000355954.3_Missense_Mutation_p.R390H|MFSD11_ENST00000593181.1_Missense_Mutation_p.R390H|MFSD11_ENST00000590070.1_3'UTR|MFSD11_ENST00000336509.4_Missense_Mutation_p.R442H|MFSD11_ENST00000590514.1_Missense_Mutation_p.R442H	NM_001242534.1	NP_001229463.1	O43934	MFS11_HUMAN	major facilitator superfamily domain containing 11	442						integral component of membrane (GO:0016021)		p.R442H(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)	17						TTTGTAGCCCGCGGCTCTGAC	0.507																																					p.R442H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1325A	17						.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	122.0	115.0	118.0		1325,1325,1325,1325,1169,1169,1325	6.1	1.0	17	dbSNP_134	118	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense	MFSD11	NM_001242532.1,NM_001242533.1,NM_001242534.1,NM_001242535.1,NM_001242536.1,NM_001242537.1,NM_024311.3	29,29,29,29,29,29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	442/450,442/450,442/450,442/450,390/398,390/398,442/450	74774409	1,13005	2203	4300	6503	72286004	SO:0001583	missense	79157	exon14			BC002753	CCDS11750.1, CCDS56045.1	17q25.1	2012-03-09			ENSG00000092931	ENSG00000092931			25458	protein-coding gene	gene with protein product						9358160	Standard	NM_001242532		Approved	FLJ22196, FLJ20226	uc002jte.3	O43934		ENST00000588460.1:c.1325G>A	17.37:g.74774409G>A	ENSP00000464932:p.Arg442His	Somatic		Capture	Illumina HiSeq	Phase_I	72286004	NM_024311	O43442|Q9NXI5	Missense_Mutation	SNP	ENST00000588460.1	37	CCDS11750.1	.	.	.	.	.	.	.	.	.	.	G	18.75	3.690686	0.68271	2.27E-4	0.0	ENSG00000092931	ENST00000336509;ENST00000355954	T;T	0.10477	3.24;2.87	6.07	6.07	0.98685	.	0.106725	0.64402	D	0.000004	T	0.22859	0.0552	L	0.40543	1.245	0.49389	D	0.999785	P;D	0.89917	0.939;1.0	P;D	0.64410	0.46;0.925	T	0.00045	-1.2215	10	0.52906	T	0.07	-10.0262	14.0103	0.64493	0.0712:0.0:0.9288:0.0	.	390;442	O43934-2;O43934	.;MFS11_HUMAN	H	442;390	ENSP00000337240:R442H;ENSP00000348225:R390H	ENSP00000337240:R442H	R	+	2	0	MFSD11	72286004	1.000000	0.71417	0.997000	0.53966	0.306000	0.27790	6.767000	0.74975	2.885000	0.99019	0.655000	0.94253	CGC		0.507	MFSD11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451516.1	NM_024311	
WRAP53	55135	broad.mit.edu	37	17	7606672	7606672	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:7606672G>A	ENST00000316024.5	+	10	3863	c.1515G>A	c.(1513-1515)acG>acA	p.T505T	EFNB3_ENST00000226091.2_5'Flank|WRAP53_ENST00000396463.2_Silent_p.T505T|WRAP53_ENST00000534050.1_Silent_p.T472T|WRAP53_ENST00000457584.2_Silent_p.T505T|WRAP53_ENST00000431639.2_Silent_p.T505T			Q9BUR4	WAP53_HUMAN	WD repeat containing, antisense to TP53	505					positive regulation of telomerase activity (GO:0051973)|telomere formation via telomerase (GO:0032203)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	RNA binding (GO:0003723)	p.T505T(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(2)	18						TGCTCTCCACGCGCCACGTCC	0.647																																					p.T505T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1515A	17						.						81.0	64.0	69.0					17																	7606672		2203	4300	6503	7547397	SO:0001819	synonymous_variant	55135	exon11			AK001247, DQ431240	CCDS11119.1	17p13.1	2014-09-17	2009-02-16	2009-02-16	ENSG00000141499	ENSG00000141499		"""WD repeat domain containing"""	25522	protein-coding gene	gene with protein product	"""telomerase cajal body protein 1"", ""WD-encoding RNA antisense to p53"""	612661	"""WD repeat domain 79"""	WDR79		19179534, 19250907, 19571673, 19342896, 20494116, 21441950	Standard	NM_018081		Approved	FLJ10385, TCAB1	uc010vuh.2	Q9BUR4	OTTHUMG00000134323	ENST00000316024.5:c.1515G>A	17.37:g.7606672G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7547397	NM_001143990	B3KPR9|D3DTQ4|Q08ET9|Q9NW09	Silent	SNP	ENST00000316024.5	37	CCDS11119.1																																																																																				0.647	WRAP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259385.2	NM_018081	
CBX2	84733	broad.mit.edu	37	17	77757683	77757683	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:77757683C>T	ENST00000310942.4	+	5	545	c.441C>T	c.(439-441)gcC>gcT	p.A147A		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	147					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.A147A(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)			AGAAGAAGGCCCAGATCCTGG	0.612																																					p.A147A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C441T	17						.						47.0	46.0	46.0					17																	77757683		2198	4299	6497	75372278	SO:0001819	synonymous_variant	84733	exon5			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.441C>T	17.37:g.77757683C>T		Somatic		Capture	Illumina HiSeq	Phase_I	75372278	NM_005189	Q0VDA5|Q9BTB1	Silent	SNP	ENST00000310942.4	37	CCDS32757.1																																																																																				0.612	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
EIF4A3	9775	broad.mit.edu	37	17	78120593	78120593	+	Splice_Site	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:78120593G>A	ENST00000269349.3	-	1	389	c.168C>T	c.(166-168)taC>taT	p.Y56Y		NM_014740.3	NP_055555.1	P38919	IF4A3_HUMAN	eukaryotic translation initiation factor 4A3	56					ATP catabolic process (GO:0006200)|cytokine-mediated signaling pathway (GO:0019221)|embryonic cranial skeleton morphogenesis (GO:0048701)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|mRNA binding (GO:0003729)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)	p.Y56Y(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	10	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)			cccgcTCACCGTAAGCGTAGA	0.721																																					p.Y56Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C168T	17						.						22.0	23.0	23.0					17																	78120593		2199	4291	6490	75735188	SO:0001630	splice_region_variant	9775	exon1			BC004386	CCDS11767.1	17q25.3	2010-02-10	2010-02-10	2006-11-27		ENSG00000141543		"""DEAD-boxes"""	18683	protein-coding gene	gene with protein product		608546	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 48"", ""eukaryotic translation initiation factor 4A, isoform 3"""	DDX48		10623621, 14730019	Standard	NM_014740		Approved	KIAA0111, EIF4AIII	uc002jxs.3	P38919		ENST00000269349.3:c.169+1C>T	17.37:g.78120593G>A		Somatic		Capture	Illumina HiSeq	Phase_I	75735188	NM_014740	Q15033|Q6IBQ2|Q96A18	Silent	SNP	ENST00000269349.3	37	CCDS11767.1																																																																																				0.721	EIF4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437446.1	NM_014740	Silent
SLC26A11	284129	broad.mit.edu	37	17	78199683	78199683	+	Silent	SNP	G	G	A	rs138039526		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:78199683G>A	ENST00000361193.3	+	6	841	c.561G>A	c.(559-561)gtG>gtA	p.V187V	SLC26A11_ENST00000411502.3_Silent_p.V187V|SLC26A11_ENST00000546047.2_Silent_p.V187V|SLC26A11_ENST00000572725.1_Silent_p.V187V	NM_001166347.1|NM_173626.3	NP_001159819.1|NP_775897.3			solute carrier family 26 (anion exchanger), member 11									p.V187V(1)		central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	28	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TCCTGCAGGTGTACCACACCT	0.567																																					p.V187V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G561A	17						.	G	,,,	1,4405	2.1+/-5.4	0,1,2202	195.0	153.0	168.0		561,561,561,561	0.2	0.9	17	dbSNP_134	168	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC26A11	NM_001166347.1,NM_001166348.1,NM_001166349.1,NM_173626.3	,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,	187/607,187/607,187/607,187/607	78199683	1,13005	2203	4300	6503	75814278	SO:0001819	synonymous_variant	284129	exon5				CCDS11771.2	17q25	2013-07-18	2013-07-18		ENSG00000181045	ENSG00000181045		"""Solute carriers"""	14471	protein-coding gene	gene with protein product		610117	"""solute carrier family 26, member 11"""				Standard	NM_001166347		Approved		uc010dhv.2	Q86WA9	OTTHUMG00000133419	ENST00000361193.3:c.561G>A	17.37:g.78199683G>A		Somatic		Capture	Illumina HiSeq	Phase_I	75814278	NM_001166349		Silent	SNP	ENST00000361193.3	37	CCDS11771.2																																																																																				0.567	SLC26A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257281.1		
RNF213	57674	broad.mit.edu	37	17	78324112	78324112	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:78324112C>T	ENST00000582970.1	+	31	10243	c.10100C>T	c.(10099-10101)aCg>aTg	p.T3367M	RNF213_ENST00000336301.6_Missense_Mutation_p.T1440M|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.T3416M	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3367					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T3416M(1)|p.T1440M(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AACTGTTTAACGAATACAGCC	0.358																																					p.T3416M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C10247T	17						.						83.0	83.0	83.0					17																	78324112		2203	4300	6503	75938707	SO:0001583	missense	57674	exon32			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.10100C>T	17.37:g.78324112C>T	ENSP00000464087:p.Thr3367Met	Somatic		Capture	Illumina HiSeq	Phase_I	75938707	NM_020914	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	C	8.553	0.875968	0.17395	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.17528	2.27	5.0	-6.49	0.01890	.	1.476040	0.04054	N	0.305202	T	0.13713	0.0332	L	0.56769	1.78	0.09310	N	1	B	0.20550	0.046	B	0.11329	0.006	T	0.35599	-0.9782	10	0.49607	T	0.09	.	1.6788	0.02827	0.4489:0.1795:0.0845:0.287	.	1440	Q63HN8	RN213_HUMAN	M	3367;3416;1440	ENSP00000338218:T1440M	ENSP00000338218:T1440M	T	+	2	0	RNF213	75938707	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.207000	0.09384	-0.858000	0.04110	-0.122000	0.15005	ACG		0.358	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
RNF213	57674	broad.mit.edu	37	17	78341576	78341576	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:78341576C>T	ENST00000582970.1	+	43	12043	c.11900C>T	c.(11899-11901)aCg>aTg	p.T3967M	CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.T2040M|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.T4016M	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3967					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T2040M(1)|p.T4016M(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GACGTGAAGACGCACGGGCCT	0.592																																					p.T4016M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C12047T	17						.						73.0	67.0	69.0					17																	78341576		2203	4300	6503	75956171	SO:0001583	missense	57674	exon44			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.11900C>T	17.37:g.78341576C>T	ENSP00000464087:p.Thr3967Met	Somatic		Capture	Illumina HiSeq	Phase_I	75956171	NM_020914	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	C	12.15	1.852345	0.32699	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.25085	1.82	5.08	4.12	0.48240	.	0.169933	0.51477	N	0.000093	T	0.28995	0.0720	M	0.65975	2.015	0.28951	N	0.890382	P;B	0.48294	0.908;0.369	B;B	0.41666	0.363;0.054	T	0.30179	-0.9987	10	0.87932	D	0	.	11.7927	0.52078	0.0:0.9173:0.0:0.0827	.	4016;2040	C9JCP4;Q63HN8	.;RN213_HUMAN	M	3967;4016;2040	ENSP00000338218:T2040M	ENSP00000338218:T2040M	T	+	2	0	RNF213	75956171	0.018000	0.18449	0.777000	0.31699	0.569000	0.35902	0.147000	0.16202	1.150000	0.42419	-0.122000	0.15005	ACG		0.592	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
RNF213	57674	broad.mit.edu	37	17	78360131	78360131	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:78360131G>A	ENST00000582970.1	+	62	14764	c.14621G>A	c.(14620-14622)cGg>cAg	p.R4874Q	RNF213_ENST00000427003.3_3'UTR|CTD-2047H16.4_ENST00000573394.1_RNA|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.R2947Q|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.R4923Q	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4874					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R2947Q(1)|p.R4923Q(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CCACGCCGACGGGGCCTGGGC	0.507																																					p.R4923Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G14768A	17						.						139.0	119.0	126.0					17																	78360131		2203	4300	6503	75974726	SO:0001583	missense	57674	exon63			AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.14621G>A	17.37:g.78360131G>A	ENSP00000464087:p.Arg4874Gln	Somatic		Capture	Illumina HiSeq	Phase_I	75974726	NM_020914	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	g	0.160	-1.082110	0.01888	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301;ENST00000427003	T	0.21361	2.01	4.92	-0.984	0.10259	.	0.576582	0.17621	N	0.167711	T	0.07999	0.0200	N	0.11201	0.11	0.21499	N	0.999669	B	0.22480	0.07	B	0.08055	0.003	T	0.39272	-0.9622	10	0.05833	T	0.94	.	10.7823	0.46384	0.5687:0.0:0.4313:0.0	.	2947	Q63HN8	RN213_HUMAN	Q	4874;4923;2947;224	ENSP00000338218:R2947Q	ENSP00000338218:R2947Q	R	+	2	0	RNF213	75974726	0.486000	0.25980	0.045000	0.18777	0.062000	0.15995	0.160000	0.16462	-0.470000	0.06901	-0.226000	0.12346	CGG		0.507	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
CHD3	1107	broad.mit.edu	37	17	7802694	7802694	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:7802694C>A	ENST00000330494.7	+	15	2527	c.2377C>A	c.(2377-2379)Cca>Aca	p.P793T	CHD3_ENST00000380358.4_Missense_Mutation_p.P852T|CHD3_ENST00000358181.4_Missense_Mutation_p.P793T	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	793	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.P793T(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				GGTGAGTGCCCCACTCTCTAC	0.557																																					p.P793T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2377A	17						.						114.0	111.0	112.0					17																	7802694		2203	4300	6503	7743419	SO:0001583	missense	1107	exon15			U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"""Zinc fingers, PHD-type"""	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.2377C>A	17.37:g.7802694C>A	ENSP00000332628:p.Pro793Thr	Somatic		Capture	Illumina HiSeq	Phase_I	7743419	NM_005852	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	37	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	C	16.38	3.107871	0.56291	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	D;D;D	0.97976	-4.64;-4.64;-4.64	5.06	5.06	0.68205	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.45606	D	0.000358	D	0.99333	0.9766	H	0.98682	4.3	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.98438	1.0585	10	0.87932	D	0	-12.2857	19.0357	0.92976	0.0:1.0:0.0:0.0	.	793;793;852	Q12873-2;Q12873;E9PG89	.;CHD3_HUMAN;.	T	852;793;793	ENSP00000369716:P852T;ENSP00000350907:P793T;ENSP00000332628:P793T	ENSP00000332628:P793T	P	+	1	0	CHD3	7743419	1.000000	0.71417	0.968000	0.41197	0.988000	0.76386	7.651000	0.83577	2.809000	0.96659	0.555000	0.69702	CCA		0.557	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273	
P4HB	5034	broad.mit.edu	37	17	79817149	79817149	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:79817149T>A	ENST00000331483.4	-	2	482	c.260A>T	c.(259-261)gAg>gTg	p.E87V	P4HB_ENST00000576390.1_Intron|P4HB_ENST00000472244.1_5'Flank|P4HB_ENST00000439918.2_Missense_Mutation_p.E87V	NM_000918.3	NP_000909.2	P07237	PDIA1_HUMAN	prolyl 4-hydroxylase, beta polypeptide	87	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|protein folding (GO:0006457)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|procollagen-proline 4-dioxygenase complex (GO:0016222)	poly(A) RNA binding (GO:0044822)|procollagen-proline 4-dioxygenase activity (GO:0004656)|protein disulfide isomerase activity (GO:0003756)	p.E87V(1)		NS(1)|breast(1)|large_intestine(2)|lung(17)|urinary_tract(1)	22	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.013)|OV - Ovarian serous cystadenocarcinoma(97;0.0509)			CAGGTCAGACTCCTCCGTGGC	0.602																																					p.E87V	Colon(49;444 983 1296 7887 42561)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A260T	17						.						168.0	151.0	157.0					17																	79817149		2203	4297	6500	77410438	SO:0001583	missense	5034	exon2			J02783	CCDS11787.1	17q25	2011-10-19	2008-12-09		ENSG00000185624	ENSG00000185624	1.14.11.2, 5.3.4.1	"""Protein disulfide isomerases"""	8548	protein-coding gene	gene with protein product	"""protein disulfide isomerase-associated 1"", ""protein disulfide isomerase family A, member 1"", ""collagen prolyl 4-hydroxylase beta"""	176790	"""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase; thyroid hormone binding protein p55)"", ""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase-associated 1)"", ""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide"""	PO4DB, ERBA2L		8111381	Standard	NM_000918		Approved	PDIA1, PROHB, DSI, GIT, PDI, PO4HB, P4Hbeta	uc002kbn.1	P07237	OTTHUMG00000150269	ENST00000331483.4:c.260A>T	17.37:g.79817149T>A	ENSP00000327801:p.Glu87Val	Somatic		Capture	Illumina HiSeq	Phase_I	77410438	NM_000918	B2RDQ2|P30037|P32079|Q15205|Q6LDE5	Missense_Mutation	SNP	ENST00000331483.4	37	CCDS11787.1	.	.	.	.	.	.	.	.	.	.	T	19.64	3.865439	0.71949	.	.	ENSG00000185624	ENST00000331483;ENST00000537205;ENST00000436463	T	0.03413	3.94	4.77	4.77	0.60923	Thioredoxin domain (1);Thioredoxin-like fold (3);Disulphide isomerase (1);	0.120766	0.56097	D	0.000039	T	0.16685	0.0401	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00282	-1.1850	10	0.87932	D	0	.	13.9875	0.64345	0.0:0.0:0.0:1.0	.	87	P07237	PDIA1_HUMAN	V	87;87;71	ENSP00000327801:E87V	ENSP00000327801:E87V	E	-	2	0	P4HB	77410438	1.000000	0.71417	0.991000	0.47740	0.076000	0.17211	7.768000	0.85345	1.796000	0.52611	0.460000	0.39030	GAG		0.602	P4HB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317250.3	NM_000918	
NOTUM	147111	broad.mit.edu	37	17	79911110	79911110	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:79911110C>T	ENST00000409678.3	-	11	1601	c.1218G>A	c.(1216-1218)tcG>tcA	p.S406S		NM_178493.5	NP_848588.3	Q6P988	NOTUM_HUMAN	notum pectinacetylesterase homolog (Drosophila)	406						extracellular region (GO:0005576)	hydrolase activity (GO:0016787)	p.S340S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	15	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			CTCGGGGCAGCGACGTCCCCT	0.637																																					p.S406S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1218A	17						.						16.0	17.0	17.0					17																	79911110		2200	4296	6496	77504400	SO:0001819	synonymous_variant	147111	exon11			BC060882	CCDS32771.2	17q25.3	2008-02-05			ENSG00000185269	ENSG00000185269			27106	protein-coding gene	gene with protein product		609847					Standard	NM_178493		Approved		uc010wvg.2	Q6P988	OTTHUMG00000154416	ENST00000409678.3:c.1218G>A	17.37:g.79911110C>T		Somatic		Capture	Illumina HiSeq	Phase_I	77504400	NM_178493	Q8N410|Q8NI82	Silent	SNP	ENST00000409678.3	37	CCDS32771.2																																																																																				0.637	NOTUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335123.2	NM_178493	
CNTROB	116840	broad.mit.edu	37	17	7837492	7837492	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:7837492C>T	ENST00000563694.1	+	2	1232	c.307C>T	c.(307-309)Cgg>Tgg	p.R103W	TRAPPC1_ENST00000303731.4_5'Flank|CNTROB_ENST00000380262.3_Missense_Mutation_p.R103W|CNTROB_ENST00000565740.1_Missense_Mutation_p.R103W|TRAPPC1_ENST00000540486.1_5'Flank|CNTROB_ENST00000380255.3_Missense_Mutation_p.R103W	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	103					centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)	p.R103W(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				GGAAAGTGTTCGGGGTCAGCT	0.468																																					p.R103W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C307T	17						.						168.0	150.0	156.0					17																	7837492		2203	4300	6503	7778217	SO:0001583	missense	116840	exon2			AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"""centrobin"""	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.307C>T	17.37:g.7837492C>T	ENSP00000456335:p.Arg103Trp	Somatic		Capture	Illumina HiSeq	Phase_I	7778217	NM_053051	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Missense_Mutation	SNP	ENST00000563694.1	37	CCDS11126.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.200008	0.79015	.	.	ENSG00000170037	ENST00000380262;ENST00000380255	T;T	0.74526	-0.23;-0.85	5.48	3.46	0.39613	.	0.000000	0.56097	D	0.000030	T	0.77948	0.4207	L	0.29908	0.895	0.37199	D	0.904281	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.996	T	0.81457	-0.0924	10	0.87932	D	0	-27.315	12.2684	0.54691	0.3093:0.6907:0.0:0.0	.	103;103;103	Q8N137-3;Q8N137;Q8N137-2	.;CNTRB_HUMAN;.	W	103	ENSP00000369614:R103W;ENSP00000369605:R103W	ENSP00000369605:R103W	R	+	1	2	CNTROB	7778217	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.890000	0.28295	0.664000	0.31047	0.655000	0.94253	CGG		0.468	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051	
FASN	2194	broad.mit.edu	37	17	80041086	80041086	+	Missense_Mutation	SNP	C	C	T	rs527759350		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:80041086C>T	ENST00000306749.2	-	32	5775	c.5557G>A	c.(5557-5559)Gtc>Atc	p.V1853I	FASN_ENST00000579758.1_5'UTR	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1853	Enoyl reductase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.V1853I(1)		central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	ACCTGCACGACGACTTTGCCA	0.672													.|||	1	0.000199681	0.0008	0.0	5008	,	,		15266	0.0		0.0	False		,,,				2504	0.0				p.V1853I	Colon(59;314 1043 11189 28578 32273)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5557A	17						.						82.0	74.0	77.0					17																	80041086		2203	4300	6503	77634375	SO:0001583	missense	2194	exon32			U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	3594	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 27X, member 1"""	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.5557G>A	17.37:g.80041086C>T	ENSP00000304592:p.Val1853Ile	Somatic		Capture	Illumina HiSeq	Phase_I	77634375	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	37	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	2.909	-0.225860	0.06022	.	.	ENSG00000169710	ENST00000306749	T	0.39592	1.07	4.25	1.11	0.20524	Polyketide synthase, enoylreductase (1);	0.451537	0.21554	N	0.072691	T	0.37732	0.1014	M	0.66939	2.045	0.19300	N	0.999977	B	0.20261	0.043	B	0.17098	0.017	T	0.30765	-0.9967	10	0.48119	T	0.1	-33.1796	8.4703	0.32982	0.0:0.4195:0.4084:0.1721	.	1853	P49327	FAS_HUMAN	I	1853	ENSP00000304592:V1853I	ENSP00000304592:V1853I	V	-	1	0	FASN	77634375	0.000000	0.05858	0.034000	0.17996	0.003000	0.03518	-0.454000	0.06770	-0.142000	0.11354	-1.268000	0.01426	GTC		0.672	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
CSNK1D	1453	broad.mit.edu	37	17	80210978	80210978	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:80210978C>G	ENST00000314028.6	-	4	828	c.479G>C	c.(478-480)cGc>cCc	p.R160P	CSNK1D_ENST00000578904.1_5'UTR|CSNK1D_ENST00000398519.5_Missense_Mutation_p.R160P|CSNK1D_ENST00000392334.2_Missense_Mutation_p.R160P	NM_001893.4	NP_001884.2	P48730	KC1D_HUMAN	casein kinase 1, delta	160	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|signal transduction (GO:0007165)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle (GO:0005819)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)	p.R160P(1)		breast(2)|large_intestine(2)|lung(7)	11	Breast(20;0.00136)|all_neural(118;0.0804)|Lung NSC(278;0.128)|all_lung(278;0.145)|Ovarian(332;0.227)		OV - Ovarian serous cystadenocarcinoma(97;0.00463)|BRCA - Breast invasive adenocarcinoma(99;0.0155)			CTGGTGGGTGCGTGCATCCCG	0.602																																					p.R160P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G479C	17						.						299.0	217.0	245.0					17																	80210978		2203	4300	6503	77804267	SO:0001583	missense	1453	exon4				CCDS11805.1, CCDS11806.1	17q25	2013-01-17				ENSG00000141551			2452	protein-coding gene	gene with protein product		600864				7797465	Standard	NM_001893		Approved	HCKID, CKID, CKIdelta	uc002kej.3	P48730		ENST00000314028.6:c.479G>C	17.37:g.80210978C>G	ENSP00000324464:p.Arg160Pro	Somatic		Capture	Illumina HiSeq	Phase_I	77804267	NM_139062	A2I2P2|Q96KZ6|Q9BTN5	Missense_Mutation	SNP	ENST00000314028.6	37	CCDS11805.1	.	.	.	.	.	.	.	.	.	.	C	13.04	2.116948	0.37339	.	.	ENSG00000141551	ENST00000314028;ENST00000392334;ENST00000398519;ENST00000269361	T;T	0.06608	3.28;3.28	5.55	4.55	0.56014	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.049463	0.64402	D	0.000003	T	0.29158	0.0725	M	0.87097	2.86	0.58432	D	0.999999	D;D;D	0.76494	0.983;0.982;0.999	P;P;D	0.70935	0.85;0.855;0.971	T	0.20338	-1.0278	10	0.87932	D	0	.	15.265	0.73654	0.0:0.8593:0.1407:0.0	.	160;160;103	P48730;P48730-2;B4E0G1	KC1D_HUMAN;.;.	P	160;160;103;52	ENSP00000324464:R160P;ENSP00000376146:R160P	ENSP00000269361:R52P	R	-	2	0	CSNK1D	77804267	1.000000	0.71417	0.043000	0.18650	0.651000	0.38670	7.755000	0.85180	1.292000	0.44672	0.655000	0.94253	CGC		0.602	CSNK1D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442632.1	NM_139062	
GUCY2D	3000	broad.mit.edu	37	17	7907241	7907241	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:7907241G>A	ENST00000254854.4	+	3	943	c.793G>A	c.(793-795)Gag>Aag	p.E265K		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	265					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)	p.E265K(1)		skin(1)	1		Prostate(122;0.157)				GGCCGCAGAGGAGCTGGGCCT	0.677																																					p.E265K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G793A	17						.						84.0	78.0	80.0					17																	7907241		2203	4300	6503	7847966	SO:0001583	missense	3000	exon3			L26921	CCDS11127.1	17p13.1	2013-06-06			ENSG00000132518	ENSG00000132518			4689	protein-coding gene	gene with protein product		600179	"""cone rod dystrophy 6"""	CORD6, LCA, GUC2D, GUC1A4		1356371, 12552567	Standard	NM_000180		Approved	retGC, RETGC-1, ROS-GC1, CYGD, LCA1	uc002gjt.2	Q02846	OTTHUMG00000108169	ENST00000254854.4:c.793G>A	17.37:g.7907241G>A	ENSP00000254854:p.Glu265Lys	Somatic		Capture	Illumina HiSeq	Phase_I	7847966	NM_000180	Q6LEA7	Missense_Mutation	SNP	ENST00000254854.4	37	CCDS11127.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.847206	0.71603	.	.	ENSG00000132518	ENST00000254854	T	0.75260	-0.92	4.77	3.81	0.43845	Extracellular ligand-binding receptor (1);	0.136488	0.33290	N	0.005074	T	0.73636	0.3612	M	0.68593	2.085	0.38184	D	0.939699	B	0.32324	0.364	B	0.39465	0.3	T	0.72581	-0.4250	10	0.28530	T	0.3	.	11.7518	0.51853	0.0864:0.0:0.9136:0.0	.	265	Q02846	GUC2D_HUMAN	K	265	ENSP00000254854:E265K	ENSP00000254854:E265K	E	+	1	0	GUCY2D	7847966	1.000000	0.71417	0.925000	0.36789	0.758000	0.43043	4.944000	0.63561	1.238000	0.43771	0.561000	0.74099	GAG		0.677	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2		
RANGRF	29098	broad.mit.edu	37	17	8193299	8193299	+	3'UTR	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:8193299G>A	ENST00000226105.6	+	0	898				SLC25A35_ENST00000581320.1_5'Flank|SLC25A35_ENST00000580340.1_Nonsense_Mutation_p.R245*|RANGRF_ENST00000407006.4_3'UTR|SLC25A35_ENST00000396278.1_Missense_Mutation_p.P270L|RANGRF_ENST00000439238.3_3'UTR|SLC25A35_ENST00000380067.2_Nonsense_Mutation_p.R245*|RANGRF_ENST00000580434.1_3'UTR|SLC25A35_ENST00000579192.1_Nonsense_Mutation_p.R245*	NM_016492.4	NP_057576.2	Q9HD47	MOG1_HUMAN	RAN guanine nucleotide release factor						ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein localization to cell surface (GO:2000010)|protein exit from endoplasmic reticulum (GO:0032527)|regulation of heart rate (GO:0002027)|regulation of membrane depolarization (GO:0003254)|regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900825)|regulation of membrane potential (GO:0042391)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	guanyl-nucleotide exchange factor activity (GO:0005085)|ion channel binding (GO:0044325)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)|sodium channel regulator activity (GO:0017080)	p.R245*(1)		endometrium(1)	1						TTGGGGACTCGGTTCTGTGAG	0.463																																					p.R245X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C733T	17						.						126.0	131.0	129.0					17																	8193299		2203	4299	6502	8134024	SO:0001624	3_prime_UTR_variant	399512	exon5			AF151070	CCDS11137.1, CCDS54086.1, CCDS54087.1	17p13	2014-05-09				ENSG00000108961			17679	protein-coding gene	gene with protein product	"""MOG1 homolog (S. cerevisiae)"""	607954				11290418	Standard	NM_016492		Approved	MOG1, HSPC165, HSPC236, RANGNRF	uc002gkv.3	Q9HD47		ENST00000226105.6:c.*45G>A	17.37:g.8193299G>A		Somatic		Capture	Illumina HiSeq	Phase_I	8134024	NM_201520	D3DTR6|Q68DI3|Q9BR68|Q9HD48|Q9NRU9|Q9P001|Q9P0P2	Nonsense_Mutation	SNP	ENST00000226105.6	37	CCDS11137.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.822|0.822	-0.748324|-0.748324	0.03065|0.03065	.|.	.|.	ENSG00000125434|ENSG00000125434	ENST00000396278|ENST00000380067	T|.	0.75589|.	-0.95|.	4.72|4.72	-9.43|-9.43	0.00607|0.00607	.|.	.|1.825500	.|0.02842	.|N	.|0.128102	T|.	0.13415|.	0.0325|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.13072|.	-1.0523|.	6|.	0.28530|0.15499	T|T	0.3|0.54	.|.	2.3731|2.3731	0.04335|0.04335	0.1198:0.3921:0.2326:0.2555|0.1198:0.3921:0.2326:0.2555	.|.	.|.	.|.	.|.	L|X	270|245	ENSP00000379574:P270L|.	ENSP00000379574:P270L|ENSP00000369407:R245X	P|R	-|-	2|1	0|2	SLC25A35|SLC25A35	8134024|8134024	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.044000|0.044000	0.14063|0.14063	-1.674000|-1.674000	0.01949|0.01949	-2.266000|-2.266000	0.00687|0.00687	-0.320000|-0.320000	0.08662|0.08662	CCG|CGA		0.463	RANGRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442127.1	NM_016492	
KRBA2	124751	broad.mit.edu	37	17	8273378	8273378	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:8273378G>A	ENST00000331336.2	-	2	558	c.553C>T	c.(553-555)Cgg>Tgg	p.R185W	RP11-849F2.7_ENST00000582471.1_3'UTR|RP11-849F2.5_ENST00000580537.1_RNA|RP11-849F2.5_ENST00000583963.1_RNA|KRBA2_ENST00000396267.1_Missense_Mutation_p.R103W	NM_213597.2	NP_998762.1	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	185					DNA integration (GO:0015074)|regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)	p.R185W(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(5)|stomach(1)|urinary_tract(1)	18						ACATAATACCGTATTCGATCA	0.448																																					p.R185W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C553T	17						.						197.0	178.0	185.0					17																	8273378		2203	4300	6503	8214103	SO:0001583	missense	124751	exon2			BC024723	CCDS11141.1	17p13.1	2013-01-08	2006-08-15		ENSG00000184619	ENSG00000184619		"""-"""	26989	protein-coding gene	gene with protein product			"""KRAB A domain containing 2"""			12477932	Standard	NM_213597		Approved		uc002glf.1	Q6ZNG9	OTTHUMG00000132864	ENST00000331336.2:c.553C>T	17.37:g.8273378G>A	ENSP00000328017:p.Arg185Trp	Somatic		Capture	Illumina HiSeq	Phase_I	8214103	NM_213597	Q8IYY0	Missense_Mutation	SNP	ENST00000331336.2	37	CCDS11141.1	.	.	.	.	.	.	.	.	.	.	G	6.582	0.475632	0.12521	.	.	ENSG00000184619	ENST00000396267;ENST00000331336	T;T	0.27104	1.69;1.74	2.42	-1.86	0.07760	.	.	.	.	.	T	0.15176	0.0366	L	0.40543	1.245	0.09310	N	1	P	0.46859	0.885	B	0.35039	0.194	T	0.13899	-1.0492	9	0.87932	D	0	.	6.1576	0.20346	0.589:0.0:0.411:0.0	.	185	Q6ZNG9	KRBA2_HUMAN	W	103;185	ENSP00000379565:R103W;ENSP00000328017:R185W	ENSP00000328017:R185W	R	-	1	2	KRBA2	8214103	0.000000	0.05858	0.044000	0.18714	0.599000	0.36880	-0.388000	0.07352	-0.436000	0.07254	-0.266000	0.10368	CGG		0.448	KRBA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256338.1	NM_213597	
KRBA2	124751	broad.mit.edu	37	17	8273550	8273550	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:8273550G>A	ENST00000331336.2	-	2	386	c.381C>T	c.(379-381)agC>agT	p.S127S	RP11-849F2.7_ENST00000582471.1_3'UTR|RP11-849F2.5_ENST00000580537.1_RNA|RP11-849F2.5_ENST00000583963.1_RNA|KRBA2_ENST00000396267.1_Silent_p.S45S	NM_213597.2	NP_998762.1	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	127					DNA integration (GO:0015074)|regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)	p.S127S(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(5)|stomach(1)|urinary_tract(1)	18						AAAATACCTTGCTGTTGTAAC	0.343																																					p.S127S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C381T	17						.						117.0	113.0	115.0					17																	8273550		2203	4300	6503	8214275	SO:0001819	synonymous_variant	124751	exon2			BC024723	CCDS11141.1	17p13.1	2013-01-08	2006-08-15		ENSG00000184619	ENSG00000184619		"""-"""	26989	protein-coding gene	gene with protein product			"""KRAB A domain containing 2"""			12477932	Standard	NM_213597		Approved		uc002glf.1	Q6ZNG9	OTTHUMG00000132864	ENST00000331336.2:c.381C>T	17.37:g.8273550G>A		Somatic		Capture	Illumina HiSeq	Phase_I	8214275	NM_213597	Q8IYY0	Silent	SNP	ENST00000331336.2	37	CCDS11141.1																																																																																				0.343	KRBA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256338.1	NM_213597	
USP43	124739	broad.mit.edu	37	17	9546427	9546427	+	5'Flank	SNP	G	G	A	rs566597331		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:9546427G>A	ENST00000285199.7	+	0	0				RP11-55L4.2_ENST00000584676.1_RNA|WDR16_ENST00000396219.3_Missense_Mutation_p.R524H|WDR16_ENST00000299764.5_Missense_Mutation_p.R602H|USP43_ENST00000570475.1_5'Flank|WDR16_ENST00000352665.5_Missense_Mutation_p.R592H	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43						ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.R592H(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						AACATCACACGCATCCGCATA	0.443													G|||	1	0.000199681	0.0	0.0	5008	,	,		18265	0.0		0.0	False		,,,				2504	0.001				p.R592H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1775A	17						.						158.0	138.0	145.0					17																	9546427		2203	4300	6503	9487152	SO:0001631	upstream_gene_variant	146845	exon14			AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"""Ubiquitin-specific peptidases"""	20072	protein-coding gene	gene with protein product			"""ubiquitin specific protease 43"""			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4			17.37:g.9546427G>A	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	9487152	NM_145054	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Missense_Mutation	SNP	ENST00000285199.7	37	CCDS45610.1	.	.	.	.	.	.	.	.	.	.	G	11.00	1.511481	0.27036	.	.	ENSG00000166596	ENST00000352665;ENST00000396219;ENST00000299764	T;T;T	0.59772	0.24;0.24;0.24	5.88	4.9	0.64082	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.453231	0.28606	N	0.014756	T	0.47303	0.1438	N	0.25426	0.745	0.09310	N	1	B;B;B	0.21753	0.06;0.042;0.03	B;B;B	0.19946	0.023;0.023;0.027	T	0.43376	-0.9395	10	0.49607	T	0.09	-6.1704	16.2072	0.82135	0.0:0.1332:0.8668:0.0	.	602;524;592	Q8N1V2-2;Q8N1V2-3;Q8N1V2	.;.;WDR16_HUMAN	H	592;524;602	ENSP00000339449:R592H;ENSP00000379521:R524H;ENSP00000299764:R602H	ENSP00000299764:R602H	R	+	2	0	WDR16	9487152	0.983000	0.35010	0.003000	0.11579	0.160000	0.22226	6.230000	0.72301	1.462000	0.47948	0.655000	0.94253	CGC		0.443	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210	
RCVRN	5957	broad.mit.edu	37	17	9804370	9804370	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:9804370G>A	ENST00000226193.5	-	2	869	c.429C>T	c.(427-429)gaC>gaT	p.D143D	RCVRN_ENST00000570909.3_5'UTR	NM_002903.2	NP_002894.1	P35243	RECO_HUMAN	recoverin	143					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.D143D(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	12						TGTTTTCATCGTCTGGAAGGA	0.438																																					p.D143D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C429T	17						.						105.0	99.0	101.0					17																	9804370		2203	4300	6503	9745095	SO:0001819	synonymous_variant	5957	exon2			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.429C>T	17.37:g.9804370G>A		Somatic		Capture	Illumina HiSeq	Phase_I	9745095	NM_002903	Q53XL0	Silent	SNP	ENST00000226193.5	37	CCDS11151.1																																																																																				0.438	RCVRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252600.2	NM_002903	
WNK4	65266	broad.mit.edu	37	17	40939448	40939449	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	TG	TG	TG	-	TG	TG	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:40939448_40939449delTG	ENST00000246914.5	+	7	1650_1651	c.1629_1630delTG	c.(1627-1632)actgtgfs	p.V544fs	WNK4_ENST00000587705.1_3'UTR	NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	544					chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)	p.V532fs*13(1)|p.V544fs*13(1)		NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		CACCAGCAACTGTGCCCATGGC	0.629																																					p.543_544del	Esophageal Squamous(6;201 374 4964 23855 42828)											.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1629_1630del	17						.																																			38192975	SO:0001589	frameshift_variant	65266	exon7			AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"""protein kinase, lysine deficient 4"""	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.1629_1630delTG	17.37:g.40939450_40939451delTG	ENSP00000246914:p.Val544fs	Somatic		Capture	Illumina HiSeq	Phase_I	38192974	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Frame_Shift_Del	DEL	ENST00000246914.5	37	CCDS11439.1																																																																																				0.629	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1		
TSPAN10	83882	broad.mit.edu	37	17	79612317	79612317	+	RNA	DEL	G	G	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:79612317delG	ENST00000572675.1	+	0	336				TSPAN10_ENST00000328585.4_RNA			Q9H1Z9	TSN10_HUMAN	tetraspanin 10						establishment of protein localization to organelle (GO:0072594)	integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)	p.L116fs*19(1)		ovary(1)	1	all_neural(118;0.0878)|all_lung(278;0.175)|Lung NSC(278;0.192)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			GAAGTGATCTGGGGGGGCCCC	0.682																																					p.L112fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.336delG	17						.						25.0	30.0	29.0					17																	79612317		1895	4104	5999	77222722			83882	exon2			BC032802		17q25.3	2013-10-02			ENSG00000182612	ENSG00000182612		"""Tetraspanins"""	29942	protein-coding gene	gene with protein product	"""oculospanin"""					12107410	Standard	NM_031945		Approved	OCSP	uc010die.3	Q9H1Z9	OTTHUMG00000178037		17.37:g.79612317delG		Somatic		Capture	Illumina HiSeq	Phase_I	77222722	NM_031945	Q8N548	Frame_Shift_Del	DEL	ENST00000572675.1	37																																																																																					0.682	TSPAN10-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000440313.1	NM_031945	
FOXK2	3607	broad.mit.edu	37	17	80540697	80540697	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr17:80540697G>A	ENST00000335255.5	+	5	1164	c.990G>A	c.(988-990)tcG>tcA	p.S330S	snoU13_ENST00000459591.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	330	DNA-binding; minor groove.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S330S(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			GCAAAGGCTCGTTCTGGAGGA	0.463																																					p.S330S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G990A	17						.						59.0	60.0	60.0					17																	80540697		2203	4300	6503	78133986	SO:0001819	synonymous_variant	3607	exon5			U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"""Forkhead boxes"""	6036	protein-coding gene	gene with protein product		147685	"""interleukin enhancer binding factor 1"""	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.990G>A	17.37:g.80540697G>A		Somatic		Capture	Illumina HiSeq	Phase_I	78133986	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Silent	SNP	ENST00000335255.5	37	CCDS11813.1																																																																																				0.463	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430	
MC5R	4161	broad.mit.edu	37	18	13826537	13826537	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:13826537T>C	ENST00000324750.3	+	1	995	c.773T>C	c.(772-774)cTc>cCc	p.L258P	AP001525.1_ENST00000390194.2_RNA	NM_005913.2	NP_005904.1	P33032	MC5R_HUMAN	melanocortin 5 receptor	258					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hormone binding (GO:0042562)|melanocortin receptor activity (GO:0004977)	p.L258P(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|upper_aerodigestive_tract(1)	41						TTCCTTCATCTCACTTTAATG	0.542																																					p.L258P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T773C	18						.						233.0	183.0	200.0					18																	13826537		2203	4300	6503	13816537	SO:0001583	missense	4161	exon1			AY268429	CCDS11868.1	18p11.2	2012-08-10			ENSG00000176136	ENSG00000176136		"""GPCR / Class A : Melanocortin receptors"""	6933	protein-coding gene	gene with protein product		600042				8396929	Standard	NM_005913		Approved		uc010xaf.2	P33032	OTTHUMG00000131720	ENST00000324750.3:c.773T>C	18.37:g.13826537T>C	ENSP00000318077:p.Leu258Pro	Somatic		Capture	Illumina HiSeq	Phase_I	13816537	NM_005913	B0YJ34|Q502V1	Missense_Mutation	SNP	ENST00000324750.3	37	CCDS11868.1	.	.	.	.	.	.	.	.	.	.	T	14.20	2.464682	0.43736	.	.	ENSG00000176136	ENST00000324750	T	0.39787	1.06	4.88	4.88	0.63580	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.75287	0.3829	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84080	0.0384	10	0.87932	D	0	.	13.6551	0.62333	0.0:0.0:0.0:1.0	.	258	P33032	MC5R_HUMAN	P	258	ENSP00000318077:L258P	ENSP00000318077:L258P	L	+	2	0	MC5R	13816537	1.000000	0.71417	0.739000	0.30968	0.095000	0.18619	5.920000	0.70017	1.821000	0.53095	0.254000	0.18369	CTC		0.542	MC5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254638.1	NM_005913	
ROCK1	6093	broad.mit.edu	37	18	18566985	18566985	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:18566985G>T	ENST00000399799.2	-	19	3170	c.2230C>A	c.(2230-2232)Cta>Ata	p.L744I		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	744	Glu-rich.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L744I(2)		NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					TCAACGTCTAGCATGGAACAC	0.383																																					p.L744I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2230A	18						.						154.0	140.0	145.0					18																	18566985		2203	4300	6503	16820983	SO:0001583	missense	6093	exon19				CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.2230C>A	18.37:g.18566985G>T	ENSP00000382697:p.Leu744Ile	Somatic		Capture	Illumina HiSeq	Phase_I	16820983	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	37	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	G	20.9	4.070696	0.76301	.	.	ENSG00000067900	ENST00000399799	T	0.70986	-0.53	5.32	2.54	0.30619	.	0.000000	0.64402	D	0.000001	T	0.80798	0.4692	M	0.78223	2.4	0.49582	D	0.999802	D	0.76494	0.999	D	0.65987	0.94	T	0.81667	-0.0829	10	0.87932	D	0	.	10.2144	0.43160	0.2922:0.0:0.7078:0.0	.	744	Q13464	ROCK1_HUMAN	I	744	ENSP00000382697:L744I	ENSP00000382697:L744I	L	-	1	2	ROCK1	16820983	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.174000	0.31932	0.820000	0.34516	-0.218000	0.12543	CTA		0.383	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406	
GATA6	2627	broad.mit.edu	37	18	19761423	19761423	+	Missense_Mutation	SNP	C	C	T	rs144512170		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:19761423C>T	ENST00000269216.3	+	4	1589	c.1312C>T	c.(1312-1314)Cgg>Tgg	p.R438W	GATA6_ENST00000581694.1_Missense_Mutation_p.R438W|RNU6-702P_ENST00000364982.1_RNA	NM_005257.4	NP_005248.2	Q92908	GATA6_HUMAN	GATA binding protein 6	438					blood coagulation (GO:0007596)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cellular response to BMP stimulus (GO:0071773)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to hypoxia (GO:0071456)|Clara cell differentiation (GO:0060486)|endodermal cell fate determination (GO:0007493)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|liver development (GO:0001889)|lung saccule development (GO:0060430)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|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 beta1 production (GO:0032911)|negative regulation of transforming growth factor beta2 production (GO:0032912)|organ formation (GO:0048645)|outflow tract septum morphogenesis (GO:0003148)|pancreatic A cell differentiation (GO:0003310)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to growth factor (GO:0070848)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)|tube morphogenesis (GO:0035239)|type B pancreatic cell differentiation (GO:0003309)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.R438W(1)		NS(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	18	all_cancers(21;0.00271)|all_epithelial(16;7.31e-05)|Ovarian(2;0.116)|Lung NSC(20;0.123)|all_lung(20;0.246)		STAD - Stomach adenocarcinoma(5;0.106)			GCCTTCATCACGGCGGCTTGG	0.428																																					p.R438W	Colon(8;48 282 46199 46856)|Melanoma(177;170 2725 12489 26999)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1312T	18						.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	108.0	100.0	103.0		1312	3.1	1.0	18	dbSNP_134	103	0,8600		0,0,4300	no	missense	GATA6	NM_005257.3	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	438/596	19761423	1,13005	2203	4300	6503	18015421	SO:0001583	missense	2627	exon4			U66075	CCDS11872.1	18q11-q12	2013-01-25	2001-11-28		ENSG00000141448	ENSG00000141448		"""GATA zinc finger domain containing"""	4174	protein-coding gene	gene with protein product		601656	"""GATA-binding protein 6"""			8975704	Standard	XM_005258248		Approved		uc002ktt.2	Q92908	OTTHUMG00000131767	ENST00000269216.3:c.1312C>T	18.37:g.19761423C>T	ENSP00000269216:p.Arg438Trp	Somatic		Capture	Illumina HiSeq	Phase_I	18015421	NM_005257	B0YJ17|P78327	Missense_Mutation	SNP	ENST00000269216.3	37	CCDS11872.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.554534	0.65425	2.27E-4	0.0	ENSG00000141448	ENST00000269216	D	0.99683	-6.39	5.87	3.07	0.35406	Zinc finger, NHR/GATA-type (1);Zinc finger, GATA-type (3);	0.000000	0.85682	D	0.000000	D	0.99708	0.9888	H	0.94734	3.575	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	D	0.98713	1.0705	10	0.87932	D	0	-9.0245	8.9699	0.35899	0.3809:0.5543:0.0:0.0648	.	438	Q92908	GATA6_HUMAN	W	438	ENSP00000269216:R438W	ENSP00000269216:R438W	R	+	1	2	GATA6	18015421	0.056000	0.20664	0.997000	0.53966	0.929000	0.56500	0.464000	0.21988	0.455000	0.26910	-0.181000	0.13052	CGG		0.428	GATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254696.1	NM_005257	
TTC39C	125488	broad.mit.edu	37	18	21712467	21712467	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:21712467G>A	ENST00000317571.3	+	14	1917	c.1681G>A	c.(1681-1683)Gac>Aac	p.D561N	TTC39C_ENST00000304621.6_Missense_Mutation_p.D500N|TTC39C_ENST00000540918.2_Missense_Mutation_p.D254N	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	561								p.D500N(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						CTCTGGCTACGACTTTGAAAA	0.478																																					p.D561N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1681A	18						.						121.0	110.0	114.0					18																	21712467		2203	4300	6503	19966465	SO:0001583	missense	125488	exon14			AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"""Tetratricopeptide (TTC) repeat domain containing"""	26595	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 17"""	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.1681G>A	18.37:g.21712467G>A	ENSP00000323645:p.Asp561Asn	Somatic		Capture	Illumina HiSeq	Phase_I	19966465	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Missense_Mutation	SNP	ENST00000317571.3	37	CCDS45839.1	.	.	.	.	.	.	.	.	.	.	G	35	5.496473	0.96355	.	.	ENSG00000168234	ENST00000304621;ENST00000317571;ENST00000540918	T;T;T	0.45668	0.9;1.48;0.89	5.81	5.81	0.92471	.	0.041692	0.85682	D	0.000000	T	0.41558	0.1164	M	0.65975	2.015	0.80722	D	1	P	0.45768	0.866	B	0.31245	0.126	T	0.52087	-0.8622	10	0.59425	D	0.04	-27.1661	20.0714	0.97726	0.0:0.0:1.0:0.0	.	561	Q8N584	TT39C_HUMAN	N	500;561;254	ENSP00000306598:D500N;ENSP00000323645:D561N;ENSP00000443016:D254N	ENSP00000306598:D500N	D	+	1	0	TTC39C	19966465	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.450000	0.97607	2.749000	0.94314	0.655000	0.94253	GAC		0.478	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211	
ZNF521	25925	broad.mit.edu	37	18	22806877	22806877	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:22806877C>T	ENST00000361524.3	-	4	1153	c.1005G>A	c.(1003-1005)ccG>ccA	p.P335P	ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000538137.2_Silent_p.P335P|ZNF521_ENST00000584787.1_Silent_p.P115P	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	335					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.P335P(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)					TGCATGACTCCGGTTGCTGGT	0.527			T	PAX5	ALL																																p.P335P			Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1005A	18						.						103.0	92.0	95.0					18																	22806877		2203	4300	6503	21060875	SO:0001819	synonymous_variant	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.1005G>A	18.37:g.22806877C>T		Somatic		Capture	Illumina HiSeq	Phase_I	21060875	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	37	CCDS32806.1																																																																																				0.527	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
PSMA8	143471	broad.mit.edu	37	18	23758809	23758809	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:23758809C>T	ENST00000308268.6	+	5	600	c.511C>T	c.(511-513)Cga>Tga	p.R171*	PSMA8_ENST00000415576.2_Nonsense_Mutation_p.R165*|PSMA8_ENST00000343848.6_Nonsense_Mutation_p.R127*	NM_001025096.1|NM_144662.2	NP_001020267.1|NP_653263.2	Q8TAA3	PSA7L_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 8	171					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)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome core complex, alpha-subunit complex (GO:0019773)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)	p.R171*(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|skin(2)	16	all_cancers(21;0.000585)|Lung NSC(5;0.00148)|all_lung(6;0.0038)|Ovarian(20;0.124)		OV - Ovarian serous cystadenocarcinoma(3;0.000324)|all cancers(3;0.000954)|LUSC - Lung squamous cell carcinoma(2;0.181)			TGCAATAGGCCGAAGTGCTAA	0.323																																					p.R171X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C511T	18						.						34.0	37.0	36.0					18																	23758809		2203	4299	6502	22012807	SO:0001587	stop_gained	143471	exon5			BC047355	CCDS32808.1, CCDS45842.1, CCDS45843.1	18q11.2	2006-12-18				ENSG00000154611		"""Proteasome (prosome, macropain) subunits"""	22985	protein-coding gene	gene with protein product							Standard	XM_005258199		Approved	MGC26605, PSMA7L	uc002kvq.3	Q8TAA3		ENST00000308268.6:c.511C>T	18.37:g.23758809C>T	ENSP00000311121:p.Arg171*	Somatic		Capture	Illumina HiSeq	Phase_I	22012807	NM_144662	B0YJ75|Q8IVP4|Q8TA98|Q8TAA2	Nonsense_Mutation	SNP	ENST00000308268.6	37	CCDS32808.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.954683	0.92726	.	.	ENSG00000154611	ENST00000308268;ENST00000415576;ENST00000343848;ENST00000538664;ENST00000536423	.	.	.	5.15	1.23	0.21249	.	0.064920	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.3701	7.4482	0.27223	0.5657:0.354:0.0:0.0803	.	.	.	.	X	171;165;127;139;127	.	ENSP00000311121:R171X	R	+	1	2	PSMA8	22012807	1.000000	0.71417	0.995000	0.50966	0.969000	0.65631	1.576000	0.36504	0.041000	0.15688	-0.975000	0.02590	CGA		0.323	PSMA8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000446255.1	NM_144662	
CDH2	1000	broad.mit.edu	37	18	25568526	25568526	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:25568526T>C	ENST00000269141.3	-	11	2126	c.1703A>G	c.(1702-1704)aAc>aGc	p.N568S	CDH2_ENST00000399380.3_Missense_Mutation_p.N537S	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	568	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.N568S(1)		NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						ATATATATTGTTTTTCACATT	0.353																																					p.N568S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1703G	18						.						119.0	124.0	123.0					18																	25568526		2203	4300	6503	23822524	SO:0001583	missense	1000	exon11			S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"""CD molecules"", ""Cadherins / Major cadherins"""	1759	protein-coding gene	gene with protein product	"""N-cadherin"""	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.1703A>G	18.37:g.25568526T>C	ENSP00000269141:p.Asn568Ser	Somatic		Capture	Illumina HiSeq	Phase_I	23822524	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.866577	0.51588	.	.	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.60040	0.26;0.22	5.61	3.2	0.36748	Cadherin (4);Cadherin-like (1);	0.172380	0.64402	D	0.000006	T	0.54870	0.1885	M	0.73962	2.25	0.49915	D	0.999834	B;B	0.13594	0.008;0.002	B;B	0.17722	0.019;0.01	T	0.57510	-0.7799	10	0.72032	D	0.01	.	8.3149	0.32093	0.0:0.0689:0.1343:0.7967	.	537;568	A8MWK3;P19022	.;CADH2_HUMAN	S	568;537	ENSP00000269141:N568S;ENSP00000382312:N537S	ENSP00000269141:N568S	N	-	2	0	CDH2	23822524	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.965000	0.56788	1.046000	0.40249	0.533000	0.62120	AAC		0.353	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792	
DSC1	1823	broad.mit.edu	37	18	28736086	28736086	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:28736086G>A	ENST00000257198.5	-	4	652	c.391C>T	c.(391-393)Cgc>Tgc	p.R131C	RP11-408H20.2_ENST00000581836.1_RNA|DSC1_ENST00000257197.3_Missense_Mutation_p.R131C	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	131					homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R131C(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CTCTTGCTGCGCTTGAGGGCT	0.418																																					p.R131C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C391T	18						.						141.0	119.0	127.0					18																	28736086		2203	4300	6503	26990084	SO:0001583	missense	1823	exon4			AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.391C>T	18.37:g.28736086G>A	ENSP00000257198:p.Arg131Cys	Somatic		Capture	Illumina HiSeq	Phase_I	26990084	NM_004948	Q9HB01	Missense_Mutation	SNP	ENST00000257198.5	37	CCDS11894.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.435632	0.83885	.	.	ENSG00000134765	ENST00000257197;ENST00000257198	T;T	0.63744	-0.06;-0.06	5.66	3.76	0.43208	Cadherin-like (1);	0.277613	0.24083	N	0.041706	T	0.80732	0.4679	M	0.91561	3.22	0.80722	D	1	D;D	0.89917	0.999;1.0	P;P	0.60609	0.791;0.877	D	0.86178	0.1604	10	0.87932	D	0	.	14.689	0.69070	0.0:0.0:0.74:0.26	.	131;131	Q08554;Q9HB00	DSC1_HUMAN;.	C	131	ENSP00000257197:R131C;ENSP00000257198:R131C	ENSP00000257197:R131C	R	-	1	0	DSC1	26990084	0.989000	0.36119	0.953000	0.39169	0.987000	0.75469	2.123000	0.41996	1.502000	0.48669	0.655000	0.94253	CGC		0.418	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
DSG4	147409	broad.mit.edu	37	18	28966732	28966732	+	Missense_Mutation	SNP	G	G	A	rs200219673		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:28966732G>A	ENST00000308128.4	+	3	301	c.166G>A	c.(166-168)Gca>Aca	p.A56T	RP11-534N16.1_ENST00000581856.1_RNA|DSG4_ENST00000359747.4_Missense_Mutation_p.A56T|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	56	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A56T(1)		NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CAAGTTTGCCGCAGCCTGTCG	0.448													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19815	0.0		0.0	False		,,,				2504	0.0				p.A56T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G166A	18						.						108.0	100.0	103.0					18																	28966732		2203	4300	6503	27220730	SO:0001583	missense	147409	exon3			AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.166G>A	18.37:g.28966732G>A	ENSP00000311859:p.Ala56Thr	Somatic		Capture	Illumina HiSeq	Phase_I	27220730	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	37	CCDS11897.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	17.86	3.493027	0.64186	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.55234	0.53;0.53	5.22	5.22	0.72569	Cadherin (1);	0.000000	0.34603	N	0.003835	T	0.65322	0.2680	L	0.43152	1.355	0.40441	D	0.98004	D;P	0.89917	1.0;0.9	D;B	0.91635	0.999;0.362	T	0.61392	-0.7072	10	0.30078	T	0.28	.	17.3107	0.87208	0.0:0.0:1.0:0.0	.	56;56	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	T	56	ENSP00000311859:A56T;ENSP00000352785:A56T	ENSP00000311859:A56T	A	+	1	0	DSG4	27220730	0.991000	0.36638	0.334000	0.25495	0.917000	0.54804	4.814000	0.62627	2.589000	0.87451	0.650000	0.86243	GCA		0.448	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	
DSG4	147409	broad.mit.edu	37	18	28992845	28992845	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:28992845C>G	ENST00000308128.4	+	16	2545	c.2410C>G	c.(2410-2412)Ctc>Gtc	p.L804V	RP11-534N16.1_ENST00000581856.1_RNA|DSG4_ENST00000359747.4_Missense_Mutation_p.L823V|RP11-534N16.1_ENST00000578477.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	804					anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L804V(1)		NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			TGACTGCTTGCTCATTTATGA	0.408																																					p.L823V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2467G	18						.						105.0	97.0	100.0					18																	28992845		2203	4300	6503	27246843	SO:0001583	missense	147409	exon15			AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.2410C>G	18.37:g.28992845C>G	ENSP00000311859:p.Leu804Val	Somatic		Capture	Illumina HiSeq	Phase_I	27246843	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	37	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	C	17.14	3.313084	0.60414	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.77877	-1.13;-1.13	5.64	5.64	0.86602	Cadherin, cytoplasmic domain (1);	0.000000	0.31577	N	0.007419	D	0.88844	0.6547	M	0.90483	3.12	0.34236	D	0.677039	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.92807	0.6261	10	0.66056	D	0.02	.	9.8953	0.41316	0.0:0.8433:0.0:0.1567	.	823;804	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	V	804;823	ENSP00000311859:L804V;ENSP00000352785:L823V	ENSP00000311859:L804V	L	+	1	0	DSG4	27246843	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.599000	0.46231	2.650000	0.89964	0.650000	0.86243	CTC		0.408	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	
DSG3	1830	broad.mit.edu	37	18	29046693	29046693	+	Missense_Mutation	SNP	G	G	A	rs144565301	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:29046693G>A	ENST00000257189.4	+	11	1695	c.1612G>A	c.(1612-1614)Gta>Ata	p.V538I		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	538					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.V538I(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)			GTTGCCTGCCGTATGGAGTAT	0.408													G|||	2	0.000399361	0.0	0.0	5008	,	,		18487	0.001		0.001	False		,,,				2504	0.0				p.V538I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1612A	18						.	G	ILE/VAL	0,4406		0,0,2203	87.0	83.0	84.0		1612	-9.4	0.0	18	dbSNP_134	84	10,8590	7.7+/-29.5	0,10,4290	yes	missense	DSG3	NM_001944.2	29	0,10,6493	AA,AG,GG		0.1163,0.0,0.0769	benign	538/1000	29046693	10,12996	2203	4300	6503	27300691	SO:0001583	missense	1830	exon11			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.1612G>A	18.37:g.29046693G>A	ENSP00000257189:p.Val538Ile	Somatic		Capture	Illumina HiSeq	Phase_I	27300691	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	6.818	0.519964	0.13005	0.0	0.001163	ENSG00000134757	ENST00000257189	T	0.58506	0.33	5.82	-9.44	0.00603	.	1.281300	0.05828	N	0.616991	T	0.35653	0.0939	L	0.31065	0.9	0.09310	N	1	B	0.14438	0.01	B	0.08055	0.003	T	0.10776	-1.0615	10	0.20046	T	0.44	.	7.3522	0.26697	0.5122:0.0:0.1983:0.2895	.	538	P32926	DSG3_HUMAN	I	538	ENSP00000257189:V538I	ENSP00000257189:V538I	V	+	1	0	DSG3	27300691	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-1.401000	0.02502	-2.022000	0.00938	-0.813000	0.03139	GTA		0.408	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
DSG3	1830	broad.mit.edu	37	18	29049248	29049248	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:29049248G>A	ENST00000257189.4	+	12	1916	c.1833G>A	c.(1831-1833)ccG>ccA	p.P611P		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	611					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.P611P(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)			ATGGCAGGCCGCACTCAGGGA	0.592																																					p.P611P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1833A	18						.						49.0	51.0	50.0					18																	29049248		2203	4299	6502	27303246	SO:0001819	synonymous_variant	1830	exon12			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.1833G>A	18.37:g.29049248G>A		Somatic		Capture	Illumina HiSeq	Phase_I	27303246	NM_001944	A8K2V2	Silent	SNP	ENST00000257189.4	37	CCDS11898.1																																																																																				0.592	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
SMCHD1	23347	broad.mit.edu	37	18	2796462	2796462	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:2796462C>T	ENST00000320876.6	+	47	6274	c.5936C>T	c.(5935-5937)aCg>aTg	p.T1979M	RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1979					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)	p.T1979M(1)		NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						AAGGTTGAGACGACAGATTGT	0.368																																					p.T1979M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5936T	18						.						58.0	53.0	55.0					18																	2796462		1887	4128	6015	2786462	SO:0001583	missense	23347	exon47			AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.5936C>T	18.37:g.2796462C>T	ENSP00000326603:p.Thr1979Met	Somatic		Capture	Illumina HiSeq	Phase_I	2786462	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.315302	0.23908	.	.	ENSG00000101596	ENST00000320876	T	0.22336	1.96	5.11	2.71	0.32032	.	.	.	.	.	T	0.06371	0.0164	N	0.01048	-1.04	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25813	-1.0121	9	0.21014	T	0.42	0.2179	8.6884	0.34251	0.0:0.1593:0.0:0.8407	.	1979	A6NHR9	SMHD1_HUMAN	M	1979	ENSP00000326603:T1979M	ENSP00000326603:T1979M	T	+	2	0	SMCHD1	2786462	0.944000	0.32072	0.174000	0.22961	0.984000	0.73092	2.367000	0.44213	0.364000	0.24374	-0.238000	0.12139	ACG		0.368	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
DSG2	1829	broad.mit.edu	37	18	29122693	29122693	+	Missense_Mutation	SNP	G	G	A	rs397516705		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:29122693G>A	ENST00000261590.8	+	14	2421	c.2212G>A	c.(2212-2214)Gct>Act	p.A738T	RP11-75N4.2_ENST00000583706.1_RNA	NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	738					apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|regulation of heart rate by cardiac conduction (GO:0086091)|response to progesterone (GO:0032570)|ventricular cardiac muscle cell action potential (GO:0086005)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|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)	p.A738T(1)		breast(2)|central_nervous_system(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(2)|prostate(4)|skin(2)|urinary_tract(1)	49			OV - Ovarian serous cystadenocarcinoma(10;0.0068)			GGCCACAGGCGCTATCATGAC	0.547																																					p.A738T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2212A	18						.						101.0	107.0	105.0					18																	29122693		2021	4189	6210	27376691	SO:0001583	missense	1829	exon14			Z26317	CCDS42423.1	18q12.1	2014-09-17				ENSG00000046604		"""Cadherins / Major cadherins"""	3049	protein-coding gene	gene with protein product		125671				1612610	Standard	NM_001943		Approved	CDHF5	uc002kwu.4	Q14126		ENST00000261590.8:c.2212G>A	18.37:g.29122693G>A	ENSP00000261590:p.Ala738Thr	Somatic		Capture	Illumina HiSeq	Phase_I	27376691	NM_001943	Q4KKU6	Missense_Mutation	SNP	ENST00000261590.8	37	CCDS42423.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.898527	0.33535	.	.	ENSG00000046604	ENST00000261590	T	0.58797	0.31	5.97	0.782	0.18567	.	1.169400	0.06175	N	0.678309	T	0.32285	0.0824	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.15464	-1.0436	10	0.11794	T	0.64	.	0.8387	0.01145	0.2621:0.1205:0.3692:0.2481	.	738	Q14126	DSG2_HUMAN	T	738	ENSP00000261590:A738T	ENSP00000261590:A738T	A	+	1	0	DSG2	27376691	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	0.621000	0.24418	0.110000	0.17919	-0.136000	0.14681	GCT		0.547	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943	
MEP1B	4225	broad.mit.edu	37	18	29793082	29793082	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:29793082T>C	ENST00000269202.6	+	11	1186	c.1139T>C	c.(1138-1140)aTa>aCa	p.I380T	MEP1B_ENST00000581447.1_Missense_Mutation_p.I380T	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	380	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.I380T(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TTTGCAGAAATACCCACTGGG	0.393																																					p.I380T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1139C	18						.						63.0	59.0	60.0					18																	29793082		1873	4107	5980	28047080	SO:0001583	missense	4225	exon11			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.1139T>C	18.37:g.29793082T>C	ENSP00000269202:p.Ile380Thr	Somatic		Capture	Illumina HiSeq	Phase_I	28047080	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	37	CCDS45846.1	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.550754	0.00918	.	.	ENSG00000141434	ENST00000269202	T	0.01887	4.58	5.43	3.0	0.34707	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.782790	0.12811	N	0.437150	T	0.02012	0.0063	L	0.33137	0.985	0.09310	N	0.999995	B	0.29646	0.253	B	0.33960	0.173	T	0.47522	-0.9111	10	0.22109	T	0.4	-18.7327	1.8219	0.03112	0.1494:0.127:0.1549:0.5687	.	380	Q16820	MEP1B_HUMAN	T	380	ENSP00000269202:I380T	ENSP00000269202:I380T	I	+	2	0	MEP1B	28047080	0.887000	0.30362	0.814000	0.32528	0.221000	0.24807	1.147000	0.31602	0.978000	0.38470	0.383000	0.25322	ATA		0.393	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
GAREM	64762	broad.mit.edu	37	18	29867974	29867974	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:29867974G>A	ENST00000269209.6	-	4	589	c.586C>T	c.(586-588)Ccg>Tcg	p.P196S	RP11-344B2.2_ENST00000579580.1_RNA|GAREM_ENST00000578619.1_5'UTR|GAREM_ENST00000399218.4_Missense_Mutation_p.P196S			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	196	CABIT.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)	p.P196S(1)									ATGAGGCACGGCATTTTGCCT	0.453																																					p.P196S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C586T	18						.						111.0	91.0	98.0					18																	29867974		2203	4300	6503	28121972	SO:0001583	missense	64762	exon4			AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"""Grb2-associated and regulator of Erk/MAPK"""		"""chromosome 18 open reading frame 11"", ""family with sequence similarity 59, member A"""	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.586C>T	18.37:g.29867974G>A	ENSP00000269209:p.Pro196Ser	Somatic		Capture	Illumina HiSeq	Phase_I	28121972	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Missense_Mutation	SNP	ENST00000269209.6	37	CCDS56057.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.568378	0.86439	.	.	ENSG00000141441	ENST00000399218;ENST00000269209	T;T	0.19394	2.15;2.15	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.51550	0.1681	M	0.77616	2.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.51888	-0.8648	10	0.87932	D	0	-16.0239	20.1095	0.97908	0.0:0.0:1.0:0.0	.	196;196	Q9H706;Q9H706-3	FA59A_HUMAN;.	S	196	ENSP00000382165:P196S;ENSP00000269209:P196S	ENSP00000269209:P196S	P	-	1	0	FAM59A	28121972	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.357000	0.97099	2.831000	0.97527	0.655000	0.94253	CCG		0.453	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751	
MYOM1	8736	broad.mit.edu	37	18	3102489	3102489	+	Silent	SNP	G	G	A	rs200901326		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:3102489G>A	ENST00000356443.4	-	23	3891	c.3558C>T	c.(3556-3558)gtC>gtT	p.V1186V	MYOM1_ENST00000261606.7_Silent_p.V1090V|MYOM1_ENST00000400569.3_Silent_p.V1186V	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1186	Ig-like C2-type 3.				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.V1186V(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						CCTTGCTTTCGACTTCCAATC	0.423													G|||	1	0.000199681	0.0	0.0	5008	,	,		19464	0.001		0.0	False		,,,				2504	0.0				p.V1090V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3270T	18						.						214.0	208.0	210.0					18																	3102489		1905	4136	6041	3092489	SO:0001819	synonymous_variant	8736	exon22			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.3558C>T	18.37:g.3102489G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3092489	NM_019856	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																				0.423	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
DTNA	1837	broad.mit.edu	37	18	32438277	32438277	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:32438277C>T	ENST00000399113.3	+	15	1480	c.1480C>T	c.(1480-1482)Cgg>Tgg	p.R494W	DTNA_ENST00000595022.1_Missense_Mutation_p.R434W|DTNA_ENST00000269191.6_Missense_Mutation_p.R494W|DTNA_ENST00000599844.1_Missense_Mutation_p.R116W|DTNA_ENST00000556414.3_Missense_Mutation_p.R146W|DTNA_ENST00000598774.1_Missense_Mutation_p.R437W|DTNA_ENST00000348997.5_Missense_Mutation_p.R491W|DTNA_ENST00000283365.9_Missense_Mutation_p.R437W|DTNA_ENST00000444659.1_Missense_Mutation_p.R494W|DTNA_ENST00000597599.1_Missense_Mutation_p.R434W|DTNA_ENST00000399097.3_Missense_Mutation_p.R142W|DTNA_ENST00000596745.1_Missense_Mutation_p.R244W|DTNA_ENST00000597674.1_Missense_Mutation_p.R116W|DTNA_ENST00000598142.1_Missense_Mutation_p.R437W|DTNA_ENST00000399121.5_Missense_Mutation_p.R434W|DTNA_ENST00000598334.1_Missense_Mutation_p.R434W|DTNA_ENST00000269192.7_Missense_Mutation_p.R203W|DTNA_ENST00000591182.1_Missense_Mutation_p.R142W|DTNA_ENST00000269190.7_Missense_Mutation_p.R495W|DTNA_ENST00000601125.1_Missense_Mutation_p.R116W			Q9Y4J8	DTNA_HUMAN	dystrobrevin, alpha	494					neuromuscular synaptic transmission (GO:0007274)|signal transduction (GO:0007165)|striated muscle contraction (GO:0006941)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.R494W(1)|p.R142W(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(2)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	29						CCAGAGACTTCGGCTAGAGCA	0.522																																					p.R434W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1300T	18						.						58.0	57.0	58.0					18																	32438277		2203	4300	6503	30692275	SO:0001583	missense	1837	exon14			U84540	CCDS11908.1, CCDS11909.1, CCDS42426.1, CCDS45848.1, CCDS56060.1, CCDS56061.1, CCDS56062.1, CCDS56063.1, CCDS59309.1, CCDS59310.1, CCDS59311.1, CCDS59312.1, CCDS59313.1, CCDS59314.1	18q12	2014-09-17			ENSG00000134769	ENSG00000134769			3057	protein-coding gene	gene with protein product	"""dystrophin-related protein 3"""	601239				8081380, 15834686	Standard	NM_001390		Approved	D18S892E, DTN, DTN-1, DTN-2, DTN-3, DRP3	uc010dmn.1	Q9Y4J8	OTTHUMG00000132309	ENST00000399113.3:c.1480C>T	18.37:g.32438277C>T	ENSP00000382064:p.Arg494Trp	Somatic		Capture	Illumina HiSeq	Phase_I	30692275	NM_001198938	A8K541|A8MSZ0|A8MUY4|B4DGS6|B4DIR0|B4DIU8|M0QYX6|M0R397|O15332|O15333|O75697|Q13197|Q13198|Q13199|Q13498|Q13499|Q13500|Q59GK7|Q9BS59	Missense_Mutation	SNP	ENST00000399113.3	37	CCDS59311.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.856070	0.71834	.	.	ENSG00000134769	ENST00000399119;ENST00000283365;ENST00000399114;ENST00000269190;ENST00000399097;ENST00000348997;ENST00000399121;ENST00000444659;ENST00000269191;ENST00000399113;ENST00000269192;ENST00000450377;ENST00000556414	D;D;D;D;D;D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77	5.76	2.79	0.32731	.	0.000000	0.85682	D	0.000000	D	0.89952	0.6864	M	0.76328	2.33	0.58432	D	0.999997	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;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.998;1.0;0.991;0.999;0.999;0.998;0.999;0.997;0.999;0.997;0.999;0.997;0.998;0.999;0.994	D	0.90702	0.4621	10	0.87932	D	0	-17.8019	14.3687	0.66823	0.5113:0.4887:0.0:0.0	.	146;203;184;244;116;494;494;434;437;142;491;434;445;437;437	B4DIU8;B4DIR0;B7Z3X3;B4DGS6;Q9Y4J8-8;Q9Y4J8;Q9Y4J8-3;A8K541;F5H5C1;Q9Y4J8-6;Q9Y4J8-4;E9PEH8;Q59GK7;Q9Y4J8-2;Q9Y4J8-5	.;.;.;.;.;DTNA_HUMAN;.;.;.;.;.;.;.;.;.	W	437;437;434;495;142;491;494;494;494;494;203;142;146	ENSP00000283365:R437W;ENSP00000269190:R495W;ENSP00000382048:R142W;ENSP00000336682:R491W;ENSP00000405819:R494W;ENSP00000269191:R494W;ENSP00000382064:R494W;ENSP00000269192:R203W;ENSP00000452255:R146W	ENSP00000269190:R495W	R	+	1	2	DTNA	30692275	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	1.909000	0.39917	0.709000	0.31976	0.650000	0.86243	CGG		0.522	DTNA-005	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255422.2	NM_001390	
FHOD3	80206	broad.mit.edu	37	18	34205488	34205488	+	Silent	SNP	C	C	T	rs201237691		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:34205488C>T	ENST00000359247.4	+	10	972	c.972C>T	c.(970-972)caC>caT	p.H324H	FHOD3_ENST00000445677.1_Silent_p.H324H|FHOD3_ENST00000591635.1_5'UTR|FHOD3_ENST00000590592.1_Silent_p.H324H|FHOD3_ENST00000257209.4_Silent_p.H324H	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	324	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)		p.H324H(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				CGCTCAGGCACGAGGATGGCG	0.652													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16242	0.0		0.0	False		,,,				2504	0.0				p.H324H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C972T	18						.						51.0	51.0	51.0					18																	34205488		2203	4300	6503	32459486	SO:0001819	synonymous_variant	80206	exon10			AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.972C>T	18.37:g.34205488C>T		Somatic		Capture	Illumina HiSeq	Phase_I	32459486	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Silent	SNP	ENST00000359247.4	37																																																																																					0.652	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114	
CELF4	56853	broad.mit.edu	37	18	34833780	34833780	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:34833780C>T	ENST00000591282.1	-	12	1454	c.1455G>A	c.(1453-1455)ccG>ccA	p.P485P	CELF4_ENST00000601019.1_Silent_p.P483P|CELF4_ENST00000590011.1_5'UTR|CELF4_ENST00000603232.1_Silent_p.P484P|CELF4_ENST00000334919.5_Silent_p.P447P|CELF4_ENST00000412753.1_Silent_p.P484P|CELF4_ENST00000361795.5_Silent_p.P483P|CELF4_ENST00000591287.1_Silent_p.P483P|CELF4_ENST00000420428.2_Silent_p.P485P			Q9BZC1	CELF4_HUMAN	CUGBP, Elav-like family member 4	485					alternative mRNA splicing, via spliceosome (GO:0000380)|embryo development (GO:0009790)|germ cell development (GO:0007281)|mRNA splice site selection (GO:0006376)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of translation (GO:0017148)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	BRE binding (GO:0042835)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|translation repressor activity, nucleic acid binding (GO:0000900)	p.P485P(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	44						GCGCTCAGTACGGGCGATTGG	0.706																																					p.P447P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1341A	18						.						50.0	50.0	50.0					18																	34833780		2203	4300	6503	33087778	SO:0001819	synonymous_variant	56853	exon11			AF248651	CCDS32818.1, CCDS45857.1, CCDS45858.1	18q12	2013-02-12	2010-02-19	2010-02-19				"""RNA binding motif (RRM) containing"""	14015	protein-coding gene	gene with protein product		612679	"""Bruno (Drosophila) -like 4, RNA binding protein"", ""bruno-like 4, RNA binding protein (Drosophila)"""	BRUNOL4		10893231	Standard	NM_020180		Approved		uc002lae.2	Q9BZC1		ENST00000591282.1:c.1455G>A	18.37:g.34833780C>T		Somatic		Capture	Illumina HiSeq	Phase_I	33087778	NM_001025089	Q59EN7|Q86XB9|Q8N2M6|Q9BQ96|Q9NR84|Q9NR85	Silent	SNP	ENST00000591282.1	37	CCDS32818.1																																																																																				0.706	CELF4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440892.1	NM_020180	
CELF4	56853	broad.mit.edu	37	18	34854409	34854409	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:34854409C>T	ENST00000591282.1	-	6	665	c.666G>A	c.(664-666)tcG>tcA	p.S222S	CELF4_ENST00000601019.1_Silent_p.S221S|CELF4_ENST00000603232.1_Silent_p.S222S|CELF4_ENST00000334919.5_Silent_p.S212S|CELF4_ENST00000412753.1_Silent_p.S222S|CELF4_ENST00000588597.1_Silent_p.S211S|CELF4_ENST00000361795.5_Silent_p.S221S|RP11-797E24.3_ENST00000588766.1_RNA|CELF4_ENST00000591287.1_Silent_p.S221S|CELF4_ENST00000420428.2_Silent_p.S222S|RP11-797E24.3_ENST00000586610.1_RNA			Q9BZC1	CELF4_HUMAN	CUGBP, Elav-like family member 4	222	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.|Sufficient for RNA-binding and MSE- dependent splicing activity.				alternative mRNA splicing, via spliceosome (GO:0000380)|embryo development (GO:0009790)|germ cell development (GO:0007281)|mRNA splice site selection (GO:0006376)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of translation (GO:0017148)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	BRE binding (GO:0042835)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|translation repressor activity, nucleic acid binding (GO:0000900)	p.S222S(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	44						CCAGACTGGACGAGGCTCCCT	0.701																																					p.S212S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G636A	18						.						81.0	72.0	75.0					18																	34854409		2203	4300	6503	33108407	SO:0001819	synonymous_variant	56853	exon6			AF248651	CCDS32818.1, CCDS45857.1, CCDS45858.1	18q12	2013-02-12	2010-02-19	2010-02-19				"""RNA binding motif (RRM) containing"""	14015	protein-coding gene	gene with protein product		612679	"""Bruno (Drosophila) -like 4, RNA binding protein"", ""bruno-like 4, RNA binding protein (Drosophila)"""	BRUNOL4		10893231	Standard	NM_020180		Approved		uc002lae.2	Q9BZC1		ENST00000591282.1:c.666G>A	18.37:g.34854409C>T		Somatic		Capture	Illumina HiSeq	Phase_I	33108407	NM_001025089	Q59EN7|Q86XB9|Q8N2M6|Q9BQ96|Q9NR84|Q9NR85	Missense_Mutation	SNP	ENST00000591282.1	37	CCDS32818.1																																																																																				0.701	CELF4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440892.1	NM_020180	
PIK3C3	5289	broad.mit.edu	37	18	39584444	39584444	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:39584444A>G	ENST00000262039.4	+	10	1195	c.1109A>G	c.(1108-1110)cAt>cGt	p.H370R	PIK3C3_ENST00000398870.3_Missense_Mutation_p.H307R	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	370	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				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.H370R(1)		breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						TTATCCTCTCATTACACCAAC	0.468										TSP Lung(28;0.18)																											p.H370R	NSCLC(37;552 1060 2683 16430 37914)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1109G	18						.						121.0	107.0	112.0					18																	39584444		2203	4300	6503	37838442	SO:0001583	missense	5289	exon10			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.1109A>G	18.37:g.39584444A>G	ENSP00000262039:p.His370Arg	Somatic		Capture	Illumina HiSeq	Phase_I	37838442	NM_002647	Q15134	Missense_Mutation	SNP	ENST00000262039.4	37	CCDS11920.1	.	.	.	.	.	.	.	.	.	.	A	10.67	1.414958	0.25465	.	.	ENSG00000078142	ENST00000262039;ENST00000398870	T;T	0.62232	0.04;0.04	5.45	5.45	0.79879	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.094493	0.85682	D	0.000000	T	0.45994	0.1370	N	0.16478	0.41	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.36744	-0.9735	9	.	.	.	.	15.5116	0.75786	1.0:0.0:0.0:0.0	.	307;370	A8MYT4;Q8NEB9	.;PK3C3_HUMAN	R	370;307	ENSP00000262039:H370R;ENSP00000381845:H307R	.	H	+	2	0	PIK3C3	37838442	1.000000	0.71417	0.999000	0.59377	0.837000	0.47467	7.346000	0.79347	2.085000	0.62840	0.533000	0.62120	CAT		0.468	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647	
SETBP1	26040	broad.mit.edu	37	18	42532471	42532471	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:42532471A>C	ENST00000282030.5	+	4	3462	c.3166A>C	c.(3166-3168)Aca>Cca	p.T1056P		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1056						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.T1002P(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		AATGCCTTACACATCAATGCC	0.468									Schinzel-Giedion syndrome																												p.T1056P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3166C	18						.						108.0	89.0	95.0					18																	42532471		2203	4300	6503	40786469	SO:0001583	missense	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.3166A>C	18.37:g.42532471A>C	ENSP00000282030:p.Thr1056Pro	Somatic		Capture	Illumina HiSeq	Phase_I	40786469	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	CCDS11923.2	.	.	.	.	.	.	.	.	.	.	A	15.10	2.733490	0.48939	.	.	ENSG00000152217	ENST00000282030	D	0.90197	-2.63	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.91202	0.7228	N	0.19112	0.55	0.40085	D	0.976184	D	0.76494	0.999	D	0.67382	0.951	D	0.93061	0.6474	10	0.72032	D	0.01	.	16.1728	0.81831	1.0:0.0:0.0:0.0	.	1056	Q9Y6X0	SETBP_HUMAN	P	1056	ENSP00000282030:T1056P	ENSP00000282030:T1056P	T	+	1	0	SETBP1	40786469	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.168000	0.64978	2.228000	0.72767	0.533000	0.62120	ACA		0.468	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
EPG5	57724	broad.mit.edu	37	18	43502502	43502502	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:43502502G>A	ENST00000282041.5	-	16	2937	c.2903C>T	c.(2902-2904)gCc>gTc	p.A968V		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	968					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.A968V(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						TAAATTCCAGGCCCATTGGTT	0.413																																					p.A968V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2903T	18						.						99.0	105.0	103.0					18																	43502502		1886	4107	5993	41756500	SO:0001583	missense	57724	exon16			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.2903C>T	18.37:g.43502502G>A	ENSP00000282041:p.Ala968Val	Somatic		Capture	Illumina HiSeq	Phase_I	41756500	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	G	35	5.580829	0.96565	.	.	ENSG00000152223	ENST00000282041	T	0.10763	2.84	5.97	5.97	0.96955	.	0.324438	0.33534	N	0.004818	T	0.33440	0.0863	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.00370	-1.1783	10	0.72032	D	0.01	-13.4412	20.428	0.99075	0.0:0.0:1.0:0.0	.	968;968	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	V	968	ENSP00000282041:A968V	ENSP00000282041:A968V	A	-	2	0	EPG5	41756500	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.958000	0.87877	2.837000	0.97791	0.655000	0.94253	GCC		0.413	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
SMAD2	4087	broad.mit.edu	37	18	45374929	45374929	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:45374929G>T	ENST00000402690.2	-	8	1308	c.914C>A	c.(913-915)cCa>cAa	p.P305Q	SMAD2_ENST00000591214.1_Missense_Mutation_p.P275Q|SMAD2_ENST00000262160.6_Missense_Mutation_p.P305Q|SMAD2_ENST00000356825.4_Missense_Mutation_p.P275Q|SMAD2_ENST00000586040.1_Missense_Mutation_p.P275Q	NM_001003652.3	NP_001003652.1	Q15796	SMAD2_HUMAN	SMAD family member 2	305	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|cell fate commitment (GO:0045165)|common-partner SMAD protein phosphorylation (GO:0007182)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|endoderm formation (GO:0001706)|gastrulation (GO:0007369)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|insulin secretion (GO:0030073)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|mesoderm formation (GO:0001707)|negative regulation of cell proliferation (GO:0008285)|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)|nodal signaling pathway (GO:0038092)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primary miRNA processing (GO:0031053)|regulation of binding (GO:0051098)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to cholesterol (GO:0070723)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	activin responsive factor complex (GO:0032444)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|phosphatase binding (GO:0019902)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)	p.P305L(1)|p.P305Q(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(21)|liver(1)|lung(8)|prostate(2)|urinary_tract(1)	43						TGAATTTGATGGGTCTGTAAA	0.403																																					p.P275Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C824A	18						.						126.0	114.0	118.0					18																	45374929		2203	4300	6503	43628927	SO:0001583	missense	4087	exon7			U65019	CCDS11934.1	18q21	2006-11-06	2006-11-06	2004-05-26	ENSG00000175387	ENSG00000175387		"""SMADs"""	6768	protein-coding gene	gene with protein product		601366	"""MAD, mothers against decapentaplegic homolog 2 (Drosophila)"", ""SMAD, mothers against DPP homolog 2 (Drosophila)"""	MADH2		8752209, 8673135	Standard	NM_001003652		Approved	MADR2, JV18-1	uc002lcz.4	Q15796	OTTHUMG00000132652	ENST00000402690.2:c.914C>A	18.37:g.45374929G>T	ENSP00000384449:p.Pro305Gln	Somatic		Capture	Illumina HiSeq	Phase_I	43628927	NM_001135937		Missense_Mutation	SNP	ENST00000402690.2	37	CCDS11934.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.030962	0.93575	.	.	ENSG00000175387	ENST00000262160;ENST00000356825;ENST00000402690	D;D;D	0.97575	-4.44;-4.44;-4.44	5.81	5.81	0.92471	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98695	0.9562	M	0.87900	2.915	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.982;1.0	D	0.99094	1.0841	10	0.62326	D	0.03	.	20.0912	0.97820	0.0:0.0:1.0:0.0	.	275;275;305	B7Z5N5;Q15796-2;Q15796	.;.;SMAD2_HUMAN	Q	305;275;305	ENSP00000262160:P305Q;ENSP00000349282:P275Q;ENSP00000384449:P305Q	ENSP00000262160:P305Q	P	-	2	0	SMAD2	43628927	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	9.869000	0.99810	2.746000	0.94184	0.591000	0.81541	CCA		0.403	SMAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450571.1	NM_005901	
ZBTB7C	201501	broad.mit.edu	37	18	45566526	45566526	+	Missense_Mutation	SNP	G	G	A	rs371251738		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:45566526G>A	ENST00000588982.1	-	3	1454	c.953C>T	c.(952-954)cCg>cTg	p.P318L	ZBTB7C_ENST00000535628.2_Missense_Mutation_p.P318L|ZBTB7C_ENST00000332053.2_Missense_Mutation_p.P318L|ZBTB7C_ENST00000586438.1_Missense_Mutation_p.P318L|ZBTB7C_ENST00000590800.1_Missense_Mutation_p.P318L			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	318	Pro-rich.						metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.P318L(1)		endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						AGGCCCCCCCGGCAGGTCAGG	0.617																																					p.P318L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C953T	18						.	G	LEU/PRO	0,4406		0,0,2203	48.0	53.0	51.0		953	5.3	0.7	18		51	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZBTB7C	NM_001039360.2	98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	318/620	45566526	1,13005	2203	4300	6503	43820524	SO:0001583	missense	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.953C>T	18.37:g.45566526G>A	ENSP00000468782:p.Pro318Leu	Somatic		Capture	Illumina HiSeq	Phase_I	43820524	NM_001039360	O73453	Missense_Mutation	SNP	ENST00000588982.1	37	CCDS32830.1	.	.	.	.	.	.	.	.	.	.	G	11.23	1.576716	0.28092	0.0	1.16E-4	ENSG00000184828	ENST00000535628;ENST00000332053	T;T	0.13307	2.6;2.6	5.34	5.34	0.76211	.	0.467476	0.24752	N	0.035894	T	0.11067	0.0270	N	0.19112	0.55	0.53005	D	0.999968	P;P	0.49253	0.921;0.867	B;B	0.38880	0.284;0.284	T	0.07829	-1.0752	10	0.48119	T	0.1	.	19.0131	0.92882	0.0:0.0:1.0:0.0	.	318;318	B2RG49;A1YPR0	.;ZBT7C_HUMAN	L	318	ENSP00000439781:P318L;ENSP00000328732:P318L	ENSP00000328732:P318L	P	-	2	0	ZBTB7C	43820524	1.000000	0.71417	0.706000	0.30403	0.320000	0.28249	9.827000	0.99397	2.491000	0.84063	0.561000	0.74099	CCG		0.617	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360	
LIPG	9388	broad.mit.edu	37	18	47107950	47107950	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:47107950G>A	ENST00000261292.4	+	6	1237	c.959G>A	c.(958-960)gGc>gAc	p.G320D	LIPG_ENST00000427224.2_Missense_Mutation_p.G246D|LIPG_ENST00000577628.1_Missense_Mutation_p.G356D|LIPG_ENST00000580036.1_Missense_Mutation_p.G320D	NM_006033.2	NP_006024.1	Q9Y5X9	LIPE_HUMAN	lipase, endothelial	320					cell proliferation (GO:0008283)|cholesterol homeostasis (GO:0042632)|high-density lipoprotein particle remodeling (GO:0034375)|lipid metabolic process (GO:0006629)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|regulation of lipoprotein metabolic process (GO:0050746)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)	extracellular space (GO:0005615)	heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phosphatidylcholine 1-acylhydrolase activity (GO:0008970)|phospholipase activity (GO:0004620)	p.G320D(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(2)	18						AATAGCATTGGCTACAATGCC	0.483																																					p.G320D	Pancreas(126;280 1778 12814 26243 34948)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G959A	18						.						116.0	117.0	117.0					18																	47107950		2203	4300	6503	45361948	SO:0001583	missense	9388	exon6			AF118767	CCDS11938.1	18q21.1	2006-04-22				ENSG00000101670			6623	protein-coding gene	gene with protein product		603684				10318835, 10192396	Standard	XM_005258390		Approved	EDL	uc002ldv.3	Q9Y5X9		ENST00000261292.4:c.959G>A	18.37:g.47107950G>A	ENSP00000261292:p.Gly320Asp	Somatic		Capture	Illumina HiSeq	Phase_I	45361948	NM_006033	B0LPG6|Q6P9C8|Q6UW82	Missense_Mutation	SNP	ENST00000261292.4	37	CCDS11938.1	.	.	.	.	.	.	.	.	.	.	G	34	5.335153	0.95758	.	.	ENSG00000101670	ENST00000261292;ENST00000427224	D;D	0.98493	-4.96;-4.96	5.79	5.79	0.91817	Lipase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99456	0.9807	H	0.97983	4.12	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	0.98254	1.0495	10	0.87932	D	0	-9.4596	20.0204	0.97499	0.0:0.0:1.0:0.0	.	246;320;320	B4DTR8;Q9Y5X9;Q9Y5X9-2	.;LIPE_HUMAN;.	D	320;246	ENSP00000261292:G320D;ENSP00000387978:G246D	ENSP00000261292:G320D	G	+	2	0	LIPG	45361948	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.740000	0.93945	0.561000	0.74099	GGC		0.483	LIPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447546.1	NM_006033	
ME2	4200	broad.mit.edu	37	18	48422269	48422269	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:48422269C>T	ENST00000321341.5	+	2	351	c.79C>T	c.(79-81)Cca>Tca	p.P27S	ME2_ENST00000382927.3_Missense_Mutation_p.P27S	NM_002396.4	NP_002387.1	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	27					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.P27S(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)		AAAAGGCAAGCCACTTATGCT	0.338																																					p.P27S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C79T	18						.						90.0	78.0	82.0					18																	48422269		2203	4300	6503	46676267	SO:0001583	missense	4200	exon2			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.79C>T	18.37:g.48422269C>T	ENSP00000321070:p.Pro27Ser	Somatic		Capture	Illumina HiSeq	Phase_I	46676267	NM_001168335	B2R8J2|Q9BWL6|Q9BYG1|Q9H4B2	Missense_Mutation	SNP	ENST00000321341.5	37	CCDS11948.1	.	.	.	.	.	.	.	.	.	.	C	7.436	0.639739	0.14386	.	.	ENSG00000082212	ENST00000321341;ENST00000382927	T;T	0.39997	1.05;1.05	6.08	6.08	0.98989	.	0.048883	0.85682	D	0.000000	T	0.23330	0.0564	N	0.04724	-0.175	0.50813	D	0.999892	B;B	0.12630	0.006;0.006	B;B	0.10450	0.005;0.005	T	0.14090	-1.0485	10	0.07644	T	0.81	-15.9323	17.5802	0.87965	0.0:1.0:0.0:0.0	.	27;27	Q9BWL6;P23368	.;MAOM_HUMAN	S	27	ENSP00000321070:P27S;ENSP00000372384:P27S	ENSP00000321070:P27S	P	+	1	0	ME2	46676267	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	2.712000	0.47186	2.894000	0.99253	0.655000	0.94253	CCA		0.338	ME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255991.1	NM_002396	
SMAD4	4089	broad.mit.edu	37	18	48591817	48591817	+	Missense_Mutation	SNP	C	C	T	rs377767341		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:48591817C>T	ENST00000342988.3	+	9	1518	c.980C>T	c.(979-981)gCt>gTt	p.A327V	SMAD4_ENST00000588745.1_Missense_Mutation_p.A231V|SMAD4_ENST00000398417.2_Missense_Mutation_p.A327V	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	327	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|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)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|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, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.A327V(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		TGTTCCATTGCTTACTTTGAA	0.423																																					p.A327V												.	.	39	Whole gene deletion(36)|Unknown(2)|Substitution - Missense(1)	pancreas(26)|large_intestine(4)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|oesophagus(1)	c.C980T	18						.						249.0	215.0	227.0					18																	48591817		2203	4300	6503	46845815	SO:0001583	missense	4089	exon9			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"""SMADs"""	6770	protein-coding gene	gene with protein product		600993	"""MAD, mothers against decapentaplegic homolog 4 (Drosophila)"", ""SMAD, mothers against DPP homolog 4 (Drosophila)"""	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.980C>T	18.37:g.48591817C>T	ENSP00000341551:p.Ala327Val	Somatic		Capture	Illumina HiSeq	Phase_I	46845815	NM_005359	A8K405	Missense_Mutation	SNP	ENST00000342988.3	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.299878	0.81136	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.98835	-5.17;-5.17	5.99	5.99	0.97316	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.98738	0.9576	M	0.77103	2.36	0.80722	D	1	D	0.64830	0.994	P	0.56127	0.792	D	0.98698	1.0699	10	0.25106	T	0.35	.	19.2492	0.93917	0.0:1.0:0.0:0.0	.	327	Q13485	SMAD4_HUMAN	V	327	ENSP00000341551:A327V;ENSP00000381452:A327V	ENSP00000341551:A327V	A	+	2	0	SMAD4	46845815	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.672000	0.83956	2.840000	0.97914	0.655000	0.94253	GCT		0.423	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359	
WDR7	23335	broad.mit.edu	37	18	54363651	54363651	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:54363651T>C	ENST00000254442.3	+	12	1747	c.1536T>C	c.(1534-1536)ggT>ggC	p.G512G	WDR7_ENST00000589935.1_Intron|WDR7_ENST00000357574.3_Silent_p.G512G	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	512					hematopoietic progenitor cell differentiation (GO:0002244)			p.G512G(1)		NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		GTGTTCATGGTGGTGAGATTA	0.333																																					p.G512G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1536C	18						.						130.0	125.0	127.0					18																	54363651		2203	4300	6503	52514649	SO:0001819	synonymous_variant	23335	exon12			AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"""WD repeat domain containing"""	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.1536T>C	18.37:g.54363651T>C		Somatic		Capture	Illumina HiSeq	Phase_I	52514649	NM_015285	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Silent	SNP	ENST00000254442.3	37	CCDS11962.1																																																																																				0.333	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1		
WDR7	23335	broad.mit.edu	37	18	54424440	54424440	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:54424440T>C	ENST00000254442.3	+	15	2827	c.2616T>C	c.(2614-2616)tcT>tcC	p.S872S	WDR7_ENST00000589935.1_Intron|WDR7_ENST00000357574.3_Silent_p.S872S	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	872					hematopoietic progenitor cell differentiation (GO:0002244)			p.S872S(1)		NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)		TGCCAGCGTCTGAGGGAGTAG	0.483																																					p.S872S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2616C	18						.						116.0	96.0	102.0					18																	54424440		2203	4300	6503	52575438	SO:0001819	synonymous_variant	23335	exon15			AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157		"""WD repeat domain containing"""	13490	protein-coding gene	gene with protein product		613473				10828621	Standard	XM_005266674		Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.2616T>C	18.37:g.54424440T>C		Somatic		Capture	Illumina HiSeq	Phase_I	52575438	NM_015285	A7E2C8|Q86UX5|Q86VP2|Q96PS7	Silent	SNP	ENST00000254442.3	37	CCDS11962.1																																																																																				0.483	WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1		
MALT1	10892	broad.mit.edu	37	18	56390435	56390435	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:56390435C>T	ENST00000348428.3	+	10	1432	c.1174C>T	c.(1174-1176)Cgt>Tgt	p.R392C	RP11-126O1.4_ENST00000588835.1_RNA|MALT1_ENST00000345724.3_Missense_Mutation_p.R381C	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1	392	Caspase-like.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|B-1 B cell differentiation (GO:0001923)|defense response (GO:0006952)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|nuclear export (GO:0051168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|protein oligomerization (GO:0051259)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of T cell receptor signaling pathway (GO:0050856)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)|protein self-association (GO:0043621)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)	p.R381C(1)		central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						ATATGAGATGCGTAATGCTGT	0.348			T	BIRC3	MALT																																p.R381C			Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1141T	18						.						222.0	202.0	209.0					18																	56390435		2203	4300	6503	54541415	SO:0001583	missense	10892	exon9				CCDS11967.1, CCDS11968.1	18q21	2013-01-11			ENSG00000172175	ENSG00000172175		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6819	protein-coding gene	gene with protein product	"""paracaspase"""	604860		MLT		10339464, 10406266, 10523859	Standard	NM_006785		Approved		uc002lhm.1	Q9UDY8	OTTHUMG00000132761	ENST00000348428.3:c.1174C>T	18.37:g.56390435C>T	ENSP00000319279:p.Arg392Cys	Somatic		Capture	Illumina HiSeq	Phase_I	54541415	NM_173844	Q9NTB7|Q9ULX4	Missense_Mutation	SNP	ENST00000348428.3	37	CCDS11967.1	.	.	.	.	.	.	.	.	.	.	C	12.91	2.080659	0.36758	.	.	ENSG00000172175	ENST00000348428;ENST00000345724	T;T	0.25250	1.81;1.81	5.7	3.9	0.45041	Peptidase C14, caspase catalytic (1);Peptidase C14, ICE, catalytic subunit p20 (1);	0.230279	0.43260	N	0.000582	T	0.24586	0.0596	M	0.70595	2.14	0.58432	D	0.999997	B;B	0.31459	0.277;0.324	B;B	0.29862	0.066;0.108	T	0.05084	-1.0907	10	0.40728	T	0.16	.	5.2188	0.15358	0.2756:0.5677:0.0:0.1567	.	381;392	Q9UDY8-2;Q9UDY8	.;MALT1_HUMAN	C	392;381	ENSP00000319279:R392C;ENSP00000304161:R381C	ENSP00000304161:R381C	R	+	1	0	MALT1	54541415	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	0.784000	0.26816	0.749000	0.32854	0.655000	0.94253	CGT		0.348	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2		
CETN1	1068	broad.mit.edu	37	18	580689	580689	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:580689C>T	ENST00000327228.3	+	1	323	c.281C>T	c.(280-282)aCg>aTg	p.T94M		NM_004066.1	NP_004057.1	Q12798	CETN1_HUMAN	centrin, EF-hand protein, 1	94	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular response to heat (GO:0034605)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|photoreceptor connecting cilium (GO:0032391)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|calcium ion binding (GO:0005509)|nucleic acid binding (GO:0003676)	p.T94M(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(2)	25						GCCGTGATGACGCAGAAGATG	0.507																																					p.T94M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C281T	18						.						68.0	65.0	66.0					18																	580689		2203	4300	6503	570689	SO:0001583	missense	1068	exon1			U03270	CCDS11820.1	18p11.32	2013-01-10			ENSG00000177143	ENSG00000177143		"""EF-hand domain containing"""	1866	protein-coding gene	gene with protein product		603187		CETN		8175926	Standard	NM_004066		Approved	CEN1	uc002kko.1	Q12798	OTTHUMG00000131471	ENST00000327228.3:c.281C>T	18.37:g.580689C>T	ENSP00000319052:p.Thr94Met	Somatic		Capture	Illumina HiSeq	Phase_I	570689	NM_004066	B2R536	Missense_Mutation	SNP	ENST00000327228.3	37	CCDS11820.1	.	.	.	.	.	.	.	.	.	.	C	17.96	3.515395	0.64634	.	.	ENSG00000177143	ENST00000327228	T	0.37752	1.18	5.2	5.2	0.72013	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.60117	0.2244	M	0.81614	2.55	0.80722	D	1	D	0.89917	1.0	P	0.61477	0.889	T	0.64433	-0.6409	10	0.87932	D	0	.	16.6478	0.85181	0.0:1.0:0.0:0.0	.	94	Q12798	CETN1_HUMAN	M	94	ENSP00000319052:T94M	ENSP00000319052:T94M	T	+	2	0	CETN1	570689	1.000000	0.71417	0.976000	0.42696	0.205000	0.24178	7.630000	0.83225	2.882000	0.98803	0.655000	0.94253	ACG		0.507	CETN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254314.2	NM_004066	
CETN1	1068	broad.mit.edu	37	18	580797	580797	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:580797C>T	ENST00000327228.3	+	1	431	c.389C>T	c.(388-390)gCc>gTc	p.A130V		NM_004066.1	NP_004057.1	Q12798	CETN1_HUMAN	centrin, EF-hand protein, 1	130	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular response to heat (GO:0034605)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|photoreceptor connecting cilium (GO:0032391)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|calcium ion binding (GO:0005509)|nucleic acid binding (GO:0003676)	p.A130V(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(2)	25						AAGCGTGTGGCCAACGAGCTG	0.542																																					p.A130V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C389T	18						.						93.0	93.0	93.0					18																	580797		2203	4300	6503	570797	SO:0001583	missense	1068	exon1			U03270	CCDS11820.1	18p11.32	2013-01-10			ENSG00000177143	ENSG00000177143		"""EF-hand domain containing"""	1866	protein-coding gene	gene with protein product		603187		CETN		8175926	Standard	NM_004066		Approved	CEN1	uc002kko.1	Q12798	OTTHUMG00000131471	ENST00000327228.3:c.389C>T	18.37:g.580797C>T	ENSP00000319052:p.Ala130Val	Somatic		Capture	Illumina HiSeq	Phase_I	570797	NM_004066	B2R536	Missense_Mutation	SNP	ENST00000327228.3	37	CCDS11820.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.996256	0.74818	.	.	ENSG00000177143	ENST00000327228	T	0.78246	-1.16	5.2	5.2	0.72013	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.83445	0.5256	L	0.41236	1.265	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.84372	0.0544	10	0.72032	D	0.01	.	16.6478	0.85181	0.0:1.0:0.0:0.0	.	130	Q12798	CETN1_HUMAN	V	130	ENSP00000319052:A130V	ENSP00000319052:A130V	A	+	2	0	CETN1	570797	0.998000	0.40836	0.997000	0.53966	0.157000	0.22087	3.918000	0.56432	2.882000	0.98803	0.655000	0.94253	GCC		0.542	CETN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254314.2	NM_004066	
CCBE1	147372	broad.mit.edu	37	18	57122105	57122105	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:57122105G>A	ENST00000439986.4	-	6	669	c.632C>T	c.(631-633)aCc>aTc	p.T211I	CCBE1_ENST00000398179.2_5'UTR	NM_133459.3	NP_597716.1	Q6UXH8	CCBE1_HUMAN	collagen and calcium binding EGF domains 1	211					lymphangiogenesis (GO:0001946)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of protein processing (GO:0010954)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|positive regulation vascular endothelial growth factor production (GO:0010575)|sprouting angiogenesis (GO:0002040)|venous blood vessel morphogenesis (GO:0048845)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|protease binding (GO:0002020)	p.T211I(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)|skin(3)	24		Colorectal(73;0.175)				CTGCAGCACGGTCTGCTTCAT	0.537																																					p.T211I	NSCLC(137;1340 1860 15773 39604 51087)|Esophageal Squamous(139;339 1777 2926 19691 38524)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C632T	18						.						147.0	106.0	120.0					18																	57122105		2203	4300	6503	55273085	SO:0001583	missense	147372	exon6			AB075863	CCDS32838.1	18q21.32	2005-01-18				ENSG00000183287			29426	protein-coding gene	gene with protein product		612753				11853319, 12975309	Standard	NM_133459		Approved	FLJ30681, KIAA1983	uc002lib.3	Q6UXH8		ENST00000439986.4:c.632C>T	18.37:g.57122105G>A	ENSP00000404464:p.Thr211Ile	Somatic		Capture	Illumina HiSeq	Phase_I	55273085	NM_133459	Q6MZX5|Q86SS2|Q8TF19	Missense_Mutation	SNP	ENST00000439986.4	37	CCDS32838.1	.	.	.	.	.	.	.	.	.	.	G	16.26	3.072677	0.55646	.	.	ENSG00000183287	ENST00000439986	T	0.68903	-0.36	5.48	4.42	0.53409	.	0.096927	0.64402	D	0.000001	T	0.73721	0.3623	M	0.64997	1.995	0.80722	D	1	B;D	0.58620	0.295;0.983	B;P	0.54544	0.188;0.755	T	0.77498	-0.2565	10	0.87932	D	0	-18.9976	14.0898	0.64982	0.0877:0.0:0.9123:0.0	.	211;20	Q6UXH8;Q6UXH8-3	CCBE1_HUMAN;.	I	211	ENSP00000404464:T211I	ENSP00000404464:T211I	T	-	2	0	CCBE1	55273085	1.000000	0.71417	0.999000	0.59377	0.963000	0.63663	5.928000	0.70088	2.545000	0.85829	0.561000	0.74099	ACC		0.537	CCBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449685.2	NM_133459	
KIAA1468	57614	broad.mit.edu	37	18	59888476	59888476	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:59888476G>A	ENST00000398130.2	+	4	945	c.713G>A	c.(712-714)cGa>cAa	p.R238Q	KIAA1468_ENST00000256858.6_Missense_Mutation_p.R238Q	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	238								p.R238Q(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)				TTACAGGAACGAAAAAATTAC	0.299																																					p.R238Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G713A	18						.						34.0	32.0	33.0					18																	59888476		1806	4065	5871	58039456	SO:0001583	missense	57614	exon4			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.713G>A	18.37:g.59888476G>A	ENSP00000381198:p.Arg238Gln	Somatic		Capture	Illumina HiSeq	Phase_I	58039456	NM_020854		Missense_Mutation	SNP	ENST00000398130.2	37	CCDS11979.2	.	.	.	.	.	.	.	.	.	.	G	15.93	2.978130	0.53720	.	.	ENSG00000134444	ENST00000398130;ENST00000256858	T;T	0.44083	0.93;0.93	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.35653	0.0939	L	0.34521	1.04	0.80722	D	1	B;P	0.48016	0.429;0.904	B;B	0.39531	0.105;0.302	T	0.06716	-1.0811	9	.	.	.	-7.5274	19.9542	0.97213	0.0:0.0:1.0:0.0	.	238;238	Q9P260-2;Q9P260	.;K1468_HUMAN	Q	238	ENSP00000381198:R238Q;ENSP00000256858:R238Q	.	R	+	2	0	KIAA1468	58039456	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.471000	0.97696	2.728000	0.93425	0.650000	0.86243	CGA		0.299	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854	
TNFRSF11A	8792	broad.mit.edu	37	18	60035970	60035970	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:60035970G>A	ENST00000586569.1	+	9	858	c.820G>A	c.(820-822)Gca>Aca	p.A274T	TNFRSF11A_ENST00000269485.7_Intron	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	274					adaptive immune response (GO:0002250)|cell-cell signaling (GO:0007267)|circadian temperature homeostasis (GO:0060086)|lymph node development (GO:0048535)|mammary gland alveolus development (GO:0060749)|monocyte chemotaxis (GO:0002548)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|response to cytokine (GO:0034097)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to radiation (GO:0009314)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|tumor necrosis factor-activated receptor activity (GO:0005031)	p.A274T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(13)|skin(3)|upper_aerodigestive_tract(1)	29		Colorectal(73;0.188)				TACACACACGGCAAACTTTGG	0.463																																					p.A274T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G820A	18						.						78.0	72.0	74.0					18																	60035970		2203	4300	6503	58186950	SO:0001583	missense	8792	exon9			AF018253	CCDS11980.1, CCDS59324.1, CCDS74227.1, CCDS74228.1	18q22.1	2014-09-17			ENSG00000141655	ENSG00000141655		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11908	protein-coding gene	gene with protein product		603499	"""tumor necrosis factor receptor superfamily, member 11a, activator of NFKB"", ""Paget disease of bone 2"", ""loss of heterozygosity, 18, chromosomal region 1"""	PDB2, LOH18CR1		9367155, 10615125	Standard	NM_001270951		Approved	RANK, CD265, FEO	uc002lin.4	Q9Y6Q6	OTTHUMG00000132779	ENST00000586569.1:c.820G>A	18.37:g.60035970G>A	ENSP00000465500:p.Ala274Thr	Somatic		Capture	Illumina HiSeq	Phase_I	58186950	NM_003839	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Missense_Mutation	SNP	ENST00000586569.1	37	CCDS11980.1	.	.	.	.	.	.	.	.	.	.	G	5.563	0.288680	0.10513	.	.	ENSG00000141655	ENST00000269485	.	.	.	5.21	-2.58	0.06228	.	1.001990	0.08047	N	0.996045	T	0.13286	0.0322	N	0.04880	-0.145	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.23904	-1.0175	8	.	.	.	-1.4285	1.9783	0.03421	0.2782:0.2172:0.3937:0.1109	.	274	Q9Y6Q6	TNR11_HUMAN	T	274	.	.	A	+	1	0	TNFRSF11A	58186950	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.063000	0.14410	-0.494000	0.06669	-1.283000	0.01379	GCA		0.463	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2		
SERPINB2	5055	broad.mit.edu	37	18	61570323	61570323	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:61570323G>A	ENST00000299502.4	+	8	1112	c.1032G>A	c.(1030-1032)tcG>tcA	p.S344S	SERPINB2_ENST00000457692.1_Silent_p.S344S	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	344					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S344S(1)		NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	CAGGGATGTCGGAGAGGAATG	0.498																																					p.S344S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1032A	18						.						137.0	111.0	120.0					18																	61570323		2203	4300	6503	59721303	SO:0001819	synonymous_variant	5055	exon8			Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"""Serine (or cysteine) peptidase inhibitors"""	8584	protein-coding gene	gene with protein product		173390	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"""	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.1032G>A	18.37:g.61570323G>A		Somatic		Capture	Illumina HiSeq	Phase_I	59721303	NM_002575	Q96E96	Silent	SNP	ENST00000299502.4	37	CCDS11989.1																																																																																				0.498	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575	
LAMA1	284217	broad.mit.edu	37	18	6978337	6978337	+	Silent	SNP	C	C	T	rs545116059		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:6978337C>T	ENST00000389658.3	-	43	6141	c.6048G>A	c.(6046-6048)acG>acA	p.T2016T		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2016	Domain II and I.				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.T2016T(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)				GGCTTGCAGACGTGGCCAGCT	0.512													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18209	0.0		0.0	False		,,,				2504	0.0				p.T2016T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G6048A	18						.						93.0	88.0	89.0					18																	6978337		2203	4300	6503	6968337	SO:0001819	synonymous_variant	284217	exon43			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.6048G>A	18.37:g.6978337C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6968337	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																				0.512	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
CCDC102B	79839	broad.mit.edu	37	18	66504082	66504082	+	Missense_Mutation	SNP	G	G	A	rs369503833		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:66504082G>A	ENST00000360242.5	+	2	199	c.82G>A	c.(82-84)Gac>Aac	p.D28N	CCDC102B_ENST00000319445.6_Missense_Mutation_p.D28N|CCDC102B_ENST00000577772.1_3'UTR|CCDC102B_ENST00000584156.1_Missense_Mutation_p.D28N|CCDC102B_ENST00000358653.5_Missense_Mutation_p.D28N	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	28								p.D28N(1)		breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				GTCACGCGGCGACATGGTGGC	0.438																																					p.D28N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G82A	18						.	G	ASN/ASP,ASN/ASP	0,3930		0,0,1965	67.0	68.0	68.0		82,82	2.3	0.0	18		68	1,8249		0,1,4124	no	missense,missense	CCDC102B	NM_001093729.1,NM_024781.2	23,23	0,1,6089	AA,AG,GG		0.0121,0.0,0.0082	probably-damaging,probably-damaging	28/514,28/514	66504082	1,12179	1965	4125	6090	64655062	SO:0001583	missense	79839	exon4			AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636			26295	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 14"", ""aminoacylase 1-like"""	C18orf14, ACY1L		14702039	Standard	NM_001093729		Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.82G>A	18.37:g.66504082G>A	ENSP00000353377:p.Asp28Asn	Somatic		Capture	Illumina HiSeq	Phase_I	64655062	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	.	.	.	.	.	.	.	.	.	.	G	9.836	1.189663	0.21954	0.0	1.21E-4	ENSG00000150636	ENST00000319445;ENST00000358653;ENST00000360242	T;T;T	0.20069	2.61;2.1;2.61	5.17	2.28	0.28536	.	1.068870	0.07262	N	0.867758	T	0.17704	0.0425	L	0.29908	0.895	0.09310	N	1	D;D	0.57571	0.98;0.98	P;P	0.46172	0.506;0.506	T	0.13980	-1.0489	10	0.41790	T	0.15	-0.9325	3.7791	0.08673	0.188:0.0:0.4729:0.3391	.	28;28	Q68D86-3;Q68D86	.;C102B_HUMAN	N	28	ENSP00000316237:D28N;ENSP00000351479:D28N;ENSP00000353377:D28N	ENSP00000316237:D28N	D	+	1	0	CCDC102B	64655062	0.019000	0.18553	0.000000	0.03702	0.008000	0.06430	1.059000	0.30517	0.151000	0.19162	0.460000	0.39030	GAC		0.438	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
ZNF407	55628	broad.mit.edu	37	18	72343784	72343784	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:72343784G>A	ENST00000299687.5	+	1	809	c.809G>A	c.(808-810)cGt>cAt	p.R270H	ZNF407_ENST00000309902.6_Missense_Mutation_p.R270H|ZNF407_ENST00000582337.1_Missense_Mutation_p.R270H|ZNF407_ENST00000577538.1_Missense_Mutation_p.R270H	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	270					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.R270H(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)		ACACATCTCCGTCGTCAGAAT	0.403																																					p.R270H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G809A	18						.						110.0	109.0	109.0					18																	72343784		1900	4125	6025	70472772	SO:0001583	missense	55628	exon1			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.809G>A	18.37:g.72343784G>A	ENSP00000299687:p.Arg270His	Somatic		Capture	Illumina HiSeq	Phase_I	70472772	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.296771	0.81025	.	.	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.12879	2.64;3.14	5.3	5.3	0.74995	Zinc finger, U1-type (1);	0.192884	0.20693	U	0.087439	T	0.33847	0.0877	L	0.55017	1.72	0.33001	D	0.526309	D;D;D	0.89917	1.0;1.0;1.0	D;D;P	0.91635	0.963;0.999;0.877	T	0.43956	-0.9359	10	0.87932	D	0	.	14.2053	0.65730	0.0:0.0:0.8506:0.1493	.	270;270;270	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	H	270	ENSP00000299687:R270H;ENSP00000310359:R270H	ENSP00000299687:R270H	R	+	2	0	ZNF407	70472772	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.890000	0.63178	0.227000	0.20999	-0.331000	0.08364	CGT		0.403	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
ZNF407	55628	broad.mit.edu	37	18	72775471	72775471	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:72775471G>A	ENST00000299687.5	+	8	5794	c.5794G>A	c.(5794-5796)Gag>Aag	p.E1932K		NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1932					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.E1932K(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)		CATCCTCCCCGAGCAGCTGGC	0.662																																					p.E1932K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5794A	18						.						9.0	12.0	11.0					18																	72775471		2154	4250	6404	70904459	SO:0001583	missense	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.5794G>A	18.37:g.72775471G>A	ENSP00000299687:p.Glu1932Lys	Somatic		Capture	Illumina HiSeq	Phase_I	70904459	NM_017757	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	.	.	.	.	.	.	.	.	.	.	G	18.14	3.558537	0.65538	.	.	ENSG00000215421	ENST00000299687	T	0.11385	2.78	4.83	4.83	0.62350	.	.	.	.	.	T	0.33177	0.0854	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.13150	-1.0520	9	0.87932	D	0	.	17.9534	0.89061	0.0:0.0:1.0:0.0	.	1932	Q9C0G0	ZN407_HUMAN	K	1932	ENSP00000299687:E1932K	ENSP00000299687:E1932K	E	+	1	0	ZNF407	70904459	1.000000	0.71417	0.932000	0.37286	0.050000	0.14768	4.661000	0.61518	1.809000	0.52856	0.459000	0.35465	GAG		0.662	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
TSHZ1	10194	broad.mit.edu	37	18	72998901	72998901	+	Silent	SNP	G	G	A	rs111329836	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:72998901G>A	ENST00000580243.1	+	2	1887	c.1539G>A	c.(1537-1539)gcG>gcA	p.A513A	TSHZ1_ENST00000322038.5_Silent_p.A468A			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	513				A -> T (in Ref. 5; BAD97265). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A468A(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		CTGGCGACGCGGAGAAGATCA	0.592																																					p.A468A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1404A	18						.						94.0	104.0	100.0					18																	72998901		2203	4300	6503	71127889	SO:0001819	synonymous_variant	10194	exon2			AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.1539G>A	18.37:g.72998901G>A		Somatic		Capture	Illumina HiSeq	Phase_I	71127889	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																					0.592	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
ZNF236	7776	broad.mit.edu	37	18	74583682	74583682	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:74583682C>T	ENST00000253159.8	+	5	760	c.562C>T	c.(562-564)Cgg>Tgg	p.R188W	ZNF236_ENST00000583095.1_Intron|ZNF236_ENST00000320610.9_Missense_Mutation_p.R190W	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	188					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.R188W(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)		GTCTTATAACCGGAATATCGA	0.418																																					p.R188W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C562T	18						.						145.0	128.0	134.0					18																	74583682		1911	4121	6032	72712670	SO:0001583	missense	7776	exon5			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.562C>T	18.37:g.74583682C>T	ENSP00000253159:p.Arg188Trp	Somatic		Capture	Illumina HiSeq	Phase_I	72712670	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	37	CCDS42447.1	.	.	.	.	.	.	.	.	.	.	C	12.89	2.072398	0.36566	.	.	ENSG00000130856	ENST00000253159;ENST00000543926;ENST00000320610	T;T	0.12774	2.65;2.79	5.31	2.43	0.29744	.	0.065255	0.64402	D	0.000017	T	0.22666	0.0547	N	0.24115	0.695	0.35803	D	0.823259	D;D	0.89917	1.0;1.0	D;D	0.70935	0.965;0.971	T	0.16305	-1.0407	10	0.72032	D	0.01	.	14.9127	0.70770	0.5642:0.4358:0.0:0.0	.	188;188	Q9NWI2;Q9UL36	.;ZN236_HUMAN	W	188	ENSP00000253159:R188W;ENSP00000444524:R188W	ENSP00000253159:R188W	R	+	1	2	ZNF236	72712670	1.000000	0.71417	0.469000	0.27204	0.008000	0.06430	2.217000	0.42880	0.274000	0.22072	-0.182000	0.12963	CGG		0.418	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1		
ADNP2	22850	broad.mit.edu	37	18	77896554	77896554	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:77896554T>C	ENST00000262198.4	+	4	3713	c.3258T>C	c.(3256-3258)gaT>gaC	p.D1086D		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	1086					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|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.D1086D(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		GGAAAATTGATGTGGCTTCAT	0.308																																					p.D1086D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3258C	18						.						52.0	57.0	55.0					18																	77896554		2202	4292	6494	75997545	SO:0001819	synonymous_variant	22850	exon4			AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	23803	protein-coding gene	gene with protein product			"""zinc finger protein 508"""	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.3258T>C	18.37:g.77896554T>C		Somatic		Capture	Illumina HiSeq	Phase_I	75997545	NM_014913	A8K951|O94943|Q9H9P3	Silent	SNP	ENST00000262198.4	37	CCDS32853.1																																																																																				0.308	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913	
MTCL1	23255	broad.mit.edu	37	18	8784116	8784116	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:8784116G>T	ENST00000306329.11	+	5	2086	c.2086G>T	c.(2086-2088)Gag>Tag	p.E696*	SOGA2_ENST00000306285.7_5'UTR|SOGA2_ENST00000517570.1_Nonsense_Mutation_p.E336*|SOGA2_ENST00000359865.3_Nonsense_Mutation_p.E336*|SOGA2_ENST00000400050.3_Nonsense_Mutation_p.E336*														p.E336*(1)									CCCCCTGCAGGAGGAGCTGAA	0.647																																					p.E336X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1006T	18						.						33.0	40.0	38.0					18																	8784116		2200	4294	6494	8774116	SO:0001587	stop_gained	23255	exon6																														ENST00000306329.11:c.2086G>T	18.37:g.8784116G>T	ENSP00000305027:p.Glu696*	Somatic		Capture	Illumina HiSeq	Phase_I	8774116	NM_015210		Nonsense_Mutation	SNP	ENST00000306329.11	37		.	.	.	.	.	.	.	.	.	.	G	44	10.921101	0.99489	.	.	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050	.	.	.	5.56	5.56	0.83823	.	0.122778	0.37348	N	0.002128	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-26.7014	19.519	0.95177	0.0:0.0:1.0:0.0	.	.	.	.	X	357;336;336;336	.	ENSP00000305027:E357X	E	+	1	0	CCDC165	8774116	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.596000	0.98267	2.619000	0.88677	0.650000	0.86243	GAG		0.647	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
ANKRD12	23253	broad.mit.edu	37	18	9257447	9257447	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:9257447A>G	ENST00000262126.4	+	9	4422	c.4182A>G	c.(4180-4182)ccA>ccG	p.P1394P	RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000400020.3_Silent_p.P1371P|ANKRD12_ENST00000383440.2_Silent_p.P1371P	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1394						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.P1394P(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						ATACTGCCCCAGTGAACACTG	0.413																																					p.P1394P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A4182G	18						.						106.0	102.0	103.0					18																	9257447		2203	4300	6503	9247447	SO:0001819	synonymous_variant	23253	exon9			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.4182A>G	18.37:g.9257447A>G		Somatic		Capture	Illumina HiSeq	Phase_I	9247447	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Silent	SNP	ENST00000262126.4	37	CCDS11843.1																																																																																				0.413	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
ANKRD12	23253	broad.mit.edu	37	18	9258814	9258814	+	Missense_Mutation	SNP	G	G	A	rs190468609	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:9258814G>A	ENST00000262126.4	+	9	5789	c.5549G>A	c.(5548-5550)cGc>cAc	p.R1850H	RP11-888D10.4_ENST00000609701.1_RNA|ANKRD12_ENST00000400020.3_Missense_Mutation_p.R1827H|ANKRD12_ENST00000383440.2_Missense_Mutation_p.R1827H	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1850						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R1850H(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						GAAGAAAAACGCAAATTACTG	0.363													G|||	2	0.000399361	0.0	0.0014	5008	,	,		21945	0.0		0.001	False		,,,				2504	0.0				p.R1850H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5549A	18						.						67.0	66.0	67.0					18																	9258814		2203	4300	6503	9248814	SO:0001583	missense	23253	exon9			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5549G>A	18.37:g.9258814G>A	ENSP00000262126:p.Arg1850His	Somatic		Capture	Illumina HiSeq	Phase_I	9248814	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	31	5.088210	0.94100	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.70045	-0.45;-0.45	5.44	5.44	0.79542	.	0.112447	0.64402	D	0.000008	T	0.80654	0.4664	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.81602	-0.0858	10	0.87932	D	0	-6.4881	19.6223	0.95663	0.0:0.0:1.0:0.0	.	1827;1850	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	H	1827;1850	ENSP00000372932:R1827H;ENSP00000262126:R1850H	ENSP00000262126:R1850H	R	+	2	0	ANKRD12	9248814	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.972000	0.88022	2.707000	0.92482	0.655000	0.94253	CGC		0.363	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
RALBP1	10928	broad.mit.edu	37	18	9522367	9522367	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:9522367C>T	ENST00000019317.4	+	4	1136	c.913C>T	c.(913-915)Cgt>Tgt	p.R305C	RP11-61L19.3_ENST00000609094.1_RNA|RALBP1_ENST00000383432.3_Missense_Mutation_p.R305C			Q15311	RBP1_HUMAN	ralA binding protein 1	305	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				ATP catabolic process (GO:0006200)|chemotaxis (GO:0006935)|positive regulation of Cdc42 GTPase activity (GO:0043089)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|transport (GO:0006810)	cytosol (GO:0005829)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ATPase activity, coupled to movement of substances (GO:0043492)|GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)	p.R305C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	14					Carbamazepine(DB00564)|Doxorubicin(DB00997)|Sorafenib(DB00398)|Vincristine(DB00541)	GGAATTCCAGCGTTTACTCAA	0.443																																					p.R305C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C913T	18						.						81.0	76.0	77.0					18																	9522367		2203	4298	6501	9512367	SO:0001583	missense	10928	exon4			L42542	CCDS11845.1	18p11.22	2006-04-22			ENSG00000017797	ENSG00000017797			9841	protein-coding gene	gene with protein product		605801				7673236	Standard	NM_006788		Approved	RLIP76, RIP1, RIP	uc002koc.3	Q15311	OTTHUMG00000131596	ENST00000019317.4:c.913C>T	18.37:g.9522367C>T	ENSP00000019317:p.Arg305Cys	Somatic		Capture	Illumina HiSeq	Phase_I	9512367	NM_006788	D3DUI0	Missense_Mutation	SNP	ENST00000019317.4	37	CCDS11845.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.771817	0.69992	.	.	ENSG00000017797	ENST00000019317;ENST00000383432	T;T	0.19669	2.13;2.13	5.31	5.31	0.75309	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.41511	0.1162	M	0.64997	1.995	0.80722	D	1	D	0.76494	0.999	D	0.63192	0.912	T	0.18053	-1.0349	10	0.66056	D	0.02	-6.6807	15.1022	0.72288	0.1503:0.8497:0.0:0.0	.	305	Q15311	RBP1_HUMAN	C	305	ENSP00000019317:R305C;ENSP00000372924:R305C	ENSP00000019317:R305C	R	+	1	0	RALBP1	9512367	1.000000	0.71417	0.999000	0.59377	0.958000	0.62258	5.001000	0.63946	2.647000	0.89833	0.563000	0.77884	CGT		0.443	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1	NM_006788	
RNMT	8731	broad.mit.edu	37	18	13746253	13746253	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:13746253delA	ENST00000383314.2	+	9	1414	c.1174delA	c.(1174-1176)aaafs	p.K393fs	RNMT_ENST00000592764.1_Frame_Shift_Del_p.K393fs|RNMT_ENST00000589866.1_Frame_Shift_Del_p.K393fs|RNMT_ENST00000262173.3_Frame_Shift_Del_p.K393fs|RNMT_ENST00000543302.2_Frame_Shift_Del_p.K393fs|RNMT_ENST00000535051.1_Frame_Shift_Del_p.K151fs			O43148	MCES_HUMAN	RNA (guanine-7-) methyltransferase	393	mRNA cap 0 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00895}.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA (guanine-N7)-methylation (GO:0036265)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|receptor complex (GO:0043235)	mRNA (guanine-N7-)-methyltransferase activity (GO:0004482)|RNA binding (GO:0003723)	p.T394fs*19(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|skin(2)	18						ACTAGTCTACAAAAAAACATT	0.308																																					p.K392fs	GBM(29;474 594 19092 36647 41529)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1174delA	18						.						65.0	70.0	68.0					18																	13746253		2202	4299	6501	13736253	SO:0001589	frameshift_variant	8731	exon9			AF067791	CCDS11867.1	18p11.21	2008-05-14			ENSG00000101654	ENSG00000101654	2.1.1.56		10075	protein-coding gene	gene with protein product		603514				9828141, 9705270	Standard	NM_003799		Approved	RG7MT1	uc002ksl.1	O43148	OTTHUMG00000131718	ENST00000383314.2:c.1174delA	18.37:g.13746253delA	ENSP00000372804:p.Lys393fs	Somatic		Capture	Illumina HiSeq	Phase_I	13736253	NM_003799	B0YJ90|D3DUJ5|O94996|Q9UIJ9	Frame_Shift_Del	DEL	ENST00000383314.2	37	CCDS11867.1																																																																																				0.308	RNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254636.1	NM_003799	
PARD6G	84552	broad.mit.edu	37	18	77917689	77917689	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr18:77917689C>T	ENST00000353265.3	-	3	1293	c.1096G>A	c.(1096-1098)Ggc>Agc	p.G366S	AC139100.2_ENST00000587254.1_Intron|AC139100.2_ENST00000585422.1_Intron|AC139100.2_ENST00000589574.1_Intron|AC139100.2_ENST00000586421.1_Intron	NM_032510.3	NP_115899.1	Q9BYG4	PAR6G_HUMAN	par-6 family cell polarity regulator gamma	366					cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)		p.G366S(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	8		all_cancers(4;5.63e-22)|all_epithelial(4;5.86e-15)|all_lung(4;1.32e-05)|Ovarian(4;1.33e-05)|Lung NSC(4;2.77e-05)|Esophageal squamous(42;0.0157)|all_hematologic(56;0.13)|Melanoma(33;0.144)		Epithelial(2;1.48e-13)|all cancers(1;5.77e-13)|OV - Ovarian serous cystadenocarcinoma(15;2.74e-10)|BRCA - Breast invasive adenocarcinoma(31;0.00166)|STAD - Stomach adenocarcinoma(84;0.18)|Lung(128;0.23)		TCCTCCACGCCGCCTGGCGGC	0.726																																					p.G366S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1096A	18						.						4.0	4.0	4.0					18																	77917689		1606	2974	4580	76018680	SO:0001583	missense	84552	exon3				CCDS12022.1	18q23	2013-08-28	2013-08-28		ENSG00000178184	ENSG00000178184			16076	protein-coding gene	gene with protein product		608976	"""par-6 (partitioning defective 6, C.elegans) homolog gamma"", ""par-6 partitioning defective 6 homolog gamma (C. elegans)"""			11260256	Standard	NM_032510		Approved	PAR-6G, PAR6gamma	uc002lny.3	Q9BYG4	OTTHUMG00000132922	ENST00000353265.3:c.1096G>A	18.37:g.77917689C>T	ENSP00000343144:p.Gly366Ser	Somatic		Capture	Illumina HiSeq	Phase_I	76018680	NM_032510	A8QM57	Missense_Mutation	SNP	ENST00000353265.3	37	CCDS12022.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.180043	0.57800	.	.	ENSG00000178184	ENST00000353265	T	0.27104	1.69	4.96	4.96	0.65561	.	0.051889	0.85682	D	0.000000	T	0.24547	0.0595	L	0.32530	0.975	0.80722	D	1	D	0.58268	0.982	P	0.44921	0.464	T	0.01323	-1.1385	9	.	.	.	-40.24	17.1382	0.86745	0.0:1.0:0.0:0.0	.	366	Q9BYG4	PAR6G_HUMAN	S	366	ENSP00000343144:G366S	.	G	-	1	0	PARD6G	76018680	0.877000	0.30153	0.317000	0.25265	0.118000	0.20060	3.652000	0.54439	2.587000	0.87381	0.585000	0.79938	GGC		0.726	PARD6G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256435.2	NM_032510	
C19orf66	55337	broad.mit.edu	37	19	10201988	10201988	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:10201988C>T	ENST00000253110.11	+	6	745	c.447C>T	c.(445-447)ggC>ggT	p.G149G	C19orf66_ENST00000397881.3_Silent_p.G98G|C19orf66_ENST00000591813.1_Silent_p.G149G|CTD-2240E14.4_ENST00000589622.1_RNA	NM_018381.2	NP_060851.2	Q9NUL5	CS066_HUMAN	chromosome 19 open reading frame 66	149								p.G149G(1)		large_intestine(3)|skin(1)	4						AGATGTGGGGCCTGGCTGAGT	0.667																																					p.G149G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C447T	19						.						36.0	40.0	39.0					19																	10201988		2067	4196	6263	10062988	SO:0001819	synonymous_variant	55337	exon6				CCDS45957.1	19p13.2	2012-10-26			ENSG00000130813	ENSG00000130813			25649	protein-coding gene	gene with protein product						12477932	Standard	NM_018381		Approved	FLJ11286	uc002mmu.4	Q9NUL5		ENST00000253110.11:c.447C>T	19.37:g.10201988C>T		Somatic		Capture	Illumina HiSeq	Phase_I	10062988	NM_018381	A8MQT9|Q4G188|Q8IYH6|Q8N8V1	Silent	SNP	ENST00000253110.11	37	CCDS45957.1																																																																																				0.667	C19orf66-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451129.1	NM_018381	
DNMT1	1786	broad.mit.edu	37	19	10259658	10259658	+	Silent	SNP	G	G	A	rs375136816		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:10259658G>A	ENST00000340748.4	-	26	2809	c.2574C>T	c.(2572-2574)gaC>gaT	p.D858D	DNMT1_ENST00000540357.1_Silent_p.D858D|DNMT1_ENST00000359526.4_Silent_p.D874D			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	858	BAH 1. {ECO:0000255|PROSITE- ProRule:PRU00370}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.D858D(1)		breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	TCTTCCCGTCGTCCCCCTCCA	0.552																																					p.D874D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2622T	19						.	G	,	0,4406		0,0,2203	130.0	98.0	109.0		2622,2574	-2.4	0.0	19		109	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	DNMT1	NM_001130823.1,NM_001379.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	874/1633,858/1617	10259658	1,13005	2203	4300	6503	10120658	SO:0001819	synonymous_variant	1786	exon27			X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.2574C>T	19.37:g.10259658G>A		Somatic		Capture	Illumina HiSeq	Phase_I	10120658	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Silent	SNP	ENST00000340748.4	37	CCDS12228.1																																																																																				0.552	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379	
ZGLP1	100125288	broad.mit.edu	37	19	10418872	10418872	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:10418872G>A	ENST00000403903.3	-	1	1684	c.486C>T	c.(484-486)atC>atT	p.I162I	CTD-2369P2.10_ENST00000452032.2_3'UTR|FDX1L_ENST00000492239.1_5'Flank|ZGLP1_ENST00000403352.1_Silent_p.I78I|FDX1L_ENST00000541276.1_3'UTR	NM_001103167.1	NP_001096637.1	P0C6A0	ZGLP1_HUMAN	zinc finger, GATA-like protein 1	162					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oocyte development (GO:0048599)|spermatogenesis (GO:0007283)|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.I162I(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(2)|ovary(1)	6						TGTACGTGGGGATGATCTGCA	0.627																																					p.I162I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C486T	19						.						47.0	52.0	51.0					19																	10418872		1961	4143	6104	10279872	SO:0001819	synonymous_variant	100125288	exon1			AK096830	CCDS45959.1	19p13.2	2013-01-25			ENSG00000220201	ENSG00000220201		"""GATA zinc finger domain containing"""	37245	protein-coding gene	gene with protein product	"""GATA like protein 1"", ""GATA zinc finger domain containing 3"""	611639				16982049	Standard	NM_001103167		Approved	GLP1, GLP-1, GATAD3	uc002mnw.4	P0C6A0	OTTHUMG00000152114	ENST00000403903.3:c.486C>T	19.37:g.10418872G>A		Somatic		Capture	Illumina HiSeq	Phase_I	10279872	NM_001103167		Silent	SNP	ENST00000403903.3	37	CCDS45959.1																																																																																				0.627	ZGLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325278.1	NM_001103167	
ILF3	3609	broad.mit.edu	37	19	10793313	10793313	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:10793313C>T	ENST00000590261.1	+	12	1481	c.1481C>T	c.(1480-1482)gCc>gTc	p.A494V	ILF3_ENST00000250241.8_Missense_Mutation_p.A494V|ILF3_ENST00000407004.3_Missense_Mutation_p.A494V|ILF3_ENST00000592763.1_Missense_Mutation_p.A494V|ILF3_ENST00000589998.1_Missense_Mutation_p.A494V|ILF3_ENST00000318511.3_Missense_Mutation_p.A494V|ILF3_ENST00000588657.1_Missense_Mutation_p.A494V|ILF3_ENST00000420083.1_Missense_Mutation_p.A494V|ILF3_ENST00000449870.1_Missense_Mutation_p.A494V			Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3, 90kDa	494					defense response to virus (GO:0051607)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A494V(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31			Epithelial(33;6.86e-06)|all cancers(31;1.65e-05)			GCAGTGGTGGCCCCTGCCCCA	0.652																																					p.A494V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1481T	19						.						53.0	46.0	48.0					19																	10793313		2203	4300	6503	10654313	SO:0001583	missense	3609	exon13			U10324	CCDS12246.1, CCDS12247.1, CCDS45965.1, CCDS45966.1, CCDS45967.1	19p13.2	2012-08-10	2002-08-29		ENSG00000129351	ENSG00000129351			6038	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 4"""	603182	"""interleukin enhancer binding factor 3, 90kD"""			7519613, 8885239	Standard	NM_012218		Approved	NF90, MPHOSPH4, MPP4, DRBP76, NFAR-1	uc002mpo.3	Q12906		ENST00000590261.1:c.1481C>T	19.37:g.10793313C>T	ENSP00000468156:p.Ala494Val	Somatic		Capture	Illumina HiSeq	Phase_I	10654313	NM_012218	A8K6F2|G5E9M5|O43409|Q6P1X1|Q86XY7|Q99544|Q99545|Q9BZH4|Q9BZH5|Q9NQ95|Q9NQ96|Q9NQ97|Q9NQ98|Q9NQ99|Q9NQA0|Q9NQA1|Q9NQA2|Q9NRN2|Q9NRN3|Q9NRN4|Q9UMZ9|Q9UN00|Q9UN84|Q9UNA2	Missense_Mutation	SNP	ENST00000590261.1	37	CCDS12246.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.756578	0.49362	.	.	ENSG00000129351	ENST00000336059;ENST00000449870;ENST00000318511;ENST00000420083;ENST00000407004;ENST00000250241	T;T;T;T;T	0.15017	2.46;2.5;2.52;2.48;2.52	5.22	5.22	0.72569	.	0.520552	0.20489	N	0.091327	T	0.13927	0.0337	N	0.19112	0.55	0.42449	D	0.992742	B;B;B;B;B;B	0.21225	0.046;0.018;0.053;0.019;0.017;0.003	B;B;B;B;B;B	0.22880	0.005;0.042;0.019;0.007;0.009;0.002	T	0.06935	-1.0799	10	0.46703	T	0.11	.	16.055	0.80794	0.0:1.0:0.0:0.0	.	494;494;494;494;494;494	Q12906-4;G5E9M5;Q12906;Q12906-6;Q12906-2;Q12906-5	.;.;ILF3_HUMAN;.;.;.	V	494	ENSP00000404121:A494V;ENSP00000315205:A494V;ENSP00000405436:A494V;ENSP00000384660:A494V;ENSP00000250241:A494V	ENSP00000250241:A494V	A	+	2	0	ILF3	10654313	0.001000	0.12720	1.000000	0.80357	0.181000	0.23173	0.065000	0.14466	2.594000	0.87642	0.650000	0.86243	GCC		0.652	ILF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452074.1		
DNM2	1785	broad.mit.edu	37	19	10939823	10939823	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:10939823C>T	ENST00000355667.6	+	19	2250	c.2170C>T	c.(2170-2172)Cgc>Tgc	p.R724C	DNM2_ENST00000585892.1_Missense_Mutation_p.R724C|DNM2_ENST00000314646.5_Missense_Mutation_p.R724C|DNM2_ENST00000359692.6_Missense_Mutation_p.R720C|DNM2_ENST00000389253.4_Missense_Mutation_p.R724C|DNM2_ENST00000408974.4_Missense_Mutation_p.R720C	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	724	GED. {ECO:0000255|PROSITE- ProRule:PRU00720}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)	p.R720C(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			CGACATGCTGCGCATGTACCA	0.622			"""F, N, Splice, Mis, O"""		ETP ALL																																p.R724C			Rec	yes		19	19p13.2	1785	dynamin 2		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2170T	19						.						59.0	44.0	49.0					19																	10939823		2203	4300	6503	10800823	SO:0001583	missense	1785	exon19				CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"""Pleckstrin homology (PH) domain containing"""	2974	protein-coding gene	gene with protein product	"""dynamin II"", ""cytoskeletal protein"""	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.2170C>T	19.37:g.10939823C>T	ENSP00000347890:p.Arg724Cys	Somatic		Capture	Illumina HiSeq	Phase_I	10800823	NM_001190716	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	37	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	C	13.72	2.320230	0.41096	.	.	ENSG00000079805	ENST00000408974;ENST00000355667;ENST00000359692;ENST00000389253;ENST00000314646;ENST00000545324	T;T;T	0.56444	0.46;0.46;0.46	4.92	4.92	0.64577	GTPase effector domain, GED (1);Dynamin GTPase effector (2);	0.000000	0.85682	D	0.000000	T	0.75867	0.3908	M	0.89904	3.07	0.80722	D	1	P;D;D;D;D;D;D	0.89917	0.955;0.999;0.996;0.996;1.0;1.0;1.0	P;D;D;D;D;D;D	0.91635	0.557;0.947;0.976;0.953;0.947;0.969;0.999	T	0.80901	-0.1175	10	0.87932	D	0	.	12.0601	0.53559	0.1727:0.8273:0.0:0.0	.	318;724;453;720;720;724;724	Q8N1K8;F5H4R9;B4DJ53;A8K1B6;P50570-2;P50570;E9PEQ4	.;.;.;.;.;DYN2_HUMAN;.	C	720;720;724;724;724;331	ENSP00000386192:R720C;ENSP00000373905:R724C;ENSP00000313164:R724C	ENSP00000313164:R724C	R	+	1	0	DNM2	10800823	1.000000	0.71417	1.000000	0.80357	0.046000	0.14306	1.702000	0.37836	2.282000	0.76494	0.313000	0.20887	CGC		0.622	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945	
CARM1	10498	broad.mit.edu	37	19	11031515	11031515	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:11031515C>T	ENST00000327064.4	+	13	1620	c.1430C>T	c.(1429-1431)aCg>aTg	p.T477M	CARM1_ENST00000344150.4_Missense_Mutation_p.T477M	NM_199141.1	NP_954592.1	Q86X55	CARM1_HUMAN	coactivator-associated arginine methyltransferase 1	477					cellular lipid metabolic process (GO:0044255)|endochondral bone morphogenesis (GO:0060350)|histone H3-R17 methylation (GO:0034971)|histone H3-R2 methylation (GO:0034970)|histone methylation (GO:0016571)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of protein binding (GO:0032091)|pathogenesis (GO:0009405)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-R17 specific) (GO:0035642)|histone-arginine N-methyltransferase activity (GO:0008469)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|lysine-acetylated histone binding (GO:0070577)|protein methyltransferase activity (GO:0008276)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)	p.T477M(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	13						CATAGATACACGGGCACAACG	0.652																																					p.T477M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1430T	19						.						78.0	79.0	79.0					19																	11031515		2203	4300	6503	10892515	SO:0001583	missense	10498	exon13			AF055027	CCDS12250.1	19p13.2	2010-10-11			ENSG00000142453	ENSG00000142453		"""Protein arginine methyltransferases"""	23393	protein-coding gene	gene with protein product		603934				10381882, 11724789	Standard	NM_199141		Approved	PRMT4	uc002mpz.3	Q86X55		ENST00000327064.4:c.1430C>T	19.37:g.11031515C>T	ENSP00000325690:p.Thr477Met	Somatic		Capture	Illumina HiSeq	Phase_I	10892515	NM_199141	A6NN38	Missense_Mutation	SNP	ENST00000327064.4	37	CCDS12250.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.374418	0.61735	.	.	ENSG00000142453	ENST00000327064;ENST00000344150	T;T	0.30182	1.54;1.58	4.87	4.87	0.63330	.	0.187910	0.45361	D	0.000376	T	0.45696	0.1355	L	0.61218	1.895	0.80722	D	1	D;D	0.71674	0.997;0.998	P;P	0.53035	0.716;0.608	T	0.50939	-0.8768	10	0.87932	D	0	-2.0702	16.8043	0.85622	0.0:1.0:0.0:0.0	.	477;477	Q86X55-1;Q86X55	.;CARM1_HUMAN	M	477	ENSP00000325690:T477M;ENSP00000340934:T477M	ENSP00000325690:T477M	T	+	2	0	CARM1	10892515	1.000000	0.71417	0.956000	0.39512	0.261000	0.26267	7.244000	0.78228	2.243000	0.73865	0.637000	0.83480	ACG		0.652	CARM1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452625.1	XM_032719	
LDLR	3949	broad.mit.edu	37	19	11241988	11241988	+	Missense_Mutation	SNP	C	C	T	rs13306505	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:11241988C>T	ENST00000558518.1	+	18	2766	c.2579C>T	c.(2578-2580)gCg>gTg	p.A860V	LDLR_ENST00000560628.1_Intron|LDLR_ENST00000558013.1_Missense_Mutation_p.A858V|LDLR_ENST00000535915.1_Missense_Mutation_p.A819V|LDLR_ENST00000557933.1_Missense_Mutation_p.R881C|LDLR_ENST00000545707.1_Missense_Mutation_p.A682V|LDLR_ENST00000455727.2_Missense_Mutation_p.A692V	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	860	Required for MYLIP-triggered down- regulation of LDLR.				cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.A860V(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	GATGACGTGGCGTGAACATCT	0.537											OREG0025249	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	4	0.000798722	0.0	0.0	5008	,	,		17948	0.004		0.0	False		,,,				2504	0.0				p.A739V	GBM(18;201 575 7820 21545)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2216T	19						.						241.0	201.0	215.0					19																	11241988		2203	4300	6503	11102988	SO:0001583	missense	3949	exon17			AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.2579C>T	19.37:g.11241988C>T	ENSP00000454071:p.Ala860Val	Somatic	670	Capture	Illumina HiSeq	Phase_I	11102988	NM_001195802	B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	37	CCDS12254.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	C	15.31	2.795434	0.50208	.	.	ENSG00000130164	ENST00000252444;ENST00000545707;ENST00000535915;ENST00000455727	D;D;D	0.91894	-2.93;-2.71;-2.77	4.74	2.6	0.31112	.	0.120124	0.34046	N	0.004306	D	0.91771	0.7397	L	0.54323	1.7	0.19775	N	0.99995	D;D;D;P;B;B	0.89917	1.0;1.0;1.0;0.49;0.351;0.351	D;D;D;B;B;B	0.87578	0.998;0.998;0.998;0.103;0.062;0.103	D	0.85357	0.1105	10	0.87932	D	0	.	9.8446	0.41019	0.0:0.8275:0.0:0.1725	rs13306505;rs13306505	692;682;739;819;870;860	B4DR00;B4DJZ8;B4DII3;B4DTQ3;Q59FQ1;P01130	.;.;.;.;.;LDLR_HUMAN	V	860;682;819;692	ENSP00000437639:A682V;ENSP00000440520:A819V;ENSP00000397829:A692V	ENSP00000252444:A860V	A	+	2	0	LDLR	11102988	0.826000	0.29277	0.049000	0.19019	0.212000	0.24457	1.435000	0.34969	0.531000	0.28639	0.462000	0.41574	GCG		0.537	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2		
SPC24	147841	broad.mit.edu	37	19	11258793	11258793	+	Splice_Site	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:11258793A>C	ENST00000592540.1	-	3	337	c.306T>G	c.(304-306)ctT>ctG	p.L102L		NM_182513.2	NP_872319.1	Q8NBT2	SPC24_HUMAN	SPC24, NDC80 kinetochore complex component	102	Interaction with the N-terminus of SPBC25.				mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|Ndc80 complex (GO:0031262)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.L102L(1)		autonomic_ganglia(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|prostate(1)	5						TGGTGAGCTGAGTAGGGCAGG	0.602																																					p.L102L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T306G	19						.						47.0	48.0	48.0					19																	11258793		1986	4165	6151	11119793	SO:0001630	splice_region_variant	147841	exon3			AK075287	CCDS45974.1	19p13.2	2013-06-05	2013-06-05	2007-03-02		ENSG00000161888			26913	protein-coding gene	gene with protein product		609394	"""spindle pole body component 24 homolog (S. cerevisiae)"", ""SPC24, NDC80 kinetochore complex component, homolog (S. cerevisiae)"""	SPBC24			Standard	NM_182513		Approved	FLJ90806	uc002mql.2	Q8NBT2		ENST00000592540.1:c.306-1T>G	19.37:g.11258793A>C		Somatic		Capture	Illumina HiSeq	Phase_I	11119793	NM_182513	B4DZZ7|C9JGC4	Silent	SNP	ENST00000592540.1	37	CCDS45974.1																																																																																				0.602	SPC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453059.1	NM_182513	Silent
DOCK6	57572	broad.mit.edu	37	19	11338101	11338101	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:11338101C>T	ENST00000294618.7	-	24	2878	c.2867G>A	c.(2866-2868)cGc>cAc	p.R956H	DOCK6_ENST00000319867.7_Missense_Mutation_p.R295H	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	956					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.R956H(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						GCGCAGCTTGCGGGGTGTGTC	0.632																																					p.R956H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2867A	19						.						28.0	33.0	31.0					19																	11338101		2083	4224	6307	11199101	SO:0001583	missense	57572	exon24				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.2867G>A	19.37:g.11338101C>T	ENSP00000294618:p.Arg956His	Somatic		Capture	Illumina HiSeq	Phase_I	11199101	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	37	CCDS45975.1	.	.	.	.	.	.	.	.	.	.	C	34	5.335294	0.95758	.	.	ENSG00000130158	ENST00000294618;ENST00000319867	T;T	0.28666	1.6;1.6	4.33	4.33	0.51752	.	0.136126	0.48286	D	0.000188	T	0.63070	0.2480	M	0.91663	3.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.73452	-0.3978	10	0.87932	D	0	-22.3278	14.3234	0.66502	0.0:1.0:0.0:0.0	.	295;956	C9IZV6;Q96HP0	.;DOCK6_HUMAN	H	956;295	ENSP00000294618:R956H;ENSP00000321556:R295H	ENSP00000294618:R956H	R	-	2	0	DOCK6	11199101	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.315000	0.78998	1.941000	0.56285	0.561000	0.74099	CGC		0.632	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
DOCK6	57572	broad.mit.edu	37	19	11346306	11346306	+	Missense_Mutation	SNP	C	C	T	rs372044294		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:11346306C>T	ENST00000294618.7	-	21	2533	c.2522G>A	c.(2521-2523)cGc>cAc	p.R841H	C19orf80_ENST00000591200.1_5'Flank|RN7SL298P_ENST00000581369.1_RNA|DOCK6_ENST00000319867.7_Missense_Mutation_p.R145H	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	841					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.R841H(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						GCCAGGAAGGCGAAAGGCGTA	0.612																																					p.R841H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2522A	19						.	C	HIS/ARG	1,4153		0,1,2076	19.0	24.0	22.0		2522	4.1	1.0	19		22	1,8419		0,1,4209	no	missense	DOCK6	NM_020812.2	29	0,2,6285	TT,TC,CC		0.0119,0.0241,0.0159	benign	841/2048	11346306	2,12572	2077	4210	6287	11207306	SO:0001583	missense	57572	exon21				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.2522G>A	19.37:g.11346306C>T	ENSP00000294618:p.Arg841His	Somatic		Capture	Illumina HiSeq	Phase_I	11207306	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	37	CCDS45975.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.443947	0.43429	2.41E-4	1.19E-4	ENSG00000130158	ENST00000294618;ENST00000319867	T;T	0.32753	1.44;1.44	5.15	4.11	0.48088	.	0.133227	0.47455	D	0.000231	T	0.19967	0.0480	N	0.21373	0.66	0.44123	D	0.996902	B;B	0.24920	0.114;0.01	B;B	0.27608	0.081;0.005	T	0.05241	-1.0897	10	0.40728	T	0.16	-22.9432	8.5443	0.33413	0.0:0.8253:0.0:0.1747	.	145;841	C9IZV6;Q96HP0	.;DOCK6_HUMAN	H	841;145	ENSP00000294618:R841H;ENSP00000321556:R145H	ENSP00000294618:R841H	R	-	2	0	DOCK6	11207306	1.000000	0.71417	0.999000	0.59377	0.633000	0.38033	2.585000	0.46111	2.418000	0.82041	0.555000	0.69702	CGC		0.612	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
DOCK6	57572	broad.mit.edu	37	19	11348159	11348159	+	Silent	SNP	C	C	T	rs201212364	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:11348159C>T	ENST00000294618.7	-	18	2057	c.2046G>A	c.(2044-2046)ccG>ccA	p.P682P	C19orf80_ENST00000591200.1_5'Flank|C19orf80_ENST00000252453.8_5'Flank|DOCK6_ENST00000319867.7_5'UTR	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	682	DHR-1.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.P682P(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						AATAGCTGGGCGGCGGCTGGT	0.647													C|||	2	0.000399361	0.0	0.0	5008	,	,		12796	0.0		0.001	False		,,,				2504	0.001				p.P682P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2046A	19						.						43.0	54.0	51.0					19																	11348159		2045	4173	6218	11209159	SO:0001819	synonymous_variant	57572	exon18				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.2046G>A	19.37:g.11348159C>T		Somatic		Capture	Illumina HiSeq	Phase_I	11209159	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																				0.647	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
DOCK6	57572	broad.mit.edu	37	19	11353972	11353972	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:11353972G>A	ENST00000294618.7	-	12	1359	c.1348C>T	c.(1348-1350)Cgt>Tgt	p.R450C		NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	450					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.R450C(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						GTGGCTGGACGGAAGCCAGAG	0.677											OREG0025252	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R450C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1348T	19						.						22.0	27.0	26.0					19																	11353972		1979	4144	6123	11214972	SO:0001583	missense	57572	exon12				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.1348C>T	19.37:g.11353972G>A	ENSP00000294618:p.Arg450Cys	Somatic	671	Capture	Illumina HiSeq	Phase_I	11214972	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	37	CCDS45975.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.697317	0.88830	.	.	ENSG00000130158	ENST00000294618	T	0.38887	1.11	4.15	4.15	0.48705	.	0.000000	0.85682	D	0.000000	T	0.66694	0.2815	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.74144	-0.3760	10	0.87932	D	0	-23.5216	15.2295	0.73374	0.0:0.0:1.0:0.0	.	450	Q96HP0	DOCK6_HUMAN	C	450	ENSP00000294618:R450C	ENSP00000294618:R450C	R	-	1	0	DOCK6	11214972	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	2.464000	0.45067	1.861000	0.53984	0.462000	0.41574	CGT		0.677	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
RGL3	57139	broad.mit.edu	37	19	11513173	11513173	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:11513173C>T	ENST00000380456.3	-	11	1350	c.1287G>A	c.(1285-1287)acG>acA	p.T429T	RGL3_ENST00000393423.3_Silent_p.T429T	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	429	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)	p.T429T(1)|p.T193T(1)		breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						TAACCAGGTCCGTAAGGAAGG	0.612																																					p.T429T	GBM(174;751 2067 17998 27979 33959)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1287A	19						.						60.0	60.0	60.0					19																	11513173		2203	4300	6503	11374173	SO:0001819	synonymous_variant	57139	exon11			BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.1287G>A	19.37:g.11513173C>T		Somatic		Capture	Illumina HiSeq	Phase_I	11374173	NM_001161616	B5ME84|B7ZL22|Q0P6G0	Silent	SNP	ENST00000380456.3	37	CCDS32910.1																																																																																				0.612	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867	
RGL3	57139	broad.mit.edu	37	19	11526752	11526752	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:11526752C>T	ENST00000380456.3	-	5	561	c.498G>A	c.(496-498)tcG>tcA	p.S166S	RGL3_ENST00000393423.3_Silent_p.S166S	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	166	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)	p.S166S(1)		breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						TGCCCAGGTCCGAATGGGCAG	0.617																																					p.S166S	GBM(174;751 2067 17998 27979 33959)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G498A	19						.						34.0	41.0	39.0					19																	11526752		2203	4300	6503	11387752	SO:0001819	synonymous_variant	57139	exon5			BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.498G>A	19.37:g.11526752C>T		Somatic		Capture	Illumina HiSeq	Phase_I	11387752	NM_001161616	B5ME84|B7ZL22|Q0P6G0	Silent	SNP	ENST00000380456.3	37	CCDS32910.1																																																																																				0.617	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867	
STK11	6794	broad.mit.edu	37	19	1221293	1221293	+	Silent	SNP	C	C	T	rs9282859	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:1221293C>T	ENST00000326873.7	+	6	1989	c.816C>T	c.(814-816)taC>taT	p.Y272Y		NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	272	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Y -> H (in sporadic cancer; somatic mutation; no effect on kinase activity nor in heterotrimeric complex assembly with STRADA and CAB39).		activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.Y272Y(4)|p.?(2)|p.Y246fs*3(1)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|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)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		AGGGGAGCTACGCCATCCCGG	0.612		14	"""D, Mis, N, F, S"""		"""NSCLC, pancreatic"""	"""jejunal harmartoma, ovarian, testicular, pancreatic"""			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)			C|||	118	0.0235623	0.0862	0.0058	5008	,	,		18249	0.0		0.0	False		,,,				2504	0.0				p.Y272Y		yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"""E, M, O"""	STK11,lung,NS,Substitution - coding silent,0 	.	27	Whole gene deletion(20)|Substitution - coding silent(4)|Unknown(2)|Deletion - Frameshift(1)	cervix(14)|lung(8)|large_intestine(1)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	c.C816T	19						.	C		293,3645		8,277,1684	50.0	54.0	52.0		816	2.0	1.0	19	dbSNP_118	52	6,8252		0,6,4123	no	coding-synonymous	STK11	NM_000455.4		8,283,5807	TT,TC,CC		0.0727,7.4403,2.4516		272/434	1221293	299,11897	1969	4129	6098	1172293	SO:0001819	synonymous_variant	6794	exon6	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"""polarization-related protein LKB1"""	602216	"""serine/threonine kinase 11 (Peutz-Jeghers syndrome)"""			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.816C>T	19.37:g.1221293C>T		Somatic		Capture	Illumina HiSeq	Phase_I	1172293	NM_000455	B2RBX7|E7EW76	Silent	SNP	ENST00000326873.7	37	CCDS45896.1																																																																																				0.612	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455	
ZNF653	115950	broad.mit.edu	37	19	11606931	11606931	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:11606931C>A	ENST00000293771.5	-	3	529	c.393G>T	c.(391-393)gaG>gaT	p.E131D	ZNF653_ENST00000593191.1_5'UTR|CTC-398G3.6_ENST00000585656.1_Missense_Mutation_p.R102M	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	131					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.E131D(1)		endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						GCTTGTGGTCCTCGTACCAGA	0.637																																					p.E131D	Pancreas(83;980 1446 4542 6441 43352)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G393T	19						.						130.0	85.0	100.0					19																	11606931		2203	4300	6503	11467931	SO:0001583	missense	115950	exon3			AY072704	CCDS12261.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"""	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.393G>T	19.37:g.11606931C>A	ENSP00000293771:p.Glu131Asp	Somatic		Capture	Illumina HiSeq	Phase_I	11467931	NM_138783	Q96AS7	Missense_Mutation	SNP	ENST00000293771.5	37	CCDS12261.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.955097	0.53293	.	.	ENSG00000161914	ENST00000293771	T	0.11495	2.77	4.52	3.49	0.39957	.	0.199745	0.43579	D	0.000553	T	0.04952	0.0133	N	0.14661	0.345	0.33076	D	0.536058	P	0.37864	0.61	B	0.31946	0.138	T	0.19811	-1.0294	10	0.72032	D	0.01	-25.486	4.0262	0.09688	0.1878:0.6194:0.0:0.1928	.	131	Q96CK0	ZN653_HUMAN	D	131	ENSP00000293771:E131D	ENSP00000293771:E131D	E	-	3	2	ZNF653	11467931	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	1.624000	0.37018	1.139000	0.42245	0.561000	0.74099	GAG		0.637	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783	
ZNF491	126069	broad.mit.edu	37	19	11917410	11917410	+	Silent	SNP	G	G	A	rs376662017		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:11917410G>A	ENST00000323169.5	+	3	973	c.642G>A	c.(640-642)ccG>ccA	p.P214P	ZNF491_ENST00000492230.1_Intron	NM_152356.3	NP_689569.2	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	214					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.P214P(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(14)|lung(6)|ovary(2)|skin(1)	26						GAGAGAAGCCGTACAAATGTA	0.423																																					p.P214P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G642A	19						.	G		2,4404	4.2+/-10.8	0,2,2201	55.0	57.0	56.0		642	-1.9	0.0	19		56	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ZNF491	NM_152356.3		0,5,6498	AA,AG,GG		0.0349,0.0454,0.0384		214/438	11917410	5,13001	2203	4300	6503	11778410	SO:0001819	synonymous_variant	126069	exon3			AK092110	CCDS12267.1	19p13.2	2013-01-08			ENSG00000177599	ENSG00000177599		"""Zinc fingers, C2H2-type"""	23706	protein-coding gene	gene with protein product							Standard	XM_005259730		Approved	FLJ34791	uc002mso.1	Q8N8L2	OTTHUMG00000156529	ENST00000323169.5:c.642G>A	19.37:g.11917410G>A		Somatic		Capture	Illumina HiSeq	Phase_I	11778410	NM_152356	Q3MJ35|Q8NAT8	Silent	SNP	ENST00000323169.5	37	CCDS12267.1																																																																																				0.423	ZNF491-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344518.1	NM_152356	
ZNF491	126069	broad.mit.edu	37	19	11917899	11917899	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:11917899C>T	ENST00000323169.5	+	3	1462	c.1131C>T	c.(1129-1131)caC>caT	p.H377H	ZNF491_ENST00000492230.1_Intron	NM_152356.3	NP_689569.2	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	377					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.H377H(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(14)|lung(6)|ovary(2)|skin(1)	26						AAAGGACTCACGCTGGAGAAA	0.393																																					p.H377H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1131T	19						.						53.0	57.0	56.0					19																	11917899		2203	4300	6503	11778899	SO:0001819	synonymous_variant	126069	exon3			AK092110	CCDS12267.1	19p13.2	2013-01-08			ENSG00000177599	ENSG00000177599		"""Zinc fingers, C2H2-type"""	23706	protein-coding gene	gene with protein product							Standard	XM_005259730		Approved	FLJ34791	uc002mso.1	Q8N8L2	OTTHUMG00000156529	ENST00000323169.5:c.1131C>T	19.37:g.11917899C>T		Somatic		Capture	Illumina HiSeq	Phase_I	11778899	NM_152356	Q3MJ35|Q8NAT8	Silent	SNP	ENST00000323169.5	37	CCDS12267.1																																																																																				0.393	ZNF491-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344518.1	NM_152356	
ZNF136	7695	broad.mit.edu	37	19	12298027	12298027	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:12298027A>C	ENST00000343979.4	+	4	974	c.834A>C	c.(832-834)aaA>aaC	p.K278N	ZNF136_ENST00000398616.2_Missense_Mutation_p.K212N	NM_003437.3	NP_003428.1	P52737	ZN136_HUMAN	zinc finger protein 136	278					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)	p.K278N(1)		NS(1)|biliary_tract(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	18						CTGGAGAAAAACCCTTTAAAT	0.398																																					p.K278N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A834C	19						.						62.0	62.0	62.0					19																	12298027		2202	4300	6502	12159027	SO:0001583	missense	7695	exon4			U09367	CCDS32916.1	19p13.2	2013-01-08	2006-06-13		ENSG00000196646	ENSG00000196646		"""Zinc fingers, C2H2-type"", ""-"""	12920	protein-coding gene	gene with protein product		604078	"""zinc finger protein 136 (clone pHZ-20)"""			7557990	Standard	NM_003437		Approved	pHZ-20	uc002mti.3	P52737	OTTHUMG00000156429	ENST00000343979.4:c.834A>C	19.37:g.12298027A>C	ENSP00000344162:p.Lys278Asn	Somatic		Capture	Illumina HiSeq	Phase_I	12159027	NM_003437		Missense_Mutation	SNP	ENST00000343979.4	37	CCDS32916.1	.	.	.	.	.	.	.	.	.	.	A	11.67	1.708174	0.30322	.	.	ENSG00000196646	ENST00000343979;ENST00000398616	T;T	0.26067	1.76;1.76	1.37	-2.73	0.05950	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.45175	0.1329	M	0.80746	2.51	0.32977	D	0.52319	D	0.69078	0.997	D	0.67725	0.953	T	0.49818	-0.8899	8	.	.	.	.	9.2472	0.37534	0.4877:0.0:0.5123:0.0	.	278	P52737	ZN136_HUMAN	N	278;212	ENSP00000344162:K278N;ENSP00000381617:K212N	.	K	+	3	2	ZNF136	12159027	0.008000	0.16893	0.106000	0.21319	0.480000	0.33159	-0.296000	0.08287	-1.697000	0.01420	-1.131000	0.01979	AAA		0.398	ZNF136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344151.2	NM_003437	
ZNF44	51710	broad.mit.edu	37	19	12384425	12384425	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:12384425A>G	ENST00000356109.5	-	5	907	c.789T>C	c.(787-789)caT>caC	p.H263H	ZNF44_ENST00000355684.5_Silent_p.H215H	NM_001164276.1	NP_001157748.1	P15621	ZNF44_HUMAN	zinc finger protein 44	263					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.H215H(1)		ovary(1)	1		Renal(1328;0.157)		GBM - Glioblastoma multiforme(1328;0.0164)|Lung(535;0.179)		GAGTTCTTTCATGCATACGTA	0.383																																					p.H215H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T645C	19						.						98.0	103.0	102.0					19																	12384425		2203	4300	6503	12245425	SO:0001819	synonymous_variant	51710	exon4			X52338	CCDS45988.1, CCDS54223.1	19p13.2	2013-01-08	2006-05-11		ENSG00000197857	ENSG00000197857		"""Zinc fingers, C2H2-type"", ""-"""	13110	protein-coding gene	gene with protein product		194542	"""zinc finger protein 58"", ""zinc finger protein 44 (KOX 7)"", ""zinc finger protein 55"""	ZNF58, ZNF55		1946370, 1505991	Standard	NM_016264		Approved	KOX7, ZNF504	uc010xmj.2	P15621	OTTHUMG00000156424	ENST00000356109.5:c.789T>C	19.37:g.12384425A>G		Somatic		Capture	Illumina HiSeq	Phase_I	12245425	NM_016264	B4DML9|B9EGJ5|B9ZVM2|P17018|Q9ULZ7	Silent	SNP	ENST00000356109.5	37	CCDS54223.1																																																																																				0.383	ZNF44-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344132.1	NM_016264	
ZNF564	163050	broad.mit.edu	37	19	12637456	12637456	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:12637456G>T	ENST00000339282.7	-	4	1662	c.1466C>A	c.(1465-1467)gCc>gAc	p.A489D	CTD-2192J16.20_ENST00000593682.1_3'UTR|ZNF709_ENST00000428311.1_Intron	NM_144976.3	NP_659413.1	Q8TBZ8	ZN564_HUMAN	zinc finger protein 564	489					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.A489D(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						AATGGAACTGGCATAATTGAA	0.373																																					p.A489D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1466A	19						.						102.0	107.0	105.0					19																	12637456		2191	4294	6485	12498456	SO:0001583	missense	163050	exon4			BC028367	CCDS42505.1	19p13.2	2013-09-19			ENSG00000249709	ENSG00000249709		"""Zinc fingers, C2H2-type"", ""-"""	31106	protein-coding gene	gene with protein product							Standard	NM_144976		Approved	MGC26914		Q8TBZ8	OTTHUMG00000156418	ENST00000339282.7:c.1466C>A	19.37:g.12637456G>T	ENSP00000340004:p.Ala489Asp	Somatic		Capture	Illumina HiSeq	Phase_I	12498456	NM_144976	B9EGT4|Q6P1K6	Missense_Mutation	SNP	ENST00000339282.7	37	CCDS42505.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.141188	0.37825	.	.	ENSG00000249709	ENST00000339282	T	0.37058	1.22	1.71	-3.41	0.04839	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23727	0.0574	L	0.35793	1.09	0.09310	N	1	B	0.27166	0.17	B	0.34873	0.191	T	0.35649	-0.9780	9	0.39692	T	0.17	.	0.7642	0.01012	0.2131:0.1436:0.354:0.2893	.	489	Q8TBZ8	ZN564_HUMAN	D	489	ENSP00000340004:A489D	ENSP00000340004:A489D	A	-	2	0	ZNF564	12498456	0.000000	0.05858	0.000000	0.03702	0.996000	0.88848	-2.939000	0.00684	-1.024000	0.03338	0.643000	0.83706	GCC		0.373	ZNF564-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344120.2	NM_144976	
MAN2B1	4125	broad.mit.edu	37	19	12757524	12757524	+	Silent	SNP	C	C	T	rs192184706		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:12757524C>T	ENST00000456935.2	-	24	2986	c.2946G>A	c.(2944-2946)ccG>ccA	p.P982P	MAN2B1_ENST00000221363.4_Silent_p.P981P|CTD-2192J16.22_ENST00000597692.1_Missense_Mutation_p.V169I	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	982					cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)	p.P982P(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CCAGCTGGTACGGAGTTTGGT	0.607													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17617	0.0		0.0	False		,,,				2504	0.0				p.P982P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2946A	19						.						186.0	144.0	158.0					19																	12757524		2203	4300	6503	12618524	SO:0001819	synonymous_variant	4125	exon24				CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.2946G>A	19.37:g.12757524C>T		Somatic		Capture	Illumina HiSeq	Phase_I	12618524	NM_000528	G5E928|O15330|Q16680|Q93094|Q9BW13	Silent	SNP	ENST00000456935.2	37	CCDS32919.1																																																																																				0.607	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
BEST2	54831	broad.mit.edu	37	19	12868621	12868621	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:12868621G>A	ENST00000549706.1	+	10	1584	c.1260G>A	c.(1258-1260)aaG>aaA	p.K420K	BEST2_ENST00000553030.1_Silent_p.K420K|BEST2_ENST00000042931.1_Silent_p.K420K			Q8NFU1	BEST2_HUMAN	bestrophin 2	420					chloride transmembrane transport (GO:1902476)|membrane depolarization (GO:0051899)|sensory perception of smell (GO:0007608)	chloride channel complex (GO:0034707)|cilium (GO:0005929)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.K420K(1)		breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)	12						TACTCCGCAAGAACAGCTGCG	0.741																																					p.K420K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1260A	19						.						5.0	7.0	6.0					19																	12868621		1400	3148	4548	12729621	SO:0001819	synonymous_variant	54831	exon9			AF440756	CCDS42506.1	19p13.13	2014-08-12	2006-10-18	2006-10-18	ENSG00000039987	ENSG00000039987		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17107	protein-coding gene	gene with protein product		607335	"""vitelliform macular dystrophy 2-like 1"""	VMD2L1		12032738, 16912113	Standard	NM_017682		Approved	FLJ20132	uc002mux.3	Q8NFU1	OTTHUMG00000169293	ENST00000549706.1:c.1260G>A	19.37:g.12868621G>A		Somatic		Capture	Illumina HiSeq	Phase_I	12729621	NM_017682	Q53YQ8|Q9NXP0	Silent	SNP	ENST00000549706.1	37	CCDS42506.1																																																																																				0.741	BEST2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403343.1	NM_017682	
MAST1	22983	broad.mit.edu	37	19	12958129	12958129	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:12958129T>C	ENST00000251472.4	+	5	392	c.353T>C	c.(352-354)cTt>cCt	p.L118P	MAST1_ENST00000591495.1_Missense_Mutation_p.L114P	NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1									p.L118P(1)		NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						CAGGAGCGCCTTCACCAGCTG	0.672											OREG0025277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L118P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T353C	19						.						57.0	54.0	55.0					19																	12958129		2203	4300	6503	12819129	SO:0001583	missense	22983	exon5			AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613			19034	protein-coding gene	gene with protein product		612256					Standard	NM_014975		Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000251472.4:c.353T>C	19.37:g.12958129T>C	ENSP00000251472:p.Leu118Pro	Somatic	683	Capture	Illumina HiSeq	Phase_I	12819129	NM_014975		Missense_Mutation	SNP	ENST00000251472.4	37	CCDS32921.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.625137	0.87560	.	.	ENSG00000105613	ENST00000251472;ENST00000542153	T	0.50813	0.73	5.18	5.18	0.71444	Microtubule-associated serine/threonine-protein kinase, domain (1);	0.000000	0.56097	D	0.000023	T	0.74809	0.3765	M	0.92970	3.365	0.80722	D	1	D;D	0.89917	0.995;1.0	D;D	0.87578	0.976;0.998	T	0.81486	-0.0911	10	0.87932	D	0	-17.6612	13.2846	0.60235	0.0:0.0:0.0:1.0	.	118;118	Q9Y2H9;F5H2S9	MAST1_HUMAN;.	P	118	ENSP00000251472:L118P	ENSP00000251472:L118P	L	+	2	0	MAST1	12819129	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.698000	0.84413	2.091000	0.63221	0.459000	0.35465	CTT		0.672	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975	
CALR	811	broad.mit.edu	37	19	13054434	13054434	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:13054434C>T	ENST00000316448.5	+	8	1117	c.1044C>T	c.(1042-1044)ggC>ggT	p.G348G	CTC-425F1.4_ENST00000589120.1_RNA|RAD23A_ENST00000586534.1_5'Flank|RAD23A_ENST00000592268.1_5'Flank|RAD23A_ENST00000316856.3_5'Flank|RAD23A_ENST00000541222.1_5'Flank	NM_004343.3	NP_004334.1	P27797	CALR_HUMAN	calreticulin	348	C-domain.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|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)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|cellular response to lithium ion (GO:0071285)|cellular senescence (GO:0090398)|chaperone-mediated protein folding (GO:0061077)|cortical actin cytoskeleton organization (GO:0030866)|endoplasmic reticulum unfolded protein response (GO:0030968)|glucocorticoid receptor signaling pathway (GO:0042921)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|peptide antigen assembly with MHC class I protein complex (GO:0002502)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of DNA replication (GO:0045740)|positive regulation of gene expression (GO:0010628)|positive regulation of phagocytosis (GO:0050766)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|post-translational protein modification (GO:0043687)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein localization to nucleus (GO:0034504)|protein maturation by protein folding (GO:0022417)|protein N-linked glycosylation via asparagine (GO:0018279)|protein stabilization (GO:0050821)|regulation of apoptotic process (GO:0042981)|regulation of meiosis (GO:0040020)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to testosterone (GO:0033574)|sequestering of calcium ion (GO:0051208)|spermatogenesis (GO:0007283)	acrosomal vesicle (GO:0001669)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|intracellular (GO:0005622)|membrane (GO:0016020)|MHC class I peptide loading complex (GO:0042824)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasmic reticulum (GO:0016529)	androgen receptor binding (GO:0050681)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|chaperone binding (GO:0051087)|complement component C1q binding (GO:0001849)|DNA binding (GO:0003677)|glycoprotein binding (GO:0001948)|hormone binding (GO:0042562)|integrin binding (GO:0005178)|iron ion binding (GO:0005506)|mRNA binding (GO:0003729)|peptide binding (GO:0042277)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)	p.G348G(1)		kidney(1)|large_intestine(3)|lung(5)|ovary(1)	10					Antihemophilic Factor(DB00025)|Melatonin(DB01065)|Tenecteplase(DB00031)	AGACGTGGGGCGTAACAAAGG	0.602																																					p.G348G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1044T	19						.						137.0	112.0	121.0					19																	13054434		2203	4300	6503	12915434	SO:0001819	synonymous_variant	811	exon8			M84739	CCDS12288.1	19p13.3-p13.2	2014-09-17				ENSG00000179218			1455	protein-coding gene	gene with protein product	"""Sicca syndrome antigen A (autoantigen Ro; calreticulin)"", ""autoantigen Ro"""	109091				2365822	Standard	NM_004343		Approved	RO, SSA, cC1qR, CRT, FLJ26680	uc002mvu.2	P27797		ENST00000316448.5:c.1044C>T	19.37:g.13054434C>T		Somatic		Capture	Illumina HiSeq	Phase_I	12915434	NM_004343	Q6IAT4|Q9UDG2	Silent	SNP	ENST00000316448.5	37	CCDS12288.1																																																																																				0.602	CALR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451952.1	NM_004343	
CACNA1A	773	broad.mit.edu	37	19	13414691	13414691	+	Missense_Mutation	SNP	G	G	A	rs121908212		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:13414691G>A	ENST00000360228.5	-	16	1993	c.1994C>T	c.(1993-1995)aCg>aTg	p.T665M	CACNA1A_ENST00000573710.2_Missense_Mutation_p.T666M	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	666					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.T666M(3)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	GTCTTCGCCCGTCAGGATCTG	0.597																																					p.T666M												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.C1997T	19	GRCh37	CM960238	CACNA1A	M	rs121908212	.						121.0	123.0	122.0					19																	13414691		2003	4160	6163	13275691	SO:0001583	missense	773	exon16			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.1994C>T	19.37:g.13414691G>A	ENSP00000353362:p.Thr665Met	Somatic		Capture	Illumina HiSeq	Phase_I	13275691	NM_001174080	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	G	16.23	3.064260	0.55432	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.98889	-5.21	4.58	3.55	0.40652	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99357	0.9774	H	0.97023	3.925	0.48901	A	0.999722	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	D	0.99624	1.0984	9	0.87932	D	0	.	11.6149	0.51083	0.0887:0.0:0.9113:0.0	.	666;666;665	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	M	665;666;666;666	ENSP00000353362:T665M	ENSP00000317661:T666M	T	-	2	0	CACNA1A	13275691	1.000000	0.71417	0.966000	0.40874	0.989000	0.77384	9.507000	0.97996	1.151000	0.42436	-0.229000	0.12294	ACG		0.597	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
CCDC130	81576	broad.mit.edu	37	19	13865103	13865103	+	Splice_Site	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:13865103G>T	ENST00000586600.1	+	4	507	c.4G>T	c.(4-6)Ggt>Tgt	p.G2C	CCDC130_ENST00000221554.8_Splice_Site_p.G2C			P13994	CC130_HUMAN	coiled-coil domain containing 130	2					response to virus (GO:0009615)			p.G2C(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)			TGCTTTGCAGGGTGAAAGGAA	0.453																																					p.G2C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4T	19						.						108.0	87.0	94.0					19																	13865103		2203	4300	6503	13726103	SO:0001630	splice_region_variant	81576	exon3			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.4-1G>T	19.37:g.13865103G>T		Somatic		Capture	Illumina HiSeq	Phase_I	13726103	NM_030818	Q9BQ72	Missense_Mutation	SNP	ENST00000586600.1	37	CCDS12296.1	.	.	.	.	.	.	.	.	.	.	G	19.06	3.753557	0.69648	.	.	ENSG00000104957	ENST00000540216;ENST00000221554	T	0.38560	1.13	4.1	4.1	0.47936	.	0.000000	0.85682	D	0.000000	T	0.69260	0.3091	M	0.89904	3.07	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.982;0.999	T	0.76578	-0.2908	9	.	.	.	-22.0187	13.8781	0.63665	0.0:0.0:1.0:0.0	.	2;2	B7Z1U2;P13994	.;CC130_HUMAN	C	2	ENSP00000221554:G2C	.	G	+	1	0	CCDC130	13726103	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	8.216000	0.89764	2.124000	0.65301	0.462000	0.41574	GGT		0.453	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818	Missense_Mutation
CCDC130	81576	broad.mit.edu	37	19	13869815	13869815	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:13869815C>T	ENST00000586600.1	+	8	894	c.391C>T	c.(391-393)Ctg>Ttg	p.L131L	CCDC130_ENST00000221554.8_Silent_p.L131L			P13994	CC130_HUMAN	coiled-coil domain containing 130	131					response to virus (GO:0009615)			p.L131L(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)			TGAGCAGGTGCTGACCACAGG	0.662																																					p.L131L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C391T	19						.						38.0	36.0	37.0					19																	13869815		2203	4300	6503	13730815	SO:0001819	synonymous_variant	81576	exon7			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.391C>T	19.37:g.13869815C>T		Somatic		Capture	Illumina HiSeq	Phase_I	13730815	NM_030818	Q9BQ72	Silent	SNP	ENST00000586600.1	37	CCDS12296.1																																																																																				0.662	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818	
IL27RA	9466	broad.mit.edu	37	19	14150596	14150596	+	Silent	SNP	C	C	T	rs371298670		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:14150596C>T	ENST00000263379.2	+	4	533	c.408C>T	c.(406-408)gaC>gaT	p.D136D		NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	136	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)	p.D136D(1)		breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						TGGGCCCTGACGTGGACTTTT	0.612																																					p.D136D	Colon(164;1849 1896 4443 37792 47834)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C408T	19						.	C		0,4406		0,0,2203	54.0	59.0	57.0		408	-8.9	0.0	19		57	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	IL27RA	NM_004843.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		136/637	14150596	1,13005	2203	4300	6503	14011596	SO:0001819	synonymous_variant	9466	exon4			AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	17290	protein-coding gene	gene with protein product	"""T-cell cytokine receptor type 1"""	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.408C>T	19.37:g.14150596C>T		Somatic		Capture	Illumina HiSeq	Phase_I	14011596	NM_004843	A0N0L1|O60624	Silent	SNP	ENST00000263379.2	37	CCDS12303.1																																																																																				0.612	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843	
PRKACA	5566	broad.mit.edu	37	19	14217584	14217584	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:14217584G>A	ENST00000308677.4	-	3	421	c.225C>T	c.(223-225)ctC>ctT	p.L75L	PRKACA_ENST00000589994.1_Silent_p.L67L|PRKACA_ENST00000350356.3_5'UTR|PRKACA_ENST00000590853.1_Intron	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha	75	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.L75L(1)		central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16						TCTGTTTGTCGAGGATCTTCA	0.582																																					p.L75L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C225T	19						.						146.0	128.0	134.0					19																	14217584		2203	4300	6503	14078584	SO:0001819	synonymous_variant	5566	exon3				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.225C>T	19.37:g.14217584G>A		Somatic		Capture	Illumina HiSeq	Phase_I	14078584	NM_002730	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	Silent	SNP	ENST00000308677.4	37	CCDS12304.1																																																																																				0.582	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459004.1	NM_002730	
OR7C1	26664	broad.mit.edu	37	19	14910191	14910191	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:14910191C>T	ENST00000248073.2	-	1	832	c.758G>A	c.(757-759)gGc>gAc	p.G253D	OR7A5_ENST00000601611.1_Intron	NM_198944.1	NP_945182.1	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C, member 1	253					spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G253D(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(2)|ovary(2)|prostate(1)	18						AAAGCCCGTGCCATAGAACAA	0.502																																					p.G253D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G758A	19						.						80.0	75.0	77.0					19																	14910191		2203	4300	6503	14771191	SO:0001583	missense	26664	exon1			X89676	CCDS12317.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8373	protein-coding gene	gene with protein product				OR7C4			Standard	NM_198944		Approved	OR19-5	uc010xnz.2	O76099		ENST00000248073.2:c.758G>A	19.37:g.14910191C>T	ENSP00000248073:p.Gly253Asp	Somatic		Capture	Illumina HiSeq	Phase_I	14771191	NM_198944	Q15621|Q6IFP2|Q96R94	Missense_Mutation	SNP	ENST00000248073.2	37	CCDS12317.1	.	.	.	.	.	.	.	.	.	.	c	14.28	2.486962	0.44249	.	.	ENSG00000127530	ENST00000248073	T	0.39229	1.09	3.64	1.43	0.22495	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35585	U	0.003104	T	0.71409	0.3336	H	0.98218	4.175	0.09310	N	1	D	0.76494	0.999	D	0.81914	0.995	T	0.62115	-0.6922	10	0.59425	D	0.04	.	6.6475	0.22943	0.0:0.7104:0.1826:0.107	.	253	O76099	OR7C1_HUMAN	D	253	ENSP00000248073:G253D	ENSP00000248073:G253D	G	-	2	0	OR7C1	14771191	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.459000	0.06728	0.329000	0.23460	0.543000	0.68304	GGC		0.502	OR7C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466519.1		
OR1I1	126370	broad.mit.edu	37	19	15198754	15198754	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:15198754G>A	ENST00000209540.2	+	1	964	c.878G>A	c.(877-879)cGg>cAg	p.R293Q		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	293						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R293Q(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						TACAGCATACGGAACAAGGAT	0.542																																					p.R293Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G878A	19						.						115.0	98.0	104.0					19																	15198754		2203	4300	6503	15059754	SO:0001583	missense	126370	exon1			AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"""GPCR / Class A : Olfactory receptors"""	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.878G>A	19.37:g.15198754G>A	ENSP00000209540:p.Arg293Gln	Somatic		Capture	Illumina HiSeq	Phase_I	15059754	NM_001004713	Q96R92	Missense_Mutation	SNP	ENST00000209540.2	37	CCDS32937.1	.	.	.	.	.	.	.	.	.	.	G	11.87	1.766796	0.31320	.	.	ENSG00000094661	ENST00000209540	T	0.41065	1.01	4.64	4.64	0.57946	.	0.000000	0.34338	U	0.004058	T	0.34832	0.0911	L	0.45470	1.425	0.26554	N	0.973851	B	0.18968	0.032	B	0.17098	0.017	T	0.30031	-0.9992	10	0.72032	D	0.01	.	8.6024	0.33754	0.1028:0.0:0.8972:0.0	.	293	O60431	OR1I1_HUMAN	Q	293	ENSP00000209540:R293Q	ENSP00000209540:R293Q	R	+	2	0	OR1I1	15059754	1.000000	0.71417	0.994000	0.49952	0.221000	0.24807	2.839000	0.48207	2.423000	0.82170	0.555000	0.69702	CGG		0.542	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1		
ILVBL	10994	broad.mit.edu	37	19	15234252	15234252	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:15234252G>A	ENST00000263383.3	-	3	410	c.271C>T	c.(271-273)Cgt>Tgt	p.R91C	AC003956.1_ENST00000598450.1_RNA|ILVBL_ENST00000531635.1_5'UTR|ILVBL_ENST00000534378.1_5'UTR	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	91						integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)	p.R91C(1)		NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						TCCACCACACGGATGCCCAGT	0.637																																					p.R91C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C271T	19						.						107.0	86.0	93.0					19																	15234252		2203	4300	6503	15095252	SO:0001583	missense	10994	exon3			U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"""acetolactate synthase homolog"""	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.271C>T	19.37:g.15234252G>A	ENSP00000263383:p.Arg91Cys	Somatic		Capture	Illumina HiSeq	Phase_I	15095252	NM_006844	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Missense_Mutation	SNP	ENST00000263383.3	37	CCDS12325.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.479770	0.63849	.	.	ENSG00000105135	ENST00000263383;ENST00000269733;ENST00000527093;ENST00000533747	T	0.36878	1.23	4.19	3.15	0.36227	Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain (1);	0.109371	0.64402	N	0.000005	T	0.59742	0.2216	H	0.98901	4.365	0.80722	D	1	P	0.34837	0.472	B	0.39971	0.315	T	0.66901	-0.5806	10	0.87932	D	0	-1.6795	9.5159	0.39104	0.1073:0.0:0.8927:0.0	.	91	A1L0T0	ILVBL_HUMAN	C	91	ENSP00000263383:R91C	ENSP00000263383:R91C	R	-	1	0	ILVBL	15095252	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	7.469000	0.80959	0.753000	0.32945	0.462000	0.41574	CGT		0.637	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844	
BRD4	23476	broad.mit.edu	37	19	15367050	15367050	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:15367050C>T	ENST00000263377.2	-	9	1797	c.1576G>A	c.(1576-1578)Gca>Aca	p.A526T	BRD4_ENST00000602230.1_5'UTR|BRD4_ENST00000360016.5_Missense_Mutation_p.A526T|BRD4_ENST00000371835.4_Missense_Mutation_p.A526T	NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	526	BID region.				cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)	p.A526T(2)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			GAGAGGGCTGCAAGCTGCTCG	0.502			T	C15orf55	lethal midline carcinoma of young people																																p.A526T			Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1576A	19						.						117.0	116.0	117.0					19																	15367050		2203	4300	6503	15228050	SO:0001583	missense	23476	exon9			Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"""chromosome-associated protein"""	608749	"""bromodomain-containing 4"""			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.1576G>A	19.37:g.15367050C>T	ENSP00000263377:p.Ala526Thr	Somatic		Capture	Illumina HiSeq	Phase_I	15228050	NM_014299	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	37	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	C	31	5.086656	0.94100	.	.	ENSG00000141867	ENST00000263377;ENST00000371835;ENST00000360016	T;T;T	0.11277	2.79;4.29;4.29	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000006	T	0.27832	0.0685	L	0.43554	1.36	0.80722	D	1	D;B;D	0.89917	1.0;0.365;1.0	D;B;D	0.83275	0.996;0.3;0.994	T	0.00250	-1.1878	10	0.52906	T	0.07	-14.1346	18.2814	0.90099	0.0:1.0:0.0:0.0	.	526;526;526	Q4G0X8;O60885-2;O60885	.;.;BRD4_HUMAN	T	526	ENSP00000263377:A526T;ENSP00000360901:A526T;ENSP00000353112:A526T	ENSP00000263377:A526T	A	-	1	0	BRD4	15228050	1.000000	0.71417	0.989000	0.46669	0.992000	0.81027	7.818000	0.86416	2.627000	0.88993	0.561000	0.74099	GCA		0.502	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243	
WIZ	58525	broad.mit.edu	37	19	15538036	15538036	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:15538036C>T	ENST00000389282.4	-	6	3622	c.3409G>A	c.(3409-3411)Gcc>Acc	p.A1137T	WIZ_ENST00000545156.1_Missense_Mutation_p.A451T|WIZ_ENST00000599686.3_Missense_Mutation_p.A321T|WIZ_ENST00000599910.2_Missense_Mutation_p.A454T|WIZ_ENST00000263381.7_Missense_Mutation_p.A280T			O95785	WIZ_HUMAN	widely interspaced zinc finger motifs	1137	Pro-rich.				positive regulation of nuclear cell cycle DNA replication (GO:0010571)|protein heterotrimerization (GO:0070208)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.A280T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	24						AACTTCTTGGCCAAGGGTGAG	0.657																																					p.A280T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G838A	19						.						41.0	48.0	45.0					19																	15538036		2040	4186	6226	15399036	SO:0001583	missense	58525	exon4			AK091183	CCDS42516.1	19p13.12	2012-10-05	2007-01-18		ENSG00000011451	ENSG00000011451		"""Zinc fingers, C2H2-type"""	30917	protein-coding gene	gene with protein product			"""WIZ zinc finger"""			9795207, 12226707	Standard	NM_021241		Approved	ZNF803	uc002nbb.4	O95785		ENST00000389282.4:c.3409G>A	19.37:g.15538036C>T	ENSP00000373933:p.Ala1137Thr	Somatic		Capture	Illumina HiSeq	Phase_I	15399036	NM_021241	B3KVH1|B7ZM82|M0QY21|Q4G0E0|Q6P6B0|Q6ZN24|Q7LDY6|Q7LDZ1|Q96IG5|Q96SQ6|Q9BUR8|Q9NPT1	Missense_Mutation	SNP	ENST00000389282.4	37		.	.	.	.	.	.	.	.	.	.	C	12.82	2.053459	0.36181	.	.	ENSG00000011451	ENST00000389282;ENST00000263381;ENST00000416927;ENST00000545156	T;T;T	0.26957	1.7;1.7;1.7	5.19	2.74	0.32292	.	0.630498	0.15920	N	0.238145	T	0.11239	0.0274	N	0.12182	0.205	0.23356	N	0.997843	B;B;B	0.21071	0.0;0.051;0.0	B;B;B	0.14023	0.0;0.01;0.001	T	0.28839	-1.0031	10	0.05620	T	0.96	-10.9095	9.59	0.39539	0.0:0.7095:0.2015:0.089	.	1137;280;321	O95785;O95785-2;B3KVH1	WIZ_HUMAN;.;.	T	1137;280;321;451	ENSP00000373933:A1137T;ENSP00000263381:A280T;ENSP00000445824:A451T	ENSP00000263381:A280T	A	-	1	0	WIZ	15399036	0.963000	0.33076	1.000000	0.80357	0.963000	0.63663	0.636000	0.24644	1.297000	0.44761	0.561000	0.74099	GCC		0.657	WIZ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021241	
AD000091.2	0	broad.mit.edu	37	19	15726466	15726466	+	lincRNA	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:15726466G>A	ENST00000589196.2	-	0	0				CYP4F8_ENST00000441682.2_RNA														p.P13P(2)									GCCTCAGGCCGGTGGCAGCAT	0.682																																					p.P13P												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.G39A	19						.						25.0	29.0	27.0					19																	15726466		2201	4293	6494	15587466			11283	exon2																															19.37:g.15726466G>A		Somatic		Capture	Illumina HiSeq	Phase_I	15587466	NM_007253		Silent	SNP	ENST00000589196.2	37																																																																																					0.682	AD000091.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000460896.2		
CYP4F2	8529	broad.mit.edu	37	19	16000345	16000345	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:16000345G>A	ENST00000221700.6	-	7	901	c.806C>T	c.(805-807)gCc>gTc	p.A269V	CYP4F2_ENST00000011989.7_Missense_Mutation_p.A120V	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2									p.A269V(1)		NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CTGGATGACGGCATCTGTGAA	0.557																																					p.A269V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C806T	19						.						98.0	94.0	96.0					19																	16000345		2203	4300	6503	15861345	SO:0001583	missense	8529	exon7			U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.806C>T	19.37:g.16000345G>A	ENSP00000221700:p.Ala269Val	Somatic		Capture	Illumina HiSeq	Phase_I	15861345	NM_001082		Missense_Mutation	SNP	ENST00000221700.6	37	CCDS12336.1	.	.	.	.	.	.	.	.	.	.	g	14.42	2.529407	0.44969	.	.	ENSG00000186115	ENST00000221700;ENST00000392846;ENST00000011989	T;T	0.69435	-0.4;1.49	2.72	2.72	0.32119	.	0.638866	0.12540	U	0.459953	T	0.74898	0.3777	M	0.68317	2.08	0.09310	N	1	B;P	0.38167	0.407;0.621	P;P	0.55260	0.493;0.772	T	0.63341	-0.6659	10	0.46703	T	0.11	.	7.6591	0.28392	0.0:0.2648:0.7352:0.0	.	120;269	B4DV75;P78329	.;CP4F2_HUMAN	V	269;120;120	ENSP00000221700:A269V;ENSP00000011989:A120V	ENSP00000011989:A120V	A	-	2	0	CYP4F2	15861345	0.001000	0.12720	0.136000	0.22124	0.773000	0.43773	0.858000	0.27845	1.495000	0.48549	0.305000	0.20034	GCC		0.557	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082	
CYP4F2	8529	broad.mit.edu	37	19	16003140	16003140	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:16003140A>G	ENST00000221700.6	-	5	599	c.504T>C	c.(502-504)aaT>aaC	p.N168N	CYP4F2_ENST00000011989.7_Silent_p.N19N	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2									p.N168N(1)		NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TCACACTCTCATTGAAAATCT	0.512																																					p.N168N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T504C	19						.						133.0	135.0	134.0					19																	16003140		2203	4300	6503	15864140	SO:0001819	synonymous_variant	8529	exon5			U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.504T>C	19.37:g.16003140A>G		Somatic		Capture	Illumina HiSeq	Phase_I	15864140	NM_001082		Silent	SNP	ENST00000221700.6	37	CCDS12336.1																																																																																				0.512	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082	
TPM4	7171	broad.mit.edu	37	19	16192805	16192805	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:16192805C>T	ENST00000300933.4	+	2	475	c.215C>T	c.(214-216)aCg>aTg	p.T72M	TPM4_ENST00000538887.1_Missense_Mutation_p.T108M|TPM4_ENST00000344824.6_Missense_Mutation_p.T108M	NM_003290.2	NP_003281.1	P67936	TPM4_HUMAN	tropomyosin 4	72					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|osteoblast differentiation (GO:0001649)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|membrane (GO:0016020)|muscle thin filament tropomyosin (GO:0005862)|podosome (GO:0002102)|stress fiber (GO:0001725)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)	p.T108M(1)|p.T72M(1)	TPM4/ALK(12)	breast(1)|large_intestine(3)	4						CGACTGGCCACGGCCCTGCAG	0.572			T	ALK	ALCL																																p.T108M			Dom	yes		19	19p13.1	7171	tropomyosin 4		L	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C323T	19						.						56.0	51.0	53.0					19																	16192805		2203	4300	6503	16053805	SO:0001583	missense	7171	exon3				CCDS12338.1, CCDS46007.1	19p13.1	2013-03-11			ENSG00000167460	ENSG00000167460		"""Tropomyosins"""	12013	protein-coding gene	gene with protein product		600317				8641132	Standard	NM_003290		Approved		uc002ndi.2	P67936	OTTHUMG00000182134	ENST00000300933.4:c.215C>T	19.37:g.16192805C>T	ENSP00000300933:p.Thr72Met	Somatic		Capture	Illumina HiSeq	Phase_I	16053805	NM_001145160	P07226|Q15659|Q5U0D9|Q9BU85|Q9H8Q3|Q9UCS1|Q9UCS2|Q9UCS3|Q9UCS4	Missense_Mutation	SNP	ENST00000300933.4	37	CCDS12338.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.991355	0.74703	.	.	ENSG00000167460	ENST00000344824;ENST00000538887;ENST00000300933	D;D;D	0.97575	-4.44;-4.44;-4.44	4.62	4.62	0.57501	.	0.181985	0.31041	U	0.008380	D	0.98482	0.9494	H	0.94183	3.505	0.80722	D	1	P;B	0.43938	0.822;0.11	P;B	0.52598	0.703;0.253	D	0.99893	1.1140	10	0.87932	D	0	-0.3404	16.8417	0.85971	0.0:1.0:0.0:0.0	.	72;108	P67936;P67936-2	TPM4_HUMAN;.	M	108;108;72	ENSP00000345230:T108M;ENSP00000439135:T108M;ENSP00000300933:T72M	ENSP00000300933:T72M	T	+	2	0	TPM4	16053805	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	7.522000	0.81844	2.265000	0.75225	0.591000	0.81541	ACG		0.572	TPM4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459673.2	NM_003290	
C19orf44	84167	broad.mit.edu	37	19	16620612	16620612	+	Silent	SNP	C	C	T	rs368527845		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:16620612C>T	ENST00000221671.3	+	5	1608	c.1452C>T	c.(1450-1452)acC>acT	p.T484T	CTD-3222D19.2_ENST00000409035.1_Intron|C19orf44_ENST00000594035.1_Silent_p.T484T	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	484								p.T484T(1)		endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						CTGAGCCAACCGCCCATTCCA	0.498																																					p.T484T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1452T	19						.	T		0,4406		0,0,2203	114.0	113.0	113.0		1452	-7.6	0.0	19		113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C19orf44	NM_032207.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		484/658	16620612	1,13005	2203	4300	6503	16481612	SO:0001819	synonymous_variant	84167	exon5			AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.1452C>T	19.37:g.16620612C>T		Somatic		Capture	Illumina HiSeq	Phase_I	16481612	NM_032207	Q8N6Y7	Silent	SNP	ENST00000221671.3	37	CCDS12345.1																																																																																				0.498	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207	
NWD1	284434	broad.mit.edu	37	19	16910774	16910774	+	Silent	SNP	C	C	T	rs370525441		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:16910774C>T	ENST00000552788.1	+	15	3537	c.3537C>T	c.(3535-3537)cgC>cgT	p.R1179R	NWD1_ENST00000549814.1_Intron|NWD1_ENST00000523826.1_Silent_p.R973R|NWD1_ENST00000379808.3_Silent_p.R1179R|NWD1_ENST00000339803.6_Silent_p.R1044R|NWD1_ENST00000524140.2_Silent_p.R1179R|CTD-2538G9.6_ENST00000601661.1_RNA			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	1179							ATP binding (GO:0005524)	p.R1044R(2)|p.R1179R(1)		NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TGCTGGCCCGCGGCGGGGCTT	0.627																																					p.R1179R												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C3537T	19						.	C		1,4405	2.1+/-5.4	0,1,2202	43.0	45.0	44.0		3537	-3.8	0.0	19		44	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	NWD1	NM_001007525.3		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		1179/1433	16910774	2,13004	2203	4300	6503	16771774	SO:0001819	synonymous_variant	284434	exon17			BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.3537C>T	19.37:g.16910774C>T		Somatic		Capture	Illumina HiSeq	Phase_I	16771774	NM_001007525	C9J021|Q68CT3	Silent	SNP	ENST00000552788.1	37																																																																																					0.627	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
CPAMD8	27151	broad.mit.edu	37	19	17058003	17058003	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:17058003T>C	ENST00000443236.1	-	21	2715	c.2684A>G	c.(2683-2685)cAg>cGg	p.Q895R		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	848						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.Q895R(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CCCAACAAACTGGATGCCCTT	0.612																																					p.Q895R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2684G	19						.						163.0	162.0	162.0					19																	17058003		2058	4219	6277	16919003	SO:0001583	missense	27151	exon21			AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.2684A>G	19.37:g.17058003T>C	ENSP00000402505:p.Gln895Arg	Somatic		Capture	Illumina HiSeq	Phase_I	16919003	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.212|4.212	0.038168|0.038168	0.08148|0.08148	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	3.38|3.38	-0.635|-0.635	0.11512|0.11512	.|.	0.569034|.	0.16065|.	N|.	0.231262|.	T|T	0.15262|0.15262	0.0368|0.0368	N|N	0.00926|0.00926	-1.1|-1.1	0.80722|0.80722	D|D	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.14337|0.14337	-1.0476|-1.0476	9|5	0.15952|.	T|.	0.53|.	.|.	8.9436|8.9436	0.35745|0.35745	0.0:0.2885:0.0:0.7115|0.0:0.2885:0.0:0.7115	.|.	848|.	Q8IZJ3|.	CPMD8_HUMAN|.	R|G	895|906	.|.	ENSP00000291440:Q895R|.	Q|S	-|-	2|1	0|0	CPAMD8|CPAMD8	16919003|16919003	1.000000|1.000000	0.71417|0.71417	0.057000|0.057000	0.19452|0.19452	0.994000|0.994000	0.84299|0.84299	1.762000|1.762000	0.38451|0.38451	-0.556000|-0.556000	0.06134|0.06134	0.402000|0.402000	0.26972|0.26972	CAG|AGT		0.612	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
HAUS8	93323	broad.mit.edu	37	19	17166714	17166714	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:17166714G>A	ENST00000253669.5	-	9	934	c.744C>T	c.(742-744)ccC>ccT	p.P248P	HAUS8_ENST00000448593.2_Silent_p.P247P|HAUS8_ENST00000593360.1_Silent_p.P187P|CTD-2528A14.3_ENST00000598893.1_RNA			Q9BT25	HAUS8_HUMAN	HAUS augmin-like complex, subunit 8	248					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)		p.P248P(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)	12						TGGACCTCACGGGCAGCTCGT	0.637																																					p.P247P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C741T	19						.						131.0	102.0	112.0					19																	17166714		2203	4300	6503	17027714	SO:0001819	synonymous_variant	93323	exon9			BC004398	CCDS32948.1, CCDS46009.1	19p13.11	2013-10-11	2009-04-20	2009-04-20	ENSG00000131351	ENSG00000131351		"""HAUS augmin-like complex subunits"""	30532	protein-coding gene	gene with protein product		613434	"""HEC1/NDC80 interacting, centrosome associated 1"""	HICE1		19427217	Standard	XM_005260154		Approved	MGC20533, NY-SAR-48	uc002nfe.3	Q9BT25		ENST00000253669.5:c.744C>T	19.37:g.17166714G>A		Somatic		Capture	Illumina HiSeq	Phase_I	17027714	NM_001011699	B4DJA7|C9JBZ4|Q49AC4|Q86WF0|Q96FX3	Silent	SNP	ENST00000253669.5	37	CCDS32948.1																																																																																				0.637	HAUS8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463015.1	NM_001011699	
ANO8	57719	broad.mit.edu	37	19	17443979	17443979	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:17443979G>A	ENST00000159087.4	-	4	578	c.420C>T	c.(418-420)cgC>cgT	p.R140R	GTPBP3_ENST00000361619.5_5'Flank	NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	140					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.R140R(1)		autonomic_ganglia(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(3)	27						AGGAGAAGCCGCGGGTGCCCC	0.637																																					p.R140R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C420T	19						.						17.0	24.0	22.0					19																	17443979		2201	4293	6494	17304979	SO:0001819	synonymous_variant	57719	exon4			AB046843	CCDS32949.1	19p13.12	2014-04-09	2008-08-28	2008-08-28		ENSG00000074855		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	29329	protein-coding gene	gene with protein product		610216	"""KIAA1623"", ""transmembrane protein 16H"""	KIAA1623, TMEM16H		10997877, 24692353	Standard	NM_020959		Approved		uc002ngf.2	Q9HCE9		ENST00000159087.4:c.420C>T	19.37:g.17443979G>A		Somatic		Capture	Illumina HiSeq	Phase_I	17304979	NM_020959	A6NIJ0	Silent	SNP	ENST00000159087.4	37	CCDS32949.1																																																																																				0.637	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644	
ATP8B3	148229	broad.mit.edu	37	19	1783185	1783185	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:1783185G>A	ENST00000310127.6	-	29	3983	c.3745C>T	c.(3745-3747)Cgt>Tgt	p.R1249C	ATP8B3_ENST00000525591.1_Missense_Mutation_p.R1212C|ATP8B3_ENST00000539485.1_Missense_Mutation_p.R1259C	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	1249					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R1259C(1)		central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		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)		TAGCTGGAACGGCGGGCACGA	0.587																																					p.R1212C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3634T	19						.						48.0	49.0	49.0					19																	1783185		1993	4151	6144	1734185	SO:0001583	missense	148229	exon29			AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.3745C>T	19.37:g.1783185G>A	ENSP00000311336:p.Arg1249Cys	Somatic		Capture	Illumina HiSeq	Phase_I	1734185	NM_001178002	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	37	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.611889	0.66558	.	.	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	T;T;T	0.65732	-0.17;-0.05;-0.07	4.57	4.57	0.56435	.	0.144065	0.47852	D	0.000201	T	0.78710	0.4326	M	0.76727	2.345	0.54753	D	0.999983	D;D	0.89917	1.0;1.0	D;D	0.79108	0.988;0.992	T	0.82323	-0.0514	10	0.87932	D	0	.	16.3466	0.83134	0.0:0.0:1.0:0.0	.	1249;1212	O60423;Q7Z485	AT8B3_HUMAN;.	C	1249;1259;1212	ENSP00000311336:R1249C;ENSP00000443574:R1259C;ENSP00000437115:R1212C	ENSP00000311336:R1249C	R	-	1	0	ATP8B3	1734185	1.000000	0.71417	0.937000	0.37676	0.253000	0.25986	7.161000	0.77505	2.088000	0.63022	0.549000	0.68633	CGT		0.587	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
GTPBP3	84705	broad.mit.edu	37	19	17449774	17449774	+	Silent	SNP	C	C	T	rs150612889	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:17449774C>T	ENST00000324894.8	+	5	671	c.603C>T	c.(601-603)caC>caT	p.H201H	GTPBP3_ENST00000358792.7_Silent_p.H201H|GTPBP3_ENST00000361619.5_Silent_p.H223H|GTPBP3_ENST00000600625.1_Silent_p.H201H|GTPBP3_ENST00000598038.1_3'UTR	NM_032620.3|NM_133644.3	NP_116009.2|NP_598399.2	Q969Y2	GTPB3_HUMAN	GTP binding protein 3 (mitochondrial)	201					tRNA modification (GO:0006400)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.H201H(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)	18						CTCTGGCCCACGTGGAGGCCT	0.622																																					p.H201H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C603T	19						.	C	,,,	1,4405	2.1+/-5.4	0,1,2202	42.0	45.0	44.0		603,669,603,603	-2.5	1.0	19	dbSNP_134	44	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GTPBP3	NM_001128855.2,NM_001195422.1,NM_032620.3,NM_133644.3	,,,	0,8,6495	TT,TC,CC		0.0814,0.0227,0.0615	,,,	201/472,223/515,201/493,201/525	17449774	8,12998	2203	4300	6503	17310774	SO:0001819	synonymous_variant	84705	exon5			AF360742	CCDS32950.1, CCDS32951.1, CCDS56088.1, CCDS59364.1	19p13.2	2008-02-05				ENSG00000130299			14880	protein-coding gene	gene with protein product		608536				1290633	Standard	NM_001128855		Approved	MSS1, THDF1, GTPBG3, MTGP1, FLJ14700	uc010xpo.2	Q969Y2		ENST00000324894.8:c.603C>T	19.37:g.17449774C>T		Somatic		Capture	Illumina HiSeq	Phase_I	17310774	NM_032620	A6NFH1|A6NIG5|A6NKR4|A8K7B4|B7Z4V8|Q8TCY6|Q8WUW9|Q969G4|Q9BX61	De_novo_Start_OutOfFrame	SNP	ENST00000324894.8	37	CCDS32951.1																																																																																				0.622	GTPBP3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463624.1	NM_032620	
KCNN1	3780	broad.mit.edu	37	19	18084837	18084837	+	Missense_Mutation	SNP	C	C	T	rs202131645		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:18084837C>T	ENST00000222249.9	+	3	459	c.140C>T	c.(139-141)gCc>gTc	p.A47V	RNA5SP468_ENST00000516782.1_RNA	NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	47					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.A64V(1)		endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	GTGGTAGTGGCCAAGAGTGAG	0.741																																					p.A47V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C140T	19						.						14.0	21.0	19.0					19																	18084837		1871	4079	5950	17945837	SO:0001583	missense	3780	exon3			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.140C>T	19.37:g.18084837C>T	ENSP00000476519:p.Ala47Val	Somatic		Capture	Illumina HiSeq	Phase_I	17945837	NM_002248	Q5KR10|Q6DJU4	Missense_Mutation	SNP	ENST00000222249.9	37		.	.	.	.	.	.	.	.	.	.	C	21.5	4.151853	0.78001	.	.	ENSG00000105642	ENST00000222249;ENST00000536713	.	.	.	4.15	3.08	0.35506	.	1.031890	0.07654	N	0.932538	T	0.46776	0.1410	L	0.44542	1.39	0.30879	N	0.731675	B	0.22146	0.065	B	0.20577	0.03	T	0.46735	-0.9170	9	0.41790	T	0.15	-15.7521	10.6842	0.45833	0.1926:0.8074:0.0:0.0	.	47	Q92952	KCNN1_HUMAN	V	64;47	.	ENSP00000222249:A64V	A	+	2	0	KCNN1	17945837	1.000000	0.71417	0.996000	0.52242	0.916000	0.54674	3.541000	0.53618	0.925000	0.37094	0.561000	0.74099	GCC		0.741	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248	
KCNN1	3780	broad.mit.edu	37	19	18092781	18092781	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:18092781C>T	ENST00000222249.9	+	5	1081	c.762C>T	c.(760-762)gaC>gaT	p.D254D		NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	254					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.D271D(1)		endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	TCTTCACGGACGCCTCGAGCC	0.622																																					p.D254D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C762T	19						.						40.0	35.0	36.0					19																	18092781		2203	4300	6503	17953781	SO:0001819	synonymous_variant	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.762C>T	19.37:g.18092781C>T		Somatic		Capture	Illumina HiSeq	Phase_I	17953781	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																					0.622	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248	
MAST3	23031	broad.mit.edu	37	19	18235490	18235490	+	Silent	SNP	G	G	A	rs368862013		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:18235490G>A	ENST00000262811.6	+	10	897	c.897G>A	c.(895-897)gcG>gcA	p.A299A	MAST3_ENST00000608648.1_3'UTR	NM_015016.1	NP_055831.1	O60307	MAST3_HUMAN	microtubule associated serine/threonine kinase 3	299							ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.A321A(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						TGCTGGAGGCGGCTGAGGGCC	0.622																																					p.A299A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G897A	19						.	G		0,3938		0,0,1969	28.0	34.0	32.0		897	-6.3	0.6	19		32	1,8323		0,1,4161	no	coding-synonymous	MAST3	NM_015016.1		0,1,6130	AA,AG,GG		0.012,0.0,0.0082		299/1310	18235490	1,12261	1969	4162	6131	18096490	SO:0001819	synonymous_variant	23031	exon10			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.897G>A	19.37:g.18235490G>A		Somatic		Capture	Illumina HiSeq	Phase_I	18096490	NM_015016	Q7LDZ8|Q9UPI0	Silent	SNP	ENST00000262811.6	37	CCDS46014.1																																																																																				0.622	MAST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466526.2	XM_038150	
IFI30	10437	broad.mit.edu	37	19	18288047	18288047	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:18288047G>A	ENST00000407280.3	+	5	756	c.581G>A	c.(580-582)cGg>cAg	p.R194Q	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	194					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 II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of fibroblast proliferation (GO:0048147)|protein stabilization (GO:0050821)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	oxidoreductase activity, acting on a sulfur group of donors (GO:0016667)	p.R194Q(1)		endometrium(1)|kidney(2)|large_intestine(1)|stomach(1)	5						AACGCCCAGCGGACAGATGCT	0.592																																					p.R194Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G581A	19						.						40.0	41.0	41.0					19																	18288047		2160	4253	6413	18149047	SO:0001583	missense	10437	exon5			J03909	CCDS46015.1	19p13.1	2008-07-16				ENSG00000216490			5398	protein-coding gene	gene with protein product	"""gamma-interferon-inducible lysosomal thiol reductase"", ""interferon gamma-inducible protein 30 preproprotein"""	604664				3136170, 10639150	Standard	NM_006332		Approved	IFI-30, GILT, IP30, MGC32056	uc002nic.1	P13284		ENST00000407280.3:c.581G>A	19.37:g.18288047G>A	ENSP00000384886:p.Arg194Gln	Somatic		Capture	Illumina HiSeq	Phase_I	18149047	NM_006332	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Missense_Mutation	SNP	ENST00000407280.3	37	CCDS46015.1	.	.	.	.	.	.	.	.	.	.	G	8.805	0.933860	0.18206	.	.	ENSG00000216490	ENST00000407280	T	0.28666	1.6	5.1	1.65	0.23941	.	.	.	.	.	T	0.09202	0.0227	N	0.04355	-0.22	0.09310	N	1	P	0.48089	0.905	B	0.32533	0.147	T	0.13255	-1.0516	9	0.13470	T	0.59	-24.8756	6.1508	0.20310	0.246:0.0:0.2236:0.5304	.	194	P13284	GILT_HUMAN	Q	194	ENSP00000384886:R194Q	ENSP00000384886:R194Q	R	+	2	0	IFI30	18149047	0.136000	0.22515	0.390000	0.26220	0.007000	0.05969	0.588000	0.23924	0.286000	0.22352	-0.324000	0.08512	CGG		0.592	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3	NM_006332	
RAB3A	5864	broad.mit.edu	37	19	18313354	18313354	+	Missense_Mutation	SNP	C	C	T	rs185893715		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:18313354C>T	ENST00000222256.4	-	2	375	c.197G>A	c.(196-198)cGc>cAc	p.R66H	AC068499.10_ENST00000596473.1_RNA|RAB3A_ENST00000464076.3_Intron|AC068499.10_ENST00000594805.3_RNA|AC068499.10_ENST00000599416.2_RNA	NM_002866.4	NP_002857.1	P20336	RAB3A_HUMAN	RAB3A, member RAS oncogene family	66					axonogenesis (GO:0007409)|constitutive secretory pathway (GO:0045054)|glutamate secretion (GO:0014047)|GTP catabolic process (GO:0006184)|lung development (GO:0030324)|maintenance of presynaptic active zone structure (GO:0048790)|mitochondrion organization (GO:0007005)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|positive regulation of exocytosis (GO:0045921)|post-embryonic development (GO:0009791)|protein transport (GO:0015031)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|respiratory system process (GO:0003016)|response to electrical stimulus (GO:0051602)|sensory perception of touch (GO:0050975)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle recycling (GO:0036465)	acrosomal vesicle (GO:0001669)|axon (GO:0030424)|clathrin-sculpted acetylcholine transport vesicle membrane (GO:0060201)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|clathrin-sculpted glutamate transport vesicle membrane (GO:0060203)|clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|vesicle (GO:0031982)	ATPase activator activity (GO:0001671)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)	p.R66H(1)		NS(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	8						CTTGTCGTTGCGATAGATGGT	0.597													C|||	1	0.000199681	0.0	0.0	5008	,	,		19548	0.0		0.001	False		,,,				2504	0.0				p.R66H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G197A	19						.						200.0	160.0	173.0					19																	18313354		2203	4300	6503	18174354	SO:0001583	missense	5864	exon2				CCDS12372.1	19p13.2	2008-07-17			ENSG00000105649	ENSG00000105649		"""RAB, member RAS oncogene"""	9777	protein-coding gene	gene with protein product	"""RAS-associated protein RAB3A"""	179490				2687157, 7532276	Standard	NM_002866		Approved		uc002nie.2	P20336	OTTHUMG00000137378	ENST00000222256.4:c.197G>A	19.37:g.18313354C>T	ENSP00000222256:p.Arg66His	Somatic		Capture	Illumina HiSeq	Phase_I	18174354	NM_002866	A8K0J4|Q9NYE1	Missense_Mutation	SNP	ENST00000222256.4	37	CCDS12372.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	28.3	4.911227	0.92178	.	.	ENSG00000105649	ENST00000222256	T	0.76709	-1.04	4.23	4.23	0.50019	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.76392	0.3981	N	0.12887	0.27	0.80722	D	1	D	0.76494	0.999	D	0.67900	0.954	T	0.80084	-0.1530	10	0.52906	T	0.07	-14.044	14.0918	0.64995	0.0:1.0:0.0:0.0	.	66	P20336	RAB3A_HUMAN	H	66	ENSP00000222256:R66H	ENSP00000222256:R66H	R	-	2	0	RAB3A	18174354	1.000000	0.71417	0.941000	0.38009	0.853000	0.48598	7.709000	0.84645	1.885000	0.54596	0.313000	0.20887	CGC		0.597	RAB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268056.2	NM_002866	
PDE4C	5143	broad.mit.edu	37	19	18324189	18324189	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:18324189C>T	ENST00000355502.3	-	17	2468	c.1597G>A	c.(1597-1599)Gac>Aac	p.D533N	PDE4C_ENST00000539010.1_Missense_Mutation_p.D302N|PDE4C_ENST00000598111.2_Missense_Mutation_p.D248N|PDE4C_ENST00000597297.1_Missense_Mutation_p.D303N|PDE4C_ENST00000594465.3_Missense_Mutation_p.D533N|PDE4C_ENST00000262805.12_Missense_Mutation_p.D501N|AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000594617.3_Missense_Mutation_p.D533N|PDE4C_ENST00000447275.3_Missense_Mutation_p.D427N			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	533					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular space (GO:0005615)|primary cilium (GO:0072372)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)	p.D533N(1)		breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33					Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	TGGATTCGGTCGGAATAGTTG	0.433																																					p.D533N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1597A	19						.						119.0	95.0	103.0					19																	18324189		2203	4300	6503	18185189	SO:0001583	missense	5143	exon14				CCDS12373.1, CCDS42523.1, CCDS46016.1	19p13.11	2010-06-24	2010-06-24			ENSG00000105650	3.1.4.17	"""Phosphodiesterases"""	8782	protein-coding gene	gene with protein product	"""phosphodiesterase E1 dunce homolog (Drosophila)"""	600128	"""phosphodiesterase 4C, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E1)"""	DPDE1			Standard	NM_001098818		Approved		uc002nik.4	Q08493		ENST00000355502.3:c.1597G>A	19.37:g.18324189C>T	ENSP00000347689:p.Asp533Asn	Somatic		Capture	Illumina HiSeq	Phase_I	18185189	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Missense_Mutation	SNP	ENST00000355502.3	37	CCDS12373.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.856463	0.71834	.	.	ENSG00000105650	ENST00000536045;ENST00000355502;ENST00000536507;ENST00000262805;ENST00000447275;ENST00000545961;ENST00000336173;ENST00000539010;ENST00000543547	T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63	4.63	4.63	0.57726	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.85682	D	0.000000	T	0.82259	0.4998	M	0.65677	2.01	0.47245	D	0.999364	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;0.966;0.987;1.0	D	0.84686	0.0720	10	0.87932	D	0	.	14.9858	0.71348	0.0:1.0:0.0:0.0	.	533;501;339;248	Q08493;Q08493-3;O43850;O76104	PDE4C_HUMAN;.;.;.	N	612;533;521;501;427;339;247;302;642	ENSP00000347689:D533N;ENSP00000262805:D501N;ENSP00000402091:D427N;ENSP00000439470:D302N	ENSP00000262805:D501N	D	-	1	0	PDE4C	18185189	1.000000	0.71417	0.869000	0.34112	0.300000	0.27592	7.531000	0.81973	2.132000	0.65825	0.555000	0.69702	GAC		0.433	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1		
LSM4	25804	broad.mit.edu	37	19	18420644	18420644	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:18420644C>T	ENST00000593829.1	-	4	425	c.172G>A	c.(172-174)Gag>Aag	p.E58K	LSM4_ENST00000252816.6_Missense_Mutation_p.E44K	NM_001252129.1|NM_012321.4	NP_001239058.1|NP_036453.1	Q9Y4Z0	LSM4_HUMAN	LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)	58					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U6 snRNP (GO:0005688)	poly(A) RNA binding (GO:0044822)	p.E58K(1)		endometrium(1)|large_intestine(2)|lung(3)	6						ATGTAGCACTCGGGCATCCGC	0.667																																					p.E58K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G172A	19						.						51.0	42.0	45.0					19																	18420644		2203	4300	6503	18281644	SO:0001583	missense	25804	exon4			AF117235	CCDS12374.1, CCDS62601.1	19p13.1	2008-02-05				ENSG00000130520			17259	protein-coding gene	gene with protein product		607284				10369684, 10523320	Standard	NM_012321		Approved	YER112W	uc002niq.3	Q9Y4Z0		ENST00000593829.1:c.172G>A	19.37:g.18420644C>T	ENSP00000469468:p.Glu58Lys	Somatic		Capture	Illumina HiSeq	Phase_I	18281644	NM_012321		Missense_Mutation	SNP	ENST00000593829.1	37	CCDS12374.1	.	.	.	.	.	.	.	.	.	.	c	32	5.117333	0.94385	.	.	ENSG00000130520	ENST00000252816	.	.	.	4.47	4.47	0.54385	Like-Sm ribonucleoprotein (LSM) domain, eukaryotic/archaea-type (1);Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.000000	0.85682	D	0.000000	T	0.72104	0.3419	M	0.82433	2.59	0.80722	D	1	P	0.47302	0.893	P	0.47376	0.545	T	0.79562	-0.1752	9	0.87932	D	0	9.9037	16.5142	0.84295	0.0:1.0:0.0:0.0	.	58	Q9Y4Z0	LSM4_HUMAN	K	58	.	ENSP00000252816:E58K	E	-	1	0	LSM4	18281644	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	5.353000	0.66034	2.211000	0.71520	0.457000	0.33378	GAG		0.667	LSM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466321.1		
SUGP2	10147	broad.mit.edu	37	19	19115278	19115278	+	Silent	SNP	G	G	A	rs76482020	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:19115278G>A	ENST00000601879.1	-	7	2925	c.2628C>T	c.(2626-2628)gaC>gaT	p.D876D	SUGP2_ENST00000600377.1_Silent_p.D890D|SUGP2_ENST00000452918.2_Silent_p.D876D|SUGP2_ENST00000456085.2_Silent_p.D645D|SUGP2_ENST00000337018.6_Silent_p.D876D			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	876	Asp/Glu-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.D876D(1)		NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						GAGGGGGCTCGTCTTCAAACT	0.637													G|||	13	0.00259585	0.0083	0.0029	5008	,	,		18112	0.0		0.0	False		,,,				2504	0.0				p.D876D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2628T	19						.	G	,	28,4378	34.3+/-65.2	0,28,2175	53.0	54.0	54.0		2628,2628	-10.5	0.0	19	dbSNP_131	54	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SUGP2	NM_001017392.3,NM_014884.3	,	0,28,6475	AA,AG,GG		0.0,0.6355,0.2153	,	876/1083,876/1083	19115278	28,12978	2203	4300	6503	18976278	SO:0001819	synonymous_variant	10147	exon7			AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"""G patch domain containing"""	18641	protein-coding gene	gene with protein product		607993	"""splicing factor, arginine/serine-rich 14"""	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.2628C>T	19.37:g.19115278G>A		Somatic		Capture	Illumina HiSeq	Phase_I	18976278	NM_014884	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Silent	SNP	ENST00000601879.1	37	CCDS12392.1																																																																																				0.637	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392	
AP3D1	8943	broad.mit.edu	37	19	2110171	2110171	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:2110171C>T	ENST00000345016.5	-	26	3273	c.3042G>A	c.(3040-3042)gcG>gcA	p.A1014A	AP3D1_ENST00000356926.4_Silent_p.A973A|AP3D1_ENST00000350812.6_Silent_p.A845A|AP3D1_ENST00000355272.6_Silent_p.A1076A	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		
ZNF253	56242	broad.mit.edu	37	19	20002578	20002578	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:20002578T>C	ENST00000589717.1	+	4	614	c.522T>C	c.(520-522)tgT>tgC	p.C174C	CTC-559E9.8_ENST00000585571.1_RNA|AC011477.1_ENST00000578823.1_RNA|ZNF253_ENST00000355650.4_Silent_p.C98C	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	174					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.C174C(2)		endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TTTTCAAATGTATAATATGTG	0.303																																					p.C174C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T522C	19						.						41.0	44.0	43.0					19																	20002578		2082	4239	6321	19863578	SO:0001819	synonymous_variant	56242	exon4			AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"""Zinc fingers, C2H2-type"", ""-"""	13497	protein-coding gene	gene with protein product		606954	"""zinc finger protein 411"""	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.522T>C	19.37:g.20002578T>C		Somatic		Capture	Illumina HiSeq	Phase_I	19863578	NM_021047	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Silent	SNP	ENST00000589717.1	37	CCDS42532.1																																																																																				0.303	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047	
ZNF429	353088	broad.mit.edu	37	19	21719704	21719704	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:21719704G>A	ENST00000358491.4	+	4	1057	c.849G>A	c.(847-849)aaG>aaA	p.K283K	ZNF429_ENST00000597078.1_Intron	NM_001001415.2	NP_001001415.2	Q86V71	ZN429_HUMAN	zinc finger protein 429	283					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.K283K(1)		endometrium(2)|kidney(2)|large_intestine(13)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	34						CTGGAGAGAAGCCCTACAAAT	0.373																																					p.K283K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G849A	19						.						37.0	41.0	40.0					19																	21719704		2143	4273	6416	21511544	SO:0001819	synonymous_variant	353088	exon4			AY269786	CCDS42537.1	19p12	2014-02-14			ENSG00000197013	ENSG00000197013		"""Zinc fingers, C2H2-type"", ""-"""	20817	protein-coding gene	gene with protein product							Standard	NM_001001415		Approved		uc002nqd.1	Q86V71	OTTHUMG00000182848	ENST00000358491.4:c.849G>A	19.37:g.21719704G>A		Somatic		Capture	Illumina HiSeq	Phase_I	21511544	NM_001001415	A6NLV7|Q9BZE6	Silent	SNP	ENST00000358491.4	37	CCDS42537.1																																																																																				0.373	ZNF429-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463981.1	NM_001001415	
ZNF57	126295	broad.mit.edu	37	19	2916212	2916212	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:2916212A>G	ENST00000306908.5	+	3	415	c.267A>G	c.(265-267)gaA>gaG	p.E89E	ZNF57_ENST00000523428.1_Silent_p.E57E|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	89					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.E89E(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				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)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		AAAATTGTGAAGGCTATGGCA	0.373																																					p.E89E	NSCLC(150;910 1964 4303 10464 26498)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A267G	19						.						51.0	47.0	49.0					19																	2916212		2203	4300	6503	2867212	SO:0001819	synonymous_variant	126295	exon3			M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.267A>G	19.37:g.2916212A>G		Somatic		Capture	Illumina HiSeq	Phase_I	2867212	NM_173480	Q8N6R9	Silent	SNP	ENST00000306908.5	37	CCDS12098.1																																																																																				0.373	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
CELF5	60680	broad.mit.edu	37	19	3281334	3281334	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:3281334C>T	ENST00000292672.2	+	6	778	c.741C>T	c.(739-741)taC>taT	p.Y247Y	CELF5_ENST00000541430.2_Silent_p.Y247Y	NM_021938.3	NP_068757.2	Q8N6W0	CELF5_HUMAN	CUGBP, Elav-like family member 5	247					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.Y247Y(1)		kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						ACAGTGCCTACGCCCAGGCTG	0.647																																					p.Y247Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C741T	19						.						88.0	79.0	82.0					19																	3281334		2203	4300	6503	3232334	SO:0001819	synonymous_variant	60680	exon6			AF248649	CCDS12106.1, CCDS54197.1	19p13	2013-02-12	2010-02-19	2010-02-19		ENSG00000161082		"""RNA binding motif (RRM) containing"""	14058	protein-coding gene	gene with protein product		612680	"""Bruno (Drosophila) -like 5, RNA binding protein"", ""bruno-like 5, RNA binding protein (Drosophila)"""	BRUNOL5		10893231	Standard	NM_001172673		Approved		uc002lxm.3	Q8N6W0		ENST00000292672.2:c.741C>T	19.37:g.3281334C>T		Somatic		Capture	Illumina HiSeq	Phase_I	3232334	NM_001172673	D6W614|O75253|Q59GP2|Q86VW6|Q9BZC0|Q9NR86	Silent	SNP	ENST00000292672.2	37	CCDS12106.1																																																																																				0.647	CELF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452574.1	NM_021938	
CACTIN	58509	broad.mit.edu	37	19	3623820	3623820	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:3623820G>A	ENST00000429344.2	-	2	560	c.508C>T	c.(508-510)Cgg>Tgg	p.R170W	CACTIN_ENST00000248420.5_Missense_Mutation_p.R170W|CACTIN_ENST00000221899.3_Missense_Mutation_p.R102W	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	170					cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R102W(1)|p.R170W(1)									TTGGCCAGCCGCCGTGCGCGC	0.657																																					p.R170W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C508T	19						.						29.0	37.0	34.0					19																	3623820		2101	4206	6307	3574820	SO:0001583	missense	58509	exon2			BC019848	CCDS45920.1	19p13.3	2012-06-08	2012-06-08	2012-06-08	ENSG00000105298	ENSG00000105298			29938	protein-coding gene	gene with protein product	"""NY REN 24 antigen"", ""functional spliceosome-associated protein c"", ""cactin homolog (Drosophila)"""		"""chromosome 19 open reading frame 29"""	C19orf29		8619474, 9110174, 21429463, 20829348	Standard	NM_001080543		Approved	NY-REN-24, fSAPc, cactin	uc002lyh.3	Q8WUQ7		ENST00000429344.2:c.508C>T	19.37:g.3623820G>A	ENSP00000415078:p.Arg170Trp	Somatic		Capture	Illumina HiSeq	Phase_I	3574820	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Missense_Mutation	SNP	ENST00000429344.2	37	CCDS45920.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.479508	0.44044	.	.	ENSG00000105298	ENST00000429344;ENST00000248420;ENST00000221899	.	.	.	5.09	2.74	0.32292	.	0.199468	0.41938	D	0.000790	T	0.78162	0.4240	M	0.84773	2.715	0.54753	D	0.999986	D	0.89917	1.0	D	0.73708	0.981	T	0.80885	-0.1182	9	0.87932	D	0	.	10.7652	0.46288	0.0793:0.0:0.7392:0.1815	.	170	Q8WUQ7	CS029_HUMAN	W	170;170;102	.	ENSP00000221899:R102W	R	-	1	2	C19orf29	3574820	0.999000	0.42202	0.940000	0.37924	0.116000	0.19942	2.873000	0.48475	1.154000	0.42482	-0.258000	0.10820	CGG		0.657	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2		
ZNF208	7757	broad.mit.edu	37	19	22155439	22155439	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:22155439A>G	ENST00000397126.4	-	4	2545	c.2397T>C	c.(2395-2397)caT>caC	p.H799H	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	799					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.H799H(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				TCTCATCAGTATGAATTCTCT	0.363																																					p.H799H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2397C	19						.						56.0	66.0	63.0					19																	22155439		2097	4241	6338	21947279	SO:0001819	synonymous_variant	7757	exon4			BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2397T>C	19.37:g.22155439A>G		Somatic		Capture	Illumina HiSeq	Phase_I	21947279	NM_007153		Silent	SNP	ENST00000397126.4	37	CCDS54240.1																																																																																				0.363	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
APBA3	9546	broad.mit.edu	37	19	3751531	3751531	+	Silent	SNP	C	C	T	rs112086597	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:3751531C>T	ENST00000316757.3	-	9	1616	c.1416G>A	c.(1414-1416)tcG>tcA	p.S472S	AC005954.4_ENST00000586503.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	472	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)	p.S472S(1)		endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		TGAGTGTCACCGACGTCTGCG	0.682													C|||	7	0.00139776	0.0053	0.0	5008	,	,		13153	0.0		0.0	False		,,,				2504	0.0				p.S472S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1416A	19						.	C		25,4359		0,25,2167	38.0	38.0	38.0		1416	-6.1	0.0	19	dbSNP_132	38	0,8580		0,0,4290	no	coding-synonymous	APBA3	NM_004886.3		0,25,6457	TT,TC,CC		0.0,0.5703,0.1928		472/576	3751531	25,12939	2192	4290	6482	3702531	SO:0001819	synonymous_variant	9546	exon9			AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"""X11-like 2"""	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.1416G>A	19.37:g.3751531C>T		Somatic		Capture	Illumina HiSeq	Phase_I	3702531	NM_004886	O60483|Q9UPZ2	Silent	SNP	ENST00000316757.3	37	CCDS12110.1																																																																																				0.682	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
RAX2	84839	broad.mit.edu	37	19	3771658	3771658	+	Missense_Mutation	SNP	C	C	T	rs199546013		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:3771658C>T	ENST00000555633.1	-	2	423	c.83G>A	c.(82-84)cGg>cAg	p.R28Q	RAX2_ENST00000555978.1_Missense_Mutation_p.R28Q			Q96IS3	RAX2_HUMAN	retina and anterior neural fold homeobox 2	28					regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.R28Q(1)		large_intestine(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGGTTCCTCCGGTGCTTCTT	0.687																																					p.R28Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G83A	19						.	C	GLN/ARG	0,4402		0,0,2201	71.0	61.0	64.0		83	3.0	1.0	19		64	1,8597	1.2+/-3.3	0,1,4298	yes	missense	RAX2	NM_032753.3	43	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	28/185	3771658	1,12999	2201	4299	6500	3722658	SO:0001583	missense	84839	exon2			AY211277	CCDS12112.1	19p13.3	2013-06-06	2007-08-28	2007-08-28				"""Homeoboxes / PRD class"""	18286	protein-coding gene	gene with protein product		610362	"""retina and anterior neural fold homeobox like 1"""	RAXL1			Standard	NM_032753		Approved	MGC15631, ARMD6, CORD11	uc002lys.3	Q96IS3		ENST00000555633.1:c.83G>A	19.37:g.3771658C>T	ENSP00000450456:p.Arg28Gln	Somatic		Capture	Illumina HiSeq	Phase_I	3722658	NM_032753		Missense_Mutation	SNP	ENST00000555633.1	37	CCDS12112.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.785883	0.90282	0.0	1.16E-4	ENSG00000173976	ENST00000555633;ENST00000395106	D	0.97209	-4.29	2.98	2.98	0.34508	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	.	.	.	.	D	0.98188	0.9401	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.984;0.997	D	0.98727	1.0711	9	0.87932	D	0	.	12.8761	0.57991	0.0:1.0:0.0:0.0	.	28;74	Q96IS3;G3V243	RAX2_HUMAN;.	Q	74;28	ENSP00000450456:R74Q	ENSP00000378538:R28Q	R	-	2	0	RAX2	3722658	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.577000	0.67444	1.228000	0.43614	0.491000	0.48974	CGG		0.687	RAX2-001	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411919.2	NM_032753	
TSHZ3	57616	broad.mit.edu	37	19	31769926	31769926	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:31769926C>T	ENST00000240587.4	-	2	1100	c.773G>A	c.(772-774)cGc>cAc	p.R258H		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	258					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R258H(1)|p.R75H(1)		breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					GGAGCGTTTGCGAGGCTTGGA	0.557																																					p.R258H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G773A	19						.						217.0	190.0	199.0					19																	31769926		2203	4300	6503	36461766	SO:0001583	missense	57616	exon2			AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.773G>A	19.37:g.31769926C>T	ENSP00000240587:p.Arg258His	Somatic		Capture	Illumina HiSeq	Phase_I	36461766	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	37	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	C	24.2	4.506164	0.85282	.	.	ENSG00000121297	ENST00000240587	T	0.17691	2.26	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.35278	0.0926	L	0.36672	1.1	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	T	0.05801	-1.0863	10	0.87932	D	0	-27.9625	19.4506	0.94865	0.0:1.0:0.0:0.0	.	258	Q63HK5	TSH3_HUMAN	H	258	ENSP00000240587:R258H	ENSP00000240587:R258H	R	-	2	0	TSHZ3	36461766	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.484000	0.81180	2.567000	0.86603	0.655000	0.94253	CGC		0.557	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
LSM14A	26065	broad.mit.edu	37	19	34710328	34710328	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:34710328C>T	ENST00000433627.5	+	7	889	c.814C>T	c.(814-816)Cgt>Tgt	p.R272C	LSM14A_ENST00000544216.3_Missense_Mutation_p.R272C|LSM14A_ENST00000540746.2_Missense_Mutation_p.R231C	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	272					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.R272C(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					AAGGAGAGGGCGTGGGGGTCA	0.438																																					p.R272C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C814T	19						.						68.0	79.0	75.0					19																	34710328		2203	4300	6503	39402168	SO:0001583	missense	26065	exon7			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.814C>T	19.37:g.34710328C>T	ENSP00000413964:p.Arg272Cys	Somatic		Capture	Illumina HiSeq	Phase_I	39402168	NM_001114093	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Missense_Mutation	SNP	ENST00000433627.5	37	CCDS46040.1	.	.	.	.	.	.	.	.	.	.	c	16.68	3.190986	0.58017	.	.	ENSG00000257103	ENST00000544216;ENST00000433627;ENST00000540746	T;T;T	0.38401	1.18;1.16;1.14	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.61850	0.2380	M	0.80746	2.51	0.80722	D	1	B;D;B	0.89917	0.362;1.0;0.263	B;D;B	0.79784	0.117;0.993;0.051	T	0.62548	-0.6831	10	0.48119	T	0.1	-10.3844	14.8295	0.70137	0.1438:0.8562:0.0:0.0	.	231;272;272	B4DTG6;Q8ND56;Q8ND56-2	.;LS14A_HUMAN;.	C	272;272;231	ENSP00000446271:R272C;ENSP00000413964:R272C;ENSP00000446451:R231C	ENSP00000314768:R272C	R	+	1	0	LSM14A	39402168	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.529000	0.60588	2.734000	0.93682	0.655000	0.94253	CGT		0.438	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578	
LSM14A	26065	broad.mit.edu	37	19	34712520	34712520	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:34712520T>C	ENST00000433627.5	+	9	1320	c.1245T>C	c.(1243-1245)ctT>ctC	p.L415L	LSM14A_ENST00000544216.3_Silent_p.L415L|LSM14A_ENST00000540746.2_Silent_p.L374L	NM_001114093.1	NP_001107565.1	Q8ND56	LS14A_HUMAN	LSM14A, SCD6 homolog A (S. cerevisiae)	415					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.L415L(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(7)|skin(1)	22	Esophageal squamous(110;0.162)					GAGGAGGTCTTGGTTTCCGTG	0.582																																					p.L415L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1245C	19						.						104.0	73.0	84.0					19																	34712520		2203	4300	6503	39404360	SO:0001819	synonymous_variant	26065	exon9			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.1245T>C	19.37:g.34712520T>C		Somatic		Capture	Illumina HiSeq	Phase_I	39404360	NM_001114093	B4DTG6|Q76LX7|Q96AR3|Q96K73|Q96SN5|Q9UFR3	Silent	SNP	ENST00000433627.5	37	CCDS46040.1																																																																																				0.582	LSM14A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451576.3	NM_015578	
KMT2B	9757	broad.mit.edu	37	19	36224532	36224532	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:36224532C>T	ENST00000222270.7	+	29	6994	c.6994C>T	c.(6994-6996)Cgt>Tgt	p.R2332C	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Missense_Mutation_p.R2332C	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2332					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R2334C(2)									CCCCACAGTGCGTGGGGTCCT	0.662																																					p.R2332C												MLL4,central_nervous_system,brain,Substitution - Missense,0 	.	2	Substitution - Missense(2)	large_intestine(1)|central_nervous_system(1)	c.C6994T	19						.						28.0	37.0	34.0					19																	36224532		1993	4145	6138	40916372	SO:0001583	missense	9757	exon29			AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.6994C>T	19.37:g.36224532C>T	ENSP00000222270:p.Arg2332Cys	Somatic		Capture	Illumina HiSeq	Phase_I	40916372	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	37	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	C	12.01	1.809626	0.31961	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.85411	-1.98;-1.98	5.19	5.19	0.71726	.	0.281854	0.21510	N	0.073391	D	0.86230	0.5883	L	0.27053	0.805	0.44500	D	0.997446	D	0.89917	1.0	D	0.69654	0.965	D	0.87030	0.2134	10	0.87932	D	0	.	11.3714	0.49702	0.1808:0.8192:0.0:0.0	.	2332	Q9UMN6	MLL4_HUMAN	C	2332	ENSP00000222270:R2332C;ENSP00000398837:R2332C	ENSP00000222270:R2332C	R	+	1	0	AD000671.1	40916372	1.000000	0.71417	1.000000	0.80357	0.618000	0.37518	2.827000	0.48112	2.428000	0.82296	0.561000	0.74099	CGT		0.662	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
HSPB6	126393	broad.mit.edu	37	19	36250315	36250315	+	5'Flank	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:36250315G>A	ENST00000592984.1	-	0	0				C19orf55_ENST00000421853.2_Intron|C19orf55_ENST00000536950.1_Missense_Mutation_p.A18T|C19orf55_ENST00000544099.1_Missense_Mutation_p.A18T|HSPB6_ENST00000004982.3_5'Flank|HSPB6_ENST00000587965.1_5'Flank|C19orf55_ENST00000396908.4_Missense_Mutation_p.A18T|C19orf55_ENST00000537459.1_Missense_Mutation_p.A18T			O14558	HSPB6_HUMAN	heat shock protein, alpha-crystallin-related, B6						regulation of muscle contraction (GO:0006937)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|structural constituent of eye lens (GO:0005212)	p.A18T(1)		lung(1)	1	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTTTGGAGATGCGCCCCTGGG	0.607																																					p.A18T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G52A	19						.						37.0	41.0	40.0					19																	36250315		1930	4145	6075	40942155	SO:0001631	upstream_gene_variant	148137	exon2			AJ278121	CCDS12475.1	19q13.13	2014-06-12			ENSG00000004776	ENSG00000004776		"""Heat shock proteins / HSPB"""	26511	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 91"""	610695				12820654, 14717697	Standard	NM_144617		Approved	FLJ32389, Hsp20, PPP1R91	uc002obn.2	O14558	OTTHUMG00000048122		19.37:g.36250315G>A	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	40942155	NM_001039887	O14551|Q6NVI3|Q96MG9	Missense_Mutation	SNP	ENST00000592984.1	37	CCDS12475.1	.	.	.	.	.	.	.	.	.	.	G	12.10	1.837107	0.32513	.	.	ENSG00000167595	ENST00000396908;ENST00000301165	T	0.37411	1.2	3.53	-3.73	0.04398	.	1.741920	0.03869	N	0.275404	T	0.18045	0.0433	N	0.08118	0	0.09310	N	1	B;B;B	0.13145	0.007;0.002;0.002	B;B;B	0.10450	0.002;0.005;0.003	T	0.20240	-1.0281	10	0.18710	T	0.47	1.1504	8.7694	0.34722	0.6493:0.0:0.3507:0.0	.	18;18;18	E5RFB9;Q2NL68-3;Q2NL68-4	.;.;.	T	18	ENSP00000380116:A18T	ENSP00000301165:A18T	A	+	1	0	C19orf55	40942155	0.000000	0.05858	0.000000	0.03702	0.162000	0.22319	-0.216000	0.09266	-0.675000	0.05246	0.467000	0.42956	GCG		0.607	HSPB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109498.3	NM_144617	
NPHS1	4868	broad.mit.edu	37	19	36336632	36336632	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:36336632T>C	ENST00000378910.5	-	13	1695	c.1696A>G	c.(1696-1698)Aca>Gca	p.T566A	NPHS1_ENST00000353632.6_Missense_Mutation_p.T566A	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	566	Ig-like C2-type 6.				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.T566A(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)			CTGACGCATGTCAAGTTTAAG	0.627																																					p.T566A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1696G	19						.						53.0	50.0	51.0					19																	36336632		2203	4300	6503	41028472	SO:0001583	missense	4868	exon13				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.1696A>G	19.37:g.36336632T>C	ENSP00000368190:p.Thr566Ala	Somatic		Capture	Illumina HiSeq	Phase_I	41028472	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	.	.	.	.	.	.	.	.	.	.	T	18.94	3.729379	0.69074	.	.	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.78595	-1.19;-1.19	5.44	5.44	0.79542	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.163071	0.53938	D	0.000042	D	0.83825	0.5338	M	0.71036	2.16	0.36285	D	0.856043	D	0.56746	0.977	P	0.57152	0.814	D	0.87256	0.2276	10	0.42905	T	0.14	-15.452	13.4481	0.61153	0.0:0.0:0.0:1.0	.	566	O60500	NPHN_HUMAN	A	566	ENSP00000368190:T566A;ENSP00000343634:T566A	ENSP00000343634:T566A	T	-	1	0	NPHS1	41028472	1.000000	0.71417	1.000000	0.80357	0.571000	0.35966	3.463000	0.53050	2.082000	0.62665	0.459000	0.35465	ACA		0.627	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
KIRREL2	84063	broad.mit.edu	37	19	36349690	36349690	+	Missense_Mutation	SNP	G	G	A	rs571708243		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:36349690G>A	ENST00000360202.5	+	4	644	c.446G>A	c.(445-447)cGt>cAt	p.R149H	KIRREL2_ENST00000262625.7_Missense_Mutation_p.R149H|KIRREL2_ENST00000347900.6_Missense_Mutation_p.R99H|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_Missense_Mutation_p.R149H	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	149	Ig-like C2-type 2.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)		p.R149H(3)		breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	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)			TGTCGGAGCCGTGGGGATGCC	0.612																																					p.R149H												.	.	3	Substitution - Missense(3)	endometrium(2)|large_intestine(1)	c.G446A	19						.						97.0	96.0	96.0					19																	36349690		2203	4300	6503	41041530	SO:0001583	missense	84063	exon4			AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.446G>A	19.37:g.36349690G>A	ENSP00000353331:p.Arg149His	Somatic		Capture	Illumina HiSeq	Phase_I	41041530	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	G	1.470	-0.559959	0.03967	.	.	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	T;T;T	0.77620	-1.11;-1.11;-1.11	5.56	-1.45	0.08828	Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.378405	0.18495	N	0.139527	T	0.60327	0.2260	L	0.28504	0.86	0.21416	N	0.999692	B;B;B;B;B	0.19331	0.008;0.007;0.018;0.035;0.035	B;B;B;B;B	0.16722	0.012;0.007;0.016;0.016;0.016	T	0.45731	-0.9241	10	0.26408	T	0.33	-3.9095	8.4803	0.33038	0.4985:0.0:0.5015:0.0	.	149;149;149;99;149	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	H	149;99;149;149	ENSP00000262625:R149H;ENSP00000345067:R99H;ENSP00000353331:R149H	ENSP00000262625:R149H	R	+	2	0	KIRREL2	41041530	0.000000	0.05858	0.591000	0.28745	0.031000	0.12232	-0.395000	0.07287	-0.058000	0.13177	-1.007000	0.02485	CGT		0.612	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
CLIP3	25999	broad.mit.edu	37	19	36515512	36515512	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:36515512G>A	ENST00000360535.4	-	7	931	c.704C>T	c.(703-705)gCg>gTg	p.A235V	CLIP3_ENST00000593074.1_Missense_Mutation_p.A235V|AC002116.7_ENST00000586962.1_RNA	NM_015526.2	NP_056341.1	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	235					chaperone-mediated protein transport (GO:0072321)|fat cell differentiation (GO:0045444)|membrane biogenesis (GO:0044091)|negative regulation of microtubule polymerization (GO:0031115)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein phosphorylation (GO:0001934)	early endosome membrane (GO:0031901)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)|trans-Golgi network membrane (GO:0032588)	ganglioside binding (GO:0035594)|microtubule binding (GO:0008017)	p.A235V(1)		cervix(1)|endometrium(6)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	23	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GACCACCTCCGCCGGCACCTG	0.622																																					p.A235V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C704T	19						.						43.0	41.0	42.0					19																	36515512		2203	4300	6503	41207352	SO:0001583	missense	25999	exon6			AJ427922	CCDS12486.1	19q13.12	2014-08-12			ENSG00000105270	ENSG00000105270		"""Ankyrin repeat domain containing"""	24314	protein-coding gene	gene with protein product	"""CLIP-170-related"", ""restin-like 1"""	607382				11854307	Standard	NM_015526		Approved	CLIPR-59, RSNL1	uc002ocz.2	Q96DZ5	OTTHUMG00000181747	ENST00000360535.4:c.704C>T	19.37:g.36515512G>A	ENSP00000353732:p.Ala235Val	Somatic		Capture	Illumina HiSeq	Phase_I	41207352	NM_001199570	A8K0E4|Q8WWL1|Q96C99|Q9UFT7	Missense_Mutation	SNP	ENST00000360535.4	37	CCDS12486.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.611524	0.66558	.	.	ENSG00000105270	ENST00000360535;ENST00000544037;ENST00000534959	T	0.52057	0.68	5.88	5.88	0.94601	Ankyrin repeat-containing domain (1);	0.103095	0.64402	D	0.000004	T	0.48607	0.1509	L	0.50333	1.59	0.54753	D	0.999985	D	0.54964	0.969	P	0.45794	0.493	T	0.34453	-0.9828	10	0.27082	T	0.32	-14.6899	17.7145	0.88332	0.0:0.0:1.0:0.0	.	235	Q96DZ5	CLIP3_HUMAN	V	235;117;211	ENSP00000353732:A235V	ENSP00000353732:A235V	A	-	2	0	CLIP3	41207352	1.000000	0.71417	0.934000	0.37439	0.942000	0.58702	5.275000	0.65575	2.790000	0.95986	0.591000	0.81541	GCG		0.622	CLIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457426.1	NM_015526	
WDR62	284403	broad.mit.edu	37	19	36593664	36593664	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:36593664C>T	ENST00000270301.7	+	27	3231	c.3231C>T	c.(3229-3231)gaC>gaT	p.D1077D	WDR62_ENST00000401500.2_Silent_p.D1082D			O43379	WDR62_HUMAN	WD repeat domain 62	1077					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.D1077D(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)			CTCTGGGAGACGTGGAGGCCT	0.622																																					p.D1082D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3246T	19						.						79.0	70.0	73.0					19																	36593664		2203	4300	6503	41285504	SO:0001819	synonymous_variant	284403	exon27			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.3231C>T	19.37:g.36593664C>T		Somatic		Capture	Illumina HiSeq	Phase_I	41285504	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	37	CCDS33001.1																																																																																				0.622	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
ZFP14	57677	broad.mit.edu	37	19	36831525	36831525	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:36831525A>C	ENST00000270001.7	-	5	1318	c.1203T>G	c.(1201-1203)tgT>tgG	p.C401W		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	401					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.C401W(1)		NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					AGGTCTTCCAACATTCCATAC	0.398																																					p.C401W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1203G	19						.						116.0	107.0	110.0					19																	36831525		2203	4300	6503	41523365	SO:0001583	missense	57677	exon5			AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"""Zinc fingers, C2H2-type"", ""-"""	29312	protein-coding gene	gene with protein product			"""zinc finger protein 14 homolog (mouse)"""			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.1203T>G	19.37:g.36831525A>C	ENSP00000270001:p.Cys401Trp	Somatic		Capture	Illumina HiSeq	Phase_I	41523365	NM_020917	A7MD23	Missense_Mutation	SNP	ENST00000270001.7	37	CCDS33002.1	.	.	.	.	.	.	.	.	.	.	a	14.27	2.485868	0.44147	.	.	ENSG00000142065	ENST00000270001;ENST00000392172	D	0.85955	-2.05	3.99	1.55	0.23275	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49305	D	0.000146	D	0.93426	0.7903	H	0.97077	3.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90766	0.4668	10	0.87932	D	0	.	6.609	0.22741	0.7322:0.0:0.2678:0.0	.	401;401	A8KAN8;Q9HCL3	.;ZFP14_HUMAN	W	401	ENSP00000270001:C401W	ENSP00000270001:C401W	C	-	3	2	ZFP14	41523365	0.972000	0.33761	1.000000	0.80357	0.998000	0.95712	0.249000	0.18216	0.146000	0.19002	0.523000	0.50628	TGT		0.398	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917	
ANKRD24	170961	broad.mit.edu	37	19	4219681	4219681	+	Missense_Mutation	SNP	G	G	A	rs546339422		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:4219681G>A	ENST00000600132.1	+	19	3373	c.3097G>A	c.(3097-3099)Gag>Aag	p.E1033K	ANKRD24_ENST00000262970.5_Missense_Mutation_p.E1123K|ANKRD24_ENST00000318934.4_Missense_Mutation_p.E1033K	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	1033								p.E1033K(1)|p.E598K(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		GCTACGGACCGAGGCGGAAAG	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		17055	0.001		0.0	False		,,,				2504	0.0				p.E1033K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3097A	19						.						41.0	50.0	47.0					19																	4219681		2112	4238	6350	4170681	SO:0001583	missense	170961	exon19			AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"""Ankyrin repeat domain containing"""	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.3097G>A	19.37:g.4219681G>A	ENSP00000471252:p.Glu1033Lys	Somatic		Capture	Illumina HiSeq	Phase_I	4170681	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	37	CCDS45925.1	.	.	.	.	.	.	.	.	.	.	g	9.701	1.154577	0.21371	.	.	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.29655	1.57;1.56	3.79	3.79	0.43588	.	.	.	.	.	T	0.15912	0.0383	L	0.27053	0.805	0.28627	N	0.907878	P	0.39181	0.663	B	0.31495	0.131	T	0.04915	-1.0918	9	0.02654	T	1	.	11.8657	0.52493	0.0:0.0:1.0:0.0	.	1033	Q8TF21	ANR24_HUMAN	K	1033;1123	ENSP00000321731:E1033K;ENSP00000262970:E1123K	ENSP00000262970:E1123K	E	+	1	0	ANKRD24	4170681	0.999000	0.42202	0.849000	0.33467	0.435000	0.31806	3.400000	0.52594	2.080000	0.62538	0.313000	0.20887	GAG		0.667	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000	
ZFP14	57677	broad.mit.edu	37	19	36832354	36832354	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:36832354C>T	ENST00000270001.7	-	5	489	c.374G>A	c.(373-375)tGc>tAc	p.C125Y		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C125Y(1)		NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					CTTGCTTTTGCATTCCCAATC	0.343																																					p.C125Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G374A	19						.						116.0	112.0	113.0					19																	36832354		2203	4299	6502	41524194	SO:0001583	missense	57677	exon5			AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"""Zinc fingers, C2H2-type"", ""-"""	29312	protein-coding gene	gene with protein product			"""zinc finger protein 14 homolog (mouse)"""			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.374G>A	19.37:g.36832354C>T	ENSP00000270001:p.Cys125Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	41524194	NM_020917	A7MD23	Missense_Mutation	SNP	ENST00000270001.7	37	CCDS33002.1	.	.	.	.	.	.	.	.	.	.	c	0.008	-1.869231	0.00547	.	.	ENSG00000142065	ENST00000270001;ENST00000392172	T	0.07021	3.23	4.09	1.78	0.24846	.	0.467802	0.18383	N	0.142912	T	0.05318	0.0141	L	0.33753	1.03	0.28975	N	0.888998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.41645	-0.9497	10	0.10111	T	0.7	.	6.8167	0.23835	0.1737:0.7276:0.0:0.0986	.	125;125	A8KAN8;Q9HCL3	.;ZFP14_HUMAN	Y	125	ENSP00000270001:C125Y	ENSP00000270001:C125Y	C	-	2	0	ZFP14	41524194	0.035000	0.19736	0.993000	0.49108	0.990000	0.78478	-0.187000	0.09656	0.419000	0.25927	0.549000	0.68633	TGC		0.343	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917	
ZNF345	25850	broad.mit.edu	37	19	37369108	37369108	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:37369108G>T	ENST00000529555.1	+	2	2164	c.1376G>T	c.(1375-1377)tGt>tTt	p.C459F	ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000420450.1_Missense_Mutation_p.C459F|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000589046.1_Missense_Mutation_p.C459F			Q14585	ZN345_HUMAN	zinc finger protein 345	459					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C459F(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGTAAGAACTGTGGGAAGGCT	0.373																																					p.C459F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1376T	19						.						89.0	95.0	93.0					19																	37369108		2203	4300	6503	42060948	SO:0001583	missense	25850	exon3			X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"""Zinc fingers, C2H2-type"""	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.1376G>T	19.37:g.37369108G>T	ENSP00000431202:p.Cys459Phe	Somatic		Capture	Illumina HiSeq	Phase_I	42060948	NM_003419		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	G	6.283	0.420391	0.11928	.	.	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000344705	D;D	0.85861	-2.04;-2.04	3.03	-0.791	0.10929	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.87489	0.6190	H	0.96269	3.795	0.26270	N	0.97844	B	0.31893	0.345	B	0.30029	0.11	T	0.81204	-0.1039	9	0.87932	D	0	.	6.67	0.23064	0.4532:0.0:0.5468:0.0	.	459	Q14585	ZN345_HUMAN	F	459;459;223	ENSP00000431216:C459F;ENSP00000431202:C459F	ENSP00000442320:C223F	C	+	2	0	ZNF345	42060948	0.998000	0.40836	0.073000	0.20177	0.053000	0.15095	2.385000	0.44371	0.017000	0.15025	-0.218000	0.12543	TGT		0.373	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1		
MPND	84954	broad.mit.edu	37	19	4354087	4354087	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:4354087C>T	ENST00000262966.8	+	5	777	c.710C>T	c.(709-711)cCg>cTg	p.P237L	MPND_ENST00000359935.4_Missense_Mutation_p.P237L|AC007292.4_ENST00000594776.1_RNA|MPND_ENST00000599840.1_Missense_Mutation_p.P237L|AC007292.3_ENST00000593524.1_RNA	NM_032868.4	NP_116257.2	Q8N594	MPND_HUMAN	MPN domain containing	237							peptidase activity (GO:0008233)	p.P237L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		ATCCGGGTTCCGGTCCGCTAC	0.607																																					p.P237L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C710T	19						.						37.0	41.0	40.0					19																	4354087		1959	4149	6108	4305087	SO:0001583	missense	84954	exon5				CCDS42470.1, CCDS54200.1, CCDS74261.1	19p13.3	2014-08-12			ENSG00000008382				25934	protein-coding gene	gene with protein product							Standard	XM_005259663		Approved	FLJ14981	uc002mae.3	Q8N594	OTTHUMG00000181914	ENST00000262966.8:c.710C>T	19.37:g.4354087C>T	ENSP00000262966:p.Pro237Leu	Somatic		Capture	Illumina HiSeq	Phase_I	4305087	NM_001159846	Q96SJ0|Q9Y2P1|Q9Y2P2	Missense_Mutation	SNP	ENST00000262966.8	37	CCDS42470.1	.	.	.	.	.	.	.	.	.	.	c	14.10	2.436020	0.43224	.	.	ENSG00000008382	ENST00000262966;ENST00000359935	.	.	.	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.59432	0.2193	L	0.34521	1.04	0.80722	D	1	D;D;D	0.71674	0.996;0.997;0.998	P;P;P	0.57468	0.75;0.787;0.821	T	0.54450	-0.8292	9	0.27082	T	0.32	-17.8985	14.1996	0.65693	0.0:1.0:0.0:0.0	.	237;237;237	Q8N594-2;A6NI36;Q8N594	.;.;MPND_HUMAN	L	237	.	ENSP00000262966:P237L	P	+	2	0	MPND	4305087	0.990000	0.36364	0.882000	0.34594	0.052000	0.14988	5.566000	0.67372	2.505000	0.84491	0.550000	0.68814	CCG		0.607	MPND-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458292.1	NM_032868	
MPND	84954	broad.mit.edu	37	19	4359933	4359933	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:4359933G>A	ENST00000262966.8	+	12	1417	c.1350G>A	c.(1348-1350)acG>acA	p.T450T	MPND_ENST00000359935.4_Silent_p.T430T|MPND_ENST00000599840.1_Silent_p.T480T|AC007292.3_ENST00000593524.1_RNA	NM_032868.4	NP_116257.2	Q8N594	MPND_HUMAN	MPN domain containing	450							peptidase activity (GO:0008233)	p.T450T(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)	8				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGCAGGACGCCCAAGGACC	0.662																																					p.T430T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1290A	19						.						23.0	27.0	26.0					19																	4359933		2019	4160	6179	4310933	SO:0001819	synonymous_variant	84954	exon11				CCDS42470.1, CCDS54200.1, CCDS74261.1	19p13.3	2014-08-12			ENSG00000008382				25934	protein-coding gene	gene with protein product							Standard	XM_005259663		Approved	FLJ14981	uc002mae.3	Q8N594	OTTHUMG00000181914	ENST00000262966.8:c.1350G>A	19.37:g.4359933G>A		Somatic		Capture	Illumina HiSeq	Phase_I	4310933	NM_001159846	Q96SJ0|Q9Y2P1|Q9Y2P2	Silent	SNP	ENST00000262966.8	37	CCDS42470.1																																																																																				0.662	MPND-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458292.1	NM_032868	
ZNF540	163255	broad.mit.edu	37	19	38103040	38103040	+	Missense_Mutation	SNP	A	A	G	rs557931522		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:38103040A>G	ENST00000592533.1	+	5	1191	c.859A>G	c.(859-861)Act>Gct	p.T287A	ZNF540_ENST00000589117.1_Missense_Mutation_p.T255A|ZNF540_ENST00000343599.5_Missense_Mutation_p.T287A|ZNF540_ENST00000316433.4_Missense_Mutation_p.T287A	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	287					negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation repressor activity, nucleic acid binding (GO:0000900)	p.T287A(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(13)|lung(8)|skin(1)	28			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATTAGAACTTACTCAACATAA	0.284																																					p.T287A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A859G	19						.						27.0	32.0	30.0					19																	38103040		2170	4277	6447	42794880	SO:0001583	missense	163255	exon5			AL832315	CCDS12506.1, CCDS54258.1	19q13.13	2013-01-08				ENSG00000171817		"""Zinc fingers, C2H2-type"", ""-"""	25331	protein-coding gene	gene with protein product		613903					Standard	NM_152606		Approved	DKFZp547B0714	uc002ogq.4	Q8NDQ6		ENST00000592533.1:c.859A>G	19.37:g.38103040A>G	ENSP00000466274:p.Thr287Ala	Somatic		Capture	Illumina HiSeq	Phase_I	42794880	NM_152606	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Missense_Mutation	SNP	ENST00000592533.1	37	CCDS12506.1	.	.	.	.	.	.	.	.	.	.	A	8.921	0.961112	0.18583	.	.	ENSG00000171817	ENST00000316433;ENST00000343599	T	0.35421	1.31	2.33	1.23	0.21249	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16300	0.0392	N	0.16307	0.4	0.09310	N	1	B;B	0.23591	0.072;0.088	B;B	0.21360	0.02;0.034	T	0.28586	-1.0039	9	0.10902	T	0.67	.	2.6161	0.04903	0.6287:0.0:0.1398:0.2314	.	255;287	Q8NDQ6-2;Q8NDQ6	.;ZN540_HUMAN	A	287;255	ENSP00000324598:T287A	ENSP00000324598:T287A	T	+	1	0	ZNF540	42794880	0.000000	0.05858	0.003000	0.11579	0.809000	0.45718	0.239000	0.18023	0.115000	0.18071	0.260000	0.18958	ACT		0.284	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606	
KCNK6	9424	broad.mit.edu	37	19	38817449	38817449	+	Missense_Mutation	SNP	T	T	C	rs567646784		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:38817449T>C	ENST00000263372.3	+	2	646	c.539T>C	c.(538-540)gTa>gCa	p.V180A		NM_004823.1	NP_004814.1	Q9Y257	KCNK6_HUMAN	potassium channel, subfamily K, member 6	180					negative regulation of systemic arterial blood pressure (GO:0003085)|potassium ion transport (GO:0006813)|regulation of resting membrane potential (GO:0060075)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)	p.V180A(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)	17	all_cancers(60;5.83e-07)		Lung(45;0.00047)|LUSC - Lung squamous cell carcinoma(53;0.000613)		Ibutilide(DB00308)|Quinidine(DB00908)	TTGGGGGTCGTAGTGACCGTC	0.627																																					p.V180A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T539C	19						.						107.0	103.0	104.0					19																	38817449		2203	4300	6503	43509289	SO:0001583	missense	9424	exon2			AF117708	CCDS12513.1	19q13.1	2012-03-07				ENSG00000099337		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6281	protein-coding gene	gene with protein product		603939				10075682, 10393428, 16382106	Standard	NM_004823		Approved	K2p6.1, TWIK-2	uc002oic.3	Q9Y257		ENST00000263372.3:c.539T>C	19.37:g.38817449T>C	ENSP00000263372:p.Val180Ala	Somatic		Capture	Illumina HiSeq	Phase_I	43509289	NM_004823	Q9HB47	Missense_Mutation	SNP	ENST00000263372.3	37	CCDS12513.1	.	.	.	.	.	.	.	.	.	.	T	5.758	0.324320	0.10900	.	.	ENSG00000099337	ENST00000263372	T	0.24538	1.85	5.45	2.22	0.28083	.	0.544497	0.19336	N	0.116786	T	0.19967	0.0480	L	0.42581	1.335	0.09310	N	1	B	0.29232	0.238	B	0.37833	0.259	T	0.34650	-0.9820	10	0.02654	T	1	.	8.1615	0.31201	0.0:0.242:0.0:0.758	.	180	Q9Y257	KCNK6_HUMAN	A	180	ENSP00000263372:V180A	ENSP00000263372:V180A	V	+	2	0	KCNK6	43509289	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.921000	0.28718	0.061000	0.16311	-0.441000	0.05720	GTA		0.627	KCNK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460524.1	NM_004823	
GGN	199720	broad.mit.edu	37	19	38877251	38877251	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:38877251G>A	ENST00000334928.6	-	3	783	c.651C>T	c.(649-651)cgC>cgT	p.R217R	AC005789.9_ENST00000585411.1_RNA|GGN_ENST00000591809.1_Intron|SPRED3_ENST00000587013.1_5'Flank	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	217	Interaction with GGNBP1. {ECO:0000250}.|Pro-rich.				cell differentiation (GO:0030154)|gamete generation (GO:0007276)|multicellular organismal development (GO:0007275)|protein localization (GO:0008104)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)		p.R217R(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GCGCCCCTCCGCGAGCCCTGC	0.682																																					p.R217R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C651T	19						.						8.0	10.0	9.0					19																	38877251		2121	4177	6298	43569091	SO:0001819	synonymous_variant	199720	exon3			AF538035	CCDS12516.1	19q13.2	2008-09-04				ENSG00000179168			18869	protein-coding gene	gene with protein product		609966				12574169	Standard	NM_152657		Approved	FLJ35713, MGC33369	uc002oij.1	Q86UU5		ENST00000334928.6:c.651C>T	19.37:g.38877251G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43569091	NM_152657	Q7RTU6|Q86UU4|Q8NAA1	Silent	SNP	ENST00000334928.6	37	CCDS12516.1																																																																																				0.682	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657	
SPRED3	399473	broad.mit.edu	37	19	38882742	38882742	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:38882742G>A	ENST00000338502.4	+	2	437	c.334G>A	c.(334-336)Gca>Aca	p.A112T	SPRED3_ENST00000586301.1_Missense_Mutation_p.A112T|SPRED3_ENST00000587013.1_Missense_Mutation_p.A156T|SPRED3_ENST00000587564.2_3'UTR	NM_001042522.2	NP_001035987.1	Q2MJR0	SPRE3_HUMAN	sprouty-related, EVH1 domain containing 3	112	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)	plasma membrane (GO:0005886)		p.A112T(1)		central_nervous_system(2)|large_intestine(1)|lung(5)|skin(1)	9	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TGCGCTGGCCGCACTGGGTCG	0.617																																					p.A112T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G334A	19						.						82.0	88.0	86.0					19																	38882742		2046	4191	6237	43574582	SO:0001583	missense	399473	exon2				CCDS42560.1	19q13	2007-10-05				ENSG00000188766			31041	protein-coding gene	gene with protein product		609293				14618415	Standard	NM_001042522		Approved		uc002oim.4	Q2MJR0		ENST00000338502.4:c.334G>A	19.37:g.38882742G>A	ENSP00000345405:p.Ala112Thr	Somatic		Capture	Illumina HiSeq	Phase_I	43574582	NM_001042522	Q2MJR1	Missense_Mutation	SNP	ENST00000338502.4	37	CCDS42560.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.173869	0.57692	.	.	ENSG00000188766	ENST00000338502;ENST00000396877	D	0.85702	-2.02	3.74	3.74	0.42951	EVH1 (1);Pleckstrin homology-type (1);	0.220796	0.37219	N	0.002199	T	0.67258	0.2874	N	0.11201	0.11	0.29041	N	0.88508	P;P	0.47604	0.749;0.898	B;B	0.35312	0.142;0.2	T	0.64723	-0.6340	10	0.25106	T	0.35	-1.7124	13.41	0.60938	0.0:0.0:1.0:0.0	.	112;112	Q2MJR0;Q2MJR1	SPRE3_HUMAN;.	T	112	ENSP00000345405:A112T	ENSP00000345405:A112T	A	+	1	0	SPRED3	43574582	0.992000	0.36948	0.895000	0.35142	0.936000	0.57629	2.854000	0.48325	1.823000	0.53134	0.462000	0.41574	GCA		0.617	SPRED3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459216.1	XM_351191	
RYR1	6261	broad.mit.edu	37	19	38985136	38985136	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:38985136G>A	ENST00000359596.3	+	39	6419	c.6419G>A	c.(6418-6420)cGg>cAg	p.R2140Q	RYR1_ENST00000355481.4_Missense_Mutation_p.R2140Q|RYR1_ENST00000360985.3_Missense_Mutation_p.R2140Q			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2140	6 X approximate repeats.				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.R2140Q(1)|p.R2140L(1)		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)	GCCCTGCCGCGGGCGTACACC	0.672																																					p.R2140Q												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G6419A	19						.						55.0	50.0	52.0					19																	38985136		2203	4300	6503	43676976	SO:0001583	missense	6261	exon39			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.6419G>A	19.37:g.38985136G>A	ENSP00000352608:p.Arg2140Gln	Somatic		Capture	Illumina HiSeq	Phase_I	43676976	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.087424	0.36855	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.96774	-4.12;-4.12;-4.12	4.56	3.53	0.40419	.	0.084823	0.45361	U	0.000374	D	0.89622	0.6768	L	0.31926	0.97	0.27711	N	0.945457	P;P	0.51791	0.948;0.913	B;B	0.34418	0.182;0.089	D	0.84792	0.0779	10	0.46703	T	0.11	.	5.3797	0.16183	0.3537:0.0:0.6463:0.0	.	2140;2140	P21817-2;P21817	.;RYR1_HUMAN	Q	2140	ENSP00000352608:R2140Q;ENSP00000347667:R2140Q;ENSP00000354254:R2140Q	ENSP00000347667:R2140Q	R	+	2	0	RYR1	43676976	1.000000	0.71417	0.917000	0.36280	0.302000	0.27658	4.454000	0.60068	1.128000	0.42052	0.305000	0.20034	CGG		0.672	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
UBXN6	80700	broad.mit.edu	37	19	4452387	4452387	+	Missense_Mutation	SNP	C	C	T	rs193168940		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:4452387C>T	ENST00000301281.6	-	4	539	c.415G>A	c.(415-417)Gcc>Acc	p.A139T	UBXN6_ENST00000394765.3_Missense_Mutation_p.A86T|CTB-50L17.9_ENST00000592034.1_RNA	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	139						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.A139T(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	12						TTGATGCAGGCGTCCCGCTGG	0.632													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17664	0.0		0.0	False		,,,				2504	0.0				p.A139T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G415A	19						.						115.0	82.0	93.0					19																	4452387		2203	4300	6503	4403387	SO:0001583	missense	80700	exon4			AF272893	CCDS12129.1, CCDS54201.1	19p13	2008-07-25	2008-07-25	2008-07-25		ENSG00000167671		"""UBX domain containing"""	14928	protein-coding gene	gene with protein product		611946	"""UBX domain-containing 1"", ""UBX domain containing 1"""	UBXD1		11342112	Standard	NM_025241		Approved	UBXDC2	uc002man.2	Q9BZV1		ENST00000301281.6:c.415G>A	19.37:g.4452387C>T	ENSP00000301281:p.Ala139Thr	Somatic		Capture	Illumina HiSeq	Phase_I	4403387	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Missense_Mutation	SNP	ENST00000301281.6	37	CCDS12129.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	8.348	0.830317	0.16749	.	.	ENSG00000167671	ENST00000301281;ENST00000394765	T;T	0.48201	0.82;0.82	4.94	1.47	0.22746	.	0.782495	0.12025	N	0.506476	T	0.39489	0.1080	M	0.63428	1.95	0.09310	N	1	B	0.28208	0.203	B	0.23419	0.046	T	0.27123	-1.0083	10	0.16896	T	0.51	-10.9379	8.1335	0.31041	0.0:0.6273:0.0:0.3727	.	139	Q9BZV1	UBXN6_HUMAN	T	139;86	ENSP00000301281:A139T;ENSP00000378246:A86T	ENSP00000301281:A139T	A	-	1	0	UBXN6	4403387	0.002000	0.14202	0.005000	0.12908	0.375000	0.29983	0.562000	0.23531	0.092000	0.17331	0.484000	0.47621	GCC		0.632	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
RYR1	6261	broad.mit.edu	37	19	39057584	39057584	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:39057584C>T	ENST00000359596.3	+	92	13471	c.13471C>T	c.(13471-13473)Cca>Tca	p.P4491S	RYR1_ENST00000355481.4_Missense_Mutation_p.P4486S|RYR1_ENST00000360985.3_Missense_Mutation_p.P4486S			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4491	Pro-rich.				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.P4491S(1)		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)	CCCGCCAGAGCCAGAGCCCGA	0.647																																					p.P4486S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C13456T	19						.																																			43749424	SO:0001583	missense	6261	exon91			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.13471C>T	19.37:g.39057584C>T	ENSP00000352608:p.Pro4491Ser	Somatic		Capture	Illumina HiSeq	Phase_I	43749424	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	C	0.807	-0.753322	0.03041	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.92858	-3.12;-3.12;-3.12	3.93	2.9	0.33743	Ryanodine Receptor TM 4-6 (1);	0.606936	0.13185	U	0.407200	T	0.81197	0.4772	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.64537	-0.6384	10	0.13470	T	0.59	.	3.0487	0.06162	0.1772:0.5513:0.1721:0.0994	.	4486;4491	P21817-2;P21817	.;RYR1_HUMAN	S	4491;4486;4486	ENSP00000352608:P4491S;ENSP00000347667:P4486S;ENSP00000354254:P4486S	ENSP00000347667:P4486S	P	+	1	0	RYR1	43749424	0.452000	0.25713	0.156000	0.22583	0.014000	0.08584	1.061000	0.30542	1.251000	0.43983	-0.657000	0.03884	CCA		0.647	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
RINL	126432	broad.mit.edu	37	19	39361447	39361447	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:39361447C>T	ENST00000591812.1	-	8	873	c.787G>A	c.(787-789)Gtc>Atc	p.V263I	RINL_ENST00000598904.1_Missense_Mutation_p.V149I|RINL_ENST00000602238.1_5'UTR|RINL_ENST00000340740.3_Missense_Mutation_p.V149I|CTC-360G5.6_ENST00000593830.1_RNA			Q6ZS11	RINL_HUMAN	Ras and Rab interactor-like	263					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|ruffle (GO:0001726)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.V149I(1)		endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|urinary_tract(2)	17						AGAGACTGGACGTGAATGGTG	0.622																																					p.V149I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G445A	19						.						69.0	59.0	63.0					19																	39361447		2203	4300	6503	44053287	SO:0001583	missense	126432	exon8			AK127808	CCDS12522.1, CCDS59386.1	19q13.2	2010-07-13			ENSG00000187994	ENSG00000187994			24795	protein-coding gene	gene with protein product							Standard	NM_001195833		Approved	FLJ45909	uc010xuo.2	Q6ZS11		ENST00000591812.1:c.787G>A	19.37:g.39361447C>T	ENSP00000467107:p.Val263Ile	Somatic		Capture	Illumina HiSeq	Phase_I	44053287	NM_198445	B4DPG5	Missense_Mutation	SNP	ENST00000591812.1	37	CCDS59386.1	.	.	.	.	.	.	.	.	.	.	C	6.214	0.407645	0.11754	.	.	ENSG00000187994	ENST00000340740;ENST00000536520	T	0.42900	0.96	5.22	-6.3	0.02007	.	0.555435	0.16821	N	0.198148	T	0.15262	0.0368	N	0.05124	-0.11	0.09310	N	1	B;B	0.17038	0.02;0.011	B;B	0.10450	0.003;0.005	T	0.32375	-0.9909	10	0.09084	T	0.74	-6.56	11.7837	0.52030	0.0:0.3577:0.0:0.6423	.	263;149	B4DPG5;Q6ZS11	.;RINL_HUMAN	I	149	ENSP00000340369:V149I	ENSP00000340369:V149I	V	-	1	0	RINL	44053287	0.007000	0.16637	0.128000	0.21923	0.094000	0.18550	-1.565000	0.02150	-1.230000	0.02561	-0.458000	0.05436	GTC		0.622	RINL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460433.1	NM_198445	
FBXO27	126433	broad.mit.edu	37	19	39516061	39516061	+	Missense_Mutation	SNP	C	C	T	rs141960657	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:39516061C>T	ENST00000292853.4	-	6	961	c.842G>A	c.(841-843)cGt>cAt	p.R281H	FBXO27_ENST00000509137.2_Missense_Mutation_p.R281H|FBXO27_ENST00000600828.1_Missense_Mutation_p.R280H	NM_178820.3	NP_849142.1	Q8NI29	FBX27_HUMAN	F-box protein 27	281						SCF ubiquitin ligase complex (GO:0019005)	glycoprotein binding (GO:0001948)	p.R281H(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|urinary_tract(2)	17	all_cancers(60;3.79e-07)|all_lung(34;1.26e-07)|Lung NSC(34;1.46e-07)|all_epithelial(25;4.69e-07)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CTAGGACAGACGGACTCGCAC	0.587																																					p.R281H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G842A	19						.	C	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	118.0	102.0	107.0		842	-2.9	0.0	19	dbSNP_134	107	0,8600		0,0,4300	no	missense	FBXO27	NM_178820.3	29	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	281/284	39516061	2,13004	2203	4300	6503	44207901	SO:0001583	missense	126433	exon6			AF436061	CCDS12527.1	19q13.2	2008-02-05	2004-06-15			ENSG00000161243		"""F-boxes /  ""other"""""	18753	protein-coding gene	gene with protein product		609099	"""F-box only protein 27"""			126433	Standard	NM_178820		Approved	Fbg5, Fbx27	uc002okh.3	Q8NI29		ENST00000292853.4:c.842G>A	19.37:g.39516061C>T	ENSP00000292853:p.Arg281His	Somatic		Capture	Illumina HiSeq	Phase_I	44207901	NM_178820	Q96C87	Missense_Mutation	SNP	ENST00000292853.4	37	CCDS12527.1	.	.	.	.	.	.	.	.	.	.	C	8.486	0.860842	0.17178	4.54E-4	0.0	ENSG00000161243	ENST00000292853;ENST00000509137	T;T	0.36878	1.23;1.23	3.41	-2.88	0.05682	.	1.761420	0.03259	N	0.183013	T	0.30448	0.0765	L	0.47716	1.5	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.27331	-1.0077	10	0.54805	T	0.06	-15.2278	5.4608	0.16615	0.0:0.4302:0.1445:0.4253	.	281	Q8NI29	FBX27_HUMAN	H	281	ENSP00000292853:R281H;ENSP00000437662:R281H	ENSP00000292853:R281H	R	-	2	0	FBXO27	44207901	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.817000	0.04472	-0.834000	0.04239	-1.579000	0.00862	CGT		0.587	FBXO27-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463281.1		
SUPT5H	6829	broad.mit.edu	37	19	39963909	39963909	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:39963909G>A	ENST00000599117.1	+	25	2692	c.2325G>A	c.(2323-2325)acG>acA	p.T775T	SUPT5H_ENST00000432763.2_Silent_p.T775T|SUPT5H_ENST00000598725.1_Silent_p.T775T|SUPT5H_ENST00000402194.2_Silent_p.T771T|SUPT5H_ENST00000359191.6_Silent_p.T771T			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	775	9 X 7 AA approximate tandem repeats of G- S-[QR]-T-P-X-[YQ], motif CTR1.				7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)	p.T775T(1)		breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GCTCCCAGACGCCCATGTATG	0.657																																					p.T775T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2325A	19						.						59.0	66.0	64.0					19																	39963909		2203	4300	6503	44655749	SO:0001819	synonymous_variant	6829	exon23			U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"""suppressor of Ty (S.cerevisiae) 5 homolog"""			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.2325G>A	19.37:g.39963909G>A		Somatic		Capture	Illumina HiSeq	Phase_I	44655749	NM_003169	O43279|Q59G52|Q99639	Missense_Mutation	SNP	ENST00000599117.1	37	CCDS12536.1																																																																																				0.657	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169	
FCGBP	8857	broad.mit.edu	37	19	40382677	40382677	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:40382677C>T	ENST00000221347.6	-	22	10216	c.10209G>A	c.(10207-10209)gcG>gcA	p.A3403A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3403	VWFD 8. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.A3403A(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)			AGCCCGCGTACGCCGCCGGCA	0.692																																					p.A3403A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G10209A	19						.						21.0	27.0	25.0					19																	40382677		1672	3168	4840	45074517	SO:0001819	synonymous_variant	8857	exon22			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.10209G>A	19.37:g.40382677C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45074517	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.692	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
FCGBP	8857	broad.mit.edu	37	19	40421293	40421293	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:40421293G>A	ENST00000221347.6	-	5	2635	c.2628C>T	c.(2626-2628)gaC>gaT	p.D876D		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	876	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.D876D(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)			AGCGCCGGCCGTCGAAGCTCA	0.677																																					p.D876D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2628T	19						.						28.0	28.0	28.0					19																	40421293		2202	4300	6502	45113133	SO:0001819	synonymous_variant	8857	exon5			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.2628C>T	19.37:g.40421293G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45113133	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.677	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
PLD3	23646	broad.mit.edu	37	19	40877594	40877594	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:40877594C>T	ENST00000409587.1	+	9	1090	c.693C>T	c.(691-693)ggC>ggT	p.G231G	PLD3_ENST00000409281.1_Silent_p.G231G|PLD3_ENST00000356508.5_Silent_p.G231G|PLD3_ENST00000409735.4_Silent_p.G231G|PLD3_ENST00000409419.1_Silent_p.G231G			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	231					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)	p.G178G(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			AGGAGCTGGGCGTGGTCATGT	0.582																																					p.G231G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C693T	19						.						79.0	50.0	60.0					19																	40877594		2203	4300	6503	45569434	SO:0001819	synonymous_variant	23646	exon9			BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"""phospholipase D3"""			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.693C>T	19.37:g.40877594C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45569434	NM_001031696	Q92853|Q9BW87	Silent	SNP	ENST00000409587.1	37	CCDS33027.1																																																																																				0.582	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268	
PLD3	23646	broad.mit.edu	37	19	40884063	40884063	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:40884063G>A	ENST00000409587.1	+	13	1853	c.1456G>A	c.(1456-1458)Gcc>Acc	p.A486T	PLD3_ENST00000409281.1_Missense_Mutation_p.A486T|PLD3_ENST00000356508.5_Missense_Mutation_p.A486T|PLD3_ENST00000409735.4_Missense_Mutation_p.A486T|PLD3_ENST00000409419.1_Missense_Mutation_p.A486T			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	486					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)	p.A433T(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			CGTGGGCAACGCCTGCCGCCT	0.701																																					p.A486T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1456A	19						.						69.0	70.0	70.0					19																	40884063		2203	4299	6502	45575903	SO:0001583	missense	23646	exon13			BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"""phospholipase D3"""			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.1456G>A	19.37:g.40884063G>A	ENSP00000387050:p.Ala486Thr	Somatic		Capture	Illumina HiSeq	Phase_I	45575903	NM_001031696	Q92853|Q9BW87	Missense_Mutation	SNP	ENST00000409587.1	37	CCDS33027.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.972813	0.34848	.	.	ENSG00000105223	ENST00000409419;ENST00000409587;ENST00000356508;ENST00000409735;ENST00000409281	T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79	5.97	2.61	0.31194	.	0.367363	0.29900	N	0.010911	T	0.13372	0.0324	N	0.03608	-0.345	0.23401	N	0.997759	P	0.44659	0.84	B	0.28385	0.089	T	0.13548	-1.0505	10	0.12430	T	0.62	-22.5781	4.2512	0.10695	0.1888:0.0:0.5877:0.2235	.	486	Q8IV08	PLD3_HUMAN	T	486	ENSP00000386293:A486T;ENSP00000387050:A486T;ENSP00000348901:A486T;ENSP00000386938:A486T;ENSP00000387022:A486T	ENSP00000348901:A486T	A	+	1	0	PLD3	45575903	0.025000	0.19082	0.820000	0.32676	0.293000	0.27360	0.123000	0.15708	0.868000	0.35678	0.655000	0.94253	GCC		0.701	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268	
HIPK4	147746	broad.mit.edu	37	19	40887059	40887059	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:40887059C>T	ENST00000291823.2	-	3	1123	c.839G>A	c.(838-840)cGc>cAc	p.R280H		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	280	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R280H(2)		breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			ATACTTGCGGCGCTCCAATGG	0.627																																					p.R280H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G839A	19						.						36.0	33.0	34.0					19																	40887059		2193	4285	6478	45578899	SO:0001583	missense	147746	exon3			BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.839G>A	19.37:g.40887059C>T	ENSP00000291823:p.Arg280His	Somatic		Capture	Illumina HiSeq	Phase_I	45578899	NM_144685	A8K863|Q96M54	Missense_Mutation	SNP	ENST00000291823.2	37	CCDS12555.1	.	.	.	.	.	.	.	.	.	.	C	19.75	3.885890	0.72410	.	.	ENSG00000160396	ENST00000291823;ENST00000452139	T	0.67698	-0.28	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	0.56097	D	0.000029	T	0.53094	0.1775	N	0.19112	0.55	0.39878	D	0.973599	P	0.43519	0.809	B	0.39379	0.298	T	0.56111	-0.8033	10	0.32370	T	0.25	.	16.6992	0.85344	0.0:1.0:0.0:0.0	.	280	Q8NE63	HIPK4_HUMAN	H	280;245	ENSP00000291823:R280H	ENSP00000291823:R280H	R	-	2	0	HIPK4	45578899	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	3.493000	0.53266	2.677000	0.91161	0.561000	0.74099	CGC		0.627	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685	
PRX	57716	broad.mit.edu	37	19	40900943	40900943	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:40900943C>T	ENST00000324001.7	-	7	3586	c.3316G>A	c.(3316-3318)Gcc>Acc	p.A1106T	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	1106	Glu-rich (acidic).				axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.A1106T(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TCCTCCTGGGCGCCCAGCGTG	0.647																																					p.A1106T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3316A	19						.						56.0	54.0	55.0					19																	40900943		2203	4300	6503	45592783	SO:0001583	missense	57716	exon7			AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.3316G>A	19.37:g.40900943C>T	ENSP00000326018:p.Ala1106Thr	Somatic		Capture	Illumina HiSeq	Phase_I	45592783	NM_181882	Q9BXL9|Q9HCF2	Missense_Mutation	SNP	ENST00000324001.7	37	CCDS33028.1	.	.	.	.	.	.	.	.	.	.	C	4.203	0.036395	0.08148	.	.	ENSG00000105227	ENST00000324001	T	0.01767	4.65	4.9	0.237	0.15475	.	0.395400	0.21585	N	0.072185	T	0.01870	0.0059	L	0.57536	1.79	0.21290	N	0.999734	B	0.27416	0.178	B	0.20577	0.03	T	0.43327	-0.9398	10	0.35671	T	0.21	-9.1206	4.5086	0.11899	0.0:0.4979:0.1543:0.3477	.	1106	Q9BXM0	PRAX_HUMAN	T	1106	ENSP00000326018:A1106T	ENSP00000326018:A1106T	A	-	1	0	PRX	45592783	0.000000	0.05858	0.114000	0.21550	0.044000	0.14063	0.147000	0.16202	0.009000	0.14813	-0.333000	0.08304	GCC		0.647	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956	
BLVRB	645	broad.mit.edu	37	19	40953835	40953835	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:40953835G>A	ENST00000263368.4	-	5	733	c.582C>T	c.(580-582)taC>taT	p.Y194Y	BLVRB_ENST00000595483.1_Silent_p.Y151Y	NM_000713.2	NP_000704.1	P30043	BLVRB_HUMAN	biliverdin reductase B (flavin reductase (NADPH))	194					heme catabolic process (GO:0042167)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	biliverdin reductase activity (GO:0004074)|riboflavin reductase (NADPH) activity (GO:0042602)	p.Y194Y(1)		large_intestine(3)|lung(3)	6			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)		Riboflavin(DB00140)	TGTGTCCGTCGTACTCATCGG	0.597																																					p.Y194Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C582T	19						.						175.0	141.0	152.0					19																	40953835		2203	4300	6503	45645675	SO:0001819	synonymous_variant	645	exon5			D26308	CCDS33029.1	19q13.1-q13.2	2011-09-14				ENSG00000090013	1.3.1.24, 1.5.1.30	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	1063	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 43U, member 1"""	600941	"""Flavin reductase"""	FLR		7656592, 19027726	Standard	NM_000713		Approved	SDR43U1	uc002onw.2	P30043		ENST00000263368.4:c.582C>T	19.37:g.40953835G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45645675	NM_000713	A6NKD8|B2R5C6|P32078|P53005|Q32LZ2	Silent	SNP	ENST00000263368.4	37	CCDS33029.1																																																																																				0.597	BLVRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462563.1		
RAB4B	53916	broad.mit.edu	37	19	41292841	41292841	+	Silent	SNP	C	C	T	rs574371740		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:41292841C>T	ENST00000594800.1	+	7	775	c.615C>T	c.(613-615)gcC>gcT	p.A205A	RAB4B-EGLN2_ENST00000601949.1_3'UTR|RAB4B_ENST00000357052.2_Silent_p.A205A|RAB4B-EGLN2_ENST00000594136.1_Silent_p.A205A			P61018	RAB4B_HUMAN	RAB4B, member RAS oncogene family	205					glucose import (GO:0046323)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	insulin-responsive compartment (GO:0032593)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	GTP binding (GO:0005525)	p.A240A(1)		endometrium(2)|kidney(3)|large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	11			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			GTGCCCAGGCCGTGGCCCCTC	0.682													-|||	1	0.000199681	0.0	0.0	5008	,	,		15539	0.0		0.001	False		,,,				2504	0.0				p.A205A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C615T	19						.						30.0	31.0	31.0					19																	41292841		2203	4296	6499	45984681	SO:0001819	synonymous_variant	53916	exon7			AF165522	CCDS33030.1	19q13.2	2012-10-15			ENSG00000167578	ENSG00000167578		"""RAB, member RAS oncogene"""	9782	protein-coding gene	gene with protein product	"""ras-related GTP-binding protein 4b"", ""small GTP binding protein RAB4B"""	612945					Standard	NM_016154		Approved	FLJ78649, MGC52123	uc002opd.2	P61018		ENST00000594800.1:c.615C>T	19.37:g.41292841C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45984681	NM_016154	P22750|Q7Z514|Q9HBR6	Silent	SNP	ENST00000594800.1	37	CCDS33030.1																																																																																				0.682	RAB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463168.1	NM_016154	
CYP2A7	1549	broad.mit.edu	37	19	41383097	41383097	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:41383097T>C	ENST00000301146.4	-	7	1700	c.1159A>G	c.(1159-1161)Aag>Gag	p.K387E	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Missense_Mutation_p.K336E	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	387						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)	p.K387E(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			GATAGCACCTTAGGGAGGAAA	0.532																																					p.K387E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1159G	19						.						76.0	70.0	72.0					19																	41383097		2203	4299	6502	46074937	SO:0001583	missense	1549	exon7			NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"""Cytochrome P450s"""	2611	protein-coding gene	gene with protein product		608054	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"""			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.1159A>G	19.37:g.41383097T>C	ENSP00000301146:p.Lys387Glu	Somatic		Capture	Illumina HiSeq	Phase_I	46074937	NM_000764	Q13121	Missense_Mutation	SNP	ENST00000301146.4	37	CCDS12569.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.999930	0.74818	.	.	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.17213	4.67;2.29	2.29	2.29	0.28610	.	0.000000	0.85682	U	0.000000	T	0.36771	0.0979	M	0.74647	2.275	0.80722	D	1	D;D;P	0.89917	0.994;1.0;0.847	P;D;P	0.73708	0.884;0.981;0.73	T	0.18524	-1.0334	10	0.87932	D	0	.	9.2828	0.37737	0.0:0.0:0.0:1.0	.	387;336;387	B7ZKR0;F8W816;P20853	.;.;CP2A7_HUMAN	E	387;336	ENSP00000301146:K387E;ENSP00000291764:K336E	ENSP00000291764:K336E	K	-	1	0	CYP2A7	46074937	1.000000	0.71417	0.656000	0.29637	0.296000	0.27459	5.157000	0.64911	1.053000	0.40415	0.155000	0.16302	AAG		0.532	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
CYP2A7	1549	broad.mit.edu	37	19	41383879	41383879	+	Missense_Mutation	SNP	G	G	A	rs147586806		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:41383879G>A	ENST00000301146.4	-	6	1392	c.851C>T	c.(850-852)aCg>aTg	p.T284M	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Missense_Mutation_p.T233M	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	284						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)	p.T284M(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			GTAGAACTCCGTGTTGGGGTT	0.557																																					p.T284M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C851T	19						.	G	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	102.0	79.0	87.0		851,698	1.2	0.0	19	dbSNP_134	87	0,8598		0,0,4299	no	missense,missense	CYP2A7	NM_000764.2,NM_030589.2	81,81	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	284/495,233/444	41383879	1,13003	2203	4299	6502	46075719	SO:0001583	missense	1549	exon6			NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"""Cytochrome P450s"""	2611	protein-coding gene	gene with protein product		608054	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"""			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.851C>T	19.37:g.41383879G>A	ENSP00000301146:p.Thr284Met	Somatic		Capture	Illumina HiSeq	Phase_I	46075719	NM_000764	Q13121	Missense_Mutation	SNP	ENST00000301146.4	37	CCDS12569.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.266412	0.40095	2.27E-4	0.0	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.68903	-0.36;-0.36	2.29	1.16	0.20824	.	0.196538	0.42420	U	0.000701	T	0.71787	0.3381	L	0.54323	1.7	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.73708	0.979;0.981;0.979	T	0.60021	-0.7344	10	0.56958	D	0.05	.	6.1826	0.20480	0.0:0.2048:0.5861:0.2091	.	284;233;284	B7ZKR0;F8W816;P20853	.;.;CP2A7_HUMAN	M	284;233	ENSP00000301146:T284M;ENSP00000291764:T233M	ENSP00000291764:T233M	T	-	2	0	CYP2A7	46075719	0.015000	0.18098	0.004000	0.12327	0.466000	0.32739	1.863000	0.39459	0.273000	0.22049	0.184000	0.17185	ACG		0.557	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
BCKDHA	593	broad.mit.edu	37	19	41928158	41928158	+	Missense_Mutation	SNP	G	G	A	rs536540966	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:41928158G>A	ENST00000269980.2	+	6	1104	c.736G>A	c.(736-738)Gcc>Acc	p.A246T	BCKDHA_ENST00000535632.1_3'UTR|BCKDHA_ENST00000457836.2_Missense_Mutation_p.A224T|CTC-435M10.3_ENST00000540732.1_Missense_Mutation_p.A280T|BCKDHA_ENST00000595085.1_Missense_Mutation_p.A280T	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide	246					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.A246T(1)		central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						TGAGGGGGACGCCCATGCCGG	0.632													G|||	2	0.000399361	0.0	0.0	5008	,	,		18002	0.002		0.0	False		,,,				2504	0.0				p.A246T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G736A	19						.						84.0	74.0	77.0					19																	41928158		2203	4300	6503	46619998	SO:0001583	missense	593	exon6			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	ENST00000269980.2:c.736G>A	19.37:g.41928158G>A	ENSP00000269980:p.Ala246Thr	Somatic		Capture	Illumina HiSeq	Phase_I	46619998	NM_001164783	B4DP47|E7EW46|Q16034|Q16472	Missense_Mutation	SNP	ENST00000269980.2	37	CCDS12581.1	.	.	.	.	.	.	.	.	.	.	G	32	5.181978	0.94885	.	.	ENSG00000255730;ENSG00000248098;ENSG00000248098;ENSG00000248098;ENSG00000248098	ENST00000540732;ENST00000269980;ENST00000542943;ENST00000457836;ENST00000378196	D;D;D;D	0.95885	-3.84;-3.84;-3.84;-3.84	4.71	4.71	0.59529	Dehydrogenase, E1 component (1);	0.114055	0.64402	D	0.000017	D	0.94879	0.8345	L	0.43646	1.37	0.80722	D	1	D;D;D;D	0.63046	0.973;0.987;0.992;0.963	P;B;P;B	0.53689	0.643;0.409;0.732;0.379	D	0.93399	0.6758	10	0.25751	T	0.34	-33.1089	16.5958	0.84796	0.0:0.0:1.0:0.0	.	224;246;246;280	B4DP47;Q59EI3;P12694;F5H5P2	.;.;ODBA_HUMAN;.	T	280;246;217;224;246	ENSP00000443246:A280T;ENSP00000269980:A246T;ENSP00000440345:A217T;ENSP00000416000:A224T	ENSP00000269980:A246T	A	+	1	0	BCKDHA;CTC-435M10.3	46619998	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	8.783000	0.91813	2.450000	0.82876	0.655000	0.94253	GCC		0.632	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709	
LYPD4	147719	broad.mit.edu	37	19	42342106	42342106	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:42342106G>A	ENST00000330743.3	-	4	1652	c.441C>T	c.(439-441)ggC>ggT	p.G147G	AC020956.3_ENST00000593354.1_lincRNA|LYPD4_ENST00000601246.1_Silent_p.G112G|LYPD4_ENST00000343055.4_Silent_p.G112G	NM_173506.4	NP_775777.3	Q6UWN0	LYPD4_HUMAN	LY6/PLAUR domain containing 4	147	UPAR/Ly6.					anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.G147G(1)		breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)	12						TCATGTGCTCGCCCACACAGG	0.493																																					p.G147G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C441T	19						.						101.0	91.0	94.0					19																	42342106		2203	4300	6503	47033946	SO:0001819	synonymous_variant	147719	exon4			AY358726	CCDS12587.1	19q13.2	2008-02-05				ENSG00000273111			28659	protein-coding gene	gene with protein product						12975309	Standard	XM_005278383		Approved	MGC42718	uc002orp.1	Q6UWN0		ENST00000330743.3:c.441C>T	19.37:g.42342106G>A		Somatic		Capture	Illumina HiSeq	Phase_I	47033946	NM_173506	Q8IYW0	Silent	SNP	ENST00000330743.3	37	CCDS12587.1																																																																																				0.493	LYPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463039.1	NM_173506	
CD79A	973	broad.mit.edu	37	19	42384752	42384752	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:42384752G>A	ENST00000221972.3	+	4	699	c.514G>A	c.(514-516)Gag>Aag	p.E172K	ARHGEF1_ENST00000354532.3_5'Flank|CD79A_ENST00000444740.2_Missense_Mutation_p.E134K|ARHGEF1_ENST00000347545.4_5'Flank|ARHGEF1_ENST00000599846.1_5'Flank	NM_001783.3|NM_021601.3	NP_001774.1|NP_067612.1	P11912	CD79A_HUMAN	CD79a molecule, immunoglobulin-associated alpha	172					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)	B cell receptor complex (GO:0019815)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.E172K(1)		large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	11						ATGGCAGAACGAGAAGCTCGG	0.542			"""O, S"""		DLBCL																																p.E172K			Dom	yes		19	19q13.2	973	"""CD79a molecule, immunoglobulin-associated alpha"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G514A	19						.						19.0	19.0	19.0					19																	42384752		2022	3951	5973	47076592	SO:0001583	missense	973	exon4			M80462	CCDS12589.1, CCDS46088.1	19q13.2	2014-09-17	2006-03-28					"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1698	protein-coding gene	gene with protein product		112205	"""CD79A antigen (immunoglobulin-associated alpha)"""	IGA		1538135	Standard	NM_001783		Approved	MB-1	uc002orv.3	P11912		ENST00000221972.3:c.514G>A	19.37:g.42384752G>A	ENSP00000221972:p.Glu172Lys	Somatic		Capture	Illumina HiSeq	Phase_I	47076592	NM_001783	A0N775|Q53FB8	Missense_Mutation	SNP	ENST00000221972.3	37	CCDS12589.1	.	.	.	.	.	.	.	.	.	.	G	5.502	0.277583	0.10403	.	.	ENSG00000105369	ENST00000221972;ENST00000444740	T	0.78707	-1.2	3.7	-1.9	0.07665	.	0.575167	0.13424	N	0.388978	T	0.55257	0.1909	N	0.19112	0.55	0.19300	N	0.99998	B;B	0.22541	0.071;0.043	B;B	0.18871	0.023;0.007	T	0.34900	-0.9810	10	0.27082	T	0.32	-5.6345	4.489	0.11805	0.1405:0.0:0.5289:0.3306	.	172;134	P11912;A0N775	CD79A_HUMAN;.	K	172;134	ENSP00000221972:E172K	ENSP00000221972:E172K	E	+	1	0	CD79A	47076592	0.068000	0.21057	0.040000	0.18447	0.014000	0.08584	0.044000	0.13992	-0.394000	0.07727	0.449000	0.29647	GAG		0.542	CD79A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463058.1		
ERF	2077	broad.mit.edu	37	19	42753820	42753820	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:42753820C>T	ENST00000222329.4	-	4	601	c.444G>A	c.(442-444)acG>acA	p.T148T	ERF_ENST00000440177.2_Silent_p.T73T|ERF_ENST00000595941.1_5'Flank|AC006486.9_ENST00000594664.1_Intron	NM_006494.2	NP_006485.2	P50548	ERF_HUMAN	Ets2 repressor factor	148					cell cycle (GO:0007049)|cell differentiation (GO:0030154)|chorio-allantoic fusion (GO:0060710)|ectodermal cell differentiation (GO:0010668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription corepressor activity (GO:0003714)	p.T148T(1)		central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	17		Prostate(69;0.00682)				CCTCGGAGGGCGTTGAGGGAG	0.682																																					p.T148T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G444A	19						.						41.0	44.0	43.0					19																	42753820		2203	4299	6502	47445660	SO:0001819	synonymous_variant	2077	exon4			U58535	CCDS12600.1	19q13	2008-07-16				ENSG00000105722			3444	protein-coding gene	gene with protein product	"""Ets2 repressor factor"""	611888				7588608, 9192842	Standard	XM_005258644		Approved	PE-2, PE2	uc002ote.4	P50548		ENST00000222329.4:c.444G>A	19.37:g.42753820C>T		Somatic		Capture	Illumina HiSeq	Phase_I	47445660	NM_006494	B2RAP1|B7Z4R0|Q59G38|Q9UPI7	Silent	SNP	ENST00000222329.4	37	CCDS12600.1																																																																																				0.682	ERF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463684.1	NM_006494	
LIPE	3991	broad.mit.edu	37	19	42907042	42907042	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:42907042G>A	ENST00000244289.4	-	9	2960	c.2684C>T	c.(2683-2685)tCg>tTg	p.S895L	LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000599276.1_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000593491.2_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	895					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)	p.S895L(1)		breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				AGCTGACAGCGACATCTCGGG	0.592																																					p.S895L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2684T	19						.						97.0	77.0	84.0					19																	42907042		2203	4300	6503	47598882	SO:0001583	missense	3991	exon9			L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.2684C>T	19.37:g.42907042G>A	ENSP00000244289:p.Ser895Leu	Somatic		Capture	Illumina HiSeq	Phase_I	47598882	NM_005357	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	37	CCDS12607.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814324	0.70912	.	.	ENSG00000079435	ENST00000244289	T	0.03831	3.79	5.38	5.38	0.77491	.	0.986918	0.08240	N	0.976314	T	0.21718	0.0523	M	0.65975	2.015	0.44668	D	0.997654	D	0.76494	0.999	D	0.72625	0.978	T	0.00025	-1.2315	10	0.42905	T	0.14	-18.3884	14.9928	0.71401	0.0:0.0:1.0:0.0	.	895	Q05469	LIPS_HUMAN	L	895	ENSP00000244289:S895L	ENSP00000244289:S895L	S	-	2	0	LIPE	47598882	0.993000	0.37304	0.962000	0.40283	0.923000	0.55619	5.854000	0.69503	2.689000	0.91719	0.591000	0.81541	TCG		0.592	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357	
PSG4	5672	broad.mit.edu	37	19	43708378	43708378	+	Silent	SNP	C	C	T	rs533600298		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:43708378C>T	ENST00000405312.3	-	2	327	c.90G>A	c.(88-90)ccG>ccA	p.P30P	PSG4_ENST00000244295.9_Silent_p.P30P|PSG4_ENST00000433626.2_Silent_p.P30P	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	30					female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)		p.P30P(2)		central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				CAGTTGTGGGCGGATTCCAGA	0.468													C|||	1	0.000199681	0.0	0.0014	5008	,	,		15815	0.0		0.0	False		,,,				2504	0.0				p.P30P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G90A	19						.						118.0	131.0	127.0					19																	43708378		2137	4270	6407	48400218	SO:0001819	synonymous_variant	5672	exon2				CCDS33039.1, CCDS46093.1, CCDS62695.1	19q13.2	2013-01-29			ENSG00000243137	ENSG00000243137		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9521	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1-glycoprotein 4"""	176393				2783133	Standard	NM_002780		Approved		uc002ovy.4	Q00888	OTTHUMG00000151544	ENST00000405312.3:c.90G>A	19.37:g.43708378C>T		Somatic		Capture	Illumina HiSeq	Phase_I	48400218	NM_002780	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Silent	SNP	ENST00000405312.3	37	CCDS46093.1																																																																																				0.468	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633	
PSG9	5678	broad.mit.edu	37	19	43772053	43772053	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:43772053C>T	ENST00000270077.3	-	2	409	c.313G>A	c.(313-315)Gca>Aca	p.A105T	PSG9_ENST00000596730.1_Missense_Mutation_p.A105T|PSG9_ENST00000291752.5_Missense_Mutation_p.A105T|PSG9_ENST00000244293.7_Missense_Mutation_p.A105T|PSG9_ENST00000443718.3_Missense_Mutation_p.A105T|PSG9_ENST00000418820.2_Missense_Mutation_p.A105T|PSG9_ENST00000593948.1_Missense_Mutation_p.A105T	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9	105	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.A105T(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				AGCAGGGATGCGTTGGAATAT	0.403																																					p.A105T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G313A	19						.						290.0	267.0	275.0					19																	43772053		2203	4300	6503	48463893	SO:0001583	missense	5678	exon2			M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.313G>A	19.37:g.43772053C>T	ENSP00000270077:p.Ala105Thr	Somatic		Capture	Illumina HiSeq	Phase_I	48463893	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000270077.3	37	CCDS12618.1	.	.	.	.	.	.	.	.	.	.	c	14.40	2.525003	0.44969	.	.	ENSG00000183668	ENST00000270077;ENST00000291752;ENST00000443718;ENST00000435220;ENST00000244293	T;T;T;T	0.01548	4.78;4.78;4.78;4.78	1.56	1.56	0.23342	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.11410	0.0278	M	0.92970	3.365	0.09310	N	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.996;0.999	D;D;D;D;D;D	0.81914	0.995;0.993;0.991;0.99;0.957;0.989	T	0.03773	-1.1005	9	0.72032	D	0.01	.	6.5953	0.22669	0.0:1.0:0.0:0.0	.	105;54;105;105;105;105	E7EW65;Q15225;Q15227;G3XAA7;Q6LEU7;Q00887	.;.;.;.;.;PSG9_HUMAN	T	105;105;105;66;105	ENSP00000270077:A105T;ENSP00000291752:A105T;ENSP00000396753:A105T;ENSP00000244293:A105T	ENSP00000244293:A105T	A	-	1	0	PSG9	48463893	0.011000	0.17503	0.242000	0.24170	0.060000	0.15804	0.628000	0.24522	1.175000	0.42826	0.298000	0.19748	GCA		0.403	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784	
ZNF575	284346	broad.mit.edu	37	19	44038608	44038608	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:44038608G>A	ENST00000314228.5	+	3	546	c.34G>A	c.(34-36)Gct>Act	p.A12T	ZNF575_ENST00000458714.2_Missense_Mutation_p.A111T|ZNF575_ENST00000601282.1_Missense_Mutation_p.A12T	NM_174945.2	NP_777605.1	Q86XF7	ZN575_HUMAN	zinc finger protein 575	12					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.A12T(1)		large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	4		Prostate(69;0.0199)				CGCGGCCGGGGCTACCGATCC	0.652																																					p.A12T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G34A	19						.						19.0	19.0	19.0					19																	44038608		2196	4294	6490	48730448	SO:0001583	missense	284346	exon3			BC043611	CCDS12623.1	19q13.31	2013-09-20			ENSG00000176472	ENSG00000176472		"""Zinc fingers, C2H2-type"""	27606	protein-coding gene	gene with protein product							Standard	NM_174945		Approved	FLJ32567	uc002ows.3	Q86XF7	OTTHUMG00000182698	ENST00000314228.5:c.34G>A	19.37:g.44038608G>A	ENSP00000315870:p.Ala12Thr	Somatic		Capture	Illumina HiSeq	Phase_I	48730448	NM_174945	B4DX54	Missense_Mutation	SNP	ENST00000314228.5	37	CCDS12623.1	.	.	.	.	.	.	.	.	.	.	G	12.76	2.033093	0.35893	.	.	ENSG00000176472	ENST00000458714;ENST00000314228	T;T	0.08458	3.09;3.18	4.66	1.3	0.21679	.	2.033000	0.02331	N	0.073929	T	0.05502	0.0145	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.36407	-0.9749	10	0.72032	D	0.01	0.1153	4.9691	0.14105	0.1938:0.1741:0.6321:0.0	.	12;111	Q86XF7;B3KQ07	ZN575_HUMAN;.	T	111;12	ENSP00000413956:A111T;ENSP00000315870:A12T	ENSP00000315870:A12T	A	+	1	0	ZNF575	48730448	0.291000	0.24352	0.000000	0.03702	0.007000	0.05969	2.361000	0.44160	0.169000	0.19679	-1.121000	0.02013	GCT		0.652	ZNF575-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463191.1	NM_174945	
IRGQ	126298	broad.mit.edu	37	19	44097282	44097282	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:44097282C>T	ENST00000602269.1	-	2	953	c.768G>A	c.(766-768)tcG>tcA	p.S256S	IRGQ_ENST00000601520.1_5'Flank|IRGQ_ENST00000422989.1_Silent_p.S256S|L34079.2_ENST00000594374.1_5'Flank			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	256	IRG-type G.							p.S256S(1)		endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				CTGTGGGGACCGAAGCAGGCG	0.692																																					p.S256S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G768A	19						.						24.0	29.0	27.0					19																	44097282		2201	4299	6500	48789122	SO:0001819	synonymous_variant	126298	exon3			AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"""immunity-related GTPase family, Q1"""	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.768G>A	19.37:g.44097282C>T		Somatic		Capture	Illumina HiSeq	Phase_I	48789122	NM_001007561	B2RNP3	Silent	SNP	ENST00000602269.1	37	CCDS33040.1																																																																																				0.692	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561	
ZNF404	342908	broad.mit.edu	37	19	44377214	44377214	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:44377214T>C	ENST00000587539.1	-	3	1151	c.1152A>G	c.(1150-1152)gaA>gaG	p.E384E	ZNF404_ENST00000324394.6_Silent_p.E382E	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	384					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.E382E(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|stomach(2)|urinary_tract(1)	17		Prostate(69;0.0352)				ATTCTTTACATTCATGTGGCT	0.368																																					p.E381E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1143G	19						.						30.0	32.0	31.0					19																	44377214		2183	4294	6477	49069054	SO:0001819	synonymous_variant	342908	exon2			XM_092027	CCDS59394.1	19q13.31	2013-01-08				ENSG00000176222		"""Zinc fingers, C2H2-type"", ""-"""	19417	protein-coding gene	gene with protein product							Standard	NM_001033719		Approved		uc002oxs.5	Q494X3		ENST00000587539.1:c.1152A>G	19.37:g.44377214T>C		Somatic		Capture	Illumina HiSeq	Phase_I	49069054	NM_001033719	A4FU30|K7ELF2	Silent	SNP	ENST00000587539.1	37	CCDS59394.1																																																																																				0.368	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719	
ZNF285	26974	broad.mit.edu	37	19	44891743	44891743	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:44891743G>A	ENST00000330997.4	-	4	728	c.664C>T	c.(664-666)Cgt>Tgt	p.R222C	ZNF285_ENST00000544719.2_Missense_Mutation_p.R222C|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000591679.1_Missense_Mutation_p.R229C	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	222					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.R222C(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						GCCGCATTACGTTTTTCAACC	0.463																																					p.R222C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C664T	19						.						105.0	102.0	103.0					19																	44891743		2203	4300	6503	49583583	SO:0001583	missense	26974	exon4			AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.664C>T	19.37:g.44891743G>A	ENSP00000333595:p.Arg222Cys	Somatic		Capture	Illumina HiSeq	Phase_I	49583583	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	G	15.04	2.715721	0.48622	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.28666	1.6	3.07	-0.585	0.11698	.	.	.	.	.	T	0.12135	0.0295	N	0.08118	0	0.18873	N	0.999988	B;B	0.30068	0.092;0.267	B;B	0.06405	0.002;0.002	T	0.16453	-1.0402	9	0.87932	D	0	.	4.654	0.12608	0.2114:0.0:0.6057:0.1829	.	246;222	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	C	245;222	ENSP00000333595:R222C	ENSP00000333595:R222C	R	-	1	0	ZNF285	49583583	0.000000	0.05858	0.002000	0.10522	0.077000	0.17291	-0.391000	0.07323	-0.148000	0.11234	0.454000	0.30748	CGT		0.463	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
KDM4B	23030	broad.mit.edu	37	19	5077406	5077406	+	Silent	SNP	C	C	T	rs202178470	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:5077406C>T	ENST00000159111.4	+	8	923	c.705C>T	c.(703-705)tgC>tgT	p.C235C	KDM4B_ENST00000536461.1_Silent_p.C235C|KDM4B_ENST00000592175.1_3'UTR|KDM4B_ENST00000381759.4_Silent_p.C235C	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	235	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)	p.C235C(2)		breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						CGCAGGGCTGCGACGCCTTCC	0.657													C|||	2	0.000399361	0.0	0.0	5008	,	,		17231	0.001		0.0	False		,,,				2504	0.001				p.C235C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C705T	19						.						128.0	133.0	131.0					19																	5077406		2203	4300	6503	5028406	SO:0001819	synonymous_variant	23030	exon8			AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	29136	protein-coding gene	gene with protein product	"""tudor domain containing 14B"""	609765	"""jumonji domain containing 2B"""	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.705C>T	19.37:g.5077406C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5028406	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Silent	SNP	ENST00000159111.4	37	CCDS12138.1																																																																																				0.657	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015	
ZNF180	7733	broad.mit.edu	37	19	44981655	44981655	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:44981655G>T	ENST00000221327.4	-	5	1324	c.1043C>A	c.(1042-1044)tCt>tAt	p.S348Y	AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000391956.4_Missense_Mutation_p.S323Y|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000592529.1_Missense_Mutation_p.S321Y	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	348					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.S348Y(1)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				TTTCTCTTCAGAATTATTTCT	0.388																																					p.S348Y	Esophageal Squamous(180;1353 2003 32862 46574 49854)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1043A	19						.						72.0	75.0	74.0					19																	44981655		2203	4300	6503	49673495	SO:0001583	missense	7733	exon5			AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1043C>A	19.37:g.44981655G>T	ENSP00000221327:p.Ser348Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	49673495	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.744334	0.49151	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.08458	3.09;3.09	5.28	4.18	0.49190	.	0.000000	0.41396	D	0.000892	T	0.28466	0.0704	M	0.81497	2.545	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74348	0.971;0.983;0.983	T	0.02053	-1.1222	10	0.87932	D	0	-13.1236	12.3854	0.55328	0.0:0.0:0.8309:0.1691	.	323;347;348	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	Y	348;323	ENSP00000221327:S348Y;ENSP00000375818:S323Y	ENSP00000221327:S348Y	S	-	2	0	ZNF180	49673495	0.000000	0.05858	0.997000	0.53966	0.953000	0.61014	0.664000	0.25068	2.444000	0.82710	0.655000	0.94253	TCT		0.388	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
TRAPPC6A	79090	broad.mit.edu	37	19	45667238	45667238	+	Silent	SNP	G	G	A	rs148185826		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:45667238G>A	ENST00000585934.1	-	5	402	c.384C>T	c.(382-384)cgC>cgT	p.R128R	TRAPPC6A_ENST00000006275.4_Silent_p.R142R|TRAPPC6A_ENST00000588062.1_Missense_Mutation_p.R106W|TRAPPC6A_ENST00000592647.1_Missense_Mutation_p.R120W	NM_001270891.1	NP_001257820.1	O75865	TPC6A_HUMAN	trafficking protein particle complex 6A	128					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)		p.R142R(1)		autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	8		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00872)|GBM - Glioblastoma multiforme(486;0.233)		AGAGGGCGCCGCGCAGGAGGC	0.662													g|||	1	0.000199681	0.0	0.0	5008	,	,		17404	0.0		0.001	False		,,,				2504	0.0				p.R142R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C426T	19						.			2,4384		0,2,2191	40.0	43.0	42.0		426	-9.3	0.1	19	dbSNP_134	42	4,8568		0,4,4282	no	coding-synonymous	TRAPPC6A	NM_024108.1		0,6,6473	AA,AG,GG		0.0467,0.0456,0.0463		142/174	45667238	6,12952	2193	4286	6479	50359078	SO:0001819	synonymous_variant	79090	exon5			AF161407	CCDS12655.1, CCDS59395.1, CCDS59396.1, CCDS59397.1	19q13.32	2012-10-02				ENSG00000007255		"""Trafficking protein particle complex"""	23069	protein-coding gene	gene with protein product		610396					Standard	NM_024108		Approved	TRS33, MGC2650, HSPC289	uc002pav.4	O75865		ENST00000585934.1:c.384C>T	19.37:g.45667238G>A		Somatic		Capture	Illumina HiSeq	Phase_I	50359078	NM_024108	K7ERB1|K7ERQ4|Q9BQ45|Q9P092	Silent	SNP	ENST00000585934.1	37	CCDS59397.1																																																																																				0.662	TRAPPC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457556.1	NM_024108	
CKM	1158	broad.mit.edu	37	19	45815121	45815121	+	Missense_Mutation	SNP	G	G	A	rs145987658		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:45815121G>A	ENST00000221476.3	-	5	713	c.539C>T	c.(538-540)aCg>aTg	p.T180M		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	180	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.T180M(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)	CTCCTTCTCCGTCATGCTCTT	0.617																																					p.T180M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C539T	19						.	G	MET/THR	0,4406		0,0,2203	88.0	65.0	73.0		539	5.2	0.9	19	dbSNP_134	73	1,8599	1.2+/-3.3	0,1,4299	no	missense	CKM	NM_001824.3	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	180/382	45815121	1,13005	2203	4300	6503	50506961	SO:0001583	missense	1158	exon5			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.539C>T	19.37:g.45815121G>A	ENSP00000221476:p.Thr180Met	Somatic		Capture	Illumina HiSeq	Phase_I	50506961	NM_001824	Q96QL9	Missense_Mutation	SNP	ENST00000221476.3	37	CCDS12659.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.656808	0.88154	0.0	1.16E-4	ENSG00000104879	ENST00000221476	T	0.25250	1.81	5.18	5.18	0.71444	ATP:guanido phosphotransferase, catalytic domain (2);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.110120	0.64402	D	0.000009	T	0.62744	0.2453	H	0.95645	3.7	0.58432	D	0.999999	D	0.76494	0.999	D	0.68039	0.955	T	0.75554	-0.3277	10	0.87932	D	0	-23.8165	16.1845	0.81939	0.0:0.0:1.0:0.0	.	180	P06732	KCRM_HUMAN	M	180	ENSP00000221476:T180M	ENSP00000221476:T180M	T	-	2	0	CKM	50506961	1.000000	0.71417	0.940000	0.37924	0.953000	0.61014	7.636000	0.83301	2.425000	0.82216	0.561000	0.74099	ACG		0.617	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1		
KLC3	147700	broad.mit.edu	37	19	45852818	45852818	+	Silent	SNP	C	C	T	rs376440924		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:45852818C>T	ENST00000391946.2	+	8	1203	c.1101C>T	c.(1099-1101)ggC>ggT	p.G367G	KLC3_ENST00000585434.1_Silent_p.G366G|KLC3_ENST00000470402.1_Silent_p.G381G	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	367					axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)	p.G367G(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		AGGCACTGGGCGGGCCCCATG	0.647													C|||	1	0.000199681	0.0	0.0	5008	,	,		17376	0.0		0.0	False		,,,				2504	0.001				p.G367G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1101T	19						.	C		1,4237		0,1,2118	38.0	45.0	43.0		1101	-7.9	0.9	19		43	1,8507		0,1,4253	no	coding-synonymous	KLC3	NM_177417.2		0,2,6371	TT,TC,CC		0.0118,0.0236,0.0157		367/505	45852818	2,12744	2119	4254	6373	50544658	SO:0001819	synonymous_variant	147700	exon8			AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892		"""Tetratricopeptide (TTC) repeat domain containing"""	20717	protein-coding gene	gene with protein product		601334					Standard	XM_005258536		Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.1101C>T	19.37:g.45852818C>T		Somatic		Capture	Illumina HiSeq	Phase_I	50544658	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Silent	SNP	ENST00000391946.2	37	CCDS12660.2																																																																																				0.647	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275	
PPP1R13L	10848	broad.mit.edu	37	19	45899680	45899680	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:45899680G>A	ENST00000418234.2	-	5	805	c.727C>T	c.(727-729)Cgc>Tgc	p.R243C	PPP1R13L_ENST00000360957.5_Missense_Mutation_p.R243C	NM_001142502.1	NP_001135974.1	Q8WUF5	IASPP_HUMAN	protein phosphatase 1, regulatory subunit 13 like	243	Pro-rich.				apoptotic process (GO:0006915)|cardiac muscle contraction (GO:0060048)|cardiac right ventricle morphogenesis (GO:0003215)|embryonic camera-type eye development (GO:0031076)|hair cycle (GO:0042633)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle tissue development (GO:0003229)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.R243C(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0182)		GGCCGCCGGCGCAGCGTCAGG	0.652																																					p.R243C	Pancreas(61;1447 1663 31419 50578)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C727T	19						.						46.0	51.0	50.0					19																	45899680		2203	4300	6503	50591520	SO:0001583	missense	10848	exon5			AF078036	CCDS33050.1	19q13.32	2013-01-10	2011-10-04		ENSG00000104881	ENSG00000104881		"""Ankyrin repeat domain containing"""	18838	protein-coding gene	gene with protein product		607463	"""protein phosphatase 1, regulatory (inhibitor) subunit 13 like"""			10336463	Standard	NM_006663		Approved	RAI, IASPP	uc002pbo.3	Q8WUF5		ENST00000418234.2:c.727C>T	19.37:g.45899680G>A	ENSP00000403902:p.Arg243Cys	Somatic		Capture	Illumina HiSeq	Phase_I	50591520	NM_001142502	Q2PNZ9|Q5DU71|Q5I1X4|Q6P1R7|Q6PKF8|Q9Y290	Missense_Mutation	SNP	ENST00000418234.2	37	CCDS33050.1	.	.	.	.	.	.	.	.	.	.	G	15.31	2.795898	0.50208	.	.	ENSG00000104881	ENST00000418234;ENST00000360957	T;T	0.61274	0.12;0.12	4.64	2.35	0.29111	.	0.201359	0.42053	D	0.000770	T	0.49012	0.1532	N	0.24115	0.695	0.44366	D	0.997268	D;D	0.71674	0.998;0.99	P;B	0.53954	0.738;0.353	T	0.48896	-0.8994	10	0.62326	D	0.03	.	5.7219	0.17992	0.1085:0.1986:0.6929:0.0	.	243;243	Q6ZNZ8;Q8WUF5	.;IASPP_HUMAN	C	243	ENSP00000403902:R243C;ENSP00000354218:R243C	ENSP00000354218:R243C	R	-	1	0	PPP1R13L	50591520	0.987000	0.35691	0.989000	0.46669	0.307000	0.27823	0.831000	0.27476	0.955000	0.37878	0.462000	0.41574	CGC		0.652	PPP1R13L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457586.1	NM_006663	
EML2	24139	broad.mit.edu	37	19	46124822	46124822	+	Silent	SNP	G	G	A	rs148351202		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:46124822G>A	ENST00000245925.3	-	10	965	c.915C>T	c.(913-915)gaC>gaT	p.D305D	EML2_ENST00000587152.1_Silent_p.D506D|EML2_ENST00000586902.1_5'UTR|EML2_ENST00000536630.1_Silent_p.D452D|EML2_ENST00000589876.1_Silent_p.D305D	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	305	Tandem atypical propeller in EMLs. {ECO:0000250}.				negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.D305D(1)		NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		CCAGCGTCCCGTCCCGCAGGG	0.692																																					p.D452D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1356T	19						.		,,	1,4405	2.1+/-5.4	0,1,2202	46.0	47.0	47.0		1518,1356,915	3.2	1.0	19	dbSNP_134	47	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	,,	0,3,6498	AA,AG,GG		0.0233,0.0227,0.0231	,,	506/851,452/797,305/650	46124822	3,12999	2203	4298	6501	50816662	SO:0001819	synonymous_variant	24139	exon13			AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.915C>T	19.37:g.46124822G>A		Somatic		Capture	Illumina HiSeq	Phase_I	50816662	NM_001193269	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1																																																																																				0.692	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
FBXO46	23403	broad.mit.edu	37	19	46216448	46216448	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:46216448G>T	ENST00000317683.3	-	2	439	c.306C>A	c.(304-306)gcC>gcA	p.A102A		NM_001080469.1	NP_001073938.1	Q6PJ61	FBX46_HUMAN	F-box protein 46	102								p.A102A(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(2)|skin(1)	15		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00568)|GBM - Glioblastoma multiforme(486;0.0844)|Epithelial(262;0.201)		CCACAAAGAAGGCCACCTTCT	0.637																																					p.A102A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C306A	19						.						47.0	52.0	50.0					19																	46216448		2008	4168	6176	50908288	SO:0001819	synonymous_variant	23403	exon2			BC021978	CCDS46116.1	19q13.3	2008-02-05	2004-06-15	2004-06-16		ENSG00000177051		"""F-boxes /  ""other"""""	25069	protein-coding gene	gene with protein product		609117	"""F-box only protein 34-like"""	FBXO34L		9585442	Standard	NM_001080469		Approved	20D7-FC4, Fbx46	uc002pcz.3	Q6PJ61		ENST00000317683.3:c.306C>A	19.37:g.46216448G>T		Somatic		Capture	Illumina HiSeq	Phase_I	50908288	NM_001080469		Silent	SNP	ENST00000317683.3	37	CCDS46116.1																																																																																				0.637	FBXO46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459661.1	XM_371179	
DMWD	1762	broad.mit.edu	37	19	46289743	46289743	+	Silent	SNP	G	G	A	rs201586261		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:46289743G>A	ENST00000270223.6	-	3	1056	c.1011C>T	c.(1009-1011)gaC>gaT	p.D337D	DMWD_ENST00000377735.3_Silent_p.D337D|AC011530.4_ENST00000593999.1_5'Flank|DMWD_ENST00000601370.1_5'Flank	NM_004943.1	NP_004934.1	Q09019	DMWD_HUMAN	dystrophia myotonica, WD repeat containing	337								p.D337D(1)		central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)		CGTAGCGGCCGTCAGGGCTCC	0.647													G|||	1	0.000199681	0.0	0.0	5008	,	,		16604	0.001		0.0	False		,,,				2504	0.0				p.D337D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1011T	19						.						61.0	62.0	62.0					19																	46289743		2203	4300	6503	50981583	SO:0001819	synonymous_variant	1762	exon3			L19267	CCDS33054.1	19q13.32	2013-01-09	2007-02-20		ENSG00000185800	ENSG00000185800		"""WD repeat domain containing"""	2936	protein-coding gene	gene with protein product		609857	"""dystrophia myotonica-containing WD repeat motif"""			1302022	Standard	NM_004943		Approved	DMR-N9, gene59, D19S593E	uc021uwc.1	Q09019	OTTHUMG00000169044	ENST00000270223.6:c.1011C>T	19.37:g.46289743G>A		Somatic		Capture	Illumina HiSeq	Phase_I	50981583	NM_004943		Silent	SNP	ENST00000270223.6	37	CCDS33054.1																																																																																				0.647	DMWD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402063.1	NM_004943	
RSPH6A	81492	broad.mit.edu	37	19	46308171	46308171	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:46308171T>G	ENST00000221538.3	-	3	1134	c.992A>C	c.(991-993)aAa>aCa	p.K331T	RSPH6A_ENST00000597055.1_Missense_Mutation_p.K331T|RSPH6A_ENST00000600188.1_Missense_Mutation_p.K67T	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	331						intracellular (GO:0005622)		p.K331T(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						CACCAGCTGTTTCATGGCCAG	0.602																																					p.K331T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A992C	19						.						69.0	58.0	62.0					19																	46308171		2203	4300	6503	51000011	SO:0001583	missense	81492	exon3			AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"""radial spokehead-like 1"""	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.992A>C	19.37:g.46308171T>G	ENSP00000221538:p.Lys331Thr	Somatic		Capture	Illumina HiSeq	Phase_I	51000011	NM_030785	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	37	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.209523	0.58343	.	.	ENSG00000104941	ENST00000221538	T	0.19250	2.16	4.08	3.04	0.35103	.	0.051448	0.85682	D	0.000000	T	0.38348	0.1037	M	0.67625	2.065	0.38311	D	0.943249	D	0.69078	0.997	D	0.71414	0.973	T	0.24941	-1.0146	10	0.45353	T	0.12	-0.5114	8.3607	0.32357	0.0:0.0983:0.0:0.9017	.	331	Q9H0K4	RSH6A_HUMAN	T	331	ENSP00000221538:K331T	ENSP00000221538:K331T	K	-	2	0	RSPH6A	51000011	1.000000	0.71417	1.000000	0.80357	0.597000	0.36814	3.829000	0.55760	0.860000	0.35481	0.374000	0.22700	AAA		0.602	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1		
PPP5C	5536	broad.mit.edu	37	19	46893361	46893361	+	Missense_Mutation	SNP	G	G	A	rs148346594		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:46893361G>A	ENST00000012443.4	+	12	1512	c.1409G>A	c.(1408-1410)cGg>cAg	p.R470Q	PPP5C_ENST00000391919.1_Missense_Mutation_p.R342Q|AC007193.8_ENST00000598616.1_RNA	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	470	Catalytic.				cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)	p.R470Q(1)		endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		TCTGACCTACGGCCTCAGTTC	0.637																																					p.R470Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1409A	19						.	G	GLN/ARG,GLN/ARG	4,4402	9.9+/-24.2	0,4,2199	146.0	117.0	127.0		1343,1409	4.4	1.0	19	dbSNP_134	127	1,8599		0,1,4299	yes	missense,missense	PPP5C	NM_001204284.1,NM_006247.3	43,43	0,5,6498	AA,AG,GG		0.0116,0.0908,0.0384	benign,benign	448/478,470/500	46893361	5,13001	2203	4300	6503	51585201	SO:0001583	missense	5536	exon12				CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	9322	protein-coding gene	gene with protein product		600658		PPP5		8666404	Standard	NM_006247		Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000012443.4:c.1409G>A	19.37:g.46893361G>A	ENSP00000012443:p.Arg470Gln	Somatic		Capture	Illumina HiSeq	Phase_I	51585201	NM_006247	Q16722|Q53XV2	Missense_Mutation	SNP	ENST00000012443.4	37	CCDS12684.1	.	.	.	.	.	.	.	.	.	.	G	16.37	3.103047	0.56183	9.08E-4	1.16E-4	ENSG00000011485	ENST00000012443;ENST00000451918;ENST00000391919	T;T	0.13538	3.58;2.58	5.46	4.43	0.53597	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);	0.651527	0.15332	N	0.267955	T	0.07324	0.0185	N	0.05592	-0.015	0.43471	D	0.995682	B;B	0.18863	0.031;0.011	B;B	0.08055	0.003;0.0	T	0.19160	-1.0314	10	0.51188	T	0.08	-19.6633	8.3976	0.32566	0.1763:0.0:0.8237:0.0	.	470;470	B2R6R6;P53041	.;PPP5_HUMAN	Q	470;457;342	ENSP00000012443:R470Q;ENSP00000375786:R342Q	ENSP00000012443:R470Q	R	+	2	0	PPP5C	51585201	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	6.738000	0.74822	1.316000	0.45131	-0.253000	0.11424	CGG		0.637	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247	
PNMAL1	55228	broad.mit.edu	37	19	46973219	46973219	+	Silent	SNP	G	G	A	rs561312279		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:46973219G>A	ENST00000313683.10	-	2	1379	c.1074C>T	c.(1072-1074)ccC>ccT	p.P358P	PNMAL1_ENST00000602246.1_Intron|PNMAL1_ENST00000438932.2_Silent_p.P358P	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	358								p.P358P(1)		cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		TCATGGGAGCGGGGTTCTTGG	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		17155	0.0		0.0	False		,,,				2504	0.001				p.P358P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1074T	19						.						132.0	142.0	139.0					19																	46973219		2203	4300	6503	51665059	SO:0001819	synonymous_variant	55228	exon2			BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"""Paraneoplastic Ma antigens"""	25578	protein-coding gene	gene with protein product			"""PNMA-like 1"""			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.1074C>T	19.37:g.46973219G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51665059	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Silent	SNP	ENST00000313683.10	37	CCDS33059.1																																																																																				0.572	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215	
PTPRS	5802	broad.mit.edu	37	19	5245842	5245842	+	Silent	SNP	G	G	A	rs201711435		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:5245842G>A	ENST00000587303.1	-	9	1032	c.933C>T	c.(931-933)tgC>tgT	p.C311C	PTPRS_ENST00000353284.2_Silent_p.C298C|PTPRS_ENST00000357368.4_Silent_p.C311C|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Silent_p.C307C|PTPRS_ENST00000372412.4_Silent_p.C312C|PTPRS_ENST00000588012.1_Silent_p.C298C|PTPRS_ENST00000592099.1_Silent_p.C298C|PTPRS_ENST00000348075.2_Silent_p.C298C			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	311	Ig-like C2-type 3.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.C311C(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	ACATGGCCACGCAGGTGTAGT	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		16825	0.001		0.0	False		,,,				2504	0.0				p.C311C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C933T	19						.						80.0	65.0	70.0					19																	5245842		2203	4300	6503	5196842	SO:0001819	synonymous_variant	5802	exon10			U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.933C>T	19.37:g.5245842G>A		Somatic		Capture	Illumina HiSeq	Phase_I	5196842	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	CCDS45930.1																																																																																				0.637	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
PRKD2	25865	broad.mit.edu	37	19	47207620	47207620	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:47207620C>T	ENST00000291281.4	-	5	920	c.695G>A	c.(694-696)cGc>cAc	p.R232H	PRKD2_ENST00000601806.1_Missense_Mutation_p.R75H|PRKD2_ENST00000595515.1_Missense_Mutation_p.R232H|PRKD2_ENST00000433867.1_Missense_Mutation_p.R232H|PRKD2_ENST00000600194.1_Missense_Mutation_p.R75H			Q9BZL6	KPCD2_HUMAN	protein kinase D2	232					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.R232H(1)		central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		CGGGGGACGGCGAGGCAGGAG	0.622											OREG0025578	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R232H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G695A	19						.						209.0	164.0	179.0					19																	47207620		2203	4300	6503	51899460	SO:0001583	missense	25865	exon6			AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"""Pleckstrin homology (PH) domain containing"""	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.695G>A	19.37:g.47207620C>T	ENSP00000291281:p.Arg232His	Somatic	945	Capture	Illumina HiSeq	Phase_I	51899460	NM_001079881	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000291281.4	37	CCDS12689.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.562852	0.45694	.	.	ENSG00000105287	ENST00000291281;ENST00000433867	T;T	0.66099	-0.19;-0.19	5.18	5.18	0.71444	.	0.315297	0.26366	N	0.024788	T	0.41558	0.1164	N	0.08118	0	0.39392	D	0.966435	B;B	0.16603	0.012;0.018	B;B	0.08055	0.003;0.002	T	0.33137	-0.9880	10	0.24483	T	0.36	-27.4096	14.5551	0.68094	0.0:1.0:0.0:0.0	.	232;232	E7ER94;Q9BZL6	.;KPCD2_HUMAN	H	232	ENSP00000291281:R232H;ENSP00000393978:R232H	ENSP00000291281:R232H	R	-	2	0	PRKD2	51899460	1.000000	0.71417	0.857000	0.33713	0.843000	0.47879	3.181000	0.50903	2.579000	0.87056	0.448000	0.29417	CGC		0.622	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457	
ARHGAP35	2909	broad.mit.edu	37	19	47423942	47423942	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:47423942G>A	ENST00000404338.3	+	1	2010	c.2010G>A	c.(2008-2010)tcG>tcA	p.S670S		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	670					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)	p.S670S(1)									CAAAGGAATCGCTATCCTATG	0.473																																					p.S670S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2010A	19						.						37.0	37.0	37.0					19																	47423942		1908	4133	6041	52115782	SO:0001819	synonymous_variant	2909	exon1			M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"""Rho GTPase activating proteins"""	4591	protein-coding gene	gene with protein product		605277	"""glucocorticoid receptor DNA binding factor 1"""	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.2010G>A	19.37:g.47423942G>A		Somatic		Capture	Illumina HiSeq	Phase_I	52115782	NM_004491	A7E2A4|Q14452|Q9C0E1	Silent	SNP	ENST00000404338.3	37	CCDS46127.1																																																																																				0.473	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491	
ZC3H4	23211	broad.mit.edu	37	19	47570689	47570689	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:47570689C>T	ENST00000253048.5	-	15	2873	c.2836G>A	c.(2836-2838)Ggg>Agg	p.G946R	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	946							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.G946R(1)		NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		AGAGGGTGCCCGGGGAGTGGG	0.677																																					p.G946R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2836A	19						.						85.0	101.0	96.0					19																	47570689		2021	4178	6199	52262529	SO:0001583	missense	23211	exon15			AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.2836G>A	19.37:g.47570689C>T	ENSP00000253048:p.Gly946Arg	Somatic		Capture	Illumina HiSeq	Phase_I	52262529	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	37	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	C	13.27	2.188346	0.38609	.	.	ENSG00000130749	ENST00000253048	T	0.34072	1.38	5.17	5.17	0.71159	.	0.124537	0.52532	D	0.000061	T	0.56673	0.2001	M	0.67397	2.05	0.54753	D	0.999983	D	0.89917	1.0	D	0.91635	0.999	T	0.59123	-0.7513	10	0.87932	D	0	.	12.034	0.53415	0.0:0.9153:0.0:0.0847	.	946	Q9UPT8	ZC3H4_HUMAN	R	946	ENSP00000253048:G946R	ENSP00000253048:G946R	G	-	1	0	ZC3H4	52262529	0.904000	0.30761	0.895000	0.35142	0.082000	0.17680	2.794000	0.47853	2.571000	0.86741	0.563000	0.77884	GGG		0.677	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
ZC3H4	23211	broad.mit.edu	37	19	47572527	47572527	+	Silent	SNP	G	G	A	rs377220591		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:47572527G>A	ENST00000253048.5	-	14	2257	c.2220C>T	c.(2218-2220)ccC>ccT	p.P740P	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	740							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.P740P(1)		NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		AGAAGCTGTCGGGCTCCAGAG	0.672													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14907	0.0		0.0	False		,,,				2504	0.0				p.P740P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2220T	19						.	G		3,3777		0,3,1887	24.0	29.0	28.0		2220	-9.8	0.7	19		28	1,8211		0,1,4105	no	coding-synonymous	ZC3H4	NM_015168.1		0,4,5992	AA,AG,GG		0.0122,0.0794,0.0334		740/1304	47572527	4,11988	1890	4106	5996	52264367	SO:0001819	synonymous_variant	23211	exon14			AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.2220C>T	19.37:g.47572527G>A		Somatic		Capture	Illumina HiSeq	Phase_I	52264367	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																				0.672	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
NAPA	8775	broad.mit.edu	37	19	48006732	48006732	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:48006732G>A	ENST00000263354.3	-	2	425	c.126C>T	c.(124-126)tgC>tgT	p.C42C	NAPA_ENST00000595227.1_Silent_p.C42C|NAPA-AS1_ENST00000594367.1_RNA|NAPA_ENST00000593785.1_5'UTR	NM_003827.3	NP_003818.2	P54920	SNAA_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, alpha	42					apical protein localization (GO:0045176)|brain development (GO:0007420)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron differentiation (GO:0030182)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of synaptic vesicle priming (GO:0010807)|SNARE complex disassembly (GO:0035494)|synaptic transmission, glutamatergic (GO:0035249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)		p.C42C(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)	11		all_cancers(25;1.55e-10)|all_epithelial(76;3.4e-08)|all_lung(116;1.73e-07)|Lung NSC(112;3.95e-07)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		OV - Ovarian serous cystadenocarcinoma(262;0.000466)|all cancers(93;0.000739)|Epithelial(262;0.0168)|GBM - Glioblastoma multiforme(486;0.049)		CGTAGATTTCGCATGCTTCCT	0.483																																					p.C42C	Ovarian(185;1135 2042 27703 31345 42493)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C126T	19						.						187.0	164.0	172.0					19																	48006732		2203	4300	6503	52698544	SO:0001819	synonymous_variant	8775	exon2			U39412	CCDS12702.1	19q13.33	2012-08-16			ENSG00000105402	ENSG00000105402			7641	protein-coding gene	gene with protein product	"""alpha SNAP"""	603215				9269766	Standard	NM_003827		Approved		uc002pha.2	P54920		ENST00000263354.3:c.126C>T	19.37:g.48006732G>A		Somatic		Capture	Illumina HiSeq	Phase_I	52698544	NM_003827	A8K879|Q96IK3|Q9BVJ3	Silent	SNP	ENST00000263354.3	37	CCDS12702.1																																																																																				0.483	NAPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466048.2	NM_003827	
EHD2	30846	broad.mit.edu	37	19	48229431	48229431	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:48229431G>A	ENST00000263277.3	+	4	1116	c.865G>A	c.(865-867)Gca>Aca	p.A289T	EHD2_ENST00000538399.1_Missense_Mutation_p.A153T|CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	289					blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|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.A289T(1)		endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		GCCCCGGCACGCAGCCTTGCG	0.672																																					p.A289T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G865A	19						.						17.0	18.0	18.0					19																	48229431		2203	4297	6500	52921243	SO:0001583	missense	30846	exon4			AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"""EF-hand domain containing"""	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.865G>A	19.37:g.48229431G>A	ENSP00000263277:p.Ala289Thr	Somatic		Capture	Illumina HiSeq	Phase_I	52921243	NM_014601	B2RDH9|B4DNU6|Q96CB6	Missense_Mutation	SNP	ENST00000263277.3	37	CCDS12704.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.194957	0.58017	.	.	ENSG00000024422	ENST00000263277;ENST00000539439;ENST00000540364;ENST00000538399	D;D	0.95518	-3.73;-3.73	3.66	3.66	0.41972	.	0.211530	0.38663	N	0.001606	D	0.91868	0.7426	M	0.63428	1.95	0.80722	D	1	P	0.40180	0.705	B	0.31751	0.135	D	0.91090	0.4906	10	0.54805	T	0.06	-17.9002	8.8606	0.35256	0.0:0.0:0.7761:0.2239	.	289	Q9NZN4	EHD2_HUMAN	T	289;289;279;153	ENSP00000263277:A289T;ENSP00000439036:A153T	ENSP00000263277:A289T	A	+	1	0	EHD2	52921243	1.000000	0.71417	0.993000	0.49108	0.851000	0.48451	4.412000	0.59787	1.793000	0.52555	0.456000	0.33151	GCA		0.672	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1		
GLTSCR2	29997	broad.mit.edu	37	19	48248898	48248898	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:48248898A>G	ENST00000246802.5	+	1	120	c.82A>G	c.(82-84)Act>Gct	p.T28A	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	28						intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.T28A(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		GCTGCGGCCCACTTCGGTGGA	0.652																																					p.T28A	Colon(58;613 1041 9473 10089 15241)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A82G	19						.						56.0	66.0	62.0					19																	48248898		2203	4300	6503	52940710	SO:0001583	missense	29997	exon1			AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.82A>G	19.37:g.48248898A>G	ENSP00000246802:p.Thr28Ala	Somatic		Capture	Illumina HiSeq	Phase_I	52940710	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Missense_Mutation	SNP	ENST00000246802.5	37	CCDS12705.1	.	.	.	.	.	.	.	.	.	.	A	15.82	2.946794	0.53186	.	.	ENSG00000105373	ENST00000246802;ENST00000325566;ENST00000446535	T	0.29655	1.56	4.55	3.27	0.37495	.	0.515813	0.19747	N	0.106991	T	0.18425	0.0442	L	0.32530	0.975	0.38465	D	0.947305	B;B;B	0.22800	0.075;0.075;0.075	B;B;B	0.22601	0.04;0.04;0.027	T	0.09164	-1.0687	10	0.19147	T	0.46	-11.4215	4.5866	0.12285	0.8141:0.0:0.1859:0.0	.	28;28;26	Q53YP0;Q9NZM5;Q96CS0	.;GSCR2_HUMAN;.	A	28	ENSP00000246802:T28A	ENSP00000246802:T28A	T	+	1	0	GLTSCR2	52940710	0.458000	0.25760	0.991000	0.47740	0.756000	0.42949	1.259000	0.32956	1.806000	0.52798	0.533000	0.62120	ACT		0.652	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
LIG1	3978	broad.mit.edu	37	19	48624522	48624522	+	Missense_Mutation	SNP	C	C	T	rs368406296		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:48624522C>T	ENST00000263274.7	-	24	2709	c.2290G>A	c.(2290-2292)Gcc>Acc	p.A764T	CTC-453G23.5_ENST00000596563.1_RNA|LIG1_ENST00000536218.1_Missense_Mutation_p.A696T|CTC-453G23.5_ENST00000596839.1_RNA|LIG1_ENST00000427526.2_Missense_Mutation_p.A733T	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	764					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)	p.A764T(1)		breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	CCCAGGTAGGCGCCGATCACC	0.652								Nucleotide excision repair (NER)					C|||	1	0.000199681	0.0008	0.0	5008	,	,		13631	0.0		0.0	False		,,,				2504	0.0				p.A764T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2290A	19						.	C	THR/ALA	4,4400	8.1+/-20.4	0,4,2198	34.0	37.0	36.0		2290	5.3	1.0	19		36	0,8600		0,0,4300	no	missense	LIG1	NM_000234.1	58	0,4,6498	TT,TC,CC		0.0,0.0908,0.0308	probably-damaging	764/920	48624522	4,13000	2202	4300	6502	53316334	SO:0001583	missense	3978	exon24				CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.2290G>A	19.37:g.48624522C>T	ENSP00000263274:p.Ala764Thr	Somatic		Capture	Illumina HiSeq	Phase_I	53316334	NM_000234	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	37	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	C	35	5.574845	0.96553	9.08E-4	0.0	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526;ENST00000536218	T;T;T	0.66995	-0.24;-0.24;-0.24	5.29	5.29	0.74685	Nucleic acid-binding, OB-fold-like (1);DNA ligase, ATP-dependent, central (1);Nucleic acid-binding, OB-fold (1);	0.051269	0.85682	D	0.000000	D	0.85274	0.5659	M	0.91038	3.17	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	P;D;D	0.72338	0.82;0.939;0.977	D	0.88259	0.2922	10	0.72032	D	0.01	-26.9163	16.8046	0.85623	0.0:1.0:0.0:0.0	.	733;696;764	B4DTU4;F5GZ28;P18858	.;.;DNLI1_HUMAN	T	764;795;733;696	ENSP00000263274:A764T;ENSP00000442841:A733T;ENSP00000441531:A696T	ENSP00000263274:A764T	A	-	1	0	LIG1	53316334	1.000000	0.71417	0.965000	0.40720	0.967000	0.64934	6.982000	0.76173	2.647000	0.89833	0.655000	0.94253	GCC		0.652	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234	
ZNF114	163071	broad.mit.edu	37	19	48789444	48789444	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:48789444C>T	ENST00000595607.1	+	6	1057	c.563C>T	c.(562-564)cCg>cTg	p.P188L	ZNF114_ENST00000597695.1_Missense_Mutation_p.P154L|ZNF114_ENST00000600687.1_Missense_Mutation_p.P188L|ZNF114_ENST00000315849.1_Missense_Mutation_p.P188L			Q8NC26	ZN114_HUMAN	zinc finger protein 114	188					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P188L(1)		endometrium(1)|large_intestine(6)|lung(11)	18		all_epithelial(76;8.01e-05)|all_lung(116;0.000112)|Lung NSC(112;0.000192)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;7.56e-05)|all cancers(93;0.000113)|Epithelial(262;0.00962)|GBM - Glioblastoma multiforme(486;0.0153)		CAGTGGGTTCCGTGTGGGAGA	0.433																																					p.P188L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C563T	19						.						84.0	77.0	79.0					19																	48789444		2203	4300	6503	53481256	SO:0001583	missense	163071	exon5			BC014935	CCDS12713.1, CCDS74412.1	19q13.32	2013-01-08			ENSG00000178150	ENSG00000178150		"""Zinc fingers, C2H2-type"", ""-"""	12894	protein-coding gene	gene with protein product		603996					Standard	XM_005258580		Approved	MGC17986	uc002pim.1	Q8NC26		ENST00000595607.1:c.563C>T	19.37:g.48789444C>T	ENSP00000469998:p.Pro188Leu	Somatic		Capture	Illumina HiSeq	Phase_I	53481256	NM_153608	A8K6B0|Q08AQ6	Missense_Mutation	SNP	ENST00000595607.1	37	CCDS12713.1	.	.	.	.	.	.	.	.	.	.	C	0.458	-0.890432	0.02491	.	.	ENSG00000178150	ENST00000315849	T	0.05319	3.46	2.0	2.0	0.26442	.	.	.	.	.	T	0.10809	0.0264	N	0.19112	0.55	0.09310	N	1	D	0.89917	1.0	D	0.67548	0.952	T	0.32771	-0.9894	9	0.40728	T	0.16	.	10.0692	0.42322	0.0:1.0:0.0:0.0	.	188	Q8NC26	ZN114_HUMAN	L	188	ENSP00000318898:P188L	ENSP00000318898:P188L	P	+	2	0	ZNF114	53481256	0.000000	0.05858	0.002000	0.10522	0.365000	0.29674	0.170000	0.16663	1.470000	0.48102	0.411000	0.27672	CCG		0.433	ZNF114-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465601.1	NM_153608	
GRIN2D	2906	broad.mit.edu	37	19	48922532	48922532	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:48922532T>C	ENST00000263269.3	+	8	1865	c.1777T>C	c.(1777-1779)Tgc>Cgc	p.C593R		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	593					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)	p.C593R(1)		autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GTTCGTCATGTGCCTCACTGT	0.592																																					p.C593R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1777C	19						.						157.0	103.0	121.0					19																	48922532		2203	4300	6503	53614344	SO:0001583	missense	2906	exon8			U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4588	protein-coding gene	gene with protein product	"""N-methyl-d-aspartate receptor subunit 2D"""	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.1777T>C	19.37:g.48922532T>C	ENSP00000263269:p.Cys593Arg	Somatic		Capture	Illumina HiSeq	Phase_I	53614344	NM_000836		Missense_Mutation	SNP	ENST00000263269.3	37	CCDS12719.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.337842	0.81911	.	.	ENSG00000105464	ENST00000263269	T	0.52754	0.65	4.33	4.33	0.51752	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.61664	0.2365	L	0.50333	1.59	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65257	-0.6212	10	0.87932	D	0	.	12.9237	0.58247	0.0:0.0:0.0:1.0	.	593	O15399	NMDE4_HUMAN	R	593	ENSP00000263269:C593R	ENSP00000263269:C593R	C	+	1	0	GRIN2D	53614344	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.821000	0.86641	1.960000	0.56953	0.533000	0.62120	TGC		0.592	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1		
BCAT2	587	broad.mit.edu	37	19	49303036	49303036	+	Silent	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:49303036C>A	ENST00000316273.6	-	6	603	c.591G>T	c.(589-591)gtG>gtT	p.V197V	BCAT2_ENST00000402551.1_Silent_p.V157V|BCAT2_ENST00000599246.1_Silent_p.V105V|BCAT2_ENST00000545387.2_Silent_p.V105V|BCAT2_ENST00000598162.1_Silent_p.V197V|BCAT2_ENST00000597011.1_Silent_p.V157V	NM_001190.3	NP_001181.2	O15382	BCAT2_HUMAN	branched chain amino-acid transaminase 2, mitochondrial	197					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.V197V(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)	AGTAGGCACCCACTGGGCAGA	0.687																																					p.V105V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G315T	19						.						26.0	24.0	24.0					19																	49303036		2167	4253	6420	53994848	SO:0001819	synonymous_variant	587	exon4			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.591G>T	19.37:g.49303036C>A		Somatic		Capture	Illumina HiSeq	Phase_I	53994848	NM_001164773	B2RB87|O00269|Q96KG1|Q9BTB6|Q9BUU6	Silent	SNP	ENST00000316273.6	37	CCDS12735.1																																																																																				0.687	BCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466202.1		
HSD17B14	51171	broad.mit.edu	37	19	49316573	49316573	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:49316573G>A	ENST00000263278.4	-	9	938	c.672C>T	c.(670-672)gtC>gtT	p.V224V	HSD17B14_ENST00000599157.1_Silent_p.V200V|BCAT2_ENST00000402551.1_5'Flank|BCAT2_ENST00000599246.1_5'Flank|BCAT2_ENST00000545387.2_5'Flank|BCAT2_ENST00000598162.1_5'Flank|BCAT2_ENST00000597011.1_5'Flank|BCAT2_ENST00000316273.6_5'Flank|BCAT2_ENST00000601496.1_5'Flank	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	224					steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)	p.V224V(1)		large_intestine(3)|lung(1)|skin(1)	5		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;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		CCGCAGCCCCGACCTCAGCGG	0.672																																					p.V224V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C672T	19						.						22.0	19.0	20.0					19																	49316573		2188	4288	6476	54008385	SO:0001819	synonymous_variant	51171	exon9			AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	23238	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 3"", ""short chain dehydrogenase/reductase family 47C, member 1"""	612832	"""dehydrogenase/reductase (SDR family) member 10"""	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.672C>T	19.37:g.49316573G>A		Somatic		Capture	Illumina HiSeq	Phase_I	54008385	NM_016246	Q9UKU3	Missense_Mutation	SNP	ENST00000263278.4	37	CCDS12736.1																																																																																				0.672	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246	
ZNRF4	148066	broad.mit.edu	37	19	5455699	5455699	+	Missense_Mutation	SNP	C	C	T	rs201511283		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:5455699C>T	ENST00000222033.4	+	1	274	c.197C>T	c.(196-198)gCg>gTg	p.A66V		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	66						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.A66V(1)		NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		ACACAGACAGCGAAGCGGGTG	0.697													C|||	1	0.000199681	0.0	0.0	5008	,	,		15669	0.001		0.0	False		,,,				2504	0.0				p.A66V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C197T	19						.	C	VAL/ALA	0,4120		0,0,2060	42.0	51.0	48.0		197	-4.4	0.0	19		48	1,8357		0,1,4178	no	missense	ZNRF4	NM_181710.3	64	0,1,6238	TT,TC,CC		0.012,0.0,0.0080	possibly-damaging	66/430	5455699	1,12477	2060	4179	6239	5406699	SO:0001583	missense	148066	exon1			AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"""RING-type (C3HC4) zinc fingers"""	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.197C>T	19.37:g.5455699C>T	ENSP00000222033:p.Ala66Val	Somatic		Capture	Illumina HiSeq	Phase_I	5406699	NM_181710	A8K886|O75866	Missense_Mutation	SNP	ENST00000222033.4	37	CCDS42475.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	9.569	1.120575	0.20877	0.0	1.2E-4	ENSG00000105428	ENST00000222033	T	0.04706	3.57	3.22	-4.37	0.03633	.	.	.	.	.	T	0.02230	0.0069	N	0.08118	0	0.09310	N	1	P	0.45396	0.857	B	0.35240	0.198	T	0.46005	-0.9222	9	0.54805	T	0.06	.	10.7534	0.46221	0.3551:0.6449:0.0:0.0	.	66	Q8WWF5	ZNRF4_HUMAN	V	66	ENSP00000222033:A66V	ENSP00000222033:A66V	A	+	2	0	ZNRF4	5406699	0.015000	0.18098	0.001000	0.08648	0.016000	0.09150	-0.968000	0.03817	-0.629000	0.05575	0.313000	0.20887	GCG		0.697	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710	
HSD17B14	51171	broad.mit.edu	37	19	49339661	49339661	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:49339661G>A	ENST00000263278.4	-	1	274	c.8C>T	c.(7-9)aCg>aTg	p.T3M	HSD17B14_ENST00000599157.1_Missense_Mutation_p.T3M	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	3					steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)	p.T3M(1)		large_intestine(3)|lung(1)|skin(1)	5		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;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		GCGCGTTCCCGTAGCCATCCC	0.642											OREG0025610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T3M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C8T	19						.						67.0	54.0	58.0					19																	49339661		2203	4300	6503	54031473	SO:0001583	missense	51171	exon1			AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	23238	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 3"", ""short chain dehydrogenase/reductase family 47C, member 1"""	612832	"""dehydrogenase/reductase (SDR family) member 10"""	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.8C>T	19.37:g.49339661G>A	ENSP00000263278:p.Thr3Met	Somatic	961	Capture	Illumina HiSeq	Phase_I	54031473	NM_016246	Q9UKU3	Missense_Mutation	SNP	ENST00000263278.4	37	CCDS12736.1	.	.	.	.	.	.	.	.	.	.	-	11.95	1.790229	0.31685	.	.	ENSG00000087076	ENST00000263278	D	0.85411	-1.98	4.22	3.17	0.36434	.	1.131490	0.06656	N	0.763620	T	0.68943	0.3056	N	0.03608	-0.345	0.09310	N	1	B	0.16396	0.017	B	0.06405	0.002	T	0.56613	-0.7950	10	0.29301	T	0.29	.	8.5094	0.33208	0.1107:0.0:0.8893:0.0	.	3	Q9BPX1	DHB14_HUMAN	M	3	ENSP00000263278:T3M	ENSP00000263278:T3M	T	-	2	0	HSD17B14	54031473	0.002000	0.14202	0.001000	0.08648	0.003000	0.03518	1.126000	0.31344	0.941000	0.37499	0.546000	0.68486	ACG		0.642	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246	
GYS1	2997	broad.mit.edu	37	19	49472590	49472590	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:49472590G>A	ENST00000323798.3	-	16	2365	c.2169C>T	c.(2167-2169)agC>agT	p.S723S	GYS1_ENST00000263276.6_Silent_p.S659S|GYS1_ENST00000544287.1_Silent_p.S356S|GYS1_ENST00000541188.1_Silent_p.S643S	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	723					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)	p.S723S(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		TGAGGGGCTCGCTCGGGGTGC	0.682																																					p.S723S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2169T	19						.						21.0	20.0	21.0					19																	49472590		2196	4293	6489	54164402	SO:0001819	synonymous_variant	2997	exon16				CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.2169C>T	19.37:g.49472590G>A		Somatic		Capture	Illumina HiSeq	Phase_I	54164402	NM_002103	Q9BTT9	Silent	SNP	ENST00000323798.3	37	CCDS12747.1																																																																																				0.682	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319791.1	NM_002103	
RUVBL2	10856	broad.mit.edu	37	19	49517745	49517745	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:49517745C>T	ENST00000595090.1	+	12	1470	c.1006C>T	c.(1006-1008)Cgg>Tgg	p.R336W	RUVBL2_ENST00000601968.1_Missense_Mutation_p.R291W|RUVBL2_ENST00000413176.2_Missense_Mutation_p.R291W	NM_006666.1	NP_006657.1	Q9Y230	RUVB2_HUMAN	RuvB-like AAA ATPase 2	336					ATP catabolic process (GO:0006200)|cellular response to estradiol stimulus (GO:0071392)|cellular response to UV (GO:0034644)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|establishment of protein localization to chromatin (GO:0071169)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of estrogen receptor binding (GO:0071899)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein folding (GO:0006457)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)|transcriptional activation by promoter-enhancer looping (GO:0071733)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Ino80 complex (GO:0031011)|intracellular (GO:0005622)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent DNA helicase activity (GO:0004003)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA helicase activity (GO:0003678)|identical protein binding (GO:0042802)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|unfolded protein binding (GO:0051082)	p.R291W(1)		large_intestine(1)|upper_aerodigestive_tract(1)	2		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000449)|OV - Ovarian serous cystadenocarcinoma(262;0.000555)|GBM - Glioblastoma multiforme(486;0.00585)|Epithelial(262;0.047)		CCTCAGAATCCGGGGCACCAG	0.597																																					p.R336W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1006T	19						.						50.0	56.0	54.0					19																	49517745		1993	4158	6151	54209557	SO:0001583	missense	10856	exon12			AF155138	CCDS42588.1	19q13.3	2013-09-12	2013-09-12					"""INO80 complex subunits"", ""ATPases / AAA-type"""	10475	protein-coding gene	gene with protein product	"""reptin"", ""INO80 complex subunit J"""	604788	"""RuvB (E coli homolog)-like 2"", ""RuvB-like 2 (E. coli)"""			10428817, 10998447	Standard	XM_005258426		Approved	RVB2, TIP48, TIP49b, Reptin52, ECP51, TIH2, INO80J, Rvb2	uc002plr.1	Q9Y230		ENST00000595090.1:c.1006C>T	19.37:g.49517745C>T	ENSP00000473172:p.Arg336Trp	Somatic		Capture	Illumina HiSeq	Phase_I	54209557	NM_006666	B3KQ59|E7ETE5|Q6FIB9|Q6PK27|Q9Y361	Missense_Mutation	SNP	ENST00000595090.1	37	CCDS42588.1	.	.	.	.	.	.	.	.	.	.	C	18.83	3.707886	0.68615	.	.	ENSG00000183207	ENST00000221413;ENST00000413176	T	0.60797	0.16	5.19	2.94	0.34122	TIP49, C-terminal (1);ATPase, AAA+ type, core (1);	0.116703	0.56097	D	0.000022	D	0.83622	0.5294	H	0.98901	4.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85951	0.1464	10	0.87932	D	0	-18.9849	10.0583	0.42259	0.1555:0.6946:0.1499:0.0	.	336;302	Q9Y230;B3KNL2	RUVB2_HUMAN;.	W	336;291	ENSP00000413890:R291W	ENSP00000221413:R336W	R	+	1	2	RUVBL2	54209557	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	5.188000	0.65093	0.631000	0.30412	0.561000	0.74099	CGG		0.597	RUVBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466235.1		
HRC	3270	broad.mit.edu	37	19	49656834	49656834	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:49656834T>C	ENST00000252825.4	-	1	1847	c.1661A>G	c.(1660-1662)gAg>gGg	p.E554G	HRC_ENST00000595625.1_Missense_Mutation_p.E554G	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	554					cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)	p.E554G(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		CTCAGCCCTCTCTTCcctcct	0.607																																					p.E554G	Melanoma(37;75 1097 24567 25669 30645)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1661G	19						.						54.0	26.0	36.0					19																	49656834		2203	4300	6503	54348646	SO:0001583	missense	3270	exon1				CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.1661A>G	19.37:g.49656834T>C	ENSP00000252825:p.Glu554Gly	Somatic		Capture	Illumina HiSeq	Phase_I	54348646	NM_002152	Q504Y6	Missense_Mutation	SNP	ENST00000252825.4	37	CCDS12759.1	.	.	.	.	.	.	.	.	.	.	T	1.269	-0.613569	0.03690	.	.	ENSG00000130528	ENST00000252825;ENST00000391863	T	0.51325	0.71	2.63	1.59	0.23543	.	.	.	.	.	T	0.30230	0.0758	L	0.29908	0.895	0.22489	N	0.99906	B	0.12630	0.006	B	0.12837	0.008	T	0.19549	-1.0302	9	0.25106	T	0.35	-4.0E-4	4.5759	0.12234	0.0:0.1589:0.0:0.8411	.	554	P23327	SRCH_HUMAN	G	554;244	ENSP00000252825:E554G	ENSP00000252825:E554G	E	-	2	0	HRC	54348646	0.000000	0.05858	0.163000	0.22734	0.125000	0.20455	0.056000	0.14256	0.427000	0.26145	0.379000	0.24179	GAG		0.607	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
HRC	3270	broad.mit.edu	37	19	49657559	49657559	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:49657559A>G	ENST00000252825.4	-	1	1122	c.936T>C	c.(934-936)acT>acC	p.T312T	HRC_ENST00000595625.1_Silent_p.T312T	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	312	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)	p.T312T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		GTCCATACTCAGTGGAGACAT	0.532																																					p.T312T	Melanoma(37;75 1097 24567 25669 30645)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T936C	19						.						202.0	153.0	169.0					19																	49657559		2203	4300	6503	54349371	SO:0001819	synonymous_variant	3270	exon1				CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.936T>C	19.37:g.49657559A>G		Somatic		Capture	Illumina HiSeq	Phase_I	54349371	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	37	CCDS12759.1																																																																																				0.532	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
SCAF1	58506	broad.mit.edu	37	19	50154498	50154498	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:50154498G>C	ENST00000360565.3	+	7	976	c.852G>C	c.(850-852)gaG>gaC	p.E284D		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	284	Glu-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)	p.E284D(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		aggaagacgaggaggaggagg	0.617																																					p.E284D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G852C	19						.						22.0	23.0	23.0					19																	50154498		2203	4300	6503	54846310	SO:0001583	missense	58506	exon7			AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.852G>C	19.37:g.50154498G>C	ENSP00000353769:p.Glu284Asp	Somatic		Capture	Illumina HiSeq	Phase_I	54846310	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	37	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	G	1.109	-0.658770	0.03454	.	.	ENSG00000126461	ENST00000360565	T	0.48836	0.8	3.89	0.436	0.16549	.	.	.	.	.	T	0.22627	0.0546	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.11329	0.006	T	0.23297	-1.0192	8	.	.	.	-16.1427	5.9939	0.19483	0.3506:0.0:0.6494:0.0	.	284	Q9H7N4	SFR19_HUMAN	D	284	ENSP00000353769:E284D	.	E	+	3	2	SCAF1	54846310	0.344000	0.24827	0.002000	0.10522	0.002000	0.02628	-1.200000	0.03029	0.073000	0.16731	0.655000	0.94253	GAG		0.617	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
ATF5	22809	broad.mit.edu	37	19	50436244	50436244	+	Silent	SNP	C	C	T	rs373471926		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:50436244C>T	ENST00000423777.2	+	3	1121	c.744C>T	c.(742-744)cgC>cgT	p.R248R	MIR4751_ENST00000578027.1_RNA|CTC-326K19.6_ENST00000451973.1_Intron|ATF5_ENST00000595125.1_Silent_p.R248R	NM_001193646.1	NP_001180575.1	Q9Y2D1	ATF5_HUMAN	activating transcription factor 5	248	Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|olfactory bulb interneuron development (GO:0021891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 positive regulation of transcription (GO:0001228)|transcription corepressor activity (GO:0003714)	p.R248R(1)		NS(1)|endometrium(2)|large_intestine(1)|skin(3)	7		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00221)|OV - Ovarian serous cystadenocarcinoma(262;0.017)	Pseudoephedrine(DB00852)	CACGGAATCGCGAGCTGAAGG	0.652																																					p.R248R	GBM(48;768 989 9196 9511 26329)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C744T	19						.	C	,	0,4406		0,0,2203	34.0	37.0	36.0		744,744	-0.6	0.7	19		36	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ATF5	NM_001193646.1,NM_012068.5	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	248/283,248/283	50436244	1,13005	2203	4300	6503	55128056	SO:0001819	synonymous_variant	22809	exon4			AF101388	CCDS12789.1	19q13.33	2013-09-20			ENSG00000169136	ENSG00000169136		"""basic leucine zipper proteins"""	790	protein-coding gene	gene with protein product		606398				10373550	Standard	NM_012068		Approved		uc002prd.3	Q9Y2D1	OTTHUMG00000183065	ENST00000423777.2:c.744C>T	19.37:g.50436244C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55128056	NM_012068	B3KND3|Q9BSA1|Q9UNQ3	Silent	SNP	ENST00000423777.2	37	CCDS12789.1																																																																																				0.652	ATF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464915.2		
ZNF473	25888	broad.mit.edu	37	19	50549092	50549092	+	Silent	SNP	C	C	T	rs140202862	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:50549092C>T	ENST00000595661.1	+	6	1887	c.1392C>T	c.(1390-1392)tgC>tgT	p.C464C	CTD-2126E3.3_ENST00000599410.1_RNA|ZNF473_ENST00000270617.3_Silent_p.C464C|ZNF473_ENST00000601364.1_Intron|ZNF473_ENST00000445728.3_Silent_p.C452C|CTD-2126E3.3_ENST00000599914.1_RNA|ZNF473_ENST00000391821.2_Silent_p.C464C			Q8WTR7	ZN473_HUMAN	zinc finger protein 473	464	Interaction with SLBP/pre-mRNA complex.				gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.C464C(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37		all_neural(266;0.0459)|Ovarian(192;0.0728)		GBM - Glioblastoma multiforme(134;0.00111)|OV - Ovarian serous cystadenocarcinoma(262;0.0058)		GTCAGGAATGCGTCAGGAGTT	0.522													c|||	19	0.00379393	0.0	0.0	5008	,	,		20002	0.0179		0.0	False		,,,				2504	0.001				p.C464C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1392T	19						.						66.0	60.0	62.0					19																	50549092		2203	4300	6503	55240904	SO:0001819	synonymous_variant	25888	exon5			AB032967	CCDS33077.1	19q13.33	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	23239	protein-coding gene	gene with protein product						11782445	Standard	NM_015428		Approved	KIAA1141, DKFZP434N043, HZFP100	uc002prn.3	Q8WTR7		ENST00000595661.1:c.1392C>T	19.37:g.50549092C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55240904	NM_001006656	A8K8T7|Q9ULS9|Q9Y4Q7	Silent	SNP	ENST00000595661.1	37	CCDS33077.1																																																																																				0.522	ZNF473-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464833.1	XM_046390	
SAFB2	9667	broad.mit.edu	37	19	5610040	5610040	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:5610040G>A	ENST00000252542.4	-	9	1526	c.1262C>T	c.(1261-1263)aCg>aTg	p.T421M	SAFB2_ENST00000591310.1_5'UTR	NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	421	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T421M(1)		endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		CTTGAGATCCGTAGCGCGTGT	0.557																																					p.T421M	Ovarian(127;888 1728 23957 44128 52668)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1262T	19						.						126.0	89.0	101.0					19																	5610040		2203	4300	6503	5561040	SO:0001583	missense	9667	exon9			D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"""RNA binding motif (RRM) containing"""	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.1262C>T	19.37:g.5610040G>A	ENSP00000252542:p.Thr421Met	Somatic		Capture	Illumina HiSeq	Phase_I	5561040	NM_014649	B4DKG3|Q8TB13	Missense_Mutation	SNP	ENST00000252542.4	37	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.174665	0.78452	.	.	ENSG00000130254	ENST00000434962;ENST00000415313;ENST00000394625;ENST00000252542	T	0.16073	2.37	5.05	4.0	0.46444	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.232971	0.30126	N	0.010341	T	0.15305	0.0369	L	0.50333	1.59	0.58432	D	0.99999	D	0.55385	0.971	B	0.36608	0.229	T	0.07888	-1.0749	10	0.87932	D	0	-10.6202	13.8359	0.63408	0.0758:0.0:0.9242:0.0	.	421	Q14151	SAFB2_HUMAN	M	317;172;421;421	ENSP00000252542:T421M	ENSP00000252542:T421M	T	-	2	0	SAFB2	5561040	1.000000	0.71417	0.017000	0.16124	0.912000	0.54170	7.900000	0.87376	2.368000	0.80403	0.591000	0.81541	ACG		0.557	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649	
MYH14	79784	broad.mit.edu	37	19	50753904	50753904	+	Missense_Mutation	SNP	C	C	T	rs200843734		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:50753904C>T	ENST00000596571.1	+	13	1765	c.1765C>T	c.(1765-1767)Cgg>Tgg	p.R589W	MYH14_ENST00000425460.1_Missense_Mutation_p.R597W|MYH14_ENST00000440075.2_Missense_Mutation_p.R597W|MYH14_ENST00000601313.1_Missense_Mutation_p.R597W|MYH14_ENST00000598205.1_Missense_Mutation_p.R597W|MYH14_ENST00000376970.2_Missense_Mutation_p.R589W|MYH14_ENST00000262269.8_Missense_Mutation_p.R597W			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	589	Myosin motor.				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.R589W(1)|p.R597W(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)		GAGGCACCTGCGGGATCAGGC	0.647																																					p.R597W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1789T	19						.	C	TRP/ARG,TRP/ARG,TRP/ARG	1,4241		0,1,2120	36.0	44.0	41.0		1789,1789,1765	4.1	1.0	19		41	0,8468		0,0,4234	yes	missense,missense,missense	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	101,101,101	0,1,6354	TT,TC,CC		0.0,0.0236,0.0079	probably-damaging,probably-damaging,probably-damaging	597/2004,597/2037,589/1996	50753904	1,12709	2121	4234	6355	55445716	SO:0001583	missense	79784	exon15			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.1765C>T	19.37:g.50753904C>T	ENSP00000472819:p.Arg589Trp	Somatic		Capture	Illumina HiSeq	Phase_I	55445716	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.052102	0.75960	2.36E-4	0.0	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36	4.09	4.09	0.47781	Myosin head, motor domain (2);	.	.	.	.	D	0.94817	0.8326	M	0.92738	3.34	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.983;0.994;0.993	D	0.94907	0.8061	9	0.87932	D	0	.	9.4136	0.38507	0.2126:0.7874:0.0:0.0	.	597;589;597	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	W	589;597;589;597;589;597	ENSP00000406273:R597W;ENSP00000366169:R589W;ENSP00000407879:R597W;ENSP00000262269:R597W	ENSP00000262269:R597W	R	+	1	2	MYH14	55445716	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.880000	0.48530	2.287000	0.76781	0.561000	0.74099	CGG		0.647	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
MYBPC2	4606	broad.mit.edu	37	19	50967707	50967707	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:50967707G>A	ENST00000357701.5	+	27	3384	c.3333G>A	c.(3331-3333)tcG>tcA	p.S1111S		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	1111	Ig-like C2-type 7.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.S1111S(1)		breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		GTCGCCCCTCGCCCTTCGACG	0.597																																					p.S1111S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3333A	19						.						43.0	46.0	45.0					19																	50967707		2137	4246	6383	55659519	SO:0001819	synonymous_variant	4606	exon27				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.3333G>A	19.37:g.50967707G>A		Somatic		Capture	Illumina HiSeq	Phase_I	55659519	NM_004533	A1L4G9	Silent	SNP	ENST00000357701.5	37	CCDS46152.1																																																																																				0.597	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
SHANK1	50944	broad.mit.edu	37	19	51205879	51205879	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:51205879G>A	ENST00000293441.1	-	11	1610	c.1592C>T	c.(1591-1593)aCg>aTg	p.T531M	SHANK1_ENST00000359082.3_Missense_Mutation_p.T531M|SHANK1_ENST00000391814.1_Missense_Mutation_p.T531M	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	531					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)	p.T531M(1)		breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		TGAGCCCCCCGTGCCCCCGGC	0.721																																					p.T531M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1592T	19						.						6.0	7.0	7.0					19																	51205879		2168	4223	6391	55897691	SO:0001583	missense	50944	exon11			AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	15474	protein-coding gene	gene with protein product	"""somatostatin receptor-interacting protein"""	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.1592C>T	19.37:g.51205879G>A	ENSP00000293441:p.Thr531Met	Somatic		Capture	Illumina HiSeq	Phase_I	55897691	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	37	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	g	13.85	2.361000	0.41801	.	.	ENSG00000161681	ENST00000293441;ENST00000359082;ENST00000391814	T;T;T	0.39997	1.17;1.15;1.05	4.08	4.08	0.47627	.	2.962870	0.03066	U	0.156504	T	0.25680	0.0625	N	0.14661	0.345	0.38263	D	0.941938	P	0.43542	0.81	B	0.24269	0.052	T	0.33394	-0.9870	10	0.41790	T	0.15	-0.4903	12.4938	0.55916	0.0:0.0:1.0:0.0	.	531	Q9Y566	SHAN1_HUMAN	M	531	ENSP00000293441:T531M;ENSP00000351984:T531M;ENSP00000375690:T531M	ENSP00000293441:T531M	T	-	2	0	SHANK1	55897691	0.926000	0.31397	0.967000	0.41034	0.966000	0.64601	1.764000	0.38471	2.217000	0.71921	0.455000	0.32223	ACG		0.721	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148	
KLK15	55554	broad.mit.edu	37	19	51330321	51330321	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:51330321G>A	ENST00000598239.1	-	3	324	c.294C>T	c.(292-294)taC>taT	p.Y98Y	KLK15_ENST00000596931.1_Silent_p.Y97Y|KLK15_ENST00000416184.1_Silent_p.Y98Y|KLK15_ENST00000301421.2_Silent_p.Y98Y|KLK15_ENST00000326856.4_Silent_p.Y97Y	NM_017509.2	NP_059979.2	Q9H2R5	KLK15_HUMAN	kallikrein-related peptidase 15	98	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.Y98Y(2)		breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(12)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00758)|GBM - Glioblastoma multiforme(134;0.0143)		TGCGCGCTTCGTAGCGCGGGT	0.662																																					p.Y98Y	Pancreas(140;10 2513 7143 9246)											.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C294T	19						.						67.0	59.0	62.0					19																	51330321		2203	4300	6503	56022133	SO:0001819	synonymous_variant	55554	exon3			AF242195	CCDS12805.1, CCDS12806.1, CCDS12806.2, CCDS62766.1	19q13.4	2008-02-05	2006-10-27			ENSG00000174562		"""Kallikreins"""	20453	protein-coding gene	gene with protein product		610601	"""kallikrein 15"""			11010966, 12439720, 16800724, 16800723	Standard	NM_017509		Approved	HSRNASPH, ACO, prostinogen	uc002ptl.3	Q9H2R5		ENST00000598239.1:c.294C>T	19.37:g.51330321G>A		Somatic		Capture	Illumina HiSeq	Phase_I	56022133	NM_017509	A0AUY8|Q15358|Q6ISI0|Q9H2R3|Q9H2R4|Q9H2R6|Q9HBG9	Silent	SNP	ENST00000598239.1	37	CCDS12805.1																																																																																				0.662	KLK15-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465160.1	NM_017509	
KLK14	43847	broad.mit.edu	37	19	51581344	51581344	+	Missense_Mutation	SNP	C	C	T	rs373194700		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:51581344C>T	ENST00000156499.2	-	7	942	c.724G>A	c.(724-726)Gcc>Acc	p.A242T	KLK14_ENST00000391802.1_Missense_Mutation_p.A242T			Q9P0G3	KLK14_HUMAN	kallikrein-related peptidase 14	242	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				epidermis morphogenesis (GO:0048730)|fertilization (GO:0009566)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|proteolysis (GO:0006508)|seminal clot liquefaction (GO:0070684)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)	p.A226T(1)		kidney(4)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	11		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		CCAGGCAGGGCGCAGCGCTCC	0.597																																					p.A242T	GBM(117;2161 2172 2448 22911)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G724A	19						.		THR/ALA	0,4168		0,0,2084	67.0	72.0	71.0		724	4.6	0.2	19		71	2,8456		0,2,4227	no	missense	KLK14	NM_022046.4	58	0,2,6311	TT,TC,CC		0.0236,0.0,0.0158	probably-damaging	242/268	51581344	2,12624	2084	4229	6313	56273156	SO:0001583	missense	43847	exon7			AF283670	CCDS12823.2	19q13.3-q13.4	2008-02-05	2006-10-27		ENSG00000129437	ENSG00000129437		"""Kallikreins"""	6362	protein-coding gene	gene with protein product		606135	"""kallikrein 14"""			16800724, 16800723	Standard	XM_006723224		Approved	KLK-L6	uc002pvs.1	Q9P0G3	OTTHUMG00000143721	ENST00000156499.2:c.724G>A	19.37:g.51581344C>T	ENSP00000156499:p.Ala242Thr	Somatic		Capture	Illumina HiSeq	Phase_I	56273156	NM_022046	A7UNK5|Q1RMZ2|Q6B089	Missense_Mutation	SNP	ENST00000156499.2	37	CCDS12823.2	.	.	.	.	.	.	.	.	.	.	c	23.9	4.464988	0.84425	0.0	2.36E-4	ENSG00000129437	ENST00000156499;ENST00000391802	D;D	0.93811	-3.29;-3.29	4.64	4.64	0.57946	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.96207	0.8763	M	0.77820	2.39	0.37347	D	0.910654	D	0.89917	1.0	D	0.68192	0.956	D	0.98378	1.0557	9	0.87932	D	0	.	15.0173	0.71597	0.0:1.0:0.0:0.0	.	242	Q9P0G3	KLK14_HUMAN	T	242	ENSP00000156499:A242T;ENSP00000375678:A242T	ENSP00000156499:A242T	A	-	1	0	KLK14	56273156	0.964000	0.33143	0.204000	0.23530	0.663000	0.39108	5.459000	0.66685	2.134000	0.65973	0.651000	0.88453	GCC		0.597	KLK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289774.2	NM_022046	
ZNF175	7728	broad.mit.edu	37	19	52090131	52090131	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:52090131C>T	ENST00000262259.2	+	5	905	c.547C>T	c.(547-549)Cgc>Tgc	p.R183C	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	183					defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R183C(1)		NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		GAAAATGATTCGCACGAGGCC	0.403																																					p.R183C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C547T	19						.						94.0	91.0	92.0					19																	52090131		2203	4300	6503	56781943	SO:0001583	missense	7728	exon5			D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"""Zinc fingers, C2H2-type"", ""-"""	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.547C>T	19.37:g.52090131C>T	ENSP00000262259:p.Arg183Cys	Somatic		Capture	Illumina HiSeq	Phase_I	56781943	NM_007147	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	37	CCDS12837.1	.	.	.	.	.	.	.	.	.	.	C	10.40	1.341030	0.24339	.	.	ENSG00000105497	ENST00000262259	T	0.07114	3.22	2.2	2.2	0.27929	.	.	.	.	.	T	0.04182	0.0116	N	0.08118	0	0.80722	D	1	B	0.24721	0.11	B	0.08055	0.003	T	0.44574	-0.9319	9	0.35671	T	0.21	.	10.4889	0.44739	0.0:1.0:0.0:0.0	.	183	Q9Y473	ZN175_HUMAN	C	183	ENSP00000262259:R183C	ENSP00000262259:R183C	R	+	1	0	ZNF175	56781943	0.000000	0.05858	0.003000	0.11579	0.089000	0.18198	-0.371000	0.07513	1.563000	0.49615	0.655000	0.94253	CGC		0.403	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147	
HAS1	3036	broad.mit.edu	37	19	52222465	52222465	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:52222465G>A	ENST00000222115.1	-	2	730	c.696C>T	c.(694-696)taC>taT	p.Y232Y	HAS1_ENST00000601714.1_Silent_p.Y239Y|HAS1_ENST00000594621.1_Silent_p.Y86Y|HAS1_ENST00000540069.2_Silent_p.Y231Y	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	232					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)	p.Y232Y(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		TCACCTGCACGTAGTCCACCG	0.587																																					p.Y232Y	NSCLC(132;636 2450 45807 47979)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C696T	19						.						43.0	38.0	40.0					19																	52222465		2198	4296	6494	56914277	SO:0001819	synonymous_variant	3036	exon2			U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.696C>T	19.37:g.52222465G>A		Somatic		Capture	Illumina HiSeq	Phase_I	56914277	NM_001523	Q14470|Q9NS49	Silent	SNP	ENST00000222115.1	37	CCDS12838.1																																																																																				0.587	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523	
FPR2	2358	broad.mit.edu	37	19	52272654	52272654	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:52272654C>T	ENST00000598776.1	+	2	1515	c.743C>T	c.(742-744)gCt>gTt	p.A248V	FPR2_ENST00000598953.1_Missense_Mutation_p.A248V|FPR2_ENST00000340023.6_Missense_Mutation_p.A248V	NM_001462.3	NP_001453.1	P25090	FPR2_HUMAN	formyl peptide receptor 2	248					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|N-formyl peptide receptor activity (GO:0004982)	p.A248V(1)		endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33						GCTGTGGTGGCTTCTTTCTTC	0.483																																					p.A248V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C743T	19						.						157.0	126.0	137.0					19																	52272654		2203	4300	6503	56964466	SO:0001583	missense	2358	exon2			M88107	CCDS12840.1	19q13.3-q13.4	2012-08-10	2008-04-17	2008-04-17		ENSG00000171049		"""GPCR / Class A : Formyl peptide receptors"", ""GPCR / Class A : Leukotriene receptors"""	3827	protein-coding gene	gene with protein product		136538	"""formyl peptide receptor-like 1"""	FPRL1		9054386	Standard	NM_001462		Approved	LXA4R, HM63, FPRH2, FMLPX, FPR2A, FMLP-R-II, ALXR	uc002pxr.3	P25090		ENST00000598776.1:c.743C>T	19.37:g.52272654C>T	ENSP00000468897:p.Ala248Val	Somatic		Capture	Illumina HiSeq	Phase_I	56964466	NM_001462	A8K3E2	Missense_Mutation	SNP	ENST00000598776.1	37	CCDS12840.1	.	.	.	.	.	.	.	.	.	.	.	10.47	1.359187	0.24598	.	.	ENSG00000171049	ENST00000340023	T	0.35048	1.33	3.79	2.7	0.31948	GPCR, rhodopsin-like superfamily (1);	0.858337	0.10061	N	0.720946	T	0.23133	0.0559	L	0.28694	0.88	0.30792	N	0.740756	B	0.17465	0.022	B	0.28991	0.097	T	0.38693	-0.9649	10	0.05721	T	0.95	.	5.7211	0.17988	0.0:0.733:0.0:0.267	.	248	P25090	FPR2_HUMAN	V	248	ENSP00000340191:A248V	ENSP00000340191:A248V	A	+	2	0	FPR2	56964466	0.000000	0.05858	0.935000	0.37517	0.971000	0.66376	-0.075000	0.11431	0.909000	0.36697	0.484000	0.47621	GCT		0.483	FPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466912.2	NM_001005738	
ZNF614	80110	broad.mit.edu	37	19	52519831	52519831	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:52519831C>T	ENST00000270649.6	-	5	1564	c.1020G>A	c.(1018-1020)gaG>gaA	p.E340E	ZNF614_ENST00000356322.6_Intron	NM_025040.3	NP_079316.2	Q8N883	ZN614_HUMAN	zinc finger protein 614	340					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.E340E(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00513)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		TATAGGGTTTCTCCCCTGTAT	0.423																																					p.E340E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1020A	19						.						124.0	116.0	118.0					19																	52519831		2203	4300	6503	57211643	SO:0001819	synonymous_variant	80110	exon5			BC022246	CCDS12847.1	19q13.41	2013-01-08				ENSG00000142556		"""Zinc fingers, C2H2-type"", ""-"""	24722	protein-coding gene	gene with protein product						12477932	Standard	NM_025040		Approved	FLJ21941	uc002pyj.3	Q8N883		ENST00000270649.6:c.1020G>A	19.37:g.52519831C>T		Somatic		Capture	Illumina HiSeq	Phase_I	57211643	NM_025040	Q494T8|Q8TCF4|Q9BSN8	Silent	SNP	ENST00000270649.6	37	CCDS12847.1																																																																																				0.423	ZNF614-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462407.1	NM_025040	
CATSPERD	257062	broad.mit.edu	37	19	5772936	5772936	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:5772936T>C	ENST00000381624.3	+	20	1962	c.1901T>C	c.(1900-1902)aTg>aCg	p.M634T	CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	634					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.M634T(1)									TGGACCACCATGATAAAGGAA	0.557																																					p.M634T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1901C	19						.						50.0	54.0	52.0					19																	5772936		1910	4131	6041	5723936	SO:0001583	missense	257062	exon20			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.1901T>C	19.37:g.5772936T>C	ENSP00000371037:p.Met634Thr	Somatic		Capture	Illumina HiSeq	Phase_I	5723936	NM_152784	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	37	CCDS12149.2	.	.	.	.	.	.	.	.	.	.	T	8.276	0.814550	0.16607	.	.	ENSG00000174898	ENST00000381624;ENST00000381613	T	0.26957	1.7	3.22	2.14	0.27477	.	1.304990	0.05620	N	0.579786	T	0.22936	0.0554	L	0.50333	1.59	0.09310	N	1	P	0.38370	0.628	B	0.33254	0.16	T	0.28681	-1.0036	10	0.87932	D	0	-9.2294	5.4717	0.16674	0.2485:0.0:0.0:0.7515	.	634	Q86XM0	TM146_HUMAN	T	634;303	ENSP00000371037:M634T	ENSP00000371026:M303T	M	+	2	0	TMEM146	5723936	0.016000	0.18221	0.006000	0.13384	0.032000	0.12392	2.835000	0.48175	0.573000	0.29400	0.459000	0.35465	ATG		0.557	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784	
ZNF432	9668	broad.mit.edu	37	19	52537438	52537438	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:52537438G>A	ENST00000594154.1	-	5	1706	c.1494C>T	c.(1492-1494)agC>agT	p.S498S	ZNF432_ENST00000221315.5_Silent_p.S498S			O94892	ZN432_HUMAN	zinc finger protein 432	498					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.S498S(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	29		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.0054)|OV - Ovarian serous cystadenocarcinoma(262;0.0182)		ACATCAGTCCGCTATTCACAA	0.438																																					p.S498S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1494T	19						.						69.0	62.0	64.0					19																	52537438		2203	4300	6503	57229250	SO:0001819	synonymous_variant	9668	exon5			AB018341	CCDS12848.1	19q13.41	2013-01-08				ENSG00000256087		"""Zinc fingers, C2H2-type"", ""-"""	20810	protein-coding gene	gene with protein product						9872452	Standard	NM_014650		Approved	KIAA0798	uc002pyk.3	O94892		ENST00000594154.1:c.1494C>T	19.37:g.52537438G>A		Somatic		Capture	Illumina HiSeq	Phase_I	57229250	NM_014650		Silent	SNP	ENST00000594154.1	37	CCDS12848.1																																																																																				0.438	ZNF432-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462410.1	NM_014650	
ZNF616	90317	broad.mit.edu	37	19	52618246	52618246	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:52618246T>C	ENST00000600228.1	-	4	2432	c.2171A>G	c.(2170-2172)aAa>aGa	p.K724R	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	724					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.K724R(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		CCCAAAGGCTTTGCCACATTC	0.393																																					p.K724R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2171G	19						.						139.0	138.0	138.0					19																	52618246		2203	4300	6503	57310058	SO:0001583	missense	90317	exon4			AK092266	CCDS33090.1	19q13.41	2013-01-08				ENSG00000204611		"""Zinc fingers, C2H2-type"", ""-"""	28062	protein-coding gene	gene with protein product							Standard	NM_178523		Approved	MGC45556	uc002pym.3	Q08AN1		ENST00000600228.1:c.2171A>G	19.37:g.52618246T>C	ENSP00000471000:p.Lys724Arg	Somatic		Capture	Illumina HiSeq	Phase_I	57310058	NM_178523	B3KRV1|Q0P658|Q658V7	Missense_Mutation	SNP	ENST00000600228.1	37	CCDS33090.1	.	.	.	.	.	.	.	.	.	.	T	13.22	2.172500	0.38315	.	.	ENSG00000204611	ENST00000330123	.	.	.	1.8	-0.994	0.10225	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.48277	0.1491	L	0.45422	1.42	0.19575	N	0.999969	D	0.64830	0.994	D	0.68192	0.956	T	0.38628	-0.9652	8	0.66056	D	0.02	.	5.3632	0.16099	0.4501:0.0:0.0:0.5499	.	724	Q08AN1	ZN616_HUMAN	R	724	.	ENSP00000328722:K724R	K	-	2	0	ZNF616	57310058	0.249000	0.23941	0.000000	0.03702	0.012000	0.07955	2.036000	0.41165	-0.591000	0.05859	-0.686000	0.03744	AAA		0.393	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892	
NRTN	4902	broad.mit.edu	37	19	5824275	5824275	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:5824275C>T	ENST00000303212.2	+	1	463	c.99C>T	c.(97-99)ctC>ctT	p.L33L	AC011499.1_ENST00000579264.1_RNA	NM_004558.3	NP_004549.1	Q99748	NRTN_HUMAN	neurturin	33					axon guidance (GO:0007411)|MAPK cascade (GO:0000165)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|extracellular region (GO:0005576)	receptor binding (GO:0005102)	p.L33L(1)		large_intestine(1)	1						GCCACCGCCTCGGACCTGCGC	0.672																																					p.L33L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C99T	19						.						41.0	34.0	36.0					19																	5824275		2203	4299	6502	5775275	SO:0001819	synonymous_variant	4902	exon1			U78110	CCDS12151.1	19p13.3	2014-01-30				ENSG00000171119		"""Endogenous ligands"""	8007	protein-coding gene	gene with protein product	"""prepro-neurturin"""	602018				8945474	Standard	NM_004558		Approved	NTN	uc002mde.3	Q99748		ENST00000303212.2:c.99C>T	19.37:g.5824275C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5775275	NM_004558	B2RPE8	Silent	SNP	ENST00000303212.2	37	CCDS12151.1																																																																																				0.672	NRTN-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451882.2	NM_004558	
ZNF616	90317	broad.mit.edu	37	19	52618353	52618353	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:52618353T>C	ENST00000600228.1	-	4	2325	c.2064A>G	c.(2062-2064)ccA>ccG	p.P688P	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	688					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.P688P(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		CACATTTATATGGTTTCTTTC	0.383																																					p.P688P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2064G	19						.						151.0	141.0	144.0					19																	52618353		2203	4300	6503	57310165	SO:0001819	synonymous_variant	90317	exon4			AK092266	CCDS33090.1	19q13.41	2013-01-08				ENSG00000204611		"""Zinc fingers, C2H2-type"", ""-"""	28062	protein-coding gene	gene with protein product							Standard	NM_178523		Approved	MGC45556	uc002pym.3	Q08AN1		ENST00000600228.1:c.2064A>G	19.37:g.52618353T>C		Somatic		Capture	Illumina HiSeq	Phase_I	57310165	NM_178523	B3KRV1|Q0P658|Q658V7	Silent	SNP	ENST00000600228.1	37	CCDS33090.1																																																																																				0.383	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892	
ZNF83	55769	broad.mit.edu	37	19	53116482	53116482	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:53116482G>T	ENST00000597597.1	-	2	3589	c.1336C>A	c.(1336-1338)Cat>Aat	p.H446N	ZNF83_ENST00000391789.4_Missense_Mutation_p.H418N|ZNF83_ENST00000544146.1_Missense_Mutation_p.H446N|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000536937.1_Missense_Mutation_p.H446N|ZNF83_ENST00000545872.1_Missense_Mutation_p.H446N|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Missense_Mutation_p.H446N|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000301096.3_Missense_Mutation_p.H446N			P51522	ZNF83_HUMAN	zinc finger protein 83	446					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.H446N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		TTCCGATGATGTGCTAGGGAT	0.378																																					p.H446N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1336A	19						.						112.0	111.0	111.0					19																	53116482		2203	4300	6503	57808294	SO:0001583	missense	55769	exon4			M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.1336C>A	19.37:g.53116482G>T	ENSP00000472619:p.His446Asn	Somatic		Capture	Illumina HiSeq	Phase_I	57808294	NM_001105552	A8MT75|Q3ZCX0|Q6PI08	Missense_Mutation	SNP	ENST00000597597.1	37	CCDS12854.1	.	.	.	.	.	.	.	.	.	.	-	0.134	-1.110102	0.01813	.	.	ENSG00000167766	ENST00000536937;ENST00000301096;ENST00000544146;ENST00000434535;ENST00000545872;ENST00000541777;ENST00000391789	T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76	2.11	-4.23	0.03789	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.24812	0.0602	N	0.05467	-0.045	0.09310	N	1	B;P	0.45768	0.002;0.866	B;P	0.47251	0.002;0.542	T	0.16897	-1.0387	9	0.16896	T	0.51	.	4.5811	0.12259	0.2567:0.0:0.4361:0.3071	.	418;446	P51522-2;P51522	.;ZNF83_HUMAN	N	446;446;446;418;446;446;418	ENSP00000445993:H446N;ENSP00000301096:H446N;ENSP00000445470:H446N;ENSP00000440713:H446N;ENSP00000439681:H446N;ENSP00000375666:H418N	ENSP00000301096:H446N	H	-	1	0	ZNF83	57808294	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-6.640000	0.00058	-0.908000	0.03857	0.467000	0.42956	CAT		0.378	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
ZNF83	55769	broad.mit.edu	37	19	53117461	53117461	+	Silent	SNP	C	C	T	rs77404321	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:53117461C>T	ENST00000597597.1	-	2	2610	c.357G>A	c.(355-357)acG>acA	p.T119T	ZNF83_ENST00000391789.4_Silent_p.T119T|ZNF83_ENST00000544146.1_Silent_p.T119T|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000536937.1_Silent_p.T119T|ZNF83_ENST00000545872.1_Silent_p.T119T|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Silent_p.T119T|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000301096.3_Silent_p.T119T			P51522	ZNF83_HUMAN	zinc finger protein 83	119			T -> M (in dbSNP:rs329940).		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.T119T(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		ATTTAAATTGCGTCTCTTTAG	0.338													C|||	47	0.00938498	0.0	0.0	5008	,	,		19741	0.0466		0.0	False		,,,				2504	0.0				p.T119T												.	.	2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	c.G357A	19						.	C	,,,,,,,,	2,4404		0,2,2201	65.0	63.0	64.0		357,357,357,357,357,357,357,357,357	-2.3	0.0	19	dbSNP_133	64	9,8591		0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF83	NM_001105549.1,NM_001105550.1,NM_001105551.1,NM_001105552.1,NM_001105553.1,NM_001105554.1,NM_001242531.1,NM_001242538.1,NM_018300.3	,,,,,,,,	0,11,6492	TT,TC,CC		0.1047,0.0454,0.0846	,,,,,,,,	119/517,119/517,119/517,119/517,119/489,119/489,119/489,119/489,119/517	53117461	11,12995	2203	4300	6503	57809273	SO:0001819	synonymous_variant	55769	exon4			M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.357G>A	19.37:g.53117461C>T		Somatic		Capture	Illumina HiSeq	Phase_I	57809273	NM_001105552	A8MT75|Q3ZCX0|Q6PI08	Silent	SNP	ENST00000597597.1	37	CCDS12854.1																																																																																				0.338	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
FUT3	2525	broad.mit.edu	37	19	5844492	5844492	+	Missense_Mutation	SNP	C	C	T	rs2339237		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:5844492C>T	ENST00000303225.6	-	3	993	c.359G>A	c.(358-360)cGc>cAc	p.R120H	FUT3_ENST00000589918.1_Missense_Mutation_p.R120H|AC024592.9_ENST00000589276.1_RNA|FUT3_ENST00000593144.1_5'Flank|FUT3_ENST00000589620.1_Missense_Mutation_p.R120H|FUT3_ENST00000458379.2_Missense_Mutation_p.R120H	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	120					cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)	p.R120H(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						AGGTGGGAGGCGTGACTTAGG	0.612																																					p.R120H	Esophageal Squamous(82;745 1728 24593 44831)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G359A	19						.						134.0	109.0	117.0					19																	5844492		2203	4300	6503	5795492	SO:0001583	missense	2525	exon3				CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"""CD molecules"", ""Blood group antigens"", ""Fucosyltransferases"""	4014	protein-coding gene	gene with protein product		111100	"""fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"""	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.359G>A	19.37:g.5844492C>T	ENSP00000305603:p.Arg120His	Somatic		Capture	Illumina HiSeq	Phase_I	5795492	NM_001097640	B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	37	CCDS12153.1	.	.	.	.	.	.	.	.	.	.	C	11.69	1.714240	0.30413	.	.	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.23754	1.89;1.89	2.24	-3.38	0.04883	.	1.303170	0.05565	N	0.569958	T	0.13329	0.0323	N	0.17082	0.46	0.09310	N	1	P;B;B;B	0.39551	0.678;0.1;0.1;0.1	B;B;B;B	0.40444	0.329;0.041;0.041;0.041	T	0.12477	-1.0546	10	0.42905	T	0.14	.	0.2253	0.00173	0.3868:0.1575:0.1946:0.261	.	120;120;120;120	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	H	120	ENSP00000305603:R120H;ENSP00000416443:R120H	ENSP00000305603:R120H	R	-	2	0	FUT3	5795492	0.000000	0.05858	0.020000	0.16555	0.094000	0.18550	-0.786000	0.04623	-0.371000	0.08004	0.205000	0.17691	CGC		0.612	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149	
ZNF611	81856	broad.mit.edu	37	19	53208414	53208414	+	Missense_Mutation	SNP	G	G	A	rs148655773		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:53208414G>A	ENST00000319783.1	-	7	2210	c.1894C>T	c.(1894-1896)Cgt>Tgt	p.R632C	ZNF611_ENST00000453741.2_Missense_Mutation_p.R563C|ZNF611_ENST00000543227.1_Missense_Mutation_p.R632C|ZNF611_ENST00000602162.1_Missense_Mutation_p.R563C|ZNF611_ENST00000540744.1_Missense_Mutation_p.R632C|ZNF611_ENST00000595798.1_Missense_Mutation_p.R563C	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	632					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.R632C(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		GAGCAGTGACGGAAGGTATTG	0.438																																					p.R563C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1687T	19						.						217.0	205.0	209.0					19																	53208414		2203	4300	6503	57900226	SO:0001583	missense	81856	exon5			AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"""Zinc fingers, C2H2-type"", ""-"""	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.1894C>T	19.37:g.53208414G>A	ENSP00000322427:p.Arg632Cys	Somatic		Capture	Illumina HiSeq	Phase_I	57900226	NM_001161501	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	37	CCDS12855.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	11.71	1.720574	0.30503	.	.	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000453741;ENST00000319783	T;T;T;T	0.08282	3.11;3.11;3.11;3.11	1.54	-3.08	0.05347	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11623	0.0283	L	0.58428	1.81	0.09310	N	1	D	0.69078	0.997	P	0.50270	0.636	T	0.06427	-1.0827	9	0.62326	D	0.03	.	5.3634	0.16101	0.1613:0.0:0.1688:0.6698	.	632	Q8N823	ZN611_HUMAN	C	632;632;563;632	ENSP00000437616:R632C;ENSP00000439211:R632C;ENSP00000443505:R563C;ENSP00000322427:R632C	ENSP00000322427:R632C	R	-	1	0	ZNF611	57900226	.	.	0.000000	0.03702	0.010000	0.07245	.	.	-1.102000	0.03023	-2.201000	0.00304	CGT		0.438	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972	
ZNF665	79788	broad.mit.edu	37	19	53668849	53668849	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:53668849G>A	ENST00000600412.1	-	2	814	c.699C>T	c.(697-699)tgC>tgT	p.C233C	CTD-2245F17.2_ENST00000600257.1_RNA|ZNF665_ENST00000396424.3_Silent_p.C298C			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C233C(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		TTTGAGTGAAGCACTTGCCAC	0.413																																					p.C298C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C894T	19						.						129.0	137.0	134.0					19																	53668849		2203	4300	6503	58360661	SO:0001819	synonymous_variant	79788	exon4				CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"""Zinc fingers, C2H2-type"", ""-"""	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.699C>T	19.37:g.53668849G>A		Somatic		Capture	Illumina HiSeq	Phase_I	58360661	NM_024733	A8K5T8	Silent	SNP	ENST00000600412.1	37																																																																																					0.413	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733	
ZNF677	342926	broad.mit.edu	37	19	53740413	53740413	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:53740413C>A	ENST00000598513.1	-	5	1717	c.1567G>T	c.(1567-1569)Gct>Tct	p.A523S	ZNF677_ENST00000333952.4_Missense_Mutation_p.A523S	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	523					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.A523S(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		TGGGTAAAAGCTTTGCCACAT	0.343																																					p.A523S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1567T	19						.						135.0	129.0	131.0					19																	53740413		2203	4299	6502	58432225	SO:0001583	missense	342926	exon5			BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"""Zinc fingers, C2H2-type"", ""-"""	28730	protein-coding gene	gene with protein product	"""hypothetical protein MGC48625"""					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.1567G>T	19.37:g.53740413C>A	ENSP00000469391:p.Ala523Ser	Somatic		Capture	Illumina HiSeq	Phase_I	58432225	NM_182609		Missense_Mutation	SNP	ENST00000598513.1	37	CCDS12861.1	.	.	.	.	.	.	.	.	.	.	C	11.46	1.646482	0.29246	.	.	ENSG00000197928	ENST00000333952	T	0.07567	3.18	2.12	2.12	0.27331	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.246767	0.21289	N	0.077012	T	0.05181	0.0138	N	0.01410	-0.885	0.21802	N	0.99953	D	0.56287	0.975	P	0.56563	0.801	T	0.35475	-0.9787	10	0.38643	T	0.18	.	7.8091	0.29219	0.0:1.0:0.0:0.0	.	523	Q86XU0	ZN677_HUMAN	S	523	ENSP00000334394:A523S	ENSP00000334394:A523S	A	-	1	0	ZNF677	58432225	0.000000	0.05858	0.990000	0.47175	0.672000	0.39443	0.565000	0.23578	1.509000	0.48786	0.591000	0.81541	GCT		0.343	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609	
ZNF331	55422	broad.mit.edu	37	19	54080876	54080876	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:54080876G>A	ENST00000253144.9	+	7	2395	c.1062G>A	c.(1060-1062)ccG>ccA	p.P354P	ZNF331_ENST00000411977.2_Silent_p.P354P|ZNF331_ENST00000511593.2_Silent_p.P354P|ZNF331_ENST00000512387.1_Silent_p.P354P|ZNF331_ENST00000511154.1_Silent_p.P354P|ZNF331_ENST00000513999.1_Silent_p.P354P|ZNF331_ENST00000449416.1_Silent_p.P354P|ZNF331_ENST00000513265.1_3'UTR	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	354					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.P354P(1)		NS(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		GCGAGAAGCCGTACAAGTGCA	0.527			T	?	follicular thyroid adenoma																																p.P354P			Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1062A	19						.						106.0	92.0	96.0					19																	54080876		2203	4300	6503	58772688	SO:0001819	synonymous_variant	55422	exon6			AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"""Zinc fingers, C2H2-type"", ""-"""	15489	protein-coding gene	gene with protein product	"""rearranged in thyroid adenomas"""	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.1062G>A	19.37:g.54080876G>A		Somatic		Capture	Illumina HiSeq	Phase_I	58772688	NM_001079906	Q96GJ4	Silent	SNP	ENST00000253144.9	37	CCDS33102.1																																																																																				0.527	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555	
LENG8	114823	broad.mit.edu	37	19	54966659	54966659	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:54966659C>T	ENST00000326764.5	+	8	1417	c.938C>T	c.(937-939)aCg>aTg	p.T313M	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	276								p.T313M(1)		breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		AAGGACCGCACGGAAAAGCTG	0.632																																					p.T313M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C938T	19						.						50.0	55.0	53.0					19																	54966659		2203	4300	6503	59658471	SO:0001583	missense	114823	exon8			AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.938C>T	19.37:g.54966659C>T	ENSP00000318374:p.Thr313Met	Somatic		Capture	Illumina HiSeq	Phase_I	59658471	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	37	CCDS12894.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.910239	0.92107	.	.	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000376526;ENST00000431846	T;T;T	0.33654	1.46;1.45;1.4	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.57446	0.2054	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.53528	-0.8426	10	0.38643	T	0.18	-25.7684	16.6024	0.84819	0.0:1.0:0.0:0.0	.	313;276	Q96PV6-2;F8W9Q9	.;.	M	313;276;276;313	ENSP00000318374:T313M;ENSP00000365709:T276M;ENSP00000388053:T313M	ENSP00000301196:T276M	T	+	2	0	LENG8	59658471	1.000000	0.71417	0.708000	0.30435	0.912000	0.54170	7.224000	0.78042	2.586000	0.87340	0.655000	0.94253	ACG		0.632	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925	
RDH13	112724	broad.mit.edu	37	19	55559853	55559853	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:55559853G>A	ENST00000415061.3	-	5	645	c.502C>T	c.(502-504)Cgg>Tgg	p.R168W	CTC-550B14.7_ENST00000593060.1_RNA|RDH13_ENST00000396247.3_Missense_Mutation_p.R97W|CTC-550B14.6_ENST00000585492.1_RNA	NM_001145971.1	NP_001139443.1	Q8NBN7	RDH13_HUMAN	retinol dehydrogenase 13 (all-trans/9-cis)	168					eye photoreceptor cell development (GO:0042462)|response to high light intensity (GO:0009644)|retina layer formation (GO:0010842)	mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)	p.R97W(1)		endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.199)	GBM - Glioblastoma multiforme(193;0.0504)	Vitamin A(DB00162)	TTGATGATCCGCGAAGGGGCT	0.498																																					p.R97W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C289T	19						.						76.0	78.0	77.0					19																	55559853		2007	4180	6187	60251665	SO:0001583	missense	112724	exon6				CCDS42627.1, CCDS54320.1	19q13.42	2011-09-14	2006-05-09			ENSG00000160439	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	19978	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 3"""		"""retinol dehydrogenase 13 (all-trans and 9-cis)"""			12226107, 19027726	Standard	NM_138412		Approved	SDR7C3	uc002qio.3	Q8NBN7		ENST00000415061.3:c.502C>T	19.37:g.55559853G>A	ENSP00000391121:p.Arg168Trp	Somatic		Capture	Illumina HiSeq	Phase_I	60251665	NM_138412	Q6UX79|Q96G88	Missense_Mutation	SNP	ENST00000415061.3	37	CCDS54320.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.406076	0.42715	.	.	ENSG00000160439	ENST00000415061;ENST00000396247;ENST00000291892	T;T;T	0.27557	1.66;1.66;1.66	5.29	5.29	0.74685	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.67411	0.2890	H	0.97158	3.95	0.47153	D	0.999337	D	0.89917	1.0	D	0.97110	1.0	T	0.77135	-0.2699	10	0.87932	D	0	.	11.8938	0.52646	0.0:0.0:0.8257:0.1743	.	168	Q8NBN7	RDH13_HUMAN	W	168;97;168	ENSP00000391121:R168W;ENSP00000379547:R97W;ENSP00000291892:R168W	ENSP00000291892:R168W	R	-	1	2	RDH13	60251665	0.999000	0.42202	0.225000	0.23894	0.081000	0.17604	2.775000	0.47702	2.665000	0.90641	0.549000	0.68633	CGG		0.498	RDH13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451470.1	NM_138412	
PPP1R12C	54776	broad.mit.edu	37	19	55606058	55606058	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:55606058C>T	ENST00000263433.3	-	12	1578	c.1563G>A	c.(1561-1563)gcG>gcA	p.A521A	PPP1R12C_ENST00000376393.2_Silent_p.A521A|PPP1R12C_ENST00000435544.2_Silent_p.A447A	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C									p.A521A(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		CCGCTGGGGGCGCCGTGGAGG	0.677																																					p.A521A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1563A	19						.						31.0	32.0	32.0					19																	55606058		2199	4300	6499	60297870	SO:0001819	synonymous_variant	54776	exon12			AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14947	protein-coding gene	gene with protein product	"""myosin-binding subunit 85"""	613245	"""leukocyte receptor cluster (LRC) member 3"", ""protein phosphatase 1, regulatory (inhibitor) subunit 12C"""	LENG3		11399775	Standard	NM_017607		Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.1563G>A	19.37:g.55606058C>T		Somatic		Capture	Illumina HiSeq	Phase_I	60297870	NM_017607		Silent	SNP	ENST00000263433.3	37	CCDS12916.1																																																																																				0.677	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607	
PTPRH	5794	broad.mit.edu	37	19	55710059	55710059	+	Missense_Mutation	SNP	C	C	T	rs368354556		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:55710059C>T	ENST00000376350.3	-	8	1664	c.1642G>A	c.(1642-1644)Gag>Aag	p.E548K	PTPRH_ENST00000588559.1_5'UTR|PTPRH_ENST00000263434.5_Missense_Mutation_p.E370K	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	548	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process (GO:0006915)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.E548K(1)		breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(8)|lung(27)|ovary(2)|prostate(5)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	67		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0479)		TCATTCCTCTCGGCCCAGACG	0.562																																					p.E548K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1642A	19						.						148.0	121.0	130.0					19																	55710059		2203	4300	6503	60401871	SO:0001583	missense	5794	exon8				CCDS33110.1, CCDS54321.1	19q13.4	2013-02-11				ENSG00000080031		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9672	protein-coding gene	gene with protein product		602510				8294459	Standard	XM_006723312		Approved	SAP-1	uc002qjq.3	Q9HD43		ENST00000376350.3:c.1642G>A	19.37:g.55710059C>T	ENSP00000365528:p.Glu548Lys	Somatic		Capture	Illumina HiSeq	Phase_I	60401871	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.904060	0.33628	.	.	ENSG00000080031	ENST00000376350;ENST00000263434	T;T	0.56776	0.44;0.44	2.27	-1.64	0.08318	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.40670	0.1126	L	0.55990	1.75	0.09310	N	1	D;D;P	0.59767	0.986;0.982;0.95	P;P;P	0.49301	0.606;0.471;0.59	T	0.42258	-0.9462	9	0.02654	T	1	.	1.0884	0.01658	0.2277:0.3997:0.2236:0.149	.	370;370;548	C9JCH2;Q9HD43-2;Q9HD43	.;.;PTPRH_HUMAN	K	548;370	ENSP00000365528:E548K;ENSP00000263434:E370K	ENSP00000263434:E370K	E	-	1	0	PTPRH	60401871	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.326000	0.07965	-0.239000	0.09710	-0.310000	0.09108	GAG		0.562	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
PPP6R1	22870	broad.mit.edu	37	19	55743534	55743534	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:55743534C>G	ENST00000412770.2	-	18	2600	c.2034G>C	c.(2032-2034)gaG>gaC	p.E678D	PPP6R1_ENST00000587283.1_Missense_Mutation_p.E678D|TMEM86B_ENST00000327042.4_5'Flank|AC010327.1_ENST00000581390.1_RNA	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	678	Glu-rich.|Poly-Glu.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)	p.E678D(1)		breast(1)	1						cctcctcctcctcgtcctcct	0.642																																					p.E678D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2034C	19						.						38.0	47.0	44.0					19																	55743534		2187	4274	6461	60435346	SO:0001583	missense	22870	exon18			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.2034G>C	19.37:g.55743534C>G	ENSP00000414202:p.Glu678Asp	Somatic		Capture	Illumina HiSeq	Phase_I	60435346	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Missense_Mutation	SNP	ENST00000412770.2	37	CCDS46186.1	.	.	.	.	.	.	.	.	.	.	C	8.708	0.911388	0.17833	.	.	ENSG00000105063	ENST00000412770	T	0.65178	-0.14	3.39	-4.86	0.03132	.	1.541830	0.04232	N	0.335471	T	0.38295	0.1035	L	0.27053	0.805	0.09310	N	0.999999	B;B	0.11235	0.003;0.004	B;B	0.09377	0.003;0.004	T	0.12863	-1.0531	10	0.12430	T	0.62	-1.7909	0.7185	0.00936	0.1598:0.2451:0.2894:0.3057	.	678;40	Q9UPN7;Q96ID3	PP6R1_HUMAN;.	D	678	ENSP00000414202:E678D	ENSP00000414202:E678D	E	-	3	2	PPP6R1	60435346	0.001000	0.12720	0.084000	0.20598	0.409000	0.31022	-3.395000	0.00486	-0.884000	0.03976	0.313000	0.20887	GAG		0.642	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931	
ZNF628	89887	broad.mit.edu	37	19	55992824	55992824	+	Silent	SNP	C	C	T	rs146432627	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:55992824C>T	ENST00000598519.1	+	3	817	c.264C>T	c.(262-264)ggC>ggT	p.G88G	ZNF628_ENST00000391718.2_Silent_p.G84G			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	88					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.G84G(1)		endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		GCCACACGGGCGAGCGGCCCT	0.667																																					p.G84G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C252T	19						.	C		1,4405		0,1,2202	41.0	41.0	41.0		252	-7.1	0.3	19	dbSNP_134	41	0,8594		0,0,4297	no	coding-synonymous	ZNF628	NM_033113.2		0,1,6499	TT,TC,CC		0.0,0.0227,0.0077		84/1056	55992824	1,12999	2203	4297	6500	60684636	SO:0001819	synonymous_variant	89887	exon3			AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"""Zinc fingers, C2H2-type"""	28054	protein-coding gene	gene with protein product	"""Zinc finger expressed in Embryonal cells and Certain adult organs"""	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.264C>T	19.37:g.55992824C>T		Somatic		Capture	Illumina HiSeq	Phase_I	60684636	NM_033113	Q86X34	Silent	SNP	ENST00000598519.1	37	CCDS33116.3																																																																																				0.667	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964	
NLRP11	204801	broad.mit.edu	37	19	56303801	56303801	+	Silent	SNP	G	G	A	rs114762114		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:56303801G>A	ENST00000589093.1	-	7	2472	c.2379C>T	c.(2377-2379)agC>agT	p.S793S	NLRP11_ENST00000443188.1_Silent_p.S793S|NLRP11_ENST00000592953.1_Silent_p.S694S|NLRP11_ENST00000589824.2_Silent_p.S739S|NLRP11_ENST00000360133.3_Silent_p.S739S			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	793							ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)	p.S793S(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		TTCCAAGGGCGCTGCAGCAAT	0.493													G|||	1	0.000199681	0.0	0.0	5008	,	,		19093	0.001		0.0	False		,,,				2504	0.0				p.S793S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2379T	19						.	G		0,4406		0,0,2203	116.0	107.0	110.0		2379	1.1	0.0	19	dbSNP_132	110	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	NLRP11	NM_145007.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		793/1034	56303801	1,13005	2203	4300	6503	60995613	SO:0001819	synonymous_variant	204801	exon9			AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"""Nucleotide-binding domain and leucine rich repeat containing"""	22945	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"""	609664	"""NACHT, leucine rich repeat and PYD containing 11"""	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.2379C>T	19.37:g.56303801G>A		Somatic		Capture	Illumina HiSeq	Phase_I	60995613	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Silent	SNP	ENST00000589093.1	37	CCDS12935.1																																																																																				0.493	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007	
NLRP4	147945	broad.mit.edu	37	19	56369169	56369169	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:56369169G>A	ENST00000301295.6	+	3	832	c.410G>A	c.(409-411)cGc>cAc	p.R137H	NLRP4_ENST00000346986.5_Missense_Mutation_p.R137H|NLRP4_ENST00000587891.1_Missense_Mutation_p.R62H	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	137					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.R137H(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)		CATTTGGACCGCCTTTTTGCT	0.463																																					p.R137H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G410A	19						.						143.0	131.0	135.0					19																	56369169		2203	4300	6503	61060981	SO:0001583	missense	147945	exon3			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.410G>A	19.37:g.56369169G>A	ENSP00000301295:p.Arg137His	Somatic		Capture	Illumina HiSeq	Phase_I	61060981	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.122628	0.00346	.	.	ENSG00000160505	ENST00000301295;ENST00000346986	T;T	0.74002	-0.8;-0.76	3.45	-6.89	0.01660	.	.	.	.	.	T	0.46776	0.1410	N	0.19112	0.55	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.0	T	0.19386	-1.0307	9	0.11182	T	0.66	.	2.0654	0.03601	0.386:0.1564:0.3335:0.1241	.	62;137	Q96MN2-3;Q96MN2	.;NALP4_HUMAN	H	137	ENSP00000301295:R137H;ENSP00000344787:R137H	ENSP00000301295:R137H	R	+	2	0	NLRP4	61060981	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.415000	0.02469	-4.127000	0.00071	-2.636000	0.00152	CGC		0.463	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
NLRP8	126205	broad.mit.edu	37	19	56466143	56466143	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:56466143C>T	ENST00000291971.3	+	3	790	c.719C>T	c.(718-720)gCt>gTt	p.A240V	NLRP8_ENST00000590542.1_Missense_Mutation_p.A240V	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	240	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.A240V(2)		breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CGCTGGTGTGCTTTCTACTTC	0.522																																					p.A240V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C719T	19						.						121.0	109.0	113.0					19																	56466143		2203	4300	6503	61157955	SO:0001583	missense	126205	exon3			AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.719C>T	19.37:g.56466143C>T	ENSP00000291971:p.Ala240Val	Somatic		Capture	Illumina HiSeq	Phase_I	61157955	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.647128	0.00792	.	.	ENSG00000179709	ENST00000291971	T	0.74106	-0.81	2.04	-1.48	0.08745	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.49966	0.1588	N	0.12443	0.215	0.09310	N	1	B;B	0.23591	0.088;0.065	B;B	0.34180	0.058;0.177	T	0.45056	-0.9287	9	0.02654	T	1	.	5.0601	0.14553	0.0:0.4861:0.0:0.5139	.	240;240	Q86W28-2;Q86W28	.;NALP8_HUMAN	V	240	ENSP00000291971:A240V	ENSP00000291971:A240V	A	+	2	0	NLRP8	61157955	0.003000	0.15002	0.000000	0.03702	0.012000	0.07955	1.082000	0.30803	-0.286000	0.09076	-0.351000	0.07748	GCT		0.522	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
ZNF543	125919	broad.mit.edu	37	19	57840246	57840246	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:57840246C>T	ENST00000321545.4	+	4	1761	c.1416C>T	c.(1414-1416)atC>atT	p.I472I		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	472					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.I472I(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)		ACTTCAGCATCCACACTGGAG	0.493																																					p.I472I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1416T	19						.						84.0	82.0	83.0					19																	57840246		2203	4300	6503	62532058	SO:0001819	synonymous_variant	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.1416C>T	19.37:g.57840246C>T		Somatic		Capture	Illumina HiSeq	Phase_I	62532058	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Silent	SNP	ENST00000321545.4	37	CCDS33130.1																																																																																				0.493	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
ZNF530	348327	broad.mit.edu	37	19	58115745	58115745	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:58115745T>C	ENST00000332854.6	+	2	351	c.131T>C	c.(130-132)cTg>cCg	p.L44P	ZNF530_ENST00000597864.1_Missense_Mutation_p.L11P	NM_020880.3	NP_065931.3	Q6P9A1	ZN530_HUMAN	zinc finger protein 530	44	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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.L44P(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(6)|skin(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0443)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		GATGTGATGCTGGAGAACTTT	0.532																																					p.L44P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T131C	19						.						277.0	245.0	256.0					19																	58115745		2203	4300	6503	62807557	SO:0001583	missense	348327	exon2			AK096831	CCDS12955.1	19q13.43	2013-01-08				ENSG00000183647		"""Zinc fingers, C2H2-type"", ""-"""	29297	protein-coding gene	gene with protein product						10819331	Standard	NM_020880		Approved	KIAA1508	uc002qpk.2	Q6P9A1		ENST00000332854.6:c.131T>C	19.37:g.58115745T>C	ENSP00000332861:p.Leu44Pro	Somatic		Capture	Illumina HiSeq	Phase_I	62807557	NM_020880	O43340|Q9P220	Missense_Mutation	SNP	ENST00000332854.6	37	CCDS12955.1	.	.	.	.	.	.	.	.	.	.	T	13.07	2.126541	0.37533	.	.	ENSG00000183647	ENST00000332854	T	0.03242	4.0	2.03	0.941	0.19519	Krueppel-associated box (4);	.	.	.	.	T	0.21103	0.0508	H	0.95437	3.67	0.45342	D	0.998336	D	0.89917	1.0	D	0.97110	1.0	T	0.00636	-1.1633	9	0.87932	D	0	.	5.5154	0.16904	0.2471:0.0:0.0:0.7529	.	44	Q6P9A1	ZN530_HUMAN	P	44	ENSP00000332861:L44P	ENSP00000332861:L44P	L	+	2	0	ZNF530	62807557	1.000000	0.71417	0.910000	0.35882	0.083000	0.17756	0.702000	0.25631	0.215000	0.20761	-0.654000	0.03906	CTG		0.532	ZNF530-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466797.1	NM_020880	
ZNF587	84914	broad.mit.edu	37	19	58371174	58371174	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:58371174C>T	ENST00000339656.5	+	3	1576	c.1394C>T	c.(1393-1395)gCg>gTg	p.A465V	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597652.1_5'Flank|ZNF814_ENST00000597342.1_Intron|ZNF587_ENST00000423137.1_Missense_Mutation_p.A464V|ZNF587_ENST00000419854.1_Missense_Mutation_p.A422V|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	465					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.A465V(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		AGGCCATATGCGTGTGAGGTA	0.433																																					p.A465V	Pancreas(59;641 1233 1885 20055 50741)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1394T	19						.						139.0	151.0	147.0					19																	58371174		2203	4300	6503	63062986	SO:0001583	missense	84914	exon3			AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.1394C>T	19.37:g.58371174C>T	ENSP00000345479:p.Ala465Val	Somatic		Capture	Illumina HiSeq	Phase_I	63062986	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Missense_Mutation	SNP	ENST00000339656.5	37	CCDS12964.1	.	.	.	.	.	.	.	.	.	.	.	8.648	0.897460	0.17686	.	.	ENSG00000198466	ENST00000376209;ENST00000423137;ENST00000339656;ENST00000540851;ENST00000419854	T;T;T	0.07688	3.17;3.17;3.17	1.91	-1.05	0.10036	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02533	0.0077	N	0.04275	-0.24	0.21416	N	0.999692	P;B	0.36683	0.565;0.005	B;B	0.20767	0.031;0.001	T	0.40289	-0.9571	8	0.49607	T	0.09	.	4.0262	0.09688	0.4411:0.3743:0.0:0.1845	.	464;465	G3V0H5;Q96SQ5	.;ZN587_HUMAN	V	422;464;465;465;422	ENSP00000393865:A464V;ENSP00000345479:A465V;ENSP00000406999:A422V	ENSP00000345479:A465V	A	+	2	0	ZNF587	63062986	0.000000	0.05858	0.002000	0.10522	0.134000	0.20937	-0.975000	0.03790	0.004000	0.14682	-1.450000	0.01041	GCG		0.433	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
ZNF329	79673	broad.mit.edu	37	19	58640192	58640192	+	Missense_Mutation	SNP	C	C	T	rs539267795		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:58640192C>T	ENST00000598312.1	-	4	912	c.679G>A	c.(679-681)Gga>Aga	p.G227R	ZNF329_ENST00000358067.4_Missense_Mutation_p.G227R	NM_024620.3	NP_078896.3	Q86UD4	ZN329_HUMAN	zinc finger protein 329	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.G227R(1)		NS(1)|large_intestine(10)|lung(5)|skin(3)|urinary_tract(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.029)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)|Lung(386;0.216)		GGCTTCTCTCCGGTGTGAGTT	0.433													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20241	0.0		0.0	False		,,,				2504	0.0				p.G227R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G679A	19						.						142.0	135.0	138.0					19																	58640192		2203	4300	6503	63332004	SO:0001583	missense	79673	exon4			AK022648	CCDS12972.1	19q13.43	2013-01-08				ENSG00000181894		"""Zinc fingers, C2H2-type"""	14209	protein-coding gene	gene with protein product							Standard	XM_006723381		Approved	FLJ12586	uc002qrn.3	Q86UD4		ENST00000598312.1:c.679G>A	19.37:g.58640192C>T	ENSP00000470008:p.Gly227Arg	Somatic		Capture	Illumina HiSeq	Phase_I	63332004	NM_024620	B3KR32|Q9H9R7	Missense_Mutation	SNP	ENST00000598312.1	37	CCDS12972.1	.	.	.	.	.	.	.	.	.	.	C	18.83	3.707335	0.68615	.	.	ENSG00000181894	ENST00000358067;ENST00000500161	T;T	0.26223	1.75;1.75	4.46	4.46	0.54185	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45361	D	0.000372	T	0.48003	0.1476	M	0.62154	1.92	0.47308	D	0.999384	D	0.89917	1.0	D	0.87578	0.998	T	0.45687	-0.9244	10	0.72032	D	0.01	-19.669	15.0647	0.71983	0.0:1.0:0.0:0.0	.	227	Q86UD4	ZN329_HUMAN	R	227	ENSP00000350773:G227R;ENSP00000439527:G227R	ENSP00000350773:G227R	G	-	1	0	ZNF329	63332004	0.020000	0.18652	1.000000	0.80357	0.983000	0.72400	2.329000	0.43876	2.767000	0.95098	0.655000	0.94253	GGA		0.433	ZNF329-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466724.1	NM_024620	
PALM	5064	broad.mit.edu	37	19	740362	740362	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:740362G>A	ENST00000338448.5	+	8	559	c.513G>A	c.(511-513)tcG>tcA	p.S171S	PALM_ENST00000264560.7_Intron|PALM_ENST00000593172.1_3'UTR	NM_002579.2	NP_002570.2	O75781	PALM_HUMAN	paralemmin	171					cellular component movement (GO:0006928)|cellular response to electrical stimulus (GO:0071257)|cytoskeleton organization (GO:0007010)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of dopamine receptor signaling pathway (GO:0060160)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of filopodium assembly (GO:0051491)|protein targeting to plasma membrane (GO:0072661)|regulation of cell shape (GO:0008360)|synapse maturation (GO:0060074)	apicolateral plasma membrane (GO:0016327)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cytoplasmic membrane-bounded vesicle (GO:0016023)|dendrite membrane (GO:0032590)|dendritic spine membrane (GO:0032591)|filopodium membrane (GO:0031527)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S171S(1)		endometrium(2)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_epithelial(18;2.19e-21)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)|Lung(535;0.201)		CCATGTACTCGGTTGAGATCA	0.687																																					p.S171S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G513A	19						.						53.0	32.0	39.0					19																	740362		2181	4276	6457	691362	SO:0001819	synonymous_variant	5064	exon8			Y16270	CCDS32857.1, CCDS32858.1	19p13.3	2008-07-17				ENSG00000099864			8594	protein-coding gene	gene with protein product		608134				9615234, 9813098	Standard	XM_005259565		Approved	KIAA0270	uc002lpm.1	O75781		ENST00000338448.5:c.513G>A	19.37:g.740362G>A		Somatic		Capture	Illumina HiSeq	Phase_I	691362	NM_002579	O43359|O95673|Q92559|Q9UPJ4|Q9UQS2|Q9UQS3	Silent	SNP	ENST00000338448.5	37	CCDS32857.1																																																																																				0.687	PALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457592.1	NM_002579	
ARID3A	1820	broad.mit.edu	37	19	971970	971970	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:971970G>A	ENST00000263620.3	+	9	2014	c.1687G>A	c.(1687-1689)Ggc>Agc	p.G563S		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	563	Gly-rich.					cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|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 positive regulation of transcription (GO:0001228)	p.G563S(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		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)		cAACGCAGGCGGCCGGGGAGG	0.667																																					p.G563S	Pancreas(29;54 1022 32760 50921)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1687A	19						.						25.0	29.0	27.0					19																	971970		2198	4287	6485	922970	SO:0001583	missense	1820	exon9			U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"""-"""	3031	protein-coding gene	gene with protein product		603265	"""dead ringer-like 1 (Drosophila)"", ""AT rich interactive domain 3A (BRIGHT- like)"""	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.1687G>A	19.37:g.971970G>A	ENSP00000263620:p.Gly563Ser	Somatic		Capture	Illumina HiSeq	Phase_I	922970	NM_005224	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Missense_Mutation	SNP	ENST00000263620.3	37	CCDS12050.1	.	.	.	.	.	.	.	.	.	.	G	1.822	-0.471969	0.04445	.	.	ENSG00000116017	ENST00000263620	T	0.35421	1.31	3.56	-5.64	0.02466	.	2.174400	0.02424	N	0.082834	T	0.16938	0.0407	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27400	-1.0075	10	0.09338	T	0.73	.	9.8311	0.40941	0.4597:0.0:0.5403:0.0	.	563	Q99856	ARI3A_HUMAN	S	563	ENSP00000263620:G563S	ENSP00000263620:G563S	G	+	1	0	ARID3A	922970	0.001000	0.12720	0.001000	0.08648	0.428000	0.31595	-1.593000	0.02096	-1.260000	0.02465	-1.191000	0.01696	GGC		0.667	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224	
CSNK1G2	1455	broad.mit.edu	37	19	1953991	1953991	+	Intron	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:1953991C>A	ENST00000255641.8	+	1	230				CSNK1G2-AS1_ENST00000586395.1_RNA|CSNK1G2-AS1_ENST00000314315.3_RNA	NM_001319.6	NP_001310.3	P78368	KC1G2_HUMAN	casein kinase 1, gamma 2						protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|peptide binding (GO:0042277)|protein serine/threonine kinase activity (GO:0004674)	p.R15M(1)		endometrium(1)|kidney(1)|lung(3)|prostate(1)|skin(1)|stomach(1)	8		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)		GACAGTCGCCCTTGGTCTGGT	0.677																																					.	Ovarian(91;880 1392 21236 36928 37598)											.	.	1	Substitution - Missense(1)	large_intestine(1)	.	19						.						118.0	135.0	129.0					19																	1953991		2172	4259	6431	1904991	SO:0001627	intron_variant	255193	.			AF001177	CCDS12077.1	19p13.3	2013-01-17			ENSG00000133275	ENSG00000133275			2455	protein-coding gene	gene with protein product		602214				9403068	Standard	NM_001319		Approved	CK1g2	uc002lul.4	P78368		ENST00000255641.8:c.-266+12574C>A	19.37:g.1953991C>A		Somatic		Capture	Illumina HiSeq	Phase_I	1904991	.	B5BU42|O00704|Q8WUB1	Missense_Mutation	SNP	ENST00000255641.8	37	CCDS12077.1	.	.	.	.	.	.	.	.	.	.	c	5.852	0.341321	0.11069	.	.	ENSG00000180846	ENST00000314315	.	.	.	0.493	-0.985	0.10256	.	.	.	.	.	T	0.21718	0.0523	.	.	.	0.09310	N	1	D	0.53462	0.96	B	0.41202	0.35	T	0.13845	-1.0494	6	0.87932	D	0	.	.	.	.	.	15	Q8NCQ2	CS034_HUMAN	M	15	.	ENSP00000315669:R15M	R	-	2	0	C19orf34	1904991	0.001000	0.12720	0.010000	0.14722	0.010000	0.07245	-0.035000	0.12205	-0.511000	0.06514	-0.535000	0.04281	AGG		0.677	CSNK1G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449287.1	NM_001319	
TUBB4A	10382	broad.mit.edu	37	19	6495341	6495341	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:6495341C>T	ENST00000264071.2	-	4	1540	c.1169G>A	c.(1168-1170)cGg>cAg	p.R390Q	TUBB4A_ENST00000540257.1_Missense_Mutation_p.R390Q|CTD-2396E7.9_ENST00000599292.1_RNA|CTD-2396E7.10_ENST00000596027.1_RNA			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	390					'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.R390Q(1)									GGCCTTGCGCCGGAACATGGC	0.617																																					p.R390Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1169A	19						.						153.0	139.0	144.0					19																	6495341		2203	4287	6490	6446341	SO:0001583	missense	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.1169G>A	19.37:g.6495341C>T	ENSP00000264071:p.Arg390Gln	Somatic		Capture	Illumina HiSeq	Phase_I	6446341	NM_006087	B3KQP4|Q969E5	Missense_Mutation	SNP	ENST00000264071.2	37	CCDS12168.1	.	.	.	.	.	.	.	.	.	.	C	14.56	2.570957	0.45798	.	.	ENSG00000104833	ENST00000264071;ENST00000540257;ENST00000412858	D;D	0.84442	-1.85;-1.85	3.43	3.43	0.39272	.	0.000000	0.64402	U	0.000011	D	0.85775	0.5775	M	0.91872	3.25	0.50467	D	0.999872	P	0.43909	0.821	B	0.33196	0.159	D	0.89042	0.3449	10	0.87932	D	0	.	13.6752	0.62449	0.0:1.0:0.0:0.0	.	390	P04350	TBB4A_HUMAN	Q	390;390;308	ENSP00000264071:R390Q;ENSP00000443590:R390Q	ENSP00000264071:R390Q	R	-	2	0	TUBB4	6446341	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.681000	0.84073	1.473000	0.48159	0.306000	0.20318	CGG		0.617	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087	
CD70	970	broad.mit.edu	37	19	6586039	6586039	+	Missense_Mutation	SNP	G	G	A	rs182050995		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:6586039G>A	ENST00000245903.3	-	3	723	c.574C>T	c.(574-576)Cgc>Tgc	p.R192C	CD70_ENST00000423145.3_Intron	NM_001252.3	NP_001243.1	P32970	CD70_HUMAN	CD70 molecule	192					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protease binding (GO:0002020)|receptor binding (GO:0005102)	p.R192C(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|skin(1)	11						GGTCAGGGGCGCACCCACTGC	0.507													g|||	1	0.000199681	0.0	0.0014	5008	,	,		16553	0.0		0.0	False		,,,				2504	0.0				p.R192C	Pancreas(183;2617 2876 10173 34193)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C574T	19						.						42.0	36.0	38.0					19																	6586039		2203	4300	6503	6537039	SO:0001583	missense	970	exon3			L08096	CCDS12170.1	19p13	2013-05-22	2006-10-27	2006-10-27		ENSG00000125726		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11937	protein-coding gene	gene with protein product		602840	"""tumor necrosis factor (ligand) superfamily, member 7"""	CD27LG, TNFSF7		8387892, 8120384	Standard	NM_001252		Approved	CD27L	uc002mfi.3	P32970		ENST00000245903.3:c.574C>T	19.37:g.6586039G>A	ENSP00000245903:p.Arg192Cys	Somatic		Capture	Illumina HiSeq	Phase_I	6537039	NM_001252	B4DPR8|Q53XX4|Q96J57	Missense_Mutation	SNP	ENST00000245903.3	37	CCDS12170.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	8.615	0.889979	0.17540	.	.	ENSG00000125726	ENST00000245903	.	.	.	4.32	0.578	0.17391	.	0.530353	0.17338	N	0.177829	T	0.16128	0.0388	N	0.12182	0.205	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.13229	-1.0517	9	0.33141	T	0.24	.	4.1432	0.10203	0.2241:0.1934:0.5826:0.0	.	192	P32970	CD70_HUMAN	C	192	.	ENSP00000245903:R192C	R	-	1	0	CD70	6537039	0.001000	0.12720	0.252000	0.24328	0.048000	0.14542	0.655000	0.24933	0.384000	0.24942	0.556000	0.70494	CGC		0.507	CD70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457860.1		
EMR1	2015	broad.mit.edu	37	19	6901986	6901986	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:6901986C>T	ENST00000312053.4	+	6	652	c.615C>T	c.(613-615)tcC>tcT	p.S205S	EMR1_ENST00000381404.4_Silent_p.S153S|EMR1_ENST00000450315.3_Intron|EMR1_ENST00000381407.5_Intron|EMR1_ENST00000250572.8_Silent_p.S205S	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	205	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.S205S(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					GATTTGAATCCAGCAGTGGCC	0.478																																					p.S205S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C615T	19						.						194.0	197.0	196.0					19																	6901986		2203	4300	6503	6852986	SO:0001819	synonymous_variant	2015	exon6			X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"""-"", ""GPCR / Class B : Orphans"""	3336	protein-coding gene	gene with protein product		600493	"""egf-like module containing, mucin-like, hormone receptor-like sequence 1"""	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.615C>T	19.37:g.6901986C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6852986	NM_001974	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Silent	SNP	ENST00000312053.4	37	CCDS12175.1																																																																																				0.478	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
MCOLN1	57192	broad.mit.edu	37	19	7593735	7593735	+	Missense_Mutation	SNP	G	G	A	rs368837514		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:7593735G>A	ENST00000264079.6	+	9	1138	c.1013G>A	c.(1012-1014)cGg>cAg	p.R338Q		NM_020533.2	NP_065394.1	Q9GZU1	MCLN1_HUMAN	mucolipin 1	338					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular iron ion homeostasis (GO:0006879)|ion transmembrane transport (GO:0034220)|release of sequestered calcium ion into cytosol (GO:0051209)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cation channel activity (GO:0005261)|NAADP-sensitive calcium-release channel activity (GO:0072345)	p.R338Q(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TGGCGGCAGCGGGGACGGGTC	0.617																																					p.R338Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1013A	19						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	54.0	50.0	51.0		1013	4.5	0.9	19		51	0,8600		0,0,4300	no	missense	MCOLN1	NM_020533.2	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	338/581	7593735	1,13005	2203	4300	6503	7499735	SO:0001583	missense	57192	exon9			AF249319	CCDS12180.1	19p13.2	2011-12-16				ENSG00000090674		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	13356	protein-coding gene	gene with protein product		605248				16382100	Standard	NM_020533		Approved	TRPML1, ML4, MLIV, MST080, MSTP080, TRPM-L1	uc002mgo.3	Q9GZU1		ENST00000264079.6:c.1013G>A	19.37:g.7593735G>A	ENSP00000264079:p.Arg338Gln	Somatic		Capture	Illumina HiSeq	Phase_I	7499735	NM_020533	D6W647|Q7Z4F7|Q9H292|Q9H4B3|Q9H4B5	Missense_Mutation	SNP	ENST00000264079.6	37	CCDS12180.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.970646	0.34754	2.27E-4	0.0	ENSG00000090674	ENST00000264079;ENST00000394321	T	0.76186	-1.0	5.7	4.47	0.54385	.	0.318910	0.33217	N	0.005157	T	0.49949	0.1587	N	0.08118	0	0.30835	N	0.736326	B;B	0.25955	0.138;0.011	B;B	0.15484	0.013;0.001	T	0.49986	-0.8880	10	0.31617	T	0.26	.	8.6984	0.34310	0.1752:0.0:0.8248:0.0	.	303;338	Q9GZU1-2;Q9GZU1	.;MCLN1_HUMAN	Q	338;303	ENSP00000264079:R338Q	ENSP00000264079:R338Q	R	+	2	0	MCOLN1	7499735	0.987000	0.35691	0.945000	0.38365	0.116000	0.19942	2.748000	0.47483	2.700000	0.92200	0.563000	0.77884	CGG		0.617	MCOLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458974.2	NM_020533	
XAB2	56949	broad.mit.edu	37	19	7692707	7692707	+	Silent	SNP	C	C	T	rs200672913		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:7692707C>T	ENST00000358368.4	-	3	268	c.231G>A	c.(229-231)gcG>gcA	p.A77A	XAB2_ENST00000534844.1_Silent_p.A74A|PET100_ENST00000601406.1_5'Flank|CTD-3214H19.4_ENST00000595866.1_5'Flank|PET100_ENST00000456958.3_5'Flank|PET100_ENST00000594797.1_5'Flank	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	77					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.A74A(1)		breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						GTGCCCGACGCGCCTTCAGGT	0.547								Direct reversal of damage;Nucleotide excision repair (NER)					C|||	1	0.000199681	0.0008	0.0	5008	,	,		13766	0.0		0.0	False		,,,				2504	0.0				p.A77A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G231A	19						.						117.0	101.0	106.0					19																	7692707		2203	4300	6503	7598707	SO:0001819	synonymous_variant	56949	exon3			AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"""SYF1 homolog, RNA splicing factor (S. cerevisiae)"", ""SYF1 pre-mRNA-splicing factor"""	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.231G>A	19.37:g.7692707C>T		Somatic		Capture	Illumina HiSeq	Phase_I	7598707	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Silent	SNP	ENST00000358368.4	37	CCDS32892.1																																																																																				0.547	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196	
PCP2	126006	broad.mit.edu	37	19	7698422	7698422	+	De_novo_Start_OutOfFrame	SNP	G	G	A	rs558700311		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:7698422G>A	ENST00000311069.5	-	0	212				CTD-3214H19.4_ENST00000595866.1_Intron|CTD-3214H19.6_ENST00000601797.1_RNA|PCP2_ENST00000598935.1_5'Flank	NM_174895.1	NP_777555.1	Q8IVA1	PCP2_HUMAN	Purkinje cell protein 2						rhodopsin mediated signaling pathway (GO:0016056)	neuronal cell body (GO:0043025)	GTPase regulator activity (GO:0030695)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|urinary_tract(1)	2						CGTCCAGGACGTGGGGGTGTG	0.562													G|||	1	0.000199681	0.0	0.0	5008	,	,		15031	0.001		0.0	False		,,,				2504	0.0				.												.	.	0			.	19						.																																			7604422			126006	.			BC025387	CCDS32893.1, CCDS62521.1	19p13.3	2008-02-05				ENSG00000174788			30209	protein-coding gene	gene with protein product						12477932	Standard	NM_174895		Approved	MGC41903, GPSM4	uc031rjd.1	Q8IVA1		ENST00000311069.5:c.-79C>T	19.37:g.7698422G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7604422	.	M0R2R7|Q3KRG7	De_novo_Start_OutOfFrame	SNP	ENST00000311069.5	37	CCDS32893.1																																																																																				0.562	PCP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461026.2	XM_058956	
KANK3	256949	broad.mit.edu	37	19	8398950	8398961	+	In_Frame_Del	DEL	TCGCTGTCGCCA	TCGCTGTCGCCA	-	rs111751275|rs199822445|rs201862465|rs6146458|rs200669927	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	TCGCTGTCGCCA	TCGCTGTCGCCA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:8398950_8398961delTCGCTGTCGCCA	ENST00000593649.1	-	5	1532_1543	c.1467_1478delTGGCGACAGCGA	c.(1465-1479)gatggcgacagcgag>gag	p.DGDS489del	KANK3_ENST00000330915.3_In_Frame_Del_p.DGDS489del			Q6NY19	KANK3_HUMAN	KN motif and ankyrin repeat domains 3	489								p.D489_S492delDGDS(2)		breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						GCCACCGTTCTCGCTGTCGCCATCGCTGTCGC	0.717														1760	0.351438	0.4085	0.428	5008	,	,		15278	0.2927		0.2962	False		,,,				2504	0.3374				p.489_493del												.	.	2	Deletion - In frame(2)	large_intestine(1)|breast(1)	c.1467_1478del	19						.			958,2544		287,384,1080						-7.5	0.0		dbSNP_114	6	1402,5766		338,726,2520	no	coding	KANK3	NM_198471.2		625,1110,3600	A1A1,A1R,RR		19.5592,27.3558,22.1181				2360,8310				8304961	SO:0001651	inframe_deletion	256949	exon5			AK128815	CCDS12199.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000186994		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	24796	protein-coding gene	gene with protein product		614611	"""ankyrin repeat domain 47"""	ANKRD47		17996375, 19554261	Standard	NM_198471		Approved	FLJ46061	uc010dwa.3	Q6NY19		ENST00000593649.1:c.1467_1478delTGGCGACAGCGA	19.37:g.8398950_8398961delTCGCTGTCGCCA	ENSP00000470728:p.Asp489_Ser492del	Somatic		Capture	Illumina HiSeq	Phase_I	8304950	NM_198471	Q6NZI1|Q6ZQR3|Q8IUV2	In_Frame_Del	DEL	ENST00000593649.1	37																																																																																					0.717	KANK3-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000461379.1	NM_198471	
HNRNPM	4670	broad.mit.edu	37	19	8551151	8551151	+	Silent	SNP	C	C	T	rs369110925		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:8551151C>T	ENST00000325495.4	+	14	1880	c.1839C>T	c.(1837-1839)ggC>ggT	p.G613G	HNRNPM_ENST00000348943.3_Silent_p.G574G	NM_005968.4	NP_005959.2	P52272	HNRPM_HUMAN	heterogeneous nuclear ribonucleoprotein M	613	Poly-Gly.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|RNA binding (GO:0003723)	p.G613G(1)		endometrium(5)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)	25						CCATGGGTGGCGGTGGCGGTG	0.677																																					p.G613G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1839T	19						.	C	,	0,4406		0,0,2203	31.0	35.0	34.0		1839,1722	-4.7	0.9	19		34	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous,coding-synonymous	HNRNPM	NM_005968.4,NM_031203.3	,	0,2,6500	TT,TC,CC		0.0233,0.0,0.0154	,	613/731,574/692	8551151	2,13002	2203	4299	6502	8457151	SO:0001819	synonymous_variant	4670	exon14			L03532	CCDS12203.1, CCDS12204.1	19p13.2	2013-06-12		2008-04-18	ENSG00000099783	ENSG00000099783		"""RNA binding motif (RRM) containing"""	5046	protein-coding gene	gene with protein product	"""CEA receptor"""	160994		NAGR1, HNRPM		8441656, 7558047	Standard	NM_005968		Approved	HTGR1, HNRNPM4, HNRPM4, CEAR	uc010dwe.3	P52272	OTTHUMG00000182383	ENST00000325495.4:c.1839C>T	19.37:g.8551151C>T		Somatic		Capture	Illumina HiSeq	Phase_I	8457151	NM_005968	Q15584|Q8WZ44|Q96H56|Q9BWL9|Q9Y492	Silent	SNP	ENST00000325495.4	37	CCDS12203.1																																																																																				0.677	HNRNPM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460894.1		
PRAM1	84106	broad.mit.edu	37	19	8563835	8563835	+	Missense_Mutation	SNP	G	G	A	rs533898136		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:8563835G>A	ENST00000423345.4	-	2	1377	c.857C>T	c.(856-858)cCg>cTg	p.P286L	PRAM1_ENST00000255612.3_Missense_Mutation_p.P286L			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	334	Pro-rich.				integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)	p.P286L(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						CTCAGGCTGCGGAGGCTTCTT	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		14772	0.0		0.001	False		,,,				2504	0.0				p.P286L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C857T	19						.						31.0	34.0	33.0					19																	8563835		2193	4296	6489	8469835	SO:0001583	missense	84106	exon2			BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.857C>T	19.37:g.8563835G>A	ENSP00000408342:p.Pro286Leu	Somatic		Capture	Illumina HiSeq	Phase_I	8469835	NM_032152	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	37	CCDS45954.2	.	.	.	.	.	.	.	.	.	.	G	7.721	0.697111	0.15106	.	.	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.11063	2.82;2.81	4.12	-6.52	0.01872	.	1.591210	0.04051	N	0.304714	T	0.05364	0.0142	N	0.16037	0.36	0.09310	N	1	B;B	0.18461	0.009;0.028	B;B	0.14578	0.003;0.011	T	0.45731	-0.9241	10	0.02654	T	1	.	12.0434	0.53466	0.5454:0.0:0.4546:0.0	.	286;334	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	L	286	ENSP00000255612:P286L;ENSP00000408342:P286L	ENSP00000255612:P286L	P	-	2	0	PRAM1	8469835	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.678000	0.05209	-1.184000	0.02720	-0.291000	0.09656	CCG		0.642	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152	
MYO1F	4542	broad.mit.edu	37	19	8609319	8609319	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:8609319G>A	ENST00000338257.8	-	14	1653	c.1386C>T	c.(1384-1386)gaC>gaT	p.D462D	AC092316.2_ENST00000581156.1_RNA	NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	462	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.D462D(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						CGCACACGTCGTCCAAGACGC	0.667																																					p.D462D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1386T	19						.						17.0	22.0	21.0					19																	8609319		2063	4207	6270	8515319	SO:0001819	synonymous_variant	4542	exon14			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.1386C>T	19.37:g.8609319G>A		Somatic		Capture	Illumina HiSeq	Phase_I	8515319	NM_012335	Q8WWN7	Silent	SNP	ENST00000338257.8	37	CCDS42494.1																																																																																				0.667	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2		
ACTL9	284382	broad.mit.edu	37	19	8808060	8808060	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:8808060C>T	ENST00000324436.3	-	1	1112	c.992G>A	c.(991-993)cGc>cAc	p.R331H		NM_178525.3	NP_848620.3	Q8TC94	ACTL9_HUMAN	actin-like 9	331						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R331H(2)		NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(15)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	36						CAAGTCCGCGCGCATCTCCAG	0.667																																					p.R331H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G992A	19						.						38.0	38.0	38.0					19																	8808060		2202	4297	6499	8669060	SO:0001583	missense	284382	exon1				CCDS12207.1	19p13.2	2014-08-08			ENSG00000181786	ENSG00000181786			28494	protein-coding gene	gene with protein product							Standard	NM_178525		Approved	MGC33407	uc002mkl.2	Q8TC94	OTTHUMG00000182194	ENST00000324436.3:c.992G>A	19.37:g.8808060C>T	ENSP00000316674:p.Arg331His	Somatic		Capture	Illumina HiSeq	Phase_I	8669060	NM_178525	A8K893|Q6X960	Missense_Mutation	SNP	ENST00000324436.3	37	CCDS12207.1	.	.	.	.	.	.	.	.	.	.	c	13.31	2.200241	0.38905	.	.	ENSG00000181786	ENST00000324436	D	0.95885	-3.84	4.45	1.16	0.20824	.	0.515035	0.14737	U	0.301383	D	0.93471	0.7917	M	0.78456	2.415	0.09310	N	0.999994	P	0.48911	0.917	B	0.40101	0.319	D	0.87077	0.2163	10	0.87932	D	0	.	8.0852	0.30769	0.0:0.65:0.0:0.35	.	331	Q8TC94	ACTL9_HUMAN	H	331	ENSP00000316674:R331H	ENSP00000316674:R331H	R	-	2	0	ACTL9	8669060	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	0.348000	0.20031	0.247000	0.21414	0.306000	0.20318	CGC		0.667	ACTL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459953.1	NM_178525	
MUC16	94025	broad.mit.edu	37	19	9028346	9028346	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:9028346C>T	ENST00000397910.4	-	11	36649	c.36446G>A	c.(36445-36447)cGc>cAc	p.R12149H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12151	SEA 1. {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.R12149H(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						AGGGTCAGGGCGATGTGTGCA	0.562																																					p.R12149H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G36446A	19						.						158.0	162.0	161.0					19																	9028346		2113	4229	6342	8889346	SO:0001583	missense	94025	exon11			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.36446G>A	19.37:g.9028346C>T	ENSP00000381008:p.Arg12149His	Somatic		Capture	Illumina HiSeq	Phase_I	8889346	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	C	5.937	0.356941	0.11239	.	.	ENSG00000181143	ENST00000397910	T	0.29397	1.57	2.63	-3.24	0.05094	.	.	.	.	.	T	0.14960	0.0361	L	0.34521	1.04	.	.	.	P	0.37997	0.614	B	0.26693	0.072	T	0.11446	-1.0587	8	0.87932	D	0	.	3.269	0.06875	0.2025:0.2571:0.0:0.5404	.	12149	B5ME49	.	H	12149	ENSP00000381008:R12149H	ENSP00000381008:R12149H	R	-	2	0	MUC16	8889346	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-2.439000	0.01016	-0.706000	0.05028	-0.282000	0.10007	CGC		0.562	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
OR1M1	125963	broad.mit.edu	37	19	9204355	9204355	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:9204355C>T	ENST00000429566.3	+	1	501	c.435C>T	c.(433-435)gtC>gtT	p.V145V		NM_001004456.1	NP_001004456.1	Q8NGA1	OR1M1_HUMAN	olfactory receptor, family 1, subfamily M, member 1	145						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V145V(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(17)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						GCCTGCTGGTCGGCGCCCTCT	0.577																																					p.V145V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C435T	19						.						112.0	91.0	98.0					19																	9204355		2203	4300	6503	9065355	SO:0001819	synonymous_variant	125963	exon1				CCDS32896.1	19p13.2	2013-09-20			ENSG00000170929	ENSG00000170929		"""GPCR / Class A : Olfactory receptors"""	8220	protein-coding gene	gene with protein product							Standard	NM_001004456		Approved	OR19-6	uc010xkj.2	Q8NGA1	OTTHUMG00000179930	ENST00000429566.3:c.435C>T	19.37:g.9204355C>T		Somatic		Capture	Illumina HiSeq	Phase_I	9065355	NM_001004456	B9EHA6|Q6IFJ3|Q96R91	Silent	SNP	ENST00000429566.3	37	CCDS32896.1																																																																																				0.577	OR1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448993.1		
ZNF266	10781	broad.mit.edu	37	19	9524083	9524083	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:9524083C>T	ENST00000592904.1	-	5	3594	c.1518G>A	c.(1516-1518)tcG>tcA	p.S506S	ZNF266_ENST00000590306.1_Silent_p.S506S|ZNF266_ENST00000588221.1_Silent_p.S506S|ZNF266_ENST00000588933.1_Silent_p.S506S|ZNF266_ENST00000592292.1_Silent_p.S506S|ZNF266_ENST00000361151.1_Silent_p.S506S|ZNF266_ENST00000361451.2_Silent_p.S506S			Q14584	ZN266_HUMAN	zinc finger protein 266	506					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.S506S(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						GTAACTGAAACGAATTGGAGT	0.423																																					p.S506S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1518A	19						.						103.0	76.0	85.0					19																	9524083		2203	4300	6503	9385083	SO:0001819	synonymous_variant	10781	exon11			X78924	CCDS12213.1	19p13.2	2013-01-08				ENSG00000174652		"""Zinc fingers, C2H2-type"""	13059	protein-coding gene	gene with protein product		604751				7865130	Standard	NM_006631		Approved	HZF1	uc002mlo.4	Q14584		ENST00000592904.1:c.1518G>A	19.37:g.9524083C>T		Somatic		Capture	Illumina HiSeq	Phase_I	9385083	NM_006631	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Silent	SNP	ENST00000592904.1	37	CCDS12213.1																																																																																				0.423	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1		
ZNF266	10781	broad.mit.edu	37	19	9524437	9524437	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:9524437G>T	ENST00000592904.1	-	5	3240	c.1164C>A	c.(1162-1164)gcC>gcA	p.A388A	ZNF266_ENST00000590306.1_Silent_p.A388A|ZNF266_ENST00000588221.1_Silent_p.A388A|ZNF266_ENST00000588933.1_Silent_p.A388A|ZNF266_ENST00000592292.1_Silent_p.A388A|ZNF266_ENST00000361151.1_Silent_p.A388A|ZNF266_ENST00000361451.2_Silent_p.A388A			Q14584	ZN266_HUMAN	zinc finger protein 266	388					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.A388A(1)		NS(1)|breast(2)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						ATCTGGCAAAGGCCTTTCCAC	0.453																																					p.A388A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1164A	19						.						75.0	77.0	76.0					19																	9524437		2203	4300	6503	9385437	SO:0001819	synonymous_variant	10781	exon11			X78924	CCDS12213.1	19p13.2	2013-01-08				ENSG00000174652		"""Zinc fingers, C2H2-type"""	13059	protein-coding gene	gene with protein product		604751				7865130	Standard	NM_006631		Approved	HZF1	uc002mlo.4	Q14584		ENST00000592904.1:c.1164C>A	19.37:g.9524437G>T		Somatic		Capture	Illumina HiSeq	Phase_I	9385437	NM_006631	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Silent	SNP	ENST00000592904.1	37	CCDS12213.1																																																																																				0.453	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1		
OLFM2	93145	broad.mit.edu	37	19	9965027	9965027	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:9965027C>T	ENST00000264833.4	-	6	1385	c.1200G>A	c.(1198-1200)acG>acA	p.T400T	AC008752.3_ENST00000582439.1_RNA|OLFM2_ENST00000590841.1_Silent_p.T322T	NM_058164.2	NP_477512.1	O95897	NOE2_HUMAN	olfactomedin 2	400	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				protein secretion (GO:0009306)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular region (GO:0005576)|synapse (GO:0045202)		p.T400T(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	31						CGTAACTGGACGTGTTGGTAA	0.577																																					p.T400T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1200A	19						.						136.0	119.0	125.0					19																	9965027		2203	4300	6503	9826027	SO:0001819	synonymous_variant	93145	exon6			AF131839	CCDS12221.1	19p13.2	2008-07-03				ENSG00000105088			17189	protein-coding gene	gene with protein product	"""noelin 2"""						Standard	NM_058164		Approved	OlfC, NOE2	uc002mmp.3	O95897		ENST00000264833.4:c.1200G>A	19.37:g.9965027C>T		Somatic		Capture	Illumina HiSeq	Phase_I	9826027	NM_058164	Q6IMJ3|Q96FC2	Silent	SNP	ENST00000264833.4	37	CCDS12221.1																																																																																				0.577	OLFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451119.1		
ZNF486	90649	broad.mit.edu	37	19	20308120	20308120	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:20308120delA	ENST00000335117.8	+	4	658	c.601delA	c.(601-603)aaafs	p.K202fs	CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	202					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I203fs*28(1)|p.I194fs*>22(1)		endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						TACTACACATAAAAAAATTGA	0.343																																					p.K201fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.601delA	19						.						34.0	38.0	37.0					19																	20308120		2108	4250	6358	20169120	SO:0001589	frameshift_variant	90649	exon4			BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"""Zinc fingers, C2H2-type"", ""-"""	20807	protein-coding gene	gene with protein product			"""KRAB domain only 2"""	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.601delA	19.37:g.20308120delA	ENSP00000335042:p.Lys202fs	Somatic		Capture	Illumina HiSeq	Phase_I	20169120	NM_052852	Q0VG00	Frame_Shift_Del	DEL	ENST00000335117.8	37	CCDS46029.1																																																																																				0.343	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852	
ZNF536	9745	broad.mit.edu	37	19	30934647	30934647	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:30934647delC	ENST00000355537.3	+	2	325	c.178delC	c.(178-180)cccfs	p.P61fs		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	61					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)	p.A62fs*11(1)		NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CGAGGAGAAGCCCCCCGCATC	0.672																																					p.P60fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.178delC	19						.						43.0	47.0	45.0					19																	30934647		2203	4300	6503	35626487	SO:0001589	frameshift_variant	9745	exon2				CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.178delC	19.37:g.30934647delC	ENSP00000347730:p.Pro61fs	Somatic		Capture	Illumina HiSeq	Phase_I	35626487	NM_014717	A2RU18	Frame_Shift_Del	DEL	ENST00000355537.3	37	CCDS32984.1																																																																																				0.672	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
BRSK1	84446	broad.mit.edu	37	19	55815036	55815036	+	Splice_Site	DEL	C	C	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:55815036delC	ENST00000309383.1	+	12	1405	c.1128delC	c.(1126-1128)gac>ga	p.D376fs	BRSK1_ENST00000590333.1_Splice_Site_p.D392fs|BRSK1_ENST00000326848.7_Splice_Site_p.D71fs	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	376					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)	p.R379fs*9(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		GTCCCTCAGACCCCCCCCGGA	0.582																																					p.D376fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1128delC	19						.						54.0	63.0	60.0					19																	55815036		2203	4300	6503	60506848	SO:0001630	splice_region_variant	84446	exon12			AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1127-1C>-	19.37:g.55815036delC		Somatic		Capture	Illumina HiSeq	Phase_I	60506848	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Frame_Shift_Del	DEL	ENST00000309383.1	37	CCDS12921.1																																																																																				0.582	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	Frame_Shift_Del
ZNF132	7691	broad.mit.edu	37	19	58945630	58945630	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr19:58945630T>C	ENST00000254166.3	-	3	1581	c.1181A>G	c.(1180-1182)cAg>cGg	p.Q394R		NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	394					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.Q394R(1)		NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0171)|Lung(386;0.182)		GTGAACTTTCTGATGCCGAAG	0.478																																					p.Q394R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1181G	19						.						91.0	85.0	87.0					19																	58945630		2203	4300	6503	63637442	SO:0001583	missense	7691	exon3			U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849		"""Zinc fingers, C2H2-type"", ""-"""	12916	protein-coding gene	gene with protein product		604074	"""zinc finger protein 132 (clone pHZ-12)"""			7557990	Standard	NM_003433		Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.1181A>G	19.37:g.58945630T>C	ENSP00000254166:p.Gln394Arg	Somatic		Capture	Illumina HiSeq	Phase_I	63637442	NM_003433	Q32MI9	Missense_Mutation	SNP	ENST00000254166.3	37	CCDS12980.1	.	.	.	.	.	.	.	.	.	.	T	13.45	2.240413	0.39598	.	.	ENSG00000131849	ENST00000254166	T	0.17691	2.26	4.0	1.88	0.25563	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07548	0.0190	N	0.04148	-0.265	0.09310	N	1	B	0.26775	0.159	B	0.19946	0.027	T	0.33599	-0.9862	9	0.44086	T	0.13	.	7.8075	0.29211	0.0:0.1569:0.0:0.8431	.	394	P52740	ZN132_HUMAN	R	394	ENSP00000254166:Q394R	ENSP00000254166:Q394R	Q	-	2	0	ZNF132	63637442	0.065000	0.20965	0.030000	0.17652	0.973000	0.67179	0.170000	0.16663	0.114000	0.18032	0.533000	0.62120	CAG		0.478	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467035.1	NM_003433	
SPOCD1	90853	broad.mit.edu	37	1	32256584	32256585	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:32256584_32256585insG	ENST00000360482.2	-	16	3399_3400	c.3270_3271insC	c.(3268-3273)cccagafs	p.R1091fs	RP11-84A19.3_ENST00000527035.1_RNA|SPOCD1_ENST00000257100.3_Frame_Shift_Ins_p.R571fs|SPOCD1_ENST00000533231.1_Frame_Shift_Ins_p.R1078fs|SPOCD1_ENST00000373648.2_3'UTR	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	1091					negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)			p.R1091fs*11(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		CCCCTGCCTCTGGGGGGCCTCT	0.678																																					p.R1091fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.3271_3272insC	1						.																																			32029172	SO:0001589	frameshift_variant	90853	exon16			AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 146"""					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.3271dupC	1.37:g.32256590_32256590dupG	ENSP00000353670:p.Arg1091fs	Somatic		Capture	Illumina HiSeq	Phase_I	32029171	NM_144569	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Frame_Shift_Ins	INS	ENST00000360482.2	37	CCDS347.1																																																																																				0.678	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569	
CDC14A	8556	broad.mit.edu	37	1	100963746	100963746	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:100963746G>A	ENST00000336454.3	+	14	1759	c.1404G>A	c.(1402-1404)tcG>tcA	p.S468S	CDC14A_ENST00000361544.6_Silent_p.S468S|CDC14A_ENST00000370125.2_3'UTR|CDC14A_ENST00000542213.1_Silent_p.S410S|CDC14A_ENST00000544534.1_Silent_p.S468S	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	468					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.S468S(1)		breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		CTTTGTCTTCGGGTGCCACTG	0.463																																					p.S468S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1404A	1						.						152.0	141.0	144.0					1																	100963746		2203	4300	6503	100736334	SO:0001819	synonymous_variant	8556	exon14			AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	1718	protein-coding gene	gene with protein product		603504	"""CDC10 (cell division cycle 10, S. cerevisiae, homolog)"", ""CDC14 cell division cycle 14 homolog A (S. cerevisiae)"""			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.1404G>A	1.37:g.100963746G>A		Somatic		Capture	Illumina HiSeq	Phase_I	100736334	NM_033312	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Silent	SNP	ENST00000336454.3	37	CCDS769.1																																																																																				0.463	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312	
CASZ1	54897	broad.mit.edu	37	1	10720466	10720466	+	Silent	SNP	C	C	T	rs374277022		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:10720466C>T	ENST00000377022.3	-	6	950	c.633G>A	c.(631-633)gcG>gcA	p.A211A	CASZ1_ENST00000478728.2_5'Flank|CASZ1_ENST00000344008.5_Silent_p.A211A	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	211					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A211A(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		GGGTGGAGCCCGCGTGCAGCT	0.617																																					p.A211A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G633A	1						.	C	,	1,4405	2.1+/-5.4	0,1,2202	36.0	42.0	40.0		633,633	-8.0	0.2	1		40	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CASZ1	NM_001079843.1,NM_017766.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	211/1760,211/1167	10720466	1,13005	2203	4300	6503	10643053	SO:0001819	synonymous_variant	54897	exon6			AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.633G>A	1.37:g.10720466C>T		Somatic		Capture	Illumina HiSeq	Phase_I	10643053	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	CCDS41246.1																																																																																				0.617	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
GPR88	54112	broad.mit.edu	37	1	101004860	101004860	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:101004860G>A	ENST00000315033.4	+	2	777	c.338G>A	c.(337-339)cGc>cAc	p.R113H		NM_022049.2	NP_071332.2	Q9GZN0	GPR88_HUMAN	G protein-coupled receptor 88	113					G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuronal action potential (GO:0019228)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R113H(1)		large_intestine(2)|skin(1)	3		all_epithelial(167;1.19e-05)|all_lung(203;0.00159)|Lung NSC(277;0.00171)		Epithelial(280;0.0372)|all cancers(265;0.0558)|COAD - Colon adenocarcinoma(174;0.141)|Colorectal(144;0.156)|Lung(183;0.189)		GGCAGCTACCGCCTGCTACGG	0.736																																					p.R113H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G338A	1						.						11.0	14.0	13.0					1																	101004860		2086	4221	6307	100777448	SO:0001583	missense	54112	exon2			AB042411	CCDS772.1	1p21.3	2012-08-21	2006-02-15		ENSG00000181656	ENSG00000181656		"""GPCR / Class A : Orphans"""	4539	protein-coding gene	gene with protein product		607468	"""G-protein coupled receptor 88"", ""G protein coupled receptor 88"""				Standard	NM_022049		Approved		uc001dth.3	Q9GZN0	OTTHUMG00000010981	ENST00000315033.4:c.338G>A	1.37:g.101004860G>A	ENSP00000314223:p.Arg113His	Somatic		Capture	Illumina HiSeq	Phase_I	100777448	NM_022049	Q29S24|Q6VN48	Missense_Mutation	SNP	ENST00000315033.4	37	CCDS772.1	.	.	.	.	.	.	.	.	.	.	G	15.22	2.767962	0.49680	.	.	ENSG00000181656	ENST00000315033	T	0.37058	1.22	4.61	3.68	0.42216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40385	U	0.001117	T	0.33556	0.0867	L	0.34521	1.04	0.33694	D	0.613709	D	0.89917	1.0	D	0.75484	0.986	T	0.21211	-1.0252	10	0.42905	T	0.14	-9.9112	12.6523	0.56768	0.0:0.0:0.8353:0.1647	.	113	Q9GZN0	GPR88_HUMAN	H	113	ENSP00000314223:R113H	ENSP00000314223:R113H	R	+	2	0	GPR88	100777448	0.997000	0.39634	0.999000	0.59377	0.560000	0.35617	2.685000	0.46959	1.143000	0.42306	0.563000	0.77884	CGC		0.736	GPR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030212.1	NM_022049	
AMIGO1	57463	broad.mit.edu	37	1	110050220	110050220	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:110050220G>A	ENST00000369864.4	-	2	1664	c.1315C>T	c.(1315-1317)Cgg>Tgg	p.R439W	AMIGO1_ENST00000369862.1_Missense_Mutation_p.R439W					adhesion molecule with Ig-like domain 1									p.R439W(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)		GCCACCCGCCGGTCAAAACCA	0.587																																					p.R439W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1315T	1						.						62.0	59.0	60.0					1																	110050220		2203	4300	6503	109851743	SO:0001583	missense	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.1315C>T	1.37:g.110050220G>A	ENSP00000358880:p.Arg439Trp	Somatic		Capture	Illumina HiSeq	Phase_I	109851743	NM_020703		Missense_Mutation	SNP	ENST00000369864.4	37	CCDS30795.1	.	.	.	.	.	.	.	.	.	.	G	16.28	3.079819	0.55753	.	.	ENSG00000181754	ENST00000369864;ENST00000369862	T;T	0.54279	0.58;0.58	6.17	5.26	0.73747	.	0.000000	0.64402	D	0.000010	T	0.35008	0.0917	L	0.47716	1.5	0.58432	D	0.999998	B	0.23442	0.085	B	0.21546	0.035	T	0.37526	-0.9702	10	0.87932	D	0	-8.199	15.9033	0.79400	0.0:0.0:0.8634:0.1366	.	439	Q86WK6	AMGO1_HUMAN	W	439	ENSP00000358880:R439W;ENSP00000358878:R439W	ENSP00000358878:R439W	R	-	1	2	AMIGO1	109851743	0.778000	0.28640	1.000000	0.80357	0.997000	0.91878	1.628000	0.37060	1.611000	0.50210	0.655000	0.94253	CGG		0.587	AMIGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032247.1	NM_020703	
GSTM3	2947	broad.mit.edu	37	1	110279776	110279776	+	Missense_Mutation	SNP	C	C	T	rs199933862		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:110279776C>T	ENST00000540225.1	-	9	905	c.595G>A	c.(595-597)Gct>Act	p.A199T	GSTM3_ENST00000361066.2_Missense_Mutation_p.A199T|GSTM3_ENST00000488824.1_5'UTR|GSTM3_ENST00000256594.3_Missense_Mutation_p.A199T|RP4-735C1.4_ENST00000431955.1_RNA			P21266	GSTM3_HUMAN	glutathione S-transferase mu 3 (brain)	199	GST C-terminal.				cellular detoxification of nitrogen compound (GO:0070458)|establishment of blood-nerve barrier (GO:0008065)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|nitrobenzene metabolic process (GO:0018916)|response to estrogen (GO:0043627)|small molecule metabolic process (GO:0044281)|xenobiotic catabolic process (GO:0042178)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	enzyme binding (GO:0019899)|glutathione binding (GO:0043295)|glutathione transferase activity (GO:0004364)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)	p.A199T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|skin(1)	9		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Colorectal(144;0.0339)|Lung(183;0.0426)|all cancers(265;0.113)|Epithelial(280;0.125)|COAD - Colon adenocarcinoma(174;0.134)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)|Vitamin E(DB00163)	AAGTAGGCAGCGATTTTCTCC	0.488													C|||	0	0.0	0.0	0.0	5008	,	,		19347	0.0		0.0	False		,,,				2504	0.0				p.A199T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G595A	1						.	C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	105.0	97.0	100.0		595	5.5	0.8	1		100	0,8600		0,0,4300	no	missense	GSTM3	NM_000849.4	58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	199/226	110279776	1,13005	2203	4300	6503	110081299	SO:0001583	missense	2947	exon9			BC000088	CCDS812.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134202	ENSG00000134202	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4635	protein-coding gene	gene with protein product		138390	"""glutathione S-transferase M3 (brain)"""			2345169	Standard	NM_000849		Approved	GST5	uc001dyo.2	P21266	OTTHUMG00000011640	ENST00000540225.1:c.595G>A	1.37:g.110279776C>T	ENSP00000444978:p.Ala199Thr	Somatic		Capture	Illumina HiSeq	Phase_I	110081299	NM_000849	O60550|Q96HA3	Missense_Mutation	SNP	ENST00000540225.1	37	CCDS812.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	19.41	3.822553	0.71028	2.27E-4	0.0	ENSG00000134202	ENST00000540225;ENST00000256594;ENST00000361066	T;T;T	0.03745	3.82;3.82;3.82	5.53	5.53	0.82687	Glutathione S-transferase, C-terminal-like (1);Glutathione S-transferase/chloride channel, C-terminal (1);	0.151454	0.64402	D	0.000017	T	0.02418	0.0074	L	0.60904	1.88	0.44771	D	0.997776	P;P	0.47350	0.894;0.877	B;B	0.34931	0.192;0.084	T	0.45804	-0.9236	10	0.72032	D	0.01	-7.7737	13.8801	0.63678	0.1531:0.8469:0.0:0.0	.	205;199	Q59EJ5;P21266	.;GSTM3_HUMAN	T	199	ENSP00000444978:A199T;ENSP00000256594:A199T;ENSP00000354357:A199T	ENSP00000256594:A199T	A	-	1	0	GSTM3	110081299	0.803000	0.28956	0.778000	0.31720	0.940000	0.58332	1.474000	0.35398	2.871000	0.98454	0.655000	0.94253	GCT		0.488	GSTM3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032182.1	NM_000849	
AHCYL1	10768	broad.mit.edu	37	1	110557445	110557445	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:110557445G>A	ENST00000369799.5	+	6	1008	c.641G>A	c.(640-642)cGc>cAc	p.R214H	AHCYL1_ENST00000393614.4_Missense_Mutation_p.R167H|AHCYL1_ENST00000475081.1_3'UTR|AHCYL1_ENST00000359172.3_Missense_Mutation_p.R167H	NM_001242673.1|NM_001242674.1|NM_006621.5	NP_001229602.1|NP_001229603.1|NP_006612.2	O43865	SAHH2_HUMAN	adenosylhomocysteinase-like 1	214					mRNA polyadenylation (GO:0006378)|one-carbon metabolic process (GO:0006730)|positive regulation of sodium ion transport (GO:0010765)|protein export from nucleus (GO:0006611)|regulation of anion transport (GO:0044070)|regulation of ion transmembrane transporter activity (GO:0032412)|regulation of mRNA 3'-end processing (GO:0031440)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	adenosylhomocysteinase activity (GO:0004013)	p.R214H(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)	18		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)		TGTATTGACCGCTGTGTGAAC	0.438																																					p.R214H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G641A	1						.						213.0	190.0	198.0					1																	110557445		2203	4300	6503	110358968	SO:0001583	missense	10768	exon6			U82761	CCDS818.1, CCDS55620.1	1p13	2014-06-12	2009-06-12		ENSG00000168710	ENSG00000168710			344	protein-coding gene	gene with protein product	"""inositol 1,4,5-trisphosphate receptor-binding protein"", ""protein phosphatase 1, regulatory subunit 78"""	607826	"""S-adenosylhomocysteine hydrolase-like 1"""			11904675, 16754674, 12525476	Standard	NM_006621		Approved	XPVKONA, IRBIT, PPP1R78	uc001dyx.3	O43865	OTTHUMG00000011652	ENST00000369799.5:c.641G>A	1.37:g.110557445G>A	ENSP00000358814:p.Arg214His	Somatic		Capture	Illumina HiSeq	Phase_I	110358968	NM_006621	B4E168|Q2TAJ6|Q502W8|Q5VSM0|Q6P171|Q96PK4|Q9UG84	Missense_Mutation	SNP	ENST00000369799.5	37	CCDS818.1	.	.	.	.	.	.	.	.	.	.	G	19.99	3.928987	0.73327	.	.	ENSG00000168710	ENST00000369799;ENST00000359172;ENST00000393614	T;T;T	0.78707	-1.2;-1.2;-1.2	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.73171	0.3553	M	0.70787	2.145	0.80722	D	1	B	0.22003	0.063	B	0.12837	0.008	T	0.69327	-0.5174	10	0.72032	D	0.01	-9.99	20.8794	0.99867	0.0:0.0:1.0:0.0	.	214	O43865	SAHH2_HUMAN	H	214;167;167	ENSP00000358814:R214H;ENSP00000352092:R167H;ENSP00000377238:R167H	ENSP00000352092:R167H	R	+	2	0	AHCYL1	110358968	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.946000	0.87746	2.941000	0.99782	0.655000	0.94253	CGC		0.438	AHCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032243.1		
LAMTOR5	10542	broad.mit.edu	37	1	110946655	110946655	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:110946655C>T	ENST00000602318.1	-	3	188	c.101G>A	c.(100-102)cGc>cAc	p.R34H	LAMTOR5_ENST00000602858.1_Missense_Mutation_p.R22H|LAMTOR5_ENST00000474861.2_Missense_Mutation_p.R33H|LAMTOR5_ENST00000483260.1_Missense_Mutation_p.R33H|LAMTOR5_ENST00000256644.4_Missense_Mutation_p.R116H|LAMTOR5-AS1_ENST00000590413.1_RNA			O43504	LTOR5_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 5	34					cellular response to amino acid stimulus (GO:0071230)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)|protein localization to lysosome (GO:0061462)|regulation of cell size (GO:0008361)|response to virus (GO:0009615)|viral genome replication (GO:0019079)	cytosol (GO:0005829)|lysosome (GO:0005764)|Ragulator complex (GO:0071986)		p.R116H(1)									CAGGGTCCCGCGGCCTGGAAA	0.443																																					p.R116H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G347A	1						.						80.0	75.0	77.0					1																	110946655		2203	4300	6503	110748178	SO:0001583	missense	10542	exon3			AF029890	CCDS824.1	1p12	2012-09-24	2012-09-24	2012-09-24	ENSG00000134248	ENSG00000134248			17955	protein-coding gene	gene with protein product	"""HBx-interacting protein"", ""hepatitis B virus x-interacting protein (9.6kD)"""	608521	"""hepatitis B virus x interacting protein"""	HBXIP		9499022, 22980980	Standard	NM_006402		Approved	XIP, MGC71071	uc001dzr.3	O43504	OTTHUMG00000011568	ENST00000602318.1:c.101G>A	1.37:g.110946655C>T	ENSP00000473439:p.Arg34His	Somatic		Capture	Illumina HiSeq	Phase_I	110748178	NM_006402	Q6IBD8	Missense_Mutation	SNP	ENST00000602318.1	37		.	.	.	.	.	.	.	.	.	.	C	20.1	3.936722	0.73557	.	.	ENSG00000134248	ENST00000483260;ENST00000474861;ENST00000256644	.	.	.	5.87	5.87	0.94306	.	0.109676	0.64402	N	0.000006	T	0.47040	0.1424	.	.	.	0.58432	D	0.999997	B	0.11235	0.004	B	0.12156	0.007	T	0.34576	-0.9823	8	0.48119	T	0.1	-3.5381	19.3531	0.94398	0.0:1.0:0.0:0.0	.	34	O43504	HBXIP_HUMAN	H	33;33;116	.	ENSP00000256644:R116H	R	-	2	0	HBXIP	110748178	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	6.611000	0.74183	2.941000	0.99782	0.655000	0.94253	CGC		0.443	LAMTOR5-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467909.1	NM_006402	
OVGP1	5016	broad.mit.edu	37	1	111969103	111969103	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:111969103C>A	ENST00000369732.3	-	3	271	c.216G>T	c.(214-216)caG>caT	p.Q72H	OVGP1_ENST00000540696.1_Missense_Mutation_p.Q12H	NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	72					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)	p.Q114H(1)|p.Q72H(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		TTTTCTCATCCTGGAGATCCT	0.433																																					p.Q72H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G216T	1						.						99.0	98.0	98.0					1																	111969103		2203	4300	6503	111770626	SO:0001583	missense	5016	exon3			U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.216G>T	1.37:g.111969103C>A	ENSP00000358747:p.Gln72His	Somatic		Capture	Illumina HiSeq	Phase_I	111770626	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	.	.	.	.	.	.	.	.	.	.	C	17.66	3.444340	0.63178	.	.	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000540696	T;T	0.05717	3.4;3.4	4.23	1.02	0.19986	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.279255	0.36778	N	0.002407	T	0.07279	0.0184	M	0.64404	1.975	0.25203	N	0.990033	D;D;D	0.69078	0.98;0.98;0.997	P;P;D	0.65684	0.871;0.871;0.937	T	0.10683	-1.0619	10	0.72032	D	0.01	-3.748	5.4384	0.16494	0.1603:0.648:0.0:0.1917	.	72;72;114	B2RA77;Q12889;Q59HH5	.;OVGP1_HUMAN;.	H	72;114;12	ENSP00000358747:Q72H;ENSP00000438449:Q12H	ENSP00000358743:Q114H	Q	-	3	2	OVGP1	111770626	0.957000	0.32711	0.854000	0.33618	0.980000	0.70556	1.881000	0.39638	0.522000	0.28464	0.491000	0.48974	CAG		0.433	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
ATP5F1	515	broad.mit.edu	37	1	112002187	112002187	+	Missense_Mutation	SNP	C	C	T	rs151251385		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:112002187C>T	ENST00000369722.3	+	6	1228	c.622C>T	c.(622-624)Cgt>Tgt	p.R208C	ATP5F1_ENST00000483994.1_Missense_Mutation_p.R147C|ATP5F1_ENST00000369721.4_3'UTR	NM_001688.4	NP_001679.2	P24539	AT5F1_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit B1	208					ATP catabolic process (GO:0006200)|ATP synthesis coupled proton transport (GO:0015986)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)	p.R208C(1)		breast(1)|cervix(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	8		all_cancers(81;8.16e-06)|all_epithelial(167;5.63e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		GAACATGATGCGTCGAAAGGA	0.423																																					p.R208C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C622T	1						.						89.0	91.0	90.0					1																	112002187		2203	4300	6503	111803710	SO:0001583	missense	515	exon6			X60221	CCDS836.1	1p13.2	2012-10-12	2010-06-11		ENSG00000116459	ENSG00000116459		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	840	protein-coding gene	gene with protein product		603270	"""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit b, isoform 1"", ""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit B1"""			1831354	Standard	XM_005270929		Approved		uc001ebc.3	P24539	OTTHUMG00000011745	ENST00000369722.3:c.622C>T	1.37:g.112002187C>T	ENSP00000358737:p.Arg208Cys	Somatic		Capture	Illumina HiSeq	Phase_I	111803710	NM_001688	Q9BQ68|Q9BRU8	Missense_Mutation	SNP	ENST00000369722.3	37	CCDS836.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.535605	0.45176	.	.	ENSG00000116459	ENST00000369722;ENST00000483994	T;T	0.40225	1.04;1.04	5.15	4.22	0.49857	.	0.393014	0.31577	N	0.007419	T	0.54111	0.1838	M	0.88310	2.945	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.59221	0.854;0.854	T	0.64782	-0.6326	10	0.87932	D	0	.	10.98	0.47488	0.1458:0.7137:0.1406:0.0	.	208;208	Q08ET0;P24539	.;AT5F1_HUMAN	C	208;147	ENSP00000358737:R208C;ENSP00000420366:R147C	ENSP00000358737:R208C	R	+	1	0	ATP5F1	111803710	0.999000	0.42202	0.987000	0.45799	0.046000	0.14306	2.083000	0.41615	1.147000	0.42369	0.467000	0.42956	CGT		0.423	ATP5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032455.1	NM_001688	
C1orf162	128346	broad.mit.edu	37	1	112020365	112020365	+	Missense_Mutation	SNP	G	G	T	rs145747788		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:112020365G>T	ENST00000343534.5	+	5	545	c.295G>T	c.(295-297)Gcc>Tcc	p.A99S	C1orf162_ENST00000464591.1_Intron|C1orf162_ENST00000369718.3_Missense_Mutation_p.A74S	NM_174896.2	NP_777556.1	Q8NEQ5	CA162_HUMAN	chromosome 1 open reading frame 162	99						integral component of membrane (GO:0016021)		p.A99S(1)		NS(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5		all_cancers(81;0.00116)|all_epithelial(167;0.000761)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0236)|Colorectal(144;0.0286)|all cancers(265;0.0572)|Epithelial(280;0.0862)|COAD - Colon adenocarcinoma(174;0.112)|LUSC - Lung squamous cell carcinoma(189;0.134)		CAAGCCCCAGGCCCCAGATCC	0.552																																					p.A99S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G295T	1						.						107.0	109.0	108.0					1																	112020365		2203	4300	6503	111821888	SO:0001583	missense	128346	exon5			BC017973	CCDS837.1, CCDS72837.1	1p13.2	2008-02-05			ENSG00000143110	ENSG00000143110			28344	protein-coding gene	gene with protein product						12477932	Standard	XM_005270475		Approved	MGC24133	uc001ebe.3	Q8NEQ5	OTTHUMG00000011750	ENST00000343534.5:c.295G>T	1.37:g.112020365G>T	ENSP00000344218:p.Ala99Ser	Somatic		Capture	Illumina HiSeq	Phase_I	111821888	NM_174896	Q5QNZ1	Missense_Mutation	SNP	ENST00000343534.5	37	CCDS837.1	.	.	.	.	.	.	.	.	.	.	G	9.774	1.173443	0.21704	.	.	ENSG00000143110	ENST00000343534;ENST00000369718	T;T	0.53206	0.63;0.78	4.31	0.962	0.19643	.	0.841213	0.10200	N	0.703547	T	0.13713	0.0332	N	0.24115	0.695	0.09310	N	1	B	0.25904	0.137	B	0.31614	0.133	T	0.33292	-0.9874	10	0.48119	T	0.1	-2.4297	3.4328	0.07434	0.282:0.2084:0.5096:0.0	.	99	Q8NEQ5	CA162_HUMAN	S	99;74	ENSP00000344218:A99S;ENSP00000358732:A74S	ENSP00000344218:A99S	A	+	1	0	C1orf162	111821888	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.580000	0.23803	0.207000	0.20607	0.563000	0.77884	GCC		0.552	C1orf162-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032471.1	NM_174896	
ADORA3	140	broad.mit.edu	37	1	112045646	112045646	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:112045646G>A	ENST00000241356.4	-	1	736	c.331C>T	c.(331-333)Cgg>Tgg	p.R111W	ADORA3_ENST00000369716.4_Missense_Mutation_p.R111W|ADORA3_ENST00000486342.1_5'UTR|ADORA3_ENST00000369717.4_Intron	NM_000677.3	NP_000668.1	P33765	AA3R_HUMAN	adenosine A3 receptor	111					activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)	p.R111W(2)		NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	AGCTTGACCCGCAAGTATCGG	0.537																																					p.R111W												.	.	2	Substitution - Missense(2)	large_intestine(1)|breast(1)	c.C331T	1						.						53.0	45.0	48.0					1																	112045646		2203	4300	6503	111847169	SO:0001583	missense	140	exon1			BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"""GPCR / Class A : Adenosine receptors"", ""Immunoglobulin superfamily / V-set domain containing"""	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000241356.4:c.331C>T	1.37:g.112045646G>A	ENSP00000241356:p.Arg111Trp	Somatic		Capture	Illumina HiSeq	Phase_I	111847169	NM_020683	A2A3P4|Q6UWU0|Q9BYZ1	Missense_Mutation	SNP	ENST00000241356.4	37	CCDS839.1	.	.	.	.	.	.	.	.	.	.	G	17.52	3.409278	0.62399	.	.	ENSG00000121933	ENST00000369716;ENST00000241356	T;T	0.37235	1.21;1.21	5.26	4.22	0.49857	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42548	D	0.000684	T	0.58104	0.2099	M	0.86502	2.82	0.40707	D	0.982533	D;D	0.89917	1.0;0.998	D;D	0.75484	0.986;0.981	T	0.65763	-0.6089	10	0.87932	D	0	-17.9003	14.84	0.70217	0.0:0.0:0.7987:0.2013	.	111;111	P33765;P33765-2	AA3R_HUMAN;.	W	111	ENSP00000358730:R111W;ENSP00000241356:R111W	ENSP00000241356:R111W	R	-	1	2	ADORA3	111847169	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.856000	0.39389	2.613000	0.88420	0.561000	0.74099	CGG		0.537	ADORA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033065.1	NM_000677, NM_020683	
PPM1J	333926	broad.mit.edu	37	1	113255588	113255588	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:113255588G>T	ENST00000309276.6	-	3	682	c.507C>A	c.(505-507)gcC>gcA	p.A169A	PPM1J_ENST00000359994.4_Silent_p.A2A|RP11-426L16.10_ENST00000606505.1_5'Flank|PPM1J_ENST00000464951.1_Silent_p.A2A|RP11-426L16.9_ENST00000566195.1_RNA|RP11-426L16.10_ENST00000471038.2_5'Flank	NM_005167.5	NP_005158.5	Q5JR12	PPM1J_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1J	169	PP2C-like.				protein dephosphorylation (GO:0006470)		protein serine/threonine phosphatase activity (GO:0004722)	p.A169A(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	14	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGAGCCGTGAGGCCATTTCAG	0.572																																					p.A169A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C507A	1						.						73.0	79.0	77.0					1																	113255588		2203	4300	6503	113057111	SO:0001819	synonymous_variant	333926	exon3			AK093270	CCDS855.2	1p13.1	2012-04-17	2010-03-05		ENSG00000155367	ENSG00000155367	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	20785	protein-coding gene	gene with protein product	"""protein phosphatase 2C zeta"""	609957	"""protein phosphatase 1J (PP2C domain containing)"""			12633878	Standard	NM_005167		Approved	FLJ35951, MGC19531, DKFZp434P1514, PP2Czeta, PPP2CZ	uc001ect.1	Q5JR12	OTTHUMG00000012019	ENST00000309276.6:c.507C>A	1.37:g.113255588G>T		Somatic		Capture	Illumina HiSeq	Phase_I	113057111	NM_005167	B3KSB7|Q6DKJ7|Q96EZ7|Q9UF84	Silent	SNP	ENST00000309276.6	37	CCDS855.2																																																																																				0.572	PPM1J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033251.1	NM_005167	
PTPN22	26191	broad.mit.edu	37	1	114397560	114397560	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:114397560C>A	ENST00000359785.5	-	8	787	c.652G>T	c.(652-654)Gat>Tat	p.D218Y	PTPN22_ENST00000538253.1_Intron|AP4B1-AS1_ENST00000419536.1_RNA|PTPN22_ENST00000525799.1_Intron|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000420377.2_Missense_Mutation_p.D218Y|PTPN22_ENST00000534519.1_5'Flank|PTPN22_ENST00000528414.1_Missense_Mutation_p.D218Y	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	218	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)	p.D218N(1)|p.D218Y(1)		NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACACTGTCATCCTCTTGGTAA	0.413																																					p.D218Y												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G652T	1						.						180.0	156.0	164.0					1																	114397560		2203	4300	6503	114199083	SO:0001583	missense	26191	exon8			AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9652	protein-coding gene	gene with protein product		600716	"""protein tyrosine phosphatase, non-receptor type 8"""	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.652G>T	1.37:g.114397560C>A	ENSP00000352833:p.Asp218Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	114199083	NM_012411	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Missense_Mutation	SNP	ENST00000359785.5	37	CCDS863.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.994168	0.54041	.	.	ENSG00000134242	ENST00000359785;ENST00000528414;ENST00000420377;ENST00000354605	D;T;D	0.83755	-1.76;2.72;-1.76	6.16	3.22	0.36961	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.227351	0.44097	D	0.000497	T	0.74351	0.3705	L	0.28115	0.83	0.29031	N	0.885688	B;D;P;P	0.65815	0.256;0.995;0.564;0.618	B;D;B;B	0.66602	0.195;0.945;0.347;0.358	T	0.68704	-0.5338	10	0.49607	T	0.09	.	8.2501	0.31712	0.0:0.6389:0.2233:0.1378	.	218;218;218;218	E9PMT0;E9PLD8;G5E984;Q9Y2R2	.;.;.;PTN22_HUMAN	Y	218	ENSP00000352833:D218Y;ENSP00000435176:D218Y;ENSP00000388229:D218Y	ENSP00000346621:D218Y	D	-	1	0	PTPN22	114199083	0.391000	0.25221	0.007000	0.13788	0.986000	0.74619	0.836000	0.27545	0.935000	0.37341	0.650000	0.86243	GAT		0.413	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967	
SYT6	148281	broad.mit.edu	37	1	114646338	114646338	+	Silent	SNP	G	G	A	rs368052418		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:114646338G>A	ENST00000610222.1	-	4	1223	c.1077C>T	c.(1075-1077)agC>agT	p.S359S	SYT6_ENST00000369547.1_Silent_p.S274S|SYT6_ENST00000393296.1_Silent_p.S359S|SYT6_ENST00000609117.1_Silent_p.S274S|SYT6_ENST00000607941.1_Silent_p.S274S			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	359					acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)	p.S274S(1)		central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCAAGTCCACGCTTTCCTGCA	0.572																																					p.S274S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C822T	1						.	G		0,4406		0,0,2203	91.0	63.0	73.0		822	-3.3	1.0	1		73	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SYT6	NM_205848.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		274/426	114646338	1,13005	2203	4300	6503	114447861	SO:0001819	synonymous_variant	148281	exon4				CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"""Synaptotagmins"""	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.1077C>T	1.37:g.114646338G>A		Somatic		Capture	Illumina HiSeq	Phase_I	114447861	NM_205848	B1AMB8|B3KPK1	Silent	SNP	ENST00000610222.1	37																																																																																					0.572	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848	
TRIM33	51592	broad.mit.edu	37	1	114948114	114948114	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:114948114C>T	ENST00000358465.2	-	15	2769	c.2686G>A	c.(2686-2688)Gga>Aga	p.G896R	TRIM33_ENST00000369543.2_Missense_Mutation_p.G896R|TRIM33_ENST00000476908.1_5'UTR|TRIM33_ENST00000450349.2_Missense_Mutation_p.G528R	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	896					gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G896R(1)		breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|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)		AGATCTCCTCCGTTTTGGCAG	0.448			T	RET	papillary thyroid																																p.G896R			Dom	yes		1	1p13	51592	""" tripartite motif-containing 33 (PTC7,TIF1G)"""		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2686A	1						.						273.0	241.0	252.0					1																	114948114		2203	4300	6503	114749637	SO:0001583	missense	51592	exon15			AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"", ""RING-type (C3HC4) zinc fingers"""	16290	protein-coding gene	gene with protein product	"""transcriptional intermediary factor 1 gamma"", ""ret-fused gene 7"""	605769	"""tripartite motif-containing 33"""			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.2686G>A	1.37:g.114948114C>T	ENSP00000351250:p.Gly896Arg	Somatic		Capture	Illumina HiSeq	Phase_I	114749637	NM_015906	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Missense_Mutation	SNP	ENST00000358465.2	37	CCDS872.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.992772	0.93167	.	.	ENSG00000197323	ENST00000358465;ENST00000369543;ENST00000450349	D;D;T	0.84800	-1.9;-1.9;1.04	5.32	5.32	0.75619	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.93035	0.7783	M	0.87971	2.92	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	1.0;1.0;0.999;0.999;1.0	D	0.93657	0.6978	10	0.87932	D	0	-13.0708	19.3509	0.94384	0.0:1.0:0.0:0.0	.	528;528;91;896;896	E7EN20;B3KN30;Q9HAL0;Q9UPN9-2;Q9UPN9	.;.;.;.;TRI33_HUMAN	R	896;896;528	ENSP00000351250:G896R;ENSP00000358556:G896R;ENSP00000412077:G528R	ENSP00000351250:G896R	G	-	1	0	TRIM33	114749637	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.750000	0.85110	2.644000	0.89710	0.491000	0.48974	GGA		0.448	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906	
NRAS	4893	broad.mit.edu	37	1	115251236	115251236	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:115251236G>A	ENST00000369535.4	-	5	743	c.490C>T	c.(490-492)Cgc>Tgc	p.R164C		NM_002524.4	NP_002515.1	P01111	RASN_HUMAN	neuroblastoma RAS viral (v-ras) oncogene homolog	164					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|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)|negative regulation of skeletal muscle tissue development (GO:0048642)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|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)|small GTPase mediated signal transduction (GO:0007264)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.R164C(1)		NS(134)|adrenal_gland(9)|autonomic_ganglia(9)|biliary_tract(6)|bone(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(11)|eye(3)|haematopoietic_and_lymphoid_tissue(1115)|kidney(3)|large_intestine(105)|liver(10)|lung(42)|meninges(2)|ovary(7)|pancreas(5)|prostate(8)|skin(1144)|soft_tissue(37)|stomach(5)|testis(8)|thyroid(359)|upper_aerodigestive_tract(28)|urinary_tract(13)	3085	all_epithelial(7;5.11e-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)		CGGTACTGGCGTATTTCTCTT	0.398		50	Mis		"""melanoma, MM, AML, thyroid"""				Noonan syndrome	TSP Lung(23;0.16)|Multiple Myeloma(1;<1E-6)																											p.R164C			Dom	yes		1	1p13.2	4893	neuroblastoma RAS viral (v-ras) oncogene homolog		"""L, E"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C490T	1						.						270.0	229.0	243.0					1																	115251236		2203	4300	6503	115052759	SO:0001583	missense	4893	exon5	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	BC005219	CCDS877.1	1p13.2	2014-09-17			ENSG00000213281	ENSG00000213281			7989	protein-coding gene	gene with protein product		164790					Standard	NM_002524		Approved	N-ras	uc009wgu.3	P01111	OTTHUMG00000012059	ENST00000369535.4:c.490C>T	1.37:g.115251236G>A	ENSP00000358548:p.Arg164Cys	Somatic		Capture	Illumina HiSeq	Phase_I	115052759	NM_002524	Q14971|Q15104|Q15282	Missense_Mutation	SNP	ENST00000369535.4	37	CCDS877.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.967715	0.92855	.	.	ENSG00000213281	ENST00000369535	T	0.70516	-0.49	5.86	4.89	0.63831	.	0.000000	0.46145	U	0.000308	T	0.81158	0.4764	M	0.86028	2.79	0.80722	D	1	D	0.61080	0.989	P	0.59424	0.857	D	0.83435	0.0040	10	0.87932	D	0	.	16.1475	0.81580	0.0:0.0:0.866:0.134	.	164	P01111	RASN_HUMAN	C	164	ENSP00000358548:R164C	ENSP00000358548:R164C	R	-	1	0	NRAS	115052759	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.877000	0.63086	2.937000	0.99478	0.650000	0.86243	CGC		0.398	NRAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033395.2	NM_002524	
DRAXIN	374946	broad.mit.edu	37	1	11772447	11772447	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:11772447G>A	ENST00000294485.5	+	5	943	c.808G>A	c.(808-810)Gaa>Aaa	p.E270K		NM_198545.3	NP_940947.3			dorsal inhibitory axon guidance protein									p.E270K(1)									ATCACCAGCCGAAGGGGAACC	0.582																																					p.E270K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G808A	1						.						108.0	93.0	98.0					1																	11772447		2203	4300	6503	11695034	SO:0001583	missense	374946	exon5			AY358750	CCDS135.1	1p36.22	2012-08-20	2012-08-14	2012-08-14	ENSG00000162490	ENSG00000162490			25054	protein-coding gene	gene with protein product	"""dorsal repulsive axon guidance protein"", ""neural tissue-specific cysteine-rich protein"""	612682	"""chromosome 1 open reading frame 187"""	C1orf187		19150847	Standard	NM_198545		Approved	FLJ34999, Draxin, Neucrin	uc001asr.1	Q8NBI3	OTTHUMG00000002227	ENST00000294485.5:c.808G>A	1.37:g.11772447G>A	ENSP00000294485:p.Glu270Lys	Somatic		Capture	Illumina HiSeq	Phase_I	11695034	NM_198545		Missense_Mutation	SNP	ENST00000294485.5	37	CCDS135.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.001125	0.54254	.	.	ENSG00000162490	ENST00000294485	T	0.48836	0.8	5.79	0.0526	0.14303	.	0.830937	0.10988	N	0.611940	T	0.34542	0.0901	L	0.35723	1.085	0.09310	N	0.999996	B	0.13594	0.008	B	0.09377	0.004	T	0.25537	-1.0129	10	0.42905	T	0.14	-2.3471	8.079	0.30733	0.2787:0.1097:0.6116:0.0	.	270	Q8NBI3	DRAXI_HUMAN	K	270	ENSP00000294485:E270K	ENSP00000294485:E270K	E	+	1	0	C1orf187	11695034	0.991000	0.36638	0.006000	0.13384	0.467000	0.32768	2.132000	0.42083	0.099000	0.17552	-0.258000	0.10820	GAA		0.582	DRAXIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006325.1	NM_198545	
ATP1A1	476	broad.mit.edu	37	1	116943802	116943802	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:116943802C>T	ENST00000295598.5	+	20	3021	c.2769C>T	c.(2767-2769)ttC>ttT	p.F923F	ATP1A1_ENST00000369496.4_Silent_p.F892F|ATP1A1_ENST00000537345.1_Silent_p.F923F	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	923					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.F923F(2)		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)	CAGCCTTCTTCGTCAGTATCG	0.507																																					p.F923F												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2769T	1						.						91.0	80.0	84.0					1																	116943802		2203	4300	6503	116745325	SO:0001819	synonymous_variant	476	exon20			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.2769C>T	1.37:g.116943802C>T		Somatic		Capture	Illumina HiSeq	Phase_I	116745325	NM_000701	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	37	CCDS887.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.418198	0.25552	.	.	ENSG00000163399	ENST00000339159	.	.	.	5.1	-4.5	0.03493	.	.	.	.	.	T	0.59500	0.2198	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72080	-0.4398	5	0.66056	D	0.02	.	13.8847	0.63702	0.0:0.2556:0.0:0.7444	.	.	.	.	L	655	.	ENSP00000342827:S655L	S	+	2	0	ATP1A1	116745325	0.102000	0.21896	0.973000	0.42090	0.998000	0.95712	-0.560000	0.05964	-0.728000	0.04882	0.591000	0.81541	TCG		0.507	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233	
TRIM45	80263	broad.mit.edu	37	1	117656070	117656070	+	Missense_Mutation	SNP	C	C	T	rs372269129		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:117656070C>T	ENST00000256649.4	-	5	2031	c.1505G>A	c.(1504-1506)cGc>cAc	p.R502H	TRIM45_ENST00000369461.3_Missense_Mutation_p.R445H|TRIM45_ENST00000369464.3_Missense_Mutation_p.R484H	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	502					bone development (GO:0060348)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.R502H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|prostate(1)	23	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)		TGAGTGTGGGCGGTGCTTTCT	0.562																																					p.R484H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1451A	1						.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	75.0	68.0	71.0		1451,1505	2.1	0.9	1		71	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TRIM45	NM_001145635.1,NM_025188.3	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	484/563,502/581	117656070	1,13005	2203	4300	6503	117457593	SO:0001583	missense	80263	exon5				CCDS893.1, CCDS44200.1	1p13.1	2011-04-20	2011-01-25		ENSG00000134253	ENSG00000134253		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19018	protein-coding gene	gene with protein product		609318	"""tripartite motif-containing 45"""			15351693	Standard	NM_025188		Approved	FLJ13181, RNF99	uc001egz.2	Q9H8W5	OTTHUMG00000012119	ENST00000256649.4:c.1505G>A	1.37:g.117656070C>T	ENSP00000256649:p.Arg502His	Somatic		Capture	Illumina HiSeq	Phase_I	117457593	NM_001145635	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Missense_Mutation	SNP	ENST00000256649.4	37	CCDS893.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.374504	0.42105	0.0	1.16E-4	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	D;T;T	0.81908	-1.55;0.97;-1.28	4.96	2.11	0.27256	Immunoglobulin E-set (1);	0.116446	0.56097	N	0.000027	T	0.69504	0.3118	M	0.74258	2.255	0.42471	D	0.992826	B;B	0.30236	0.274;0.18	B;B	0.28139	0.086;0.04	T	0.68262	-0.5455	10	0.66056	D	0.02	-19.2469	7.6897	0.28561	0.0:0.6739:0.0:0.3261	.	484;502	Q9H8W5-2;Q9H8W5	.;TRI45_HUMAN	H	502;484;445	ENSP00000256649:R502H;ENSP00000358476:R484H;ENSP00000358473:R445H	ENSP00000256649:R502H	R	-	2	0	TRIM45	117457593	0.958000	0.32768	0.902000	0.35471	0.688000	0.40055	2.219000	0.42899	0.301000	0.22738	-0.251000	0.11542	CGC		0.562	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188	
VTCN1	79679	broad.mit.edu	37	1	117699295	117699295	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:117699295G>A	ENST00000369458.3	-	3	424	c.346C>T	c.(346-348)Cgg>Tgg	p.R116W	VTCN1_ENST00000463461.1_5'UTR|VTCN1_ENST00000359008.4_Missense_Mutation_p.R119W|VTCN1_ENST00000539893.1_Missense_Mutation_p.R21W|VTCN1_ENST00000328189.3_Intron	NM_024626.3	NP_078902.2			V-set domain containing T cell activation inhibitor 1									p.R116W(1)		large_intestine(7)|lung(4)|upper_aerodigestive_tract(1)	12	Lung SC(450;0.225)	all_cancers(81;6.05e-06)|all_epithelial(167;5.59e-07)|all_lung(203;2.85e-06)|Lung NSC(69;2e-05)		Lung(183;0.0664)|LUSC - Lung squamous cell carcinoma(189;0.214)|Colorectal(144;0.23)		TTTTTCAGCCGCAAAGAGGCA	0.458																																					p.R116W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C346T	1						.						98.0	94.0	95.0					1																	117699295		2203	4300	6503	117500818	SO:0001583	missense	79679	exon3			BX648021	CCDS894.1, CCDS58019.1, CCDS58020.1	1p12	2013-01-29			ENSG00000134258	ENSG00000134258		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28873	protein-coding gene	gene with protein product	"""B7 family member, H4"", ""B7 superfamily member 1"""	608162				12818165, 12818166	Standard	NM_024626		Approved	B7-H4, FLJ22418, B7S1, B7X, B7H4	uc001ehb.3	Q7Z7D3	OTTHUMG00000012118	ENST00000369458.3:c.346C>T	1.37:g.117699295G>A	ENSP00000358470:p.Arg116Trp	Somatic		Capture	Illumina HiSeq	Phase_I	117500818	NM_024626		Missense_Mutation	SNP	ENST00000369458.3	37	CCDS894.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.218462	0.39201	.	.	ENSG00000134258	ENST00000369458;ENST00000359008;ENST00000539893	T;T;T	0.67345	-0.26;-0.26;-0.26	6.08	4.96	0.65561	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.172268	0.42053	D	0.000775	T	0.42200	0.1192	L	0.59436	1.845	0.27487	N	0.952408	B	0.22909	0.077	B	0.24269	0.052	T	0.47446	-0.9117	10	0.87932	D	0	-21.3003	6.0364	0.19710	0.0:0.0863:0.1754:0.7383	.	116	Q7Z7D3	VTCN1_HUMAN	W	116;119;21	ENSP00000358470:R116W;ENSP00000351899:R119W;ENSP00000444724:R21W	ENSP00000351899:R119W	R	-	1	2	VTCN1	117500818	1.000000	0.71417	1.000000	0.80357	0.734000	0.41952	2.359000	0.44142	1.128000	0.42052	-0.291000	0.09656	CGG		0.458	VTCN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000033500.2	NM_024626	
MAN1A2	10905	broad.mit.edu	37	1	118042173	118042173	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:118042173A>G	ENST00000356554.3	+	11	2409	c.1674A>G	c.(1672-1674)gcA>gcG	p.A558A		NM_006699.3	NP_006690.1	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	558					cellular protein metabolic process (GO:0044267)|lung alveolus development (GO:0048286)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.A558A(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	27	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		GGGAAGCAGCACTGGTAAATA	0.423																																					p.A558A	Ovarian(33;199 881 8228 13687 31538)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1674G	1						.						60.0	57.0	58.0					1																	118042173		2203	4299	6502	117843696	SO:0001819	synonymous_variant	10905	exon11			AF027156	CCDS895.1	1p13	2008-02-05			ENSG00000198162	ENSG00000198162			6822	protein-coding gene	gene with protein product		604345				9592125	Standard	NM_006699		Approved	MAN1B	uc001ehd.1	O60476	OTTHUMG00000012149	ENST00000356554.3:c.1674A>G	1.37:g.118042173A>G		Somatic		Capture	Illumina HiSeq	Phase_I	117843696	NM_006699	Q9H510	Silent	SNP	ENST00000356554.3	37	CCDS895.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	6.947|6.947	0.544483|0.544483	0.13312|0.13312	.|.	.|.	ENSG00000198162|ENSG00000198162	ENST00000449370|ENST00000421535	.|.	.|.	.|.	5.39|5.39	1.51|1.51	0.23008|0.23008	.|.	.|.	.|.	.|.	.|.	T|T	0.30448|0.30448	0.0765|0.0765	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.13442|0.13442	-1.0509|-1.0509	4|4	.|.	.|.	.|.	-8.7623|-8.7623	4.3392|4.3392	0.11101|0.11101	0.4808:0.0:0.0867:0.4324|0.4808:0.0:0.0867:0.4324	.|.	.|.	.|.	.|.	R|A	291|125	.|.	.|.	H|T	+|+	2|1	0|0	MAN1A2|MAN1A2	117843696|117843696	0.231000|0.231000	0.23751|0.23751	0.999000|0.999000	0.59377|0.59377	0.513000|0.513000	0.34164|0.34164	-0.229000|-0.229000	0.09098|0.09098	0.335000|0.335000	0.23614|0.23614	-0.256000|-0.256000	0.11100|0.11100	CAC|ACT		0.423	MAN1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033593.1	NM_006699	
SPAG17	200162	broad.mit.edu	37	1	118624086	118624086	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:118624086G>A	ENST00000336338.5	-	14	2007	c.1942C>T	c.(1942-1944)Cag>Tag	p.Q648*		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	648						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)		p.Q648*(1)		NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		ACATATTGCTGCCTTATCTGT	0.418																																					p.Q648X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1942T	1						.						183.0	175.0	178.0					1																	118624086		2203	4300	6503	118425609	SO:0001587	stop_gained	200162	exon14				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.1942C>T	1.37:g.118624086G>A	ENSP00000337804:p.Gln648*	Somatic		Capture	Illumina HiSeq	Phase_I	118425609	NM_206996	Q8NAZ1|Q9NT21	Nonsense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	38	7.054895	0.98032	.	.	ENSG00000155761	ENST00000336338	.	.	.	5.12	3.06	0.35304	.	0.339697	0.28109	N	0.016569	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	10.1086	0.42548	0.0:0.1487:0.697:0.1543	.	.	.	.	X	648	.	ENSP00000337804:Q648X	Q	-	1	0	SPAG17	118425609	1.000000	0.71417	0.952000	0.39060	0.577000	0.36160	1.952000	0.40343	1.259000	0.44117	0.591000	0.81541	CAG		0.418	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
WARS2	10352	broad.mit.edu	37	1	119619097	119619097	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:119619097T>C	ENST00000235521.4	-	2	250	c.224A>G	c.(223-225)gAc>gGc	p.D75G	WARS2_ENST00000369426.5_Missense_Mutation_p.D75G|WARS2_ENST00000537870.1_5'UTR	NM_015836.3|NM_201263.2	NP_056651.1|NP_957715.1	Q9UGM6	SYWM_HUMAN	tryptophanyl tRNA synthetase 2, mitochondrial	75					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)|vasculogenesis (GO:0001570)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)	p.D75G(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(2)	15	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)	GGAGTGGAGGTCAACAATGCT	0.502																																					p.D75G												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A224G	1						.						149.0	148.0	148.0					1																	119619097		2203	4300	6503	119420620	SO:0001583	missense	10352	exon2			BC021722	CCDS900.1, CCDS30817.1	1p12	2011-07-01	2007-02-23		ENSG00000116874	ENSG00000116874	6.1.1.2	"""Aminoacyl tRNA synthetases / Class I"""	12730	protein-coding gene	gene with protein product	"""tryptophan tRNA ligase 2, mitochondrial"""	604733				10072595, 10828066	Standard	NM_201263		Approved	TrpRS	uc001ehn.3	Q9UGM6	OTTHUMG00000012335	ENST00000235521.4:c.224A>G	1.37:g.119619097T>C	ENSP00000235521:p.Asp75Gly	Somatic		Capture	Illumina HiSeq	Phase_I	119420620	NM_201263	B1ALR1|B2R9D4|Q53FT4|Q5VUD2|Q86TQ0	Missense_Mutation	SNP	ENST00000235521.4	37	CCDS900.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.103348	0.76983	.	.	ENSG00000116874	ENST00000369426;ENST00000235521	T;T	0.61510	0.1;0.1	5.78	5.78	0.91487	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.79730	0.4496	H	0.94542	3.55	0.80722	D	1	D;P;D	0.89917	1.0;0.934;1.0	D;P;D	0.97110	1.0;0.788;1.0	D	0.85636	0.1273	10	0.87932	D	0	-30.2587	14.9759	0.71273	0.0:0.0:0.0:1.0	.	75;75;75	B7Z448;Q9UGM6;B1ALR1	.;SYWM_HUMAN;.	G	75	ENSP00000358434:D75G;ENSP00000235521:D75G	ENSP00000235521:D75G	D	-	2	0	WARS2	119420620	1.000000	0.71417	0.991000	0.47740	0.770000	0.43624	7.543000	0.82106	2.333000	0.79357	0.482000	0.46254	GAC		0.502	WARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034362.1	NM_015836	
MIIP	60672	broad.mit.edu	37	1	12082269	12082269	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:12082269G>A	ENST00000235332.4	+	3	401	c.232G>A	c.(232-234)Gat>Aat	p.D78N	Y_RNA_ENST00000365591.1_RNA|MIIP_ENST00000436478.2_Missense_Mutation_p.D78N	NM_021933.3	NP_068752.2	Q5JXC2	MIIP_HUMAN	migration and invasion inhibitory protein	78								p.D78N(1)		autonomic_ganglia(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(1)	15						GGGCCCACCAGATGCCTGTCG	0.657																																					p.D78N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G232A	1						.						52.0	57.0	55.0					1																	12082269		2203	4300	6503	12004856	SO:0001583	missense	60672	exon3			AK022500	CCDS143.1	1p36.22	2009-07-09			ENSG00000116691	ENSG00000116691			25715	protein-coding gene	gene with protein product	"""invasion inhibitory protein 45"""	608772				15867349, 14617774	Standard	NM_021933		Approved	FLJ12438, IIp45	uc001ato.2	Q5JXC2	OTTHUMG00000002439	ENST00000235332.4:c.232G>A	1.37:g.12082269G>A	ENSP00000235332:p.Asp78Asn	Somatic		Capture	Illumina HiSeq	Phase_I	12004856	NM_021933	C0KL22|Q96HU6|Q9H839|Q9HA00	Missense_Mutation	SNP	ENST00000235332.4	37	CCDS143.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.357689	0.61403	.	.	ENSG00000116691	ENST00000235332;ENST00000436478	T;T	0.20332	2.08;2.08	4.49	3.44	0.39384	.	0.956942	0.08620	N	0.918644	T	0.31979	0.0814	M	0.72479	2.2	0.09310	N	1	P	0.48016	0.904	P	0.47573	0.55	T	0.14476	-1.0471	10	0.52906	T	0.07	-0.2051	8.7665	0.34706	0.1213:0.0:0.8787:0.0	.	78	Q5JXC2	MIIP_HUMAN	N	78	ENSP00000235332:D78N;ENSP00000392417:D78N	ENSP00000235332:D78N	D	+	1	0	MIIP	12004856	0.003000	0.15002	0.001000	0.08648	0.017000	0.09413	1.253000	0.32886	1.017000	0.39495	0.591000	0.81541	GAT		0.657	MIIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006941.1	NM_021933	
HSD3B1	3283	broad.mit.edu	37	1	120057162	120057162	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:120057162C>T	ENST00000369413.3	+	4	1161	c.1016C>T	c.(1015-1017)gCg>gTg	p.A339V	HSD3B1_ENST00000528909.1_Missense_Mutation_p.A339V|HSD3B1_ENST00000235547.6_Missense_Mutation_p.A341V			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	339					androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)	p.A339V(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	CGAGATCTGGCGTATAAGCCA	0.512																																					p.A339V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1016T	1						.						84.0	74.0	77.0					1																	120057162		2203	4300	6503	119858685	SO:0001583	missense	3283	exon4			S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5217	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 1"""	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.1016C>T	1.37:g.120057162C>T	ENSP00000358421:p.Ala339Val	Somatic		Capture	Illumina HiSeq	Phase_I	119858685	NM_000862	A8K691|Q14545|Q8IV65	Missense_Mutation	SNP	ENST00000369413.3	37	CCDS903.1	.	.	.	.	.	.	.	.	.	.	C	9.829	1.187937	0.21954	.	.	ENSG00000203857	ENST00000369413;ENST00000235547;ENST00000528909	D;D;D	0.88201	-2.35;-2.35;-2.35	3.26	2.32	0.28847	.	0.049786	0.85682	D	0.000000	T	0.80391	0.4614	L	0.50333	1.59	0.28587	N	0.909855	B;D	0.56287	0.135;0.975	B;P	0.46825	0.019;0.528	T	0.74247	-0.3727	10	0.66056	D	0.02	-8.2779	10.0193	0.42033	0.0:0.2225:0.7774:0.0	.	341;339	Q5TDG2;P14060	.;3BHS1_HUMAN	V	339;341;339	ENSP00000358421:A339V;ENSP00000235547:A341V;ENSP00000432268:A339V	ENSP00000235547:A341V	A	+	2	0	HSD3B1	119858685	1.000000	0.71417	0.548000	0.28192	0.070000	0.16714	7.202000	0.77856	0.673000	0.31224	0.313000	0.20887	GCG		0.512	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862	
DVL1	1855	broad.mit.edu	37	1	1274017	1274017	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:1274017C>T	ENST00000378888.5	-	12	1508	c.1224G>A	c.(1222-1224)ccG>ccA	p.P408P	DVL1_ENST00000378891.5_Silent_p.P383P			O14640	DVL1_HUMAN	dishevelled segment polarity protein 1	408					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.P383P(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)		TCACCGTCAGCGGCGCCTCTT	0.657																																					p.P383P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1149A	1						.						34.0	33.0	33.0					1																	1274017		2201	4296	6497	1263880	SO:0001819	synonymous_variant	1855	exon12			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.1224G>A	1.37:g.1274017C>T		Somatic		Capture	Illumina HiSeq	Phase_I	1263880	NM_004421	Q5TA33|Q5TA35	Silent	SNP	ENST00000378888.5	37																																																																																					0.657	DVL1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000008490.1	NM_004421	
VPS13D	55187	broad.mit.edu	37	1	12336564	12336564	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:12336564G>A	ENST00000358136.3	+	19	3049	c.2919G>A	c.(2917-2919)cgG>cgA	p.R973R	VPS13D_ENST00000356315.4_Silent_p.R973R	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)									p.R973R(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)		GCAATGGCCGGTACATTTCTG	0.507											OREG0013110	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R973R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2919A	1						.						111.0	105.0	107.0					1																	12336564		2203	4300	6503	12259151	SO:0001819	synonymous_variant	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.2919G>A	1.37:g.12336564G>A		Somatic	679	Capture	Illumina HiSeq	Phase_I	12259151	NM_018156		Silent	SNP	ENST00000358136.3	37	CCDS30588.1																																																																																				0.507	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
DHRS3	9249	broad.mit.edu	37	1	12640559	12640559	+	Missense_Mutation	SNP	G	G	A	rs201342762		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:12640559G>A	ENST00000376223.2	-	2	714	c.331C>T	c.(331-333)Cgg>Tgg	p.R111W	DHRS3_ENST00000482265.1_5'UTR	NM_004753.4	NP_004744.2	O75911	DHRS3_HUMAN	dehydrogenase/reductase (SDR family) member 3	111					bone morphogenesis (GO:0060349)|cardiac septum morphogenesis (GO:0060411)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|phototransduction, visible light (GO:0007603)|regulation of ossification (GO:0030278)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|photoreceptor outer segment membrane (GO:0042622)	electron carrier activity (GO:0009055)|NADP-retinol dehydrogenase activity (GO:0052650)|nucleotide binding (GO:0000166)|retinol dehydrogenase activity (GO:0004745)	p.R111W(1)		cervix(1)|large_intestine(4)|lung(2)|prostate(1)|skin(1)	9	Ovarian(185;0.249)	Lung NSC(185;4.11e-05)|all_lung(284;4.58e-05)|Renal(390;0.000147)|Colorectal(325;0.000585)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|Colorectal(212;9.25e-07)|COAD - Colon adenocarcinoma(227;0.000326)|BRCA - Breast invasive adenocarcinoma(304;0.000344)|Kidney(185;0.00235)|KIRC - Kidney renal clear cell carcinoma(229;0.00656)|STAD - Stomach adenocarcinoma(313;0.00798)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)	ACCTTCTCCCGGACGGCCTTG	0.577													G|||	1	0.000199681	0.0	0.0	5008	,	,		17470	0.0		0.001	False		,,,				2504	0.0				p.R111W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C331T	1						.						60.0	59.0	60.0					1																	12640559		2203	4300	6503	12563146	SO:0001583	missense	9249	exon2			AF061741	CCDS146.1	1p36.1	2011-09-20			ENSG00000162496	ENSG00000162496	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	17693	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 16C, member 1"""	612830				9705317, 12226107, 19027726	Standard	XM_005263533		Approved	retSDR1, Rsdr1, SDR1, RDH17, SDR16C1	uc001auc.3	O75911	OTTHUMG00000001885	ENST00000376223.2:c.331C>T	1.37:g.12640559G>A	ENSP00000365397:p.Arg111Trp	Somatic		Capture	Illumina HiSeq	Phase_I	12563146	NM_004753	B2R7F3|Q5VUY3|Q6UY38|Q9BUC8	Missense_Mutation	SNP	ENST00000376223.2	37	CCDS146.1	5	0.0022893772893772895	3	0.006097560975609756	0	0.0	0	0.0	2	0.002638522427440633	G	16.19	3.054426	0.55218	.	.	ENSG00000162496	ENST00000376223;ENST00000430996	D;D	0.88586	-2.4;-2.4	5.43	5.43	0.79202	NAD(P)-binding domain (1);	0.050183	0.85682	D	0.000000	D	0.91068	0.7189	M	0.68728	2.09	0.58432	D	0.999998	D;D;D	0.89917	1.0;0.974;1.0	D;P;D	0.81914	0.995;0.637;0.991	D	0.91889	0.5522	10	0.87932	D	0	.	13.4078	0.60924	0.0:0.0:0.7232:0.2768	.	111;111;111	B2R7F3;O75911-2;O75911	.;.;DHRS3_HUMAN	W	111;26	ENSP00000365397:R111W;ENSP00000387903:R26W	ENSP00000365397:R111W	R	-	1	2	DHRS3	12563146	1.000000	0.71417	1.000000	0.80357	0.488000	0.33401	2.125000	0.42016	2.532000	0.85374	0.655000	0.94253	CGG		0.577	DHRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005318.1	NM_004753	
NOTCH2	4853	broad.mit.edu	37	1	120508152	120508152	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:120508152G>T	ENST00000256646.2	-	10	1824	c.1605C>A	c.(1603-1605)gaC>gaA	p.D535E		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	535	EGF-like 14; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)	p.D535E(1)		breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TACTGGAACAGTCATCAATAT	0.448			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																												p.D535E			Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1605A	1						.						256.0	233.0	241.0					1																	120508152		2203	4300	6503	120309675	SO:0001583	missense	4853	exon10	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.1605C>A	1.37:g.120508152G>T	ENSP00000256646:p.Asp535Glu	Somatic		Capture	Illumina HiSeq	Phase_I	120309675	NM_024408	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	2.190	-0.385616	0.04966	.	.	ENSG00000134250	ENST00000256646;ENST00000539617	D	0.95272	-3.66	5.15	3.28	0.37604	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.39759	U	0.001264	T	0.74913	0.3779	N	0.01188	-0.97	0.46279	D	0.998968	P;P;B	0.42827	0.791;0.512;0.083	P;B;B	0.47941	0.562;0.376;0.018	T	0.78293	-0.2260	10	0.02654	T	1	.	13.5623	0.61797	0.1409:0.0:0.8591:0.0	.	496;535;535	D2WEZ3;Q6IQ50;Q04721	.;.;NOTC2_HUMAN	E	535;496	ENSP00000256646:D535E	ENSP00000256646:D535E	D	-	3	2	NOTCH2	120309675	0.999000	0.42202	1.000000	0.80357	0.815000	0.46073	0.504000	0.22626	0.357000	0.24183	-1.151000	0.01829	GAC		0.448	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
PDE4DIP	9659	broad.mit.edu	37	1	144881600	144881600	+	Missense_Mutation	SNP	C	C	T	rs376549207		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:144881600C>T	ENST00000369354.3	-	25	3785	c.3596G>A	c.(3595-3597)cGt>cAt	p.R1199H	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.R1336H|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.R1199H|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.R1155H|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.R1336H|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1199					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.R1199H(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CCCAGGGTCACGAGGCTGGGA	0.582			T	PDGFRB	MPD																																p.R1155H			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3464A	1						.	C	HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	92.0	85.0	87.0		3596,3596,3464	-5.4	0.0	1		87	0,8592		0,0,4296	no	missense,missense,missense	PDE4DIP	NM_014644.4,NM_001198834.2,NM_001198832.1	29,29,29	0,1,6498	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign	1199/2347,1199/2363,1155/2241	144881600	1,12997	2203	4296	6499	143592957	SO:0001583	missense	9659	exon28			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.3596G>A	1.37:g.144881600C>T	ENSP00000358360:p.Arg1199His	Somatic		Capture	Illumina HiSeq	Phase_I	143592957	NM_001198832	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	C	0.921	-0.715900	0.03206	2.27E-4	0.0	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01767	4.65;4.85;4.85;4.85;4.85	5.65	-5.43	0.02632	.	.	.	.	.	T	0.00271	0.0008	N	0.02011	-0.69	0.09310	N	0.999995	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.42137	-0.9469	9	0.30854	T	0.27	.	9.211	0.37318	0.0:0.2556:0.1104:0.634	.	1155;1199	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	H	1155;1199;1199;1336;1336	ENSP00000327209:R1155H;ENSP00000358360:R1199H;ENSP00000358363:R1199H;ENSP00000435654:R1336H;ENSP00000358366:R1336H	ENSP00000327209:R1155H	R	-	2	0	PDE4DIP	143592957	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.704000	0.05058	-0.971000	0.03564	-4.234000	0.00009	CGT		0.582	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
PDE4DIP	9659	broad.mit.edu	37	1	144994721	144994721	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:144994721C>T	ENST00000369354.3	-	1	200	c.11G>A	c.(10-12)gGa>gAa	p.G4E	PDE4DIP_ENST00000369348.3_Intron|PDE4DIP_ENST00000530740.1_Intron|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.G4E|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.G4E|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000369347.4_Missense_Mutation_p.G4E|PDE4DIP_ENST00000369349.3_Missense_Mutation_p.G4E|PDE4DIP_ENST00000369359.4_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	4					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.G4E(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AGTGCGATATCCATTAGACAT	0.567			T	PDGFRB	MPD																																p.G4E			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G11A	1						.						158.0	130.0	139.0					1																	144994721		2203	4300	6503	143706078	SO:0001583	missense	9659	exon1			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.11G>A	1.37:g.144994721C>T	ENSP00000358360:p.Gly4Glu	Somatic		Capture	Illumina HiSeq	Phase_I	143706078	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	C	32	5.141240	0.94560	.	.	ENSG00000178104	ENST00000369354;ENST00000369356;ENST00000369351;ENST00000369349;ENST00000369347	T;T;T;T;T	0.10192	4.45;4.45;3.49;3.51;2.9	5.78	5.78	0.91487	.	.	.	.	.	T	0.19087	0.0458	L	0.47716	1.5	0.80722	D	1	D;P;P	0.89917	1.0;0.623;0.947	D;P;P	0.97110	1.0;0.501;0.79	T	0.00489	-1.1709	8	.	.	.	.	17.5005	0.87730	0.0:1.0:0.0:0.0	.	4;4;4	Q5VU43-7;Q5VU43;Q5VU43-10	.;MYOME_HUMAN;.	E	4	ENSP00000358360:G4E;ENSP00000358363:G4E;ENSP00000358357:G4E;ENSP00000358355:G4E;ENSP00000358353:G4E	.	G	-	2	0	PDE4DIP	143706078	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.563000	0.60823	2.731000	0.93534	0.650000	0.86243	GGA		0.567	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
SSU72	29101	broad.mit.edu	37	1	1477477	1477477	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:1477477C>T	ENST00000291386.3	-	5	865	c.554G>A	c.(553-555)cGc>cAc	p.R185H	TMEM240_ENST00000378733.4_5'Flank|TMEM240_ENST00000425828.1_5'Flank	NM_014188.2	NP_054907.1	Q9NP77	SSU72_HUMAN	SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae)	185					dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|mRNA polyadenylation (GO:0006378)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)	p.R185H(1)		large_intestine(2)|lung(5)	7	all_cancers(77;0.00125)|all_epithelial(69;0.000703)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.03e-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;5.04e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.72e-23)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;0.000188)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|BRCA - Breast invasive adenocarcinoma(365;0.00837)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		CAGAAAGGTGCGGCCACTCTT	0.567																																					p.R185H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G554A	1						.						112.0	78.0	90.0					1																	1477477		2201	4296	6497	1467340	SO:0001583	missense	29101	exon5			AJ276409	CCDS32.1	1p36	2010-03-24	2006-04-04		ENSG00000160075	ENSG00000160075			25016	protein-coding gene	gene with protein product			"""Ssu72 RNA polymerase II CTD phosphatase homolog (yeast)"""			15125841, 15659578	Standard	NM_014188		Approved	HSPC182	uc001agd.3	Q9NP77	OTTHUMG00000000576	ENST00000291386.3:c.554G>A	1.37:g.1477477C>T	ENSP00000291386:p.Arg185His	Somatic		Capture	Illumina HiSeq	Phase_I	1467340	NM_014188	Q9BZS6|Q9H933	Missense_Mutation	SNP	ENST00000291386.3	37	CCDS32.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235158	0.39498	.	.	ENSG00000160075	ENST00000291386;ENST00000378726	T	0.44881	0.91	5.07	2.14	0.27477	.	0.000000	0.85682	D	0.000000	T	0.34048	0.0884	L	0.45228	1.405	0.42507	D	0.992957	D	0.60575	0.988	P	0.45946	0.498	T	0.05869	-1.0859	10	0.39692	T	0.17	-2.7791	6.4779	0.22047	0.1465:0.6944:0.0:0.1591	.	185	Q9NP77	SSU72_HUMAN	H	185;102	ENSP00000291386:R185H	ENSP00000291386:R185H	R	-	2	0	SSU72	1467340	1.000000	0.71417	0.000000	0.03702	0.004000	0.04260	3.724000	0.54962	0.170000	0.19704	-0.181000	0.13052	CGC		0.567	SSU72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001366.1	NM_014188	
PIAS3	10401	broad.mit.edu	37	1	145578464	145578464	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:145578464C>T	ENST00000393045.2	+	2	517	c.427C>T	c.(427-429)Cgg>Tgg	p.R143W	PIAS3_ENST00000369298.1_Missense_Mutation_p.R108W|PIAS3_ENST00000369299.3_Missense_Mutation_p.R134W	NM_006099.3	NP_006090.2	Q9Y6X2	PIAS3_HUMAN	protein inhibitor of activated STAT, 3	143	PINIT. {ECO:0000255|PROSITE- ProRule:PRU00799}.				positive regulation of gene expression (GO:0010628)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein sumoylation (GO:0033235)|protein sumoylation (GO:0016925)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|nucleus (GO:0005634)|synapse (GO:0045202)	enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|SUMO ligase activity (GO:0019789)|zinc ion binding (GO:0008270)	p.R134W(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)	28	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					GGAGCTCATCCGGCCCACCAC	0.542																																					p.R143W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C427T	1						.						104.0	106.0	105.0					1																	145578464		2203	4300	6503	144289821	SO:0001583	missense	10401	exon2			AB021868	CCDS72866.1	1q21	2011-10-11			ENSG00000131788	ENSG00000131788		"""Zinc fingers, MIZ-type"""	16861	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 5"""	605987				10319586	Standard	NM_006099		Approved	FLJ14651, ZMIZ5	uc001eoc.1	Q9Y6X2	OTTHUMG00000013750	ENST00000393045.2:c.427C>T	1.37:g.145578464C>T	ENSP00000376765:p.Arg143Trp	Somatic		Capture	Illumina HiSeq	Phase_I	144289821	NM_006099	Q9UFI3	Missense_Mutation	SNP	ENST00000393045.2	37	CCDS920.2	.	.	.	.	.	.	.	.	.	.	C	17.54	3.414137	0.62511	.	.	ENSG00000131788	ENST00000393046;ENST00000369299;ENST00000393045;ENST00000369298	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	3.79	2.84	0.33178	PINIT domain (1);	0.362011	0.19502	N	0.112712	T	0.35335	0.0928	L	0.38175	1.15	0.44685	D	0.997678	D;D	0.76494	0.999;0.999	D;P	0.63283	0.913;0.875	T	0.24404	-1.0161	10	0.87932	D	0	-8.3848	8.4831	0.33054	0.4216:0.5784:0.0:0.0	.	134;143	F8WA94;Q9Y6X2	.;PIAS3_HUMAN	W	134;134;143;108	ENSP00000376766:R134W;ENSP00000358305:R134W;ENSP00000376765:R143W;ENSP00000358304:R108W	ENSP00000358304:R108W	R	+	1	2	PIAS3	144289821	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.612000	0.74187	0.755000	0.32990	0.561000	0.74099	CGG		0.542	PIAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038533.4	NM_006099	
SV2A	9900	broad.mit.edu	37	1	149877580	149877580	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:149877580C>T	ENST00000369146.3	-	12	2387	c.1897G>A	c.(1897-1899)Gtg>Atg	p.V633M	SV2A_ENST00000369145.1_Missense_Mutation_p.V633M	NM_001278719.1|NM_014849.3	NP_001265648.1|NP_055664.3	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2A	633					cellular calcium ion homeostasis (GO:0006874)|neurotransmitter transport (GO:0006836)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane transporter activity (GO:0022857)	p.V633M(1)		breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(6)|pancreas(1)|prostate(8)|skin(2)|urinary_tract(2)	55	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Levetiracetam(DB01202)	CAGGACATCACGCTGGAGCCA	0.577																																					p.V633M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1897A	1						.						86.0	69.0	75.0					1																	149877580		2203	4300	6503	148144204	SO:0001583	missense	9900	exon12			AB018279	CCDS940.1	1q21.2	2008-02-05			ENSG00000159164	ENSG00000159164			20566	protein-coding gene	gene with protein product		185860				7681585, 10611374	Standard	NM_014849		Approved	SV2, KIAA0736	uc001etg.3	Q7L0J3	OTTHUMG00000012209	ENST00000369146.3:c.1897G>A	1.37:g.149877580C>T	ENSP00000358142:p.Val633Met	Somatic		Capture	Illumina HiSeq	Phase_I	148144204	NM_014849	D3DUZ7|O94841|Q5QNX8|Q7Z3L6|Q8NBJ6|Q9BVZ9	Missense_Mutation	SNP	ENST00000369146.3	37	CCDS940.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.042572	0.75732	.	.	ENSG00000159164	ENST00000369146;ENST00000369145	T;T	0.44881	0.91;0.91	4.2	4.2	0.49525	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.448615	0.21776	N	0.069300	T	0.45216	0.1331	L	0.46157	1.445	0.80722	D	1	D;D	0.64830	0.994;0.994	D;D	0.64687	0.928;0.928	T	0.38693	-0.9649	10	0.46703	T	0.11	-16.4067	14.0842	0.64944	0.0:1.0:0.0:0.0	.	85;633	B4E000;Q7L0J3	.;SV2A_HUMAN	M	633	ENSP00000358142:V633M;ENSP00000358141:V633M	ENSP00000358141:V633M	V	-	1	0	SV2A	148144204	0.974000	0.33945	1.000000	0.80357	0.935000	0.57460	2.448000	0.44926	2.168000	0.68352	0.297000	0.19635	GTG		0.577	SV2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033754.1		
PRPF3	9129	broad.mit.edu	37	1	150297544	150297544	+	Splice_Site	SNP	C	C	T	rs370220628		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:150297544C>T	ENST00000324862.6	+	2	309	c.144C>T	c.(142-144)gcC>gcT	p.A48A	PRPF3_ENST00000543398.1_5'UTR|PRPF3_ENST00000414970.2_Splice_Site_p.A48A	NM_004698.2	NP_004689.1	O43395	PRPF3_HUMAN	pre-mRNA processing factor 3	48	PWI. {ECO:0000255|PROSITE- ProRule:PRU00627}.				mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 x U5 tri-snRNP complex (GO:0046540)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.A48A(1)		breast(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(24;5.57e-29)|Breast(34;0.000844)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)	Colorectal(1306;0.0149)		AGAAGGCAGCCGGTATGTACC	0.458																																					p.A48A	Ovarian(168;1070 2670 5178 20729)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C144T	1						.						132.0	117.0	122.0					1																	150297544		2203	4300	6503	148564168	SO:0001630	splice_region_variant	9129	exon2			AF001947	CCDS951.1	1q21.1	2013-07-16	2013-06-10		ENSG00000117360	ENSG00000117360			17348	protein-coding gene	gene with protein product		607301	"""retinitis pigmentosa 18 (autosomal dominant)"", ""PRP3 pre-mRNA processing factor 3 homolog (yeast)"", ""PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae)"""	RP18			Standard	NM_004698		Approved	Prp3, hPrp3, SNRNP90	uc001eum.4	O43395	OTTHUMG00000012807	ENST00000324862.6:c.145+1C>T	1.37:g.150297544C>T		Somatic		Capture	Illumina HiSeq	Phase_I	148564168	NM_004698	B4DSY9|O43446|Q5VT54	Silent	SNP	ENST00000324862.6	37	CCDS951.1																																																																																				0.458	PRPF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035836.1	NM_004698	Silent
RPRD2	23248	broad.mit.edu	37	1	150444647	150444647	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:150444647C>A	ENST00000369068.4	+	11	3227	c.3223C>A	c.(3223-3225)Cct>Act	p.P1075T	RPRD2_ENST00000401000.4_Missense_Mutation_p.P1049T|RPRD2_ENST00000492220.1_3'UTR	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	1075						DNA-directed RNA polymerase II, holoenzyme (GO:0016591)		p.P1075T(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						CTTAGACTTGCCTGATAGCAC	0.537																																					p.P1075T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3223A	1						.						52.0	54.0	53.0					1																	150444647		1945	4144	6089	148711271	SO:0001583	missense	23248	exon11			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.3223C>A	1.37:g.150444647C>A	ENSP00000358064:p.Pro1075Thr	Somatic		Capture	Illumina HiSeq	Phase_I	148711271	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	37	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.074749	0.55646	.	.	ENSG00000163125	ENST00000401000;ENST00000369068	T;T	0.65732	-0.17;-0.16	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.56572	0.1994	N	0.24115	0.695	0.80722	D	1	D;D	0.61697	0.983;0.99	P;P	0.56563	0.637;0.801	T	0.64101	-0.6486	10	0.87932	D	0	-10.9429	18.138	0.89627	0.0:1.0:0.0:0.0	.	1075;1049	Q5VT52;Q5VT52-3	RPRD2_HUMAN;.	T	1049;1075	ENSP00000383785:P1049T;ENSP00000358064:P1075T	ENSP00000358064:P1075T	P	+	1	0	RPRD2	148711271	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.076000	0.64413	2.600000	0.87896	0.655000	0.94253	CCT		0.537	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203	
LYSMD1	388695	broad.mit.edu	37	1	151133405	151133405	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:151133405G>A	ENST00000368908.5	-	3	1297	c.637C>T	c.(637-639)Cgg>Tgg	p.R213W	LYSMD1_ENST00000440902.2_Missense_Mutation_p.R165W	NM_212551.4	NP_997716.1	Q96S90	LYSM1_HUMAN	LysM, putative peptidoglycan-binding, domain containing 1	213								p.R213W(1)		endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7	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)			GTCCGGGTCCGAGAGGTACGG	0.557																																					p.R165W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C493T	1						.						108.0	103.0	105.0					1																	151133405		2203	4300	6503	149400029	SO:0001583	missense	388695	exon3			BX647911	CCDS986.1, CCDS44218.1	1q21.2	2008-02-05			ENSG00000163155	ENSG00000163155			32070	protein-coding gene	gene with protein product						12477932	Standard	NM_212551		Approved	SB145, MGC35223, RP11-68I18.5	uc001ewy.3	Q96S90	OTTHUMG00000012260	ENST00000368908.5:c.637C>T	1.37:g.151133405G>A	ENSP00000357904:p.Arg213Trp	Somatic		Capture	Illumina HiSeq	Phase_I	149400029	NM_001136543	B4DQA1|Q69YX9	Missense_Mutation	SNP	ENST00000368908.5	37	CCDS986.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.995171	0.74703	.	.	ENSG00000163155	ENST00000368908;ENST00000440902	T;T	0.32988	1.46;1.43	5.56	2.24	0.28232	.	0.076354	0.49916	D	0.000128	T	0.38401	0.1039	M	0.71581	2.175	0.35359	D	0.788047	D;D	0.89917	1.0;0.999	D;P	0.70935	0.971;0.857	T	0.42396	-0.9454	10	0.72032	D	0.01	-9.2885	10.4227	0.44359	0.0:0.1197:0.6081:0.2721	.	165;213	Q96S90-2;Q96S90	.;LYSM1_HUMAN	W	213;165	ENSP00000357904:R213W;ENSP00000404059:R165W	ENSP00000357904:R213W	R	-	1	2	LYSMD1	149400029	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	3.348000	0.52209	0.674000	0.31244	0.650000	0.86243	CGG		0.557	LYSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034070.3	NM_212551	
VPS72	6944	broad.mit.edu	37	1	151149371	151149371	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:151149371G>A	ENST00000354473.4	-	6	913	c.877C>T	c.(877-879)Cgg>Tgg	p.R293W	VPS72_ENST00000496809.1_5'UTR|TMOD4_ENST00000416280.2_5'Flank|TMOD4_ENST00000601585.1_5'Flank			Q15906	VPS72_HUMAN	vacuolar protein sorting 72 homolog (S. cerevisiae)	282					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)	p.R282W(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	14	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)			TTTGGGGGCCGCCCTTGGGGG	0.572																																					p.R282W	Pancreas(109;1131 2287 3209 24201)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C844T	1						.						50.0	55.0	53.0					1																	151149371		2203	4300	6503	149415995	SO:0001583	missense	6944	exon6			D43642	CCDS989.1, CCDS59201.1	1q21	2008-02-05	2006-12-19	2005-09-08	ENSG00000163159	ENSG00000163159			11644	protein-coding gene	gene with protein product		600607	"""transcription factor-like 1"", ""vacuolar protein sorting 72 (yeast)"""	TCFL1		7702631	Standard	NM_001271087		Approved	YL-1, YL1, Swc2	uc001exe.2	Q15906	OTTHUMG00000012345	ENST00000354473.4:c.877C>T	1.37:g.151149371G>A	ENSP00000346464:p.Arg293Trp	Somatic		Capture	Illumina HiSeq	Phase_I	149415995	NM_005997	A6NLK9|A6PW55|Q53GJ2|Q5U0R4	Missense_Mutation	SNP	ENST00000354473.4	37	CCDS59201.1	.	.	.	.	.	.	.	.	.	.	.	16.44	3.123642	0.56613	.	.	ENSG00000163159	ENST00000368892;ENST00000354473	.	.	.	5.41	3.41	0.39046	.	0.385177	0.29178	N	0.012919	T	0.09247	0.0228	L	0.32530	0.975	0.09310	N	1	D	0.54047	0.964	B	0.38880	0.284	T	0.06643	-1.0815	9	0.54805	T	0.06	-11.8942	8.6774	0.34187	0.0838:0.0:0.7301:0.1861	.	282	Q15906	VPS72_HUMAN	W	282;293	.	ENSP00000346464:R293W	R	-	1	2	VPS72	149415995	0.030000	0.19436	0.976000	0.42696	0.797000	0.45037	1.633000	0.37113	1.518000	0.48934	0.561000	0.74099	CGG		0.572	VPS72-002	NOVEL	mRNA_start_NF|basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000034394.3	NM_005997	
ZNF687	57592	broad.mit.edu	37	1	151259788	151259788	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:151259788A>G	ENST00000368879.2	+	2	1119	c.1021A>G	c.(1021-1023)Aat>Gat	p.N341D		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	341					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N341D(1)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|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)			ATCCTGCGGGAATATCACAAG	0.572																																					p.N341D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1021G	1						.						63.0	63.0	63.0					1																	151259788		2203	4300	6503	149526412	SO:0001583	missense	57592	exon2				CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.1021A>G	1.37:g.151259788A>G	ENSP00000357874:p.Asn341Asp	Somatic		Capture	Illumina HiSeq	Phase_I	149526412	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Missense_Mutation	SNP	ENST00000368879.2	37		.	.	.	.	.	.	.	.	.	.	A	13.93	2.382515	0.42207	.	.	ENSG00000143373	ENST00000336715;ENST00000324048;ENST00000368879	T;T;T	0.00801	5.68;5.68;6.01	5.02	5.02	0.67125	.	0.000000	0.37715	N	0.001964	T	0.00845	0.0028	L	0.44542	1.39	0.29600	N	0.847749	D;P;D	0.57571	0.98;0.863;0.98	P;P;P	0.50659	0.647;0.526;0.626	T	0.59413	-0.7459	9	.	.	.	.	13.8618	0.63566	1.0:0.0:0.0:0.0	.	341;341;341	Q8N1G0-2;Q8N1G0;F8WCX2	.;ZN687_HUMAN;.	D	341	ENSP00000336620:N341D;ENSP00000319829:N341D;ENSP00000357874:N341D	.	N	+	1	0	ZNF687	149526412	0.066000	0.20996	0.783000	0.31826	0.959000	0.62525	2.373000	0.44266	2.118000	0.64928	0.459000	0.35465	AAT		0.572	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832	
CELF3	11189	broad.mit.edu	37	1	151677567	151677567	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:151677567G>A	ENST00000290583.4	-	12	2141	c.1348C>T	c.(1348-1350)Cgc>Tgc	p.R450C	CELF3_ENST00000392706.3_Missense_Mutation_p.R245C|CELF3_ENST00000290585.4_Missense_Mutation_p.R400C|RP11-98D18.1_ENST00000457548.1_RNA|CELF3_ENST00000470688.1_5'UTR	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	450	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.R450C(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						ACTTTGAGGCGCTTCATGCCG	0.627																																					p.R450C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1348T	1						.						69.0	66.0	67.0					1																	151677567		2203	4300	6503	149944191	SO:0001583	missense	11189	exon12			U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"""Trinucleotide (CAG) repeat containing"", ""RNA binding motif (RRM) containing"""	11967	protein-coding gene	gene with protein product	"""expanded repeat domain, CAG/CTG 4"", ""CAG repeat domain"", ""CUG-BP and ETR-3 like factor 3"""	612678	"""trinucleotide repeat containing 4"""	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.1348C>T	1.37:g.151677567G>A	ENSP00000290583:p.Arg450Cys	Somatic		Capture	Illumina HiSeq	Phase_I	149944191	NM_007185	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Missense_Mutation	SNP	ENST00000290583.4	37	CCDS1002.1	.	.	.	.	.	.	.	.	.	.	.	21.9	4.222102	0.79464	.	.	ENSG00000159409	ENST00000290585;ENST00000290583;ENST00000392706	T;T;T	0.17054	2.3;2.3;2.3	5.11	5.11	0.69529	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.37046	0.0989	M	0.86864	2.845	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	0.995;1.0;1.0;0.996;0.997	T	0.30208	-0.9986	10	0.87932	D	0	-17.6043	11.027	0.47751	0.0:0.0:0.8146:0.1854	.	245;400;449;450;449	B4DQL3;Q5SZQ7;Q5SZQ8-2;Q5SZQ8;Q5SZQ8-3	.;.;.;CELF3_HUMAN;.	C	400;450;245	ENSP00000290585:R400C;ENSP00000290583:R450C;ENSP00000376470:R245C	ENSP00000290583:R450C	R	-	1	0	CELF3	149944191	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.281000	0.33214	2.657000	0.90304	0.655000	0.94253	CGC		0.627	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185	
TDRKH	11022	broad.mit.edu	37	1	151751266	151751266	+	Missense_Mutation	SNP	C	C	T	rs201963923		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:151751266C>T	ENST00000368822.1	-	6	1411	c.778G>A	c.(778-780)Gac>Aac	p.D260N	TDRKH_ENST00000440583.2_Missense_Mutation_p.D36N|TDRKH_ENST00000484421.1_5'UTR|TDRKH_ENST00000368824.3_Missense_Mutation_p.D260N|TDRKH_ENST00000458431.2_Missense_Mutation_p.D260N|TDRKH_ENST00000368827.6_Missense_Mutation_p.D260N|TDRKH_ENST00000368823.1_Missense_Mutation_p.D256N|TDRKH_ENST00000368825.3_Missense_Mutation_p.D215N			Q9Y2W6	TDRKH_HUMAN	tudor and KH domain containing	260					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	mitochondrion (GO:0005739)|pi-body (GO:0071546)|piP-body (GO:0071547)	RNA binding (GO:0003723)	p.D260N(1)		breast(5)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			ACAGCCATGTCGCCTCCTCCT	0.547																																					p.D260N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G778A	1						.	C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	0,3914		0,0,1957	80.0	78.0	79.0		778,643,778,778	4.6	0.5	1		79	2,8304		0,2,4151	yes	missense,missense,missense,missense	TDRKH	NM_001083963.1,NM_001083964.1,NM_001083965.1,NM_006862.3	23,23,23,23	0,2,6108	TT,TC,CC		0.0241,0.0,0.0164	probably-damaging,probably-damaging,probably-damaging,probably-damaging	260/562,215/517,260/562,260/562	151751266	2,12218	1957	4153	6110	150017890	SO:0001583	missense	11022	exon6			AF227192	CCDS41394.1, CCDS41395.1	1q21	2013-01-23	2003-11-07		ENSG00000182134	ENSG00000182134		"""Tudor domain containing"""	11713	protein-coding gene	gene with protein product		609501	"""tudor and KH domain containing"""			10767542	Standard	NM_001083964		Approved	TDRD2	uc001eza.4	Q9Y2W6	OTTHUMG00000013062	ENST00000368822.1:c.778G>A	1.37:g.151751266C>T	ENSP00000357812:p.Asp260Asn	Somatic		Capture	Illumina HiSeq	Phase_I	150017890	NM_001083965	D3DV24|Q5SZR3|Q5SZR5|Q8N582|Q9NYV5	Missense_Mutation	SNP	ENST00000368822.1	37	CCDS41394.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.659789	0.29515	0.0	2.41E-4	ENSG00000182134	ENST00000368827;ENST00000368825;ENST00000368824;ENST00000368823;ENST00000368822;ENST00000458431;ENST00000440583	T;T;T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38;0.38;0.38	5.48	4.58	0.56647	.	0.248969	0.28262	N	0.015998	T	0.32010	0.0815	L	0.27053	0.805	0.21020	N	0.999804	P;P;D	0.71674	0.835;0.835;0.998	B;B;P	0.55222	0.118;0.118;0.771	T	0.09796	-1.0658	10	0.20519	T	0.43	-19.7742	10.3822	0.44119	0.0:0.9125:0.0:0.0875	.	215;256;260	Q5SZR5;Q5SZR4;Q9Y2W6	.;.;TDRKH_HUMAN	N	260;215;260;256;260;260;36	ENSP00000357819:D260N;ENSP00000357817:D215N;ENSP00000357815:D260N;ENSP00000357813:D256N;ENSP00000357812:D260N;ENSP00000395718:D260N;ENSP00000416645:D36N	ENSP00000357812:D260N	D	-	1	0	TDRKH	150017890	0.244000	0.23889	0.474000	0.27266	0.220000	0.24768	1.082000	0.30803	1.573000	0.49748	-0.128000	0.14901	GAC		0.547	TDRKH-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000036648.2	NM_006862	
LINGO4	339398	broad.mit.edu	37	1	151774970	151774970	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:151774970G>A	ENST00000368820.3	-	2	1148	c.211C>T	c.(211-213)Cgc>Tgc	p.R71C		NM_001004432.2	NP_001004432.1	Q6UY18	LIGO4_HUMAN	leucine rich repeat and Ig domain containing 4	71						integral component of membrane (GO:0016021)		p.R71C(1)		breast(2)|cervix(1)|endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			CCCCACAGGCGGTTCCCACTC	0.637																																					p.R71C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C211T	1						.						47.0	38.0	41.0					1																	151774970		2203	4300	6503	150041594	SO:0001583	missense	339398	exon2				CCDS30855.1	1q21.3	2013-01-11	2007-02-01	2007-02-01	ENSG00000213171	ENSG00000213171		"""Immunoglobulin superfamily / I-set domain containing"""	31814	protein-coding gene	gene with protein product		609794	"""leucine rich repeat neuronal 6D"""	LRRN6D			Standard	NM_001004432		Approved		uc001ezf.1	Q6UY18	OTTHUMG00000013059	ENST00000368820.3:c.211C>T	1.37:g.151774970G>A	ENSP00000357810:p.Arg71Cys	Somatic		Capture	Illumina HiSeq	Phase_I	150041594	NM_001004432		Missense_Mutation	SNP	ENST00000368820.3	37	CCDS30855.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.101817	0.37048	.	.	ENSG00000213171	ENST00000368820	T	0.60672	0.17	5.28	5.28	0.74379	.	0.273612	0.26510	N	0.023966	T	0.71871	0.3391	M	0.87617	2.895	0.49687	D	0.999811	D	0.89917	1.0	D	0.79784	0.993	T	0.76146	-0.3066	10	0.72032	D	0.01	.	9.7554	0.40500	0.0911:0.0:0.9089:0.0	.	71	Q6UY18	LIGO4_HUMAN	C	71	ENSP00000357810:R71C	ENSP00000357810:R71C	R	-	1	0	LINGO4	150041594	1.000000	0.71417	1.000000	0.80357	0.230000	0.25150	2.233000	0.43027	2.753000	0.94483	0.455000	0.32223	CGC		0.637	LINGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036639.1	XM_291387	
FLG	2312	broad.mit.edu	37	1	152285230	152285230	+	Missense_Mutation	SNP	C	C	T	rs139043400	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:152285230C>T	ENST00000368799.1	-	3	2167	c.2132G>A	c.(2131-2133)cGc>cAc	p.R711H	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	711	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.R711H(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)			GAGCTGGTGGCGGGATCCATG	0.552									Ichthyosis				-|||	2	0.000399361	0.0008	0.0	5008	,	,		20145	0.0		0.001	False		,,,				2504	0.0				p.R711H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2132A	1						.						384.0	383.0	384.0					1																	152285230		2203	4300	6503	150551854	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.2132G>A	1.37:g.152285230C>T	ENSP00000357789:p.Arg711His	Somatic		Capture	Illumina HiSeq	Phase_I	150551854	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	6.761	0.509323	0.12883	.	.	ENSG00000143631	ENST00000368799	T	0.04015	3.73	3.14	-2.44	0.06502	.	.	.	.	.	T	0.00906	0.0030	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47355	-0.9124	9	0.11794	T	0.64	-0.0835	7.4962	0.27490	0.0:0.534:0.0:0.466	.	711	P20930	FILA_HUMAN	H	711	ENSP00000357789:R711H	ENSP00000357789:R711H	R	-	2	0	FLG	150551854	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-3.031000	0.00637	-0.280000	0.09154	-0.201000	0.12746	CGC		0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
FLG	2312	broad.mit.edu	37	1	152286265	152286265	+	Missense_Mutation	SNP	C	C	T	rs147509025	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:152286265C>T	ENST00000368799.1	-	3	1132	c.1097G>A	c.(1096-1098)cGt>cAt	p.R366H	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	366	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.R366H(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)			AGTCTGTCCACGAGAGGAAGT	0.562									Ichthyosis				-|||	2	0.000399361	0.0008	0.0	5008	,	,		21181	0.0		0.0	False		,,,				2504	0.001				p.R366H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1097A	1						.	C	HIS/ARG	1,4405		0,1,2202	302.0	295.0	297.0		1097	-7.4	0.0	1	dbSNP_134	297	0,8600		0,0,4300	no	missense	FLG	NM_002016.1	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	366/4062	152286265	1,13005	2203	4300	6503	150552889	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.1097G>A	1.37:g.152286265C>T	ENSP00000357789:p.Arg366His	Somatic		Capture	Illumina HiSeq	Phase_I	150552889	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	-	5.713	0.316142	0.10789	2.27E-4	0.0	ENSG00000143631	ENST00000368799	T	0.00864	5.6	3.71	-7.42	0.01388	.	.	.	.	.	T	0.00210	0.0006	L	0.31926	0.97	0.09310	N	1	P	0.38335	0.627	B	0.27380	0.079	T	0.32295	-0.9912	9	0.33940	T	0.23	0.0404	6.9106	0.24333	0.0:0.4032:0.3719:0.2249	.	366	P20930	FILA_HUMAN	H	366	ENSP00000357789:R366H	ENSP00000357789:R366H	R	-	2	0	FLG	150552889	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.053000	0.00305	-2.754000	0.00373	-0.498000	0.04607	CGT		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
LCE2D	353141	broad.mit.edu	37	1	152636817	152636817	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:152636817G>A	ENST00000368784.1	+	2	291	c.236G>A	c.(235-237)cGt>cAt	p.R79H		NM_178430.2	NP_848517.1	Q5TA82	LCE2D_HUMAN	late cornified envelope 2D	79	Cys-rich.				keratinization (GO:0031424)			p.R79H(1)		large_intestine(1)|lung(7)|prostate(2)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CACAGGCCCCGTCTCTTCCAC	0.682																																					p.R79H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G236A	1						.						40.0	55.0	50.0					1																	152636817		2192	4279	6471	150903441	SO:0001583	missense	353141	exon2			BI670513	CCDS1018.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000187223	ENSG00000187223		"""Late cornified envelopes"""	16518	protein-coding gene	gene with protein product		612612	"""small proline rich-like (epidermal differentiation complex) 1A"""	SPRL1A		11698679	Standard	NM_178430		Approved	LEP12	uc001fag.4	Q5TA82	OTTHUMG00000014400	ENST00000368784.1:c.236G>A	1.37:g.152636817G>A	ENSP00000357773:p.Arg79His	Somatic		Capture	Illumina HiSeq	Phase_I	150903441	NM_178430	A1L4M8	Missense_Mutation	SNP	ENST00000368784.1	37	CCDS1018.1	.	.	.	.	.	.	.	.	.	.	g	9.016	0.983678	0.18889	.	.	ENSG00000187223	ENST00000368784	T	0.04406	3.63	2.69	-3.13	0.05266	.	.	.	.	.	T	0.00666	0.0022	N	0.10809	0.05	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45614	-0.9249	9	0.20519	T	0.43	.	7.2396	0.26090	0.6444:0.0:0.3556:0.0	.	79	Q5TA82	LCE2D_HUMAN	H	79	ENSP00000357773:R79H	ENSP00000357773:R79H	R	+	2	0	LCE2D	150903441	0.000000	0.05858	0.000000	0.03702	0.435000	0.31806	-3.843000	0.00352	-0.961000	0.03609	-0.680000	0.03767	CGT		0.682	LCE2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040058.1	NM_178430	
SPRR2A	6700	broad.mit.edu	37	1	153029109	153029109	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:153029109G>A	ENST00000392653.2	-	2	188	c.103C>T	c.(103-105)Ccc>Tcc	p.P35S		NM_005988.2	NP_005979.1	P35326	SPR2A_HUMAN	small proline-rich protein 2A	35	3 X 9 AA tandem repeats of P-K-C-P-[EQ]- P-C-P-P.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)		p.P35S(1)		large_intestine(2)|ovary(1)	3	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGTGGGCAGGGCTCAGGGCAC	0.612																																					p.P35S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C103T	1						.						66.0	63.0	64.0					1																	153029109		2202	4278	6480	151295733	SO:0001583	missense	6700	exon2			X53064	CCDS1034.1	1q21-q22	2008-02-05			ENSG00000241794	ENSG00000241794			11261	protein-coding gene	gene with protein product		182267				8325635	Standard	NM_005988		Approved		uc001fbd.3	P35326	OTTHUMG00000014395	ENST00000392653.2:c.103C>T	1.37:g.153029109G>A	ENSP00000376423:p.Pro35Ser	Somatic		Capture	Illumina HiSeq	Phase_I	151295733	NM_005988	B2R4T3|D3DV35|Q5T529	Missense_Mutation	SNP	ENST00000392653.2	37	CCDS1034.1	.	.	.	.	.	.	.	.	.	.	G	10.52	1.372578	0.24857	.	.	ENSG00000241794	ENST00000392653	T	0.52754	0.65	2.79	2.79	0.32731	.	0.000000	0.32671	N	0.005794	T	0.51941	0.1704	.	.	.	0.19300	N	0.999974	D	0.76494	0.999	D	0.83275	0.996	T	0.34030	-0.9845	9	0.87932	D	0	.	9.1956	0.37226	0.0:0.0:1.0:0.0	.	35	P35326	SPR2A_HUMAN	S	35	ENSP00000376423:P35S	ENSP00000376423:P35S	P	-	1	0	SPRR2A	151295733	1.000000	0.71417	0.490000	0.27465	0.402000	0.30811	2.662000	0.46766	1.551000	0.49450	0.400000	0.26472	CCC		0.612	SPRR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040049.1	NM_005988	
S100A16	140576	broad.mit.edu	37	1	153580069	153580069	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:153580069C>T	ENST00000368704.1	-	3	438	c.253G>A	c.(253-255)Ggc>Agc	p.G85S	S100A16_ENST00000474991.1_5'UTR|S100A16_ENST00000368706.4_Missense_Mutation_p.G85S|S100A16_ENST00000368703.2_Missense_Mutation_p.G85S|S100A16_ENST00000368705.2_Missense_Mutation_p.G85S			Q96FQ6	S10AG_HUMAN	S100 calcium binding protein A16	85	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				response to calcium ion (GO:0051592)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.G85S(1)		breast(1)|large_intestine(1)|prostate(1)	3	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCGGTGATGCCGCCTATCAAG	0.587																																					p.G85S	Melanoma(71;1388 1729 37039 46098)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G253A	1						.						105.0	93.0	97.0					1																	153580069		2203	4300	6503	151846693	SO:0001583	missense	140576	exon3			BC010541	CCDS1045.1	1q21	2014-01-28			ENSG00000188643	ENSG00000188643		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	20441	protein-coding gene	gene with protein product						9417904	Standard	NM_080388		Approved	S100F, DT1P1A7, MGC17528	uc001fcd.1	Q96FQ6	OTTHUMG00000013545	ENST00000368704.1:c.253G>A	1.37:g.153580069C>T	ENSP00000357693:p.Gly85Ser	Somatic		Capture	Illumina HiSeq	Phase_I	151846693	NM_080388	A8K439|D3DV52|Q5RHS6	Missense_Mutation	SNP	ENST00000368704.1	37	CCDS1045.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.289967	0.40494	.	.	ENSG00000188643	ENST00000368704;ENST00000368705;ENST00000368706;ENST00000368703	T;T;T;T	0.06449	3.3;3.3;3.3;3.3	4.38	4.38	0.52667	EF-hand-like domain (1);	0.000000	0.52532	D	0.000064	T	0.04048	0.0113	N	0.17278	0.47	0.44402	D	0.99731	D	0.76494	0.999	P	0.57101	0.813	T	0.57370	-0.7823	10	0.13108	T	0.6	-14.7381	14.8714	0.70459	0.0:1.0:0.0:0.0	.	85	Q96FQ6	S10AG_HUMAN	S	85	ENSP00000357693:G85S;ENSP00000357694:G85S;ENSP00000357695:G85S;ENSP00000357692:G85S	ENSP00000357692:G85S	G	-	1	0	S100A16	151846693	0.995000	0.38212	0.994000	0.49952	0.949000	0.60115	4.162000	0.58177	2.462000	0.83206	0.456000	0.33151	GGC		0.587	S100A16-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037713.1	NM_080388	
DENND4B	9909	broad.mit.edu	37	1	153909107	153909107	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:153909107G>A	ENST00000361217.4	-	16	2768	c.2350C>T	c.(2350-2352)Cgg>Tgg	p.R784W		NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	784					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.R672W(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)			GGTGCCGACCGCACATAGGCA	0.637																																					p.R784W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2350T	1						.						44.0	48.0	47.0					1																	153909107		2129	4225	6354	152175731	SO:0001583	missense	9909	exon16			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.2350C>T	1.37:g.153909107G>A	ENSP00000354597:p.Arg784Trp	Somatic		Capture	Illumina HiSeq	Phase_I	152175731	NM_014856	Q5T4K0	Missense_Mutation	SNP	ENST00000361217.4	37	CCDS44228.1	.	.	.	.	.	.	.	.	.	.	g	16.08	3.020699	0.54576	.	.	ENSG00000198837	ENST00000361217;ENST00000368646	T;T	0.08634	3.07;3.07	4.77	3.85	0.44370	.	0.000000	0.85682	D	0.000000	T	0.16342	0.0393	M	0.69823	2.125	0.58432	D	0.999997	D	0.89917	1.0	D	0.66979	0.948	T	0.01074	-1.1460	10	0.87932	D	0	-23.0169	13.2501	0.60048	0.0:0.0:0.8396:0.1604	.	784	O75064	DEN4B_HUMAN	W	784;795	ENSP00000354597:R784W;ENSP00000357635:R795W	ENSP00000354597:R784W	R	-	1	2	DENND4B	152175731	0.005000	0.15991	0.958000	0.39756	0.401000	0.30781	1.476000	0.35420	1.196000	0.43129	0.462000	0.41574	CGG		0.637	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806	
UBAP2L	9898	broad.mit.edu	37	1	154228170	154228170	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:154228170C>T	ENST00000361546.2	+	17	2138	c.2096C>T	c.(2095-2097)aCg>aTg	p.T699M	UBAP2L_ENST00000271877.7_Missense_Mutation_p.T710M|AL590431.1_ENST00000517008.1_RNA|UBAP2L_ENST00000343815.6_Missense_Mutation_p.T699M|UBAP2L_ENST00000428931.1_Missense_Mutation_p.T699M			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	699					binding of sperm to zona pellucida (GO:0007339)		poly(A) RNA binding (GO:0044822)	p.T699M(1)|p.T195M(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)			ACGTTATCTACGCAGCAGAAT	0.443																																					p.T699M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2096T	1						.						216.0	194.0	201.0					1																	154228170		2203	4300	6503	152494794	SO:0001583	missense	9898	exon18			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.2096C>T	1.37:g.154228170C>T	ENSP00000355343:p.Thr699Met	Somatic		Capture	Illumina HiSeq	Phase_I	152494794	NM_014847	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	37	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	C	18.06	3.539919	0.65085	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000456955;ENST00000433006;ENST00000271877;ENST00000361546	T;T;T;T	0.12569	2.67;2.67;2.68;2.67	5.58	5.58	0.84498	.	0.175676	0.49916	D	0.000130	T	0.17152	0.0412	N	0.22421	0.69	0.51012	D	0.999908	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.80764	0.985;0.994;0.994;0.994;0.985	T	0.05289	-1.0894	10	0.40728	T	0.16	-6.2446	18.5347	0.91006	0.0:1.0:0.0:0.0	.	613;710;692;699;699	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	M	699;699;195;195;710;699	ENSP00000345308:T699M;ENSP00000389445:T699M;ENSP00000271877:T710M;ENSP00000355343:T699M	ENSP00000271877:T710M	T	+	2	0	UBAP2L	152494794	0.998000	0.40836	0.965000	0.40720	0.875000	0.50365	5.599000	0.67592	2.627000	0.88993	0.655000	0.94253	ACG		0.443	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847	
KAZN	23254	broad.mit.edu	37	1	15430595	15430595	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:15430595C>T	ENST00000376030.2	+	13	2252	c.1958C>T	c.(1957-1959)gCc>gTc	p.A653V		NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	653	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)		p.A653V(1)|p.A100V(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						AATGCCGAGGCCATGGCCACT	0.637																																					p.A653V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1958T	1						.						67.0	50.0	56.0					1																	15430595		2203	4300	6503	15303182	SO:0001583	missense	23254	exon13			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.1958C>T	1.37:g.15430595C>T	ENSP00000365198:p.Ala653Val	Somatic		Capture	Illumina HiSeq	Phase_I	15303182	NM_201628	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	37	CCDS152.2	.	.	.	.	.	.	.	.	.	.	C	16.74	3.206339	0.58343	.	.	ENSG00000189337	ENST00000376030	D	0.84730	-1.89	5.52	5.52	0.82312	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.000000	0.64402	D	0.000005	T	0.74473	0.3721	N	0.20986	0.625	0.80722	D	1	P	0.45176	0.852	B	0.34138	0.176	T	0.79845	-0.1631	10	0.72032	D	0.01	-29.9923	14.9421	0.71003	0.0:1.0:0.0:0.0	.	653	Q674X7	KAZRN_HUMAN	V	653	ENSP00000365198:A653V	ENSP00000365198:A653V	A	+	2	0	KAZN	15303182	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.971000	0.49248	2.591000	0.87537	0.585000	0.79938	GCC		0.637	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999	
IL6R	3570	broad.mit.edu	37	1	154408478	154408478	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:154408478G>A	ENST00000368485.3	+	6	1278	c.841G>A	c.(841-843)Gac>Aac	p.D281N	IL6R_ENST00000344086.4_Missense_Mutation_p.D281N|IL6R_ENST00000507256.1_Intron	NM_000565.3	NP_000556.1	P08887	IL6RA_HUMAN	interleukin 6 receptor	281	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				acute-phase response (GO:0006953)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|endocrine pancreas development (GO:0031018)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatic immune response (GO:0002384)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of interleukin-8 production (GO:0032717)|neutrophil mediated immunity (GO:0002446)|positive regulation of activation of Janus kinase activity (GO:0010536)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|response to cytokine (GO:0034097)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)|plasma membrane (GO:0005886)	ciliary neurotrophic factor binding (GO:0070119)|cytokine receptor activity (GO:0004896)|enzyme binding (GO:0019899)|interleukin-6 binding (GO:0019981)|protein homodimerization activity (GO:0042803)	p.D281N(1)	IL6R/ATP8B2(2)	breast(2)|large_intestine(1)|ovary(3)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)		Tocilizumab(DB06273)	TGTCATCCACGACGCCTGGAG	0.672																																					p.D281N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G841A	1						.						56.0	50.0	52.0					1																	154408478		2203	4299	6502	152675102	SO:0001583	missense	3570	exon6			X12830	CCDS1067.1, CCDS1068.1, CCDS72927.1	1q21	2013-01-11			ENSG00000160712	ENSG00000160712		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6019	protein-coding gene	gene with protein product		147880					Standard	NM_000565		Approved	CD126	uc001fez.2	P08887	OTTHUMG00000036073	ENST00000368485.3:c.841G>A	1.37:g.154408478G>A	ENSP00000357470:p.Asp281Asn	Somatic		Capture	Illumina HiSeq	Phase_I	152675102	NM_181359	A8KAE8|B2R6V4|Q16202|Q53EQ7|Q5FWG2|Q5VZ23	Missense_Mutation	SNP	ENST00000368485.3	37	CCDS1067.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.524534	0.85600	.	.	ENSG00000160712	ENST00000368485;ENST00000344086	T;T	0.23754	2.35;1.89	5.29	5.29	0.74685	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.46014	0.1371	M	0.83603	2.65	0.44956	D	0.997974	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.991	T	0.46884	-0.9159	10	0.49607	T	0.09	-34.9148	14.4682	0.67497	0.0:0.0:1.0:0.0	.	281;281	P08887-2;P08887	.;IL6RA_HUMAN	N	281	ENSP00000357470:D281N;ENSP00000340589:D281N	ENSP00000340589:D281N	D	+	1	0	IL6R	152675102	0.987000	0.35691	0.894000	0.35097	0.700000	0.40528	4.783000	0.62403	2.489000	0.83994	0.655000	0.94253	GAC		0.672	IL6R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087911.1	NM_000565	
PMVK	10654	broad.mit.edu	37	1	154901519	154901519	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:154901519C>T	ENST00000368467.3	-	3	598	c.293G>A	c.(292-294)gGc>gAc	p.G98D		NM_006556.3	NP_006547.1	Q15126	PMVK_HUMAN	phosphomevalonate kinase	98					cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|response to cholesterol (GO:0070723)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|phosphomevalonate kinase activity (GO:0004631)	p.G98D(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.142)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CTGGGAGATGCCCTCCACAAT	0.567																																					p.G98D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G293A	1						.						142.0	127.0	132.0					1																	154901519		2203	4300	6503	153168143	SO:0001583	missense	10654	exon3			L77213	CCDS1073.1	1q21.3	2012-09-20			ENSG00000163344	ENSG00000163344	2.7.4.2		9141	protein-coding gene	gene with protein product		607622				8663599, 10191291	Standard	NM_006556		Approved	PMK, PMKA, HUMPMKI	uc001ffq.3	Q15126	OTTHUMG00000037415	ENST00000368467.3:c.293G>A	1.37:g.154901519C>T	ENSP00000357452:p.Gly98Asp	Somatic		Capture	Illumina HiSeq	Phase_I	153168143	NM_006556	Q5TZW9	Missense_Mutation	SNP	ENST00000368467.3	37	CCDS1073.1	.	.	.	.	.	.	.	.	.	.	C	7.591	0.670785	0.14776	.	.	ENSG00000163344	ENST00000368467	T	0.41400	1.0	5.88	4.98	0.66077	.	0.184963	0.47852	D	0.000213	T	0.17109	0.0411	L	0.40543	1.245	0.36958	D	0.893174	B	0.30605	0.287	B	0.31751	0.135	T	0.05869	-1.0859	10	0.17369	T	0.5	-19.9065	10.9694	0.47431	0.0:0.9147:0.0:0.0853	.	98	Q15126	PMVK_HUMAN	D	98	ENSP00000357452:G98D	ENSP00000357452:G98D	G	-	2	0	PMVK	153168143	0.951000	0.32395	0.974000	0.42286	0.057000	0.15508	2.025000	0.41059	1.496000	0.48567	0.655000	0.94253	GGC		0.567	PMVK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091088.1	NM_006556	
THBS3	7059	broad.mit.edu	37	1	155166968	155166968	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:155166968G>A	ENST00000368378.3	-	21	2556	c.2536C>T	c.(2536-2538)Cga>Tga	p.R846*	RP11-263K19.4_ENST00000454348.1_RNA|THBS3_ENST00000457183.2_Nonsense_Mutation_p.R726*|THBS3_ENST00000541576.1_Nonsense_Mutation_p.R243*|RP11-263K19.4_ENST00000453136.1_RNA|RP11-263K19.4_ENST00000447623.1_RNA|MIR92B_ENST00000607575.1_RNA|RP11-263K19.4_ENST00000436772.1_RNA|THBS3_ENST00000541990.1_Nonsense_Mutation_p.R375*	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	846	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.R846*(1)		breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		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)			AGGGCATTTCGGAGGTGCTCA	0.577																																					p.R846X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2536T	1						.						89.0	84.0	85.0					1																	155166968		2203	4300	6503	153433592	SO:0001587	stop_gained	7059	exon21			L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.2536C>T	1.37:g.155166968G>A	ENSP00000357362:p.Arg846*	Somatic		Capture	Illumina HiSeq	Phase_I	153433592	NM_007112	B1AVR8|B4DQ20|Q8WV34	Nonsense_Mutation	SNP	ENST00000368378.3	37	CCDS1099.1	.	.	.	.	.	.	.	.	.	.	G	40	8.025644	0.98616	.	.	ENSG00000169231	ENST00000368378;ENST00000541576;ENST00000457183;ENST00000541990	.	.	.	4.4	3.47	0.39725	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.3435	11.4721	0.50275	0.0:0.0:0.8089:0.1911	.	.	.	.	X	846;243;726;375	.	ENSP00000357362:R846X	R	-	1	2	THBS3	153433592	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	2.353000	0.44089	1.184000	0.42957	0.491000	0.48974	CGA		0.577	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112	
GBA	2629	broad.mit.edu	37	1	155207999	155207999	+	Silent	SNP	C	C	T	rs75370695		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:155207999C>T	ENST00000327247.5	-	7	919	c.687G>A	c.(685-687)gcG>gcA	p.A229A	GBA_ENST00000536770.1_Silent_p.A116A|AL713999.1_ENST00000401290.1_RNA|GBA_ENST00000493842.1_5'Flank|GBA_ENST00000368373.3_Silent_p.A229A|GBA_ENST00000428024.3_Silent_p.A142A|GBA_ENST00000427500.3_Silent_p.A180A	NM_001005741.2|NM_001005742.2	NP_001005741.1|NP_001005742.1	P04062	GLCM_HUMAN	glucosidase, beta, acid	229			A -> E (in GD; type 2).|A -> T (in GD). {ECO:0000269|PubMed:10796875}.		carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glucosylceramide catabolic process (GO:0006680)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of MAP kinase activity (GO:0043407)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of water loss via skin (GO:0033561)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to pH (GO:0009268)|response to testosterone (GO:0033574)|response to thyroid hormone (GO:0097066)|skin morphogenesis (GO:0043589)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)|termination of signal transduction (GO:0023021)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)	glucosylceramidase activity (GO:0004348)|receptor binding (GO:0005102)	p.A229A(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	26	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)		Velaglucerase alfa(DB06720)	TCCCATTCACCGCTCCATTGG	0.572									Gaucher disease type I																												p.A229A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G687A	1						.	C	,,,,	2,4404		0,2,2201	91.0	78.0	82.0		687,687,687,426,540	-0.6	0.9	1	dbSNP_131	82	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GBA	NM_000157.3,NM_001005741.2,NM_001005742.2,NM_001171811.1,NM_001171812.1	,,,,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,,,,	229/537,229/537,229/537,142/450,180/488	155207999	2,13004	2203	4300	6503	153474623	SO:0001819	synonymous_variant	2629	exon6	Familial Cancer Database	glucocerebrosidase insufficiency	M19285	CCDS1102.1, CCDS53373.1, CCDS53374.1	1q22	2010-01-19	2010-01-19		ENSG00000177628	ENSG00000177628	3.2.1.21		4177	protein-coding gene	gene with protein product		606463	"""glucosylceramidase"", ""glucosidase, beta; acid (includes glucosylceramidase)"""	GLUC		3359914	Standard	NM_001005742		Approved	GBA1	uc001fjl.3	P04062	OTTHUMG00000035841	ENST00000327247.5:c.687G>A	1.37:g.155207999C>T		Somatic		Capture	Illumina HiSeq	Phase_I	153474623	NM_000157	A8K796|B7Z5G2|B7Z6S1|J3KQG4|J3KQK9|Q16545|Q4VX22|Q6I9R6|Q9UMJ8	Silent	SNP	ENST00000327247.5	37	CCDS1102.1																																																																																				0.572	GBA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087204.1	NM_000157	
ASH1L	55870	broad.mit.edu	37	1	155450332	155450332	+	Missense_Mutation	SNP	G	G	A	rs150671158		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:155450332G>A	ENST00000368346.3	-	3	2968	c.2329C>T	c.(2329-2331)Cgc>Tgc	p.R777C	ASH1L_ENST00000392403.3_Missense_Mutation_p.R777C			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	777					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.R777C(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)			GGCAATCGGCGTTTAAGGAAG	0.393													G|||	1	0.000199681	0.0	0.0	5008	,	,		19565	0.0		0.001	False		,,,				2504	0.0				p.R777C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2329T	1						.	G	CYS/ARG	0,4402		0,0,2201	154.0	154.0	154.0		2329	4.5	1.0	1	dbSNP_134	154	1,8595	1.2+/-3.3	0,1,4297	no	missense	ASH1L	NM_018489.2	180	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	benign	777/2965	155450332	1,12997	2201	4298	6499	153716956	SO:0001583	missense	55870	exon3			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.2329C>T	1.37:g.155450332G>A	ENSP00000357330:p.Arg777Cys	Somatic		Capture	Illumina HiSeq	Phase_I	153716956	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	9.878	1.200863	0.22121	0.0	1.16E-4	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.88896	-2.44;-2.44	5.44	4.46	0.54185	.	0.222920	0.38548	N	0.001655	T	0.65554	0.2702	N	0.03608	-0.345	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.65269	-0.6209	10	0.48119	T	0.1	.	12.4935	0.55914	0.0894:0.0:0.9106:0.0	.	777;777	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	C	777	ENSP00000357330:R777C;ENSP00000376204:R777C	ENSP00000357330:R777C	R	-	1	0	ASH1L	153716956	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.120000	0.57897	2.836000	0.97738	0.650000	0.86243	CGC		0.393	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
ASH1L	55870	broad.mit.edu	37	1	155450542	155450542	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:155450542T>C	ENST00000368346.3	-	3	2758	c.2119A>G	c.(2119-2121)Aaa>Gaa	p.K707E	ASH1L_ENST00000392403.3_Missense_Mutation_p.K707E			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	707					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.K707E(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)			TTTAATGGTTTGGACTGCAAA	0.393																																					p.K707E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2119G	1						.						43.0	45.0	45.0					1																	155450542		2199	4299	6498	153717166	SO:0001583	missense	55870	exon3			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.2119A>G	1.37:g.155450542T>C	ENSP00000357330:p.Lys707Glu	Somatic		Capture	Illumina HiSeq	Phase_I	153717166	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		.	.	.	.	.	.	.	.	.	.	T	18.89	3.719103	0.68844	.	.	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.91124	-2.79;-2.79	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	D	0.88691	0.6505	N	0.14661	0.345	0.80722	D	1	D;D	0.67145	0.993;0.996	D;D	0.76071	0.971;0.987	D	0.91646	0.5331	10	0.62326	D	0.03	.	15.2128	0.73238	0.0:0.0:0.0:1.0	.	707;707	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	E	707	ENSP00000357330:K707E;ENSP00000376204:K707E	ENSP00000357330:K707E	K	-	1	0	ASH1L	153717166	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.915000	0.69973	2.252000	0.74401	0.528000	0.53228	AAA		0.393	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
MEX3A	92312	broad.mit.edu	37	1	156047145	156047145	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:156047145G>A	ENST00000532414.2	-	2	782	c.783C>T	c.(781-783)agC>agT	p.S261S	AL355388.1_ENST00000410679.1_RNA|MEX3A_ENST00000442784.1_5'UTR	NM_001093725.1	NP_001087194.1	A1L020	MEX3A_HUMAN	mex-3 RNA binding family member A	261	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.S380S(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9	Hepatocellular(266;0.158)|all_neural(408;0.195)					CGCGGTCACGGCTTGGTGTGA	0.642																																					p.S261S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C783T	1						.						141.0	163.0	156.0					1																	156047145		2185	4283	6468	154313769	SO:0001819	synonymous_variant	92312	exon2			AK024097	CCDS53377.1	1q22	2013-09-24	2013-08-21	2007-07-18	ENSG00000254726	ENSG00000254726		"""RING-type (C3HC4) zinc fingers"", ""Mex-3 homologs"""	33482	protein-coding gene	gene with protein product		611007	"""ring finger and KH domain containing 4"", ""mex-3 homolog A (C. elegans)"""	RKHD4		17267406	Standard	NM_001093725		Approved		uc001fnd.4	A1L020	OTTHUMG00000017465	ENST00000532414.2:c.783C>T	1.37:g.156047145G>A		Somatic		Capture	Illumina HiSeq	Phase_I	154313769	NM_001093725		Silent	SNP	ENST00000532414.2	37	CCDS53377.1																																																																																				0.642	MEX3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046218.3	NM_001093725	
CCT3	7203	broad.mit.edu	37	1	156279061	156279061	+	Missense_Mutation	SNP	C	C	T	rs373870763		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:156279061C>T	ENST00000295688.3	-	14	1847	c.1567G>A	c.(1567-1569)Gtt>Att	p.V523I	CCT3_ENST00000368261.3_Missense_Mutation_p.V478I|CCT3_ENST00000472765.2_Missense_Mutation_p.V478I|CCT3_ENST00000368259.2_Missense_Mutation_p.V485I	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	523					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)	p.V523I(1)		endometrium(4)|large_intestine(1)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					TGGCCTGAAACGATGTCATCA	0.507																																					p.V485I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1453A	1						.	C	ILE/VAL,ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	110.0	111.0	110.0		1453,1567	5.4	1.0	1		110	0,8600		0,0,4300	no	missense,missense	CCT3	NM_001008800.2,NM_005998.4	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	485/508,523/546	156279061	1,13005	2203	4300	6503	154545685	SO:0001583	missense	7203	exon12			BC008019	CCDS1140.2, CCDS30888.1	1q23	2011-09-02			ENSG00000163468	ENSG00000163468		"""Heat Shock Proteins / Chaperonins"""	1616	protein-coding gene	gene with protein product		600114		TRIC5		8110840	Standard	NM_005998		Approved	Cctg	uc001fol.2	P49368	OTTHUMG00000024061	ENST00000295688.3:c.1567G>A	1.37:g.156279061C>T	ENSP00000295688:p.Val523Ile	Somatic		Capture	Illumina HiSeq	Phase_I	154545685	NM_001008800	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	37	CCDS1140.2	.	.	.	.	.	.	.	.	.	.	C	17.83	3.485835	0.63962	2.27E-4	0.0	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765	T;T;T;T	0.73681	-0.77;-0.77;-0.77;-0.77	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.71239	0.3316	L	0.45285	1.41	0.58432	D	0.999997	P;D;D	0.89917	0.466;1.0;0.959	B;D;P	0.91635	0.059;0.999;0.61	T	0.67098	-0.5756	10	0.06891	T	0.86	-28.1331	14.616	0.68549	0.0:1.0:0.0:0.0	.	485;522;523	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	I	523;485;478;478	ENSP00000295688:V523I;ENSP00000357242:V485I;ENSP00000357244:V478I;ENSP00000431543:V478I	ENSP00000295688:V523I	V	-	1	0	CCT3	154545685	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.253000	0.78320	2.827000	0.97445	0.650000	0.86243	GTT		0.507	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998	
RHBG	57127	broad.mit.edu	37	1	156351711	156351711	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:156351711A>G	ENST00000368249.1	+	6	993	c.955A>G	c.(955-957)Acg>Gcg	p.T319A	RHBG_ENST00000537040.1_Missense_Mutation_p.T157A|RHBG_ENST00000451864.2_Intron|RHBG_ENST00000368246.2_Missense_Mutation_p.T319A|RHBG_ENST00000400992.2_Missense_Mutation_p.T287A|RHBG_ENST00000255013.3_Missense_Mutation_p.T250A	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	319					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)	p.T319A(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					GACTGTCTCCACGCTGGGGTA	0.577																																					p.T319A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A955G	1						.						92.0	102.0	99.0					1																	156351711		2066	4209	6275	154618335	SO:0001583	missense	57127	exon6			AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"""Solute carriers"""	14572	protein-coding gene	gene with protein product		607079	"""Rhesus blood group, B glycoprotein"""			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.955A>G	1.37:g.156351711A>G	ENSP00000357232:p.Thr319Ala	Somatic		Capture	Illumina HiSeq	Phase_I	154618335	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Missense_Mutation	SNP	ENST00000368249.1	37		.	.	.	.	.	.	.	.	.	.	A	17.50	3.405817	0.62288	.	.	ENSG00000132677	ENST00000368249;ENST00000368246;ENST00000537040;ENST00000400992;ENST00000255013	T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99	4.44	4.44	0.53790	Ammonium transporter AmtB-like (3);	0.177905	0.49305	D	0.000151	T	0.23649	0.0572	M	0.69523	2.12	0.80722	D	1	D;P;P;P	0.56746	0.977;0.776;0.927;0.501	P;B;P;B	0.57152	0.814;0.396;0.523;0.342	T	0.04796	-1.0926	10	0.56958	D	0.05	-7.0559	6.5343	0.22344	0.8933:0.0:0.1067:0.0	.	319;157;287;356	Q9H310;F5GWZ4;Q9H310-3;Q5SZW5	RHBG_HUMAN;.;.;.	A	319;319;157;287;250	ENSP00000357232:T319A;ENSP00000357229:T319A;ENSP00000441197:T157A;ENSP00000383777:T287A;ENSP00000255013:T250A	ENSP00000255013:T250A	T	+	1	0	RHBG	154618335	0.997000	0.39634	1.000000	0.80357	0.983000	0.72400	2.654000	0.46699	1.853000	0.53794	0.459000	0.35465	ACG		0.577	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
MEF2D	4209	broad.mit.edu	37	1	156446841	156446841	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:156446841A>G	ENST00000348159.4	-	7	1298	c.818T>C	c.(817-819)aTc>aCc	p.I273T	MEF2D_ENST00000464356.2_Missense_Mutation_p.I272T|MEF2D_ENST00000368240.2_Missense_Mutation_p.I273T|MEF2D_ENST00000360595.3_Missense_Mutation_p.I273T|MEF2D_ENST00000353795.3_Missense_Mutation_p.I227T|MEF2D_ENST00000340875.5_Missense_Mutation_p.I272T	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	273					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I273T(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTGGGAAGTGATGACTCGCAG	0.602																																					p.I273T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T818C	1						.						89.0	85.0	86.0					1																	156446841		2203	4300	6503	154713465	SO:0001583	missense	4209	exon7			BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"""Myocyte enhancer factors"""	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.818T>C	1.37:g.156446841A>G	ENSP00000271555:p.Ile273Thr	Somatic		Capture	Illumina HiSeq	Phase_I	154713465	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Missense_Mutation	SNP	ENST00000348159.4	37	CCDS1143.1	.	.	.	.	.	.	.	.	.	.	A	19.52	3.842348	0.71488	.	.	ENSG00000116604	ENST00000348159;ENST00000340875;ENST00000368240;ENST00000353795;ENST00000360595;ENST00000454816	T;T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45;1.45	5.4	5.4	0.78164	.	0.049015	0.85682	D	0.000000	T	0.46444	0.1393	M	0.72118	2.19	0.58432	D	0.999997	D;P;D	0.89917	1.0;0.938;0.967	D;P;P	0.83275	0.996;0.694;0.888	T	0.51756	-0.8665	10	0.72032	D	0.01	-22.3577	14.2593	0.66073	1.0:0.0:0.0:0.0	.	278;273;273	Q4LE66;Q14814;Q14814-4	.;MEF2D_HUMAN;.	T	273;272;273;227;273;272	ENSP00000271555:I273T;ENSP00000343159:I272T;ENSP00000357223:I273T;ENSP00000344705:I227T;ENSP00000353803:I273T;ENSP00000388505:I272T	ENSP00000343159:I272T	I	-	2	0	MEF2D	154713465	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.843000	0.75384	2.042000	0.60477	0.533000	0.62120	ATC		0.602	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920	
NTRK1	4914	broad.mit.edu	37	1	156849792	156849792	+	Splice_Site	SNP	T	T	G	rs199905593		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:156849792T>G	ENST00000524377.1	+	16	2089	c.2048T>G	c.(2047-2049)gTg>gGg	p.V683G	NTRK1_ENST00000358660.3_Splice_Site_p.V680G|NTRK1_ENST00000392302.2_Splice_Site_p.V647G|NTRK1_ENST00000368196.3_Splice_Site_p.V677G	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	683	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.V683G(1)|p.V647G(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)	CCGTGGCAGGTGGGAGGCCGC	0.612			T	"""TPM3, TPR, TFG"""	papillary thyroid					TSP Lung(10;0.080)																											p.V677G			Dom	yes		1	1q21-q22	4914	"""neurotrophic tyrosine kinase, receptor, type 1"""		E	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T2030G	1						.						41.0	43.0	43.0					1																	156849792		2201	4299	6500	155116416	SO:0001630	splice_region_variant	4914	exon15			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.2047-1T>G	1.37:g.156849792T>G		None		Capture	Illumina HiSeq	Phase_I	155116416	NM_001012331	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	37	CCDS1161.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.286928	0.80803	.	.	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68	4.13	4.13	0.48395	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.50627	D	0.000115	D	0.83321	0.5229	L	0.39898	1.24	0.80722	D	1	D;D;D;D	0.89917	1.0;0.991;0.961;0.998	D;P;P;D	0.97110	1.0;0.813;0.489;0.94	D	0.85814	0.1381	10	0.72032	D	0.01	.	12.4091	0.55457	0.0:0.0:0.0:1.0	.	680;677;683;647	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	G	647;677;683;680	ENSP00000376120:V647G;ENSP00000357179:V677G;ENSP00000431418:V683G;ENSP00000351486:V680G	ENSP00000351486:V680G	V	+	2	0	NTRK1	155116416	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.382000	0.79729	1.869000	0.54173	0.459000	0.35465	GTG		0.612	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529	Missense_Mutation
MMP23B	8510	broad.mit.edu	37	1	1569946	1569946	+	Missense_Mutation	SNP	G	G	A	rs557033134		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:1569946G>A	ENST00000356026.5	+	8	1242	c.1118G>A	c.(1117-1119)cGc>cAc	p.R373H	MMP23B_ENST00000378675.3_3'UTR			O75900	MMP23_HUMAN	matrix metallopeptidase 23B	373	Ig-like C2-type.				proteolysis (GO:0006508)|reproduction (GO:0000003)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R373H(1)		large_intestine(1)	1	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-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;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)	Marimastat(DB00786)	TGCGTGGTGCGCCGCCAGCAG	0.652													.|||	1	0.000199681	0.0	0.0	5008	,	,		14894	0.001		0.0	False		,,,				2504	0.0				p.R373H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1118A	1						.						4.0	7.0	6.0					1																	1569946		1388	3530	4918	1559809	SO:0001583	missense	8510	exon8				CCDS30559.1	1p36.3	2013-01-11	2005-08-08		ENSG00000189409	ENSG00000189409		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7171	protein-coding gene	gene with protein product	"""matrix metalloproteinase 22"", ""femalysin"", ""matrix metalloproteinase in the female reproductive tract"""	603321	"""matrix metalloproteinase 23B"""	MMP22		9740677, 9750192	Standard	XM_005244810		Approved	MIFR, MIFR-1	uc001agp.3	O75900	OTTHUMG00000074713	ENST00000356026.5:c.1118G>A	1.37:g.1569946G>A	ENSP00000348308:p.Arg373His	Somatic		Capture	Illumina HiSeq	Phase_I	1559809	NM_006983	A2AGN0|A2AGN1|O75894|O75895|Q5QPQ8|Q76P96|Q7LDM6|Q7LDM7|Q9UBR9|Q9UJK8	Missense_Mutation	SNP	ENST00000356026.5	37	CCDS30559.1	.	.	.	.	.	.	.	.	.	.	G	5.490	0.275354	0.10403	.	.	ENSG00000189409	ENST00000356026;ENST00000412415	T	0.12774	2.65	3.62	2.59	0.31030	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.065249	0.56097	U	0.000021	T	0.03263	0.0095	N	0.02539	-0.55	0.80722	D	1	P	0.34724	0.465	B	0.21151	0.033	T	0.43475	-0.9389	10	0.30078	T	0.28	-34.4688	3.449	0.07491	0.3889:0.0:0.6111:0.0	.	373	O75900	MMP23_HUMAN	H	373;413	ENSP00000348308:R373H	ENSP00000348308:R373H	R	+	2	0	MMP23B	1559809	1.000000	0.71417	0.340000	0.25575	0.112000	0.19704	3.010000	0.49559	1.819000	0.53055	0.462000	0.41574	CGC		0.652	MMP23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158492.2	NM_006983	
FCRL4	83417	broad.mit.edu	37	1	157556164	157556164	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:157556164C>T	ENST00000271532.1	-	6	1064	c.929G>A	c.(928-930)tGc>tAc	p.C310Y	FCRL4_ENST00000448509.2_5'UTR	NM_031282.2	NP_112572.1	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4	310	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.C310Y(1)		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)				AGCCACGGAGCAGACAAGGAC	0.592																																					p.C310Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G929A	1						.						77.0	70.0	72.0					1																	157556164		2203	4300	6503	155822788	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.929G>A	1.37:g.157556164C>T	ENSP00000271532:p.Cys310Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	155822788	NM_031282	Q96PJ3|Q96RE0	Missense_Mutation	SNP	ENST00000271532.1	37	CCDS1166.1	.	.	.	.	.	.	.	.	.	.	C	10.99	1.507404	0.27036	.	.	ENSG00000163518	ENST00000271532	D	0.94537	-3.45	4.12	3.18	0.36537	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.42964	D	0.000630	D	0.96691	0.8920	M	0.92317	3.295	0.31033	N	0.71719	D	0.89917	1.0	D	0.97110	1.0	D	0.93963	0.7242	10	0.87932	D	0	.	9.7088	0.40231	0.0:0.788:0.212:0.0	.	310	Q96PJ5	FCRL4_HUMAN	Y	310	ENSP00000271532:C310Y	ENSP00000271532:C310Y	C	-	2	0	FCRL4	155822788	0.999000	0.42202	0.319000	0.25293	0.110000	0.19582	2.090000	0.41682	1.007000	0.39238	0.467000	0.42956	TGC		0.592	FCRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086180.1	NM_031282	
SPTA1	6708	broad.mit.edu	37	1	158615095	158615095	+	Silent	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:158615095C>A	ENST00000368147.4	-	29	4257	c.4077G>T	c.(4075-4077)ggG>ggT	p.G1359G		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1359					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.G1359G(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TAGCATGGTGCCCACTGTCGA	0.507																																					p.G1359G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4077T	1						.						102.0	95.0	97.0					1																	158615095		1932	4140	6072	156881719	SO:0001819	synonymous_variant	6708	exon29			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.4077G>T	1.37:g.158615095C>A		Somatic		Capture	Illumina HiSeq	Phase_I	156881719	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																				0.507	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
SPTA1	6708	broad.mit.edu	37	1	158639298	158639298	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:158639298A>G	ENST00000368147.4	-	14	1913	c.1733T>C	c.(1732-1734)cTg>cCg	p.L578P		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	578					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.L578P(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TGACTCCTTCAGCAATCTACG	0.438																																					p.L578P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1733C	1						.						190.0	176.0	180.0					1																	158639298		1934	4142	6076	156905922	SO:0001583	missense	6708	exon14			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.1733T>C	1.37:g.158639298A>G	ENSP00000357129:p.Leu578Pro	Somatic		Capture	Illumina HiSeq	Phase_I	156905922	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	A	18.88	3.718259	0.68844	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.80909	-1.43;-1.43	4.72	4.72	0.59763	.	0.000000	0.26518	N	0.023922	D	0.90546	0.7037	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92755	0.6219	10	0.87932	D	0	.	13.4841	0.61355	1.0:0.0:0.0:0.0	.	578	P02549	SPTA1_HUMAN	P	578	ENSP00000357130:L578P;ENSP00000357129:L578P	ENSP00000357129:L578P	L	-	2	0	SPTA1	156905922	1.000000	0.71417	0.013000	0.15412	0.039000	0.13416	8.210000	0.89753	2.117000	0.64856	0.533000	0.62120	CTG		0.438	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
OR6K6	128371	broad.mit.edu	37	1	158725357	158725357	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:158725357T>C	ENST00000368144.2	+	1	848	c.752T>C	c.(751-753)gTg>gCg	p.V251A		NM_001005184.1	NP_001005184.1	Q8NGW6	OR6K6_HUMAN	olfactory receptor, family 6, subfamily K, member 6	251						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V251A(1)		endometrium(1)|large_intestine(5)|lung(17)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0378)					ATTATTATAGTGATTCTGGGA	0.473																																					p.V251A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T752C	1						.						210.0	178.0	189.0					1																	158725357		2203	4300	6503	156991981	SO:0001583	missense	128371	exon1			BK004198	CCDS30904.1	1q23.1	2012-08-09			ENSG00000180433	ENSG00000180433		"""GPCR / Class A : Olfactory receptors"""	15033	protein-coding gene	gene with protein product							Standard	NM_001005184		Approved		uc001fsw.1	Q8NGW6	OTTHUMG00000022772	ENST00000368144.2:c.752T>C	1.37:g.158725357T>C	ENSP00000357126:p.Val251Ala	Somatic		Capture	Illumina HiSeq	Phase_I	156991981	NM_001005184	B9EIM8|Q5VUU9|Q6IFR4	Missense_Mutation	SNP	ENST00000368144.2	37	CCDS30904.1	.	.	.	.	.	.	.	.	.	.	T	0.811	-0.751968	0.03041	.	.	ENSG00000180433	ENST00000368144	T	0.00023	9.0	5.48	4.35	0.52113	GPCR, rhodopsin-like superfamily (1);	0.189702	0.25575	N	0.029738	T	0.00039	0.0001	N	0.03948	-0.315	0.09310	N	1	D	0.59357	0.985	P	0.62491	0.903	T	0.12785	-1.0534	10	0.07175	T	0.84	-6.8368	6.5881	0.22632	0.0:0.2446:0.0:0.7554	.	251	Q8NGW6	OR6K6_HUMAN	A	251	ENSP00000357126:V251A	ENSP00000357126:V251A	V	+	2	0	OR6K6	156991981	0.022000	0.18835	0.262000	0.24481	0.298000	0.27526	2.562000	0.45914	1.084000	0.41184	0.533000	0.62120	GTG		0.473	OR6K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059065.2	NM_001005184	
VSIG8	391123	broad.mit.edu	37	1	159827723	159827723	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:159827723C>T	ENST00000368100.1	-	4	599	c.464G>A	c.(463-465)gGc>gAc	p.G155D	C1orf204_ENST00000368102.1_5'Flank|RP11-190A12.7_ENST00000544342.1_3'UTR	NM_001013661.1	NP_001013683.1	Q5VU13	VSIG8_HUMAN	V-set and immunoglobulin domain containing 8	155	Ig-like V-type 2.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	poly(A) RNA binding (GO:0044822)	p.G155D(1)		central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	8	all_hematologic(112;0.0597)					TGTCATGTGGCCCTCTGTCCA	0.587																																					p.G155D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G464A	1						.						65.0	57.0	59.0					1																	159827723		2203	4300	6503	158094347	SO:0001583	missense	391123	exon4				CCDS30913.1	1q23.2	2013-01-11			ENSG00000243284	ENSG00000243284		"""Immunoglobulin superfamily / V-set domain containing"""	32063	protein-coding gene	gene with protein product							Standard	NM_001013661		Approved		uc001fuh.3	Q5VU13	OTTHUMG00000168834	ENST00000368100.1:c.464G>A	1.37:g.159827723C>T	ENSP00000357080:p.Gly155Asp	Somatic		Capture	Illumina HiSeq	Phase_I	158094347	NM_001013661	Q5VU14	Missense_Mutation	SNP	ENST00000368100.1	37	CCDS30913.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.241187	0.79912	.	.	ENSG00000243284	ENST00000368100	T	0.02709	4.19	5.15	5.15	0.70609	Immunoglobulin-like (1);	0.052379	0.85682	D	0.000000	T	0.12347	0.0300	M	0.89095	3.005	0.58432	D	0.999995	D	0.89917	1.0	D	0.97110	1.0	T	0.00408	-1.1758	10	0.66056	D	0.02	.	14.1485	0.65367	0.0:1.0:0.0:0.0	.	155	Q5VU13	VSIG8_HUMAN	D	155	ENSP00000357080:G155D	ENSP00000357080:G155D	G	-	2	0	VSIG8	158094347	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.822000	0.48073	2.409000	0.81822	0.561000	0.74099	GGC		0.587	VSIG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085978.8	NM_001013661	
TAGLN2	8407	broad.mit.edu	37	1	159888646	159888646	+	Missense_Mutation	SNP	G	G	A	rs369414441		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:159888646G>A	ENST00000368097.4	-	5	854	c.544C>T	c.(544-546)Cgc>Tgc	p.R182C	TAGLN2_ENST00000320307.4_Missense_Mutation_p.R182C|TAGLN2_ENST00000368096.1_Missense_Mutation_p.R203C|TAGLN2_ENST00000478033.1_5'UTR	NM_001277223.1|NM_003564.1	NP_001264152.1|NP_003555.1	P37802	TAGL2_HUMAN	transgelin 2	182					epithelial cell differentiation (GO:0030855)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)		p.R182C(1)		endometrium(1)|large_intestine(2)|lung(6)	9	all_hematologic(112;0.0597)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GACGCCCCGCGGTTGGTGCCC	0.587																																					p.R182C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C544T	1						.	G	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	86.0	76.0	79.0		544	4.7	1.0	1		79	0,8600		0,0,4300	no	missense	TAGLN2	NM_003564.1	180	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	182/200	159888646	2,13004	2203	4300	6503	158155270	SO:0001583	missense	8407	exon5			D21261	CCDS1189.1, CCDS60314.1	1q21-q25	2008-07-18			ENSG00000158710	ENSG00000158710			11554	protein-coding gene	gene with protein product	"""SM22-alpha homolog"""	604634				9693045	Standard	NM_001277223		Approved	KIAA0120, HA1756	uc031pqu.1	P37802	OTTHUMG00000022793	ENST00000368097.4:c.544C>T	1.37:g.159888646G>A	ENSP00000357077:p.Arg182Cys	Somatic		Capture	Illumina HiSeq	Phase_I	158155270	NM_003564	E9KL39|Q5JRQ6|Q5JRQ7|Q6FGI1|Q9BUH5|Q9H4P0	Missense_Mutation	SNP	ENST00000368097.4	37	CCDS1189.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.760822	0.69763	4.54E-4	0.0	ENSG00000158710	ENST00000368097;ENST00000368096;ENST00000320307;ENST00000397334	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	4.65	4.65	0.58169	Calponin homology domain (2);	0.237184	0.21605	U	0.071886	T	0.46619	0.1402	M	0.78801	2.425	0.52501	D	0.999956	D	0.69078	0.997	P	0.55303	0.773	T	0.49679	-0.8914	9	.	.	.	-8.4562	10.4457	0.44493	0.0:0.0:0.8056:0.1944	.	182	P37802	TAGL2_HUMAN	C	182;203;182;182	ENSP00000357077:R182C;ENSP00000357076:R203C;ENSP00000357075:R182C;ENSP00000412429:R182C	.	R	-	1	0	TAGLN2	158155270	0.634000	0.27190	1.000000	0.80357	0.996000	0.88848	0.794000	0.26958	2.573000	0.86826	0.655000	0.94253	CGC		0.587	TAGLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059105.1	NM_003564	
NCSTN	23385	broad.mit.edu	37	1	160321968	160321968	+	Missense_Mutation	SNP	G	G	A	rs200596888		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:160321968G>A	ENST00000294785.5	+	8	1093	c.968G>A	c.(967-969)cGc>cAc	p.R323H	NCSTN_ENST00000392212.4_Missense_Mutation_p.R303H|NCSTN_ENST00000368065.4_Missense_Mutation_p.R65H|NCSTN_ENST00000535857.1_Intron|NCSTN_ENST00000368063.1_Missense_Mutation_p.R303H|NCSTN_ENST00000459963.1_3'UTR	NM_015331.2	NP_056146.1	Q92542	NICA_HUMAN	nicastrin	323					amyloid precursor protein catabolic process (GO:0042987)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)|proteolysis (GO:0006508)|T cell proliferation (GO:0042098)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)	p.R323H(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(2)	34	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			ACCCTGCCCCGCAATGTCATG	0.537																																					p.R323H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G968A	1						.						95.0	89.0	91.0					1																	160321968		2203	4300	6503	158588592	SO:0001583	missense	23385	exon8			AF240468	CCDS1203.1	1q22-q23	2014-09-17			ENSG00000162736	ENSG00000162736			17091	protein-coding gene	gene with protein product		605254				9039502, 10993067	Standard	XM_005245053		Approved	KIAA0253, APH2	uc001fvx.3	Q92542	OTTHUMG00000033110	ENST00000294785.5:c.968G>A	1.37:g.160321968G>A	ENSP00000294785:p.Arg323His	Somatic		Capture	Illumina HiSeq	Phase_I	158588592	NM_015331	Q5T207|Q5T208|Q86VV5	Missense_Mutation	SNP	ENST00000294785.5	37	CCDS1203.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.01|16.01	3.002554|3.002554	0.54254|0.54254	.|.	.|.	ENSG00000162736|ENSG00000162736	ENST00000424645;ENST00000435149|ENST00000294785;ENST00000368063;ENST00000368067;ENST00000392212;ENST00000368065;ENST00000424754	.|T;T;T;T;T	.|0.75154	.|-0.91;-0.91;-0.91;-0.91;-0.91	5.03|5.03	3.16|3.16	0.36331|0.36331	.|.	.|0.108661	.|0.64402	.|N	.|0.000006	T|T	0.58221|0.58221	0.2107|0.2107	M|M	0.72118|0.72118	2.19|2.19	0.58432|0.58432	D|D	0.999998|0.999998	.|B;B	.|0.24768	.|0.042;0.111	.|B;B	.|0.25291	.|0.023;0.059	T|T	0.59958|0.59958	-0.7356|-0.7356	5|10	.|0.46703	.|T	.|0.11	-6.8002|-6.8002	10.1819|10.1819	0.42972|0.42972	0.1627:0.0:0.8373:0.0|0.1627:0.0:0.8373:0.0	.|.	.|303;323	.|Q92542-2;Q92542	.|.;NICA_HUMAN	T|H	159;35|323;303;65;303;65;67	.|ENSP00000294785:R323H;ENSP00000357042:R303H;ENSP00000376047:R303H;ENSP00000357044:R65H;ENSP00000410124:R67H	.|ENSP00000294785:R323H	A|R	+|+	1|2	0|0	NCSTN|NCSTN	158588592|158588592	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.968000|0.968000	0.65278|0.65278	3.902000|3.902000	0.56310|0.56310	0.714000|0.714000	0.32081|0.32081	-0.150000|-0.150000	0.13652|0.13652	GCA|CGC		0.537	NCSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080622.1	NM_015331	
NHLH1	4807	broad.mit.edu	37	1	160340832	160340832	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:160340832C>T	ENST00000302101.5	+	2	757	c.311C>T	c.(310-312)aCg>aTg	p.T104M		NM_005598.3	NP_005589.1	Q02575	HEN1_HUMAN	nescient helix loop helix 1	104	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell differentiation (GO:0030154)|central nervous system development (GO:0007417)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	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 positive regulation of transcription (GO:0001228)	p.T104M(1)		breast(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	7	all_cancers(52;7.11e-19)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CTGCTGCCTACGCTGCCCCCC	0.622																																					p.T104M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C311T	1						.						57.0	59.0	59.0					1																	160340832		2203	4300	6503	158607456	SO:0001583	missense	4807	exon2			BC013789	CCDS1204.1	1q22	2013-05-21			ENSG00000171786	ENSG00000171786		"""Basic helix-loop-helix proteins"""	7817	protein-coding gene	gene with protein product		162360		HEN1			Standard	NM_005598		Approved	NSCL, NSCL1, bHLHa35	uc001fwa.2	Q02575	OTTHUMG00000033121	ENST00000302101.5:c.311C>T	1.37:g.160340832C>T	ENSP00000302189:p.Thr104Met	Somatic		Capture	Illumina HiSeq	Phase_I	158607456	NM_005598		Missense_Mutation	SNP	ENST00000302101.5	37	CCDS1204.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.060179	0.76074	.	.	ENSG00000171786	ENST00000302101	D	0.98135	-4.74	4.19	4.19	0.49359	Helix-loop-helix DNA-binding (5);	0.000000	0.56097	D	0.000026	D	0.98298	0.9436	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.99308	1.0903	10	0.87932	D	0	-17.5049	15.6211	0.76808	0.0:1.0:0.0:0.0	.	104	Q02575	HEN1_HUMAN	M	104	ENSP00000302189:T104M	ENSP00000302189:T104M	T	+	2	0	NHLH1	158607456	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.744000	0.68664	2.327000	0.79052	0.655000	0.94253	ACG		0.622	NHLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080676.1	NM_005598	
SLAMF1	6504	broad.mit.edu	37	1	160607314	160607314	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:160607314G>A	ENST00000302035.6	-	2	431	c.82C>T	c.(82-84)Cgc>Tgc	p.R28C	SLAMF1_ENST00000538290.1_Missense_Mutation_p.R28C|SLAMF1_ENST00000235739.5_Missense_Mutation_p.R28C|SLAMF1_ENST00000355199.3_Missense_Mutation_p.R28C	NM_003037.2	NP_003028.1	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family member 1	28					lymphocyte activation (GO:0046649)|positive regulation of cell proliferation (GO:0008284)|regulation of catalytic activity (GO:0050790)|regulation of vesicle fusion (GO:0031338)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|phagocytic vesicle (GO:0045335)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)	p.R28C(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			TTCATCATGCGCCCACCTGTG	0.498																																					p.R28C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C82T	1						.						50.0	43.0	45.0					1																	160607314		2203	4300	6503	158873938	SO:0001583	missense	6504	exon2			U33017	CCDS1207.1	1q23.3	2013-01-11	2003-10-29	2003-10-31	ENSG00000117090	ENSG00000117090		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10903	protein-coding gene	gene with protein product		603492	"""signaling lymphocytic activation molecule"""	SLAM		7617038	Standard	XM_005245456		Approved	CD150	uc001fwl.4	Q13291	OTTHUMG00000024006	ENST00000302035.6:c.82C>T	1.37:g.160607314G>A	ENSP00000306190:p.Arg28Cys	Somatic		Capture	Illumina HiSeq	Phase_I	158873938	NM_003037	Q5W172|Q9HBE8	Missense_Mutation	SNP	ENST00000302035.6	37	CCDS1207.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.330577	0.41297	.	.	ENSG00000117090	ENST00000302035;ENST00000235739;ENST00000392208;ENST00000538290;ENST00000355199	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	3.77	-2.97	0.05530	Signaling lymphocytic activation molecule, N-terminal (2);	1.959200	0.02054	N	0.050217	T	0.23492	0.0568	N	0.22421	0.69	0.09310	N	1	D;P	0.65815	0.995;0.951	P;P	0.58520	0.84;0.553	T	0.11665	-1.0578	10	0.52906	T	0.07	-11.3237	5.4337	0.16469	0.0:0.2215:0.3419:0.4366	.	28;28	B4E2E4;Q13291	.;SLAF1_HUMAN	C	28	ENSP00000306190:R28C;ENSP00000235739:R28C;ENSP00000438406:R28C;ENSP00000347333:R28C	ENSP00000235739:R28C	R	-	1	0	SLAMF1	158873938	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.384000	0.07389	-0.651000	0.05415	-0.479000	0.04858	CGC		0.498	SLAMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060454.1		
PLEKHM2	23207	broad.mit.edu	37	1	16046395	16046395	+	Missense_Mutation	SNP	C	C	T	rs373741350		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:16046395C>T	ENST00000375799.3	+	6	859	c.632C>T	c.(631-633)gCg>gTg	p.A211V	RP11-288I21.1_ENST00000453804.1_RNA|PLEKHM2_ENST00000375793.2_Missense_Mutation_p.A211V	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	211	Interaction with KIF5B.				Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)	p.A211V(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GATGACAGTGCGATTGCCCCA	0.557																																					p.A211V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C632T	1						.	C	VAL/ALA	1,4059		0,1,2029	43.0	43.0	43.0		632	5.5	0.9	1		43	0,8386		0,0,4193	no	missense	PLEKHM2	NM_015164.2	64	0,1,6222	TT,TC,CC		0.0,0.0246,0.0080	probably-damaging	211/1020	16046395	1,12445	2030	4193	6223	15918982	SO:0001583	missense	23207	exon6			AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"""Pleckstrin homology (PH) domain containing"""	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.632C>T	1.37:g.16046395C>T	ENSP00000364956:p.Ala211Val	Somatic		Capture	Illumina HiSeq	Phase_I	15918982	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Missense_Mutation	SNP	ENST00000375799.3	37	CCDS44063.1	.	.	.	.	.	.	.	.	.	.	C	36	5.761756	0.96906	2.46E-4	0.0	ENSG00000116786	ENST00000375799;ENST00000375793	T;T	0.59906	0.23;0.7	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.54791	0.1880	L	0.32530	0.975	0.80722	D	1	D	0.59767	0.986	P	0.47402	0.546	T	0.50882	-0.8775	10	0.29301	T	0.29	-13.7216	18.9917	0.92794	0.0:1.0:0.0:0.0	.	211	Q8IWE5	PKHM2_HUMAN	V	211	ENSP00000364956:A211V;ENSP00000364950:A211V	ENSP00000364950:A211V	A	+	2	0	PLEKHM2	15918982	1.000000	0.71417	0.894000	0.35097	0.997000	0.91878	7.573000	0.82421	2.600000	0.87896	0.650000	0.86243	GCG		0.557	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164	
CD244	51744	broad.mit.edu	37	1	160811177	160811177	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:160811177C>T	ENST00000368033.3	-	3	575	c.493G>A	c.(493-495)Gtg>Atg	p.V165M	CD244_ENST00000481677.1_5'Flank|CD244_ENST00000368034.4_Missense_Mutation_p.V160M|CD244_ENST00000322302.7_Intron|CD244_ENST00000368032.2_Missense_Mutation_p.V160M			Q9BZW8	CD244_HUMAN	CD244 molecule, natural killer cell receptor 2B4	165	Ig-like 2.				blood coagulation (GO:0007596)|leukocyte migration (GO:0050900)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.V160M(1)		central_nervous_system(1)|large_intestine(3)|lung(12)|ovary(1)|urinary_tract(1)	18	all_cancers(52;2.72e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			GCATAGGACACATTGCCATCC	0.532																																					p.V165M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G493A	1						.						193.0	165.0	174.0					1																	160811177		2203	4300	6503	159077801	SO:0001583	missense	51744	exon3			AF105261	CCDS1210.1, CCDS53398.1, CCDS53399.1	1q23.1	2013-01-11	2006-03-29		ENSG00000122223	ENSG00000122223		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18171	protein-coding gene	gene with protein product		605554	"""natural killer cell receptor 2B4"", ""CD244 natural killer cell receptor 2B4"""			3772297, 10458320	Standard	NM_016382		Approved	2B4, NAIL, NKR2B4, Nmrk, SLAMF4	uc009wtq.3	Q9BZW8	OTTHUMG00000028606	ENST00000368033.3:c.493G>A	1.37:g.160811177C>T	ENSP00000357012:p.Val165Met	Somatic		Capture	Illumina HiSeq	Phase_I	159077801	NM_001166663	Q5VYI2|Q5VYI6|Q5VYI7|Q96T47|Q9NQD2|Q9NQD3|Q9Y288	Missense_Mutation	SNP	ENST00000368033.3	37	CCDS53399.1	.	.	.	.	.	.	.	.	.	.	C	16.67	3.188088	0.57909	.	.	ENSG00000122223	ENST00000368034;ENST00000368033;ENST00000368032	T;T;T	0.56444	0.46;0.46;0.46	4.73	2.74	0.32292	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.090693	0.42172	D	0.000741	T	0.56906	0.2017	M	0.79475	2.455	0.31602	N	0.652597	D;D	0.89917	1.0;1.0	D;D	0.77557	0.99;0.984	T	0.56798	-0.7919	10	0.72032	D	0.01	-15.1785	6.5711	0.22539	0.1766:0.7249:0.0:0.0986	.	165;160	Q9BZW8;Q9BZW8-2	CD244_HUMAN;.	M	160;165;160	ENSP00000357013:V160M;ENSP00000357012:V165M;ENSP00000357011:V160M	ENSP00000357011:V160M	V	-	1	0	CD244	159077801	0.164000	0.22935	0.802000	0.32245	0.185000	0.23345	0.126000	0.15769	1.147000	0.42369	-0.119000	0.15052	GTG		0.532	CD244-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071469.1	NM_016382	
FAM131C	348487	broad.mit.edu	37	1	16388654	16388654	+	Missense_Mutation	SNP	C	C	T	rs374242693		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:16388654C>T	ENST00000375662.4	-	4	391	c.208G>A	c.(208-210)Gac>Aac	p.D70N	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	70								p.D70N(1)		large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		GATCTGGAGTCGGACAGGTAG	0.652																																					p.D70N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G208A	1						.	C	ASN/ASP	0,4104		0,0,2052	77.0	78.0	78.0		208	0.4	1.0	1		78	2,8368		0,2,4183	no	missense	FAM131C	NM_182623.2	23	0,2,6235	TT,TC,CC		0.0239,0.0,0.016	benign	70/281	16388654	2,12472	2052	4185	6237	16261241	SO:0001583	missense	348487	exon4				CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.208G>A	1.37:g.16388654C>T	ENSP00000364814:p.Asp70Asn	Somatic		Capture	Illumina HiSeq	Phase_I	16261241	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Missense_Mutation	SNP	ENST00000375662.4	37	CCDS41270.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.755733	0.31046	0.0	2.39E-4	ENSG00000185519	ENST00000375662	T	0.15256	2.44	4.64	0.426	0.16479	.	0.428262	0.22187	N	0.063432	T	0.13670	0.0331	L	0.60455	1.87	0.29394	N	0.862426	B	0.21309	0.054	B	0.12156	0.007	T	0.11036	-1.0604	10	0.37606	T	0.19	.	4.7214	0.12920	0.0:0.5558:0.1572:0.287	.	70	Q96AQ9	F131C_HUMAN	N	70	ENSP00000364814:D70N	ENSP00000364814:D70N	D	-	1	0	FAM131C	16261241	0.075000	0.21258	0.966000	0.40874	0.854000	0.48673	0.068000	0.14531	0.057000	0.16193	-0.379000	0.06801	GAC		0.652	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
FBXO42	54455	broad.mit.edu	37	1	16577976	16577976	+	Missense_Mutation	SNP	G	G	A	rs561367398		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:16577976G>A	ENST00000375592.3	-	10	1559	c.1343C>T	c.(1342-1344)aCg>aTg	p.T448M		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	448								p.T448M(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)		CACAGCTGCCGTTCCTGGAGA	0.542													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18104	0.0		0.0	False		,,,				2504	0.0				p.T448M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1343T	1						.						27.0	31.0	30.0					1																	16577976		2203	4300	6503	16450563	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.1343C>T	1.37:g.16577976G>A	ENSP00000364742:p.Thr448Met	Somatic		Capture	Illumina HiSeq	Phase_I	16450563	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Missense_Mutation	SNP	ENST00000375592.3	37	CCDS30613.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.041325	0.35989	.	.	ENSG00000037637	ENST00000375592;ENST00000456164;ENST00000444116	T;T;T	0.46819	3.77;0.86;0.86	5.51	4.53	0.55603	.	0.432303	0.25833	N	0.028004	T	0.34948	0.0915	L	0.36672	1.1	0.43271	D	0.99522	P	0.42337	0.776	B	0.34452	0.183	T	0.27226	-1.0080	10	0.46703	T	0.11	-5.1739	13.5939	0.61978	0.0:0.155:0.8449:0.0	.	448	Q6P3S6	FBX42_HUMAN	M	448;166;166	ENSP00000364742:T448M;ENSP00000415663:T166M;ENSP00000412416:T166M	ENSP00000364742:T448M	T	-	2	0	FBXO42	16450563	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	4.942000	0.63547	2.763000	0.94921	0.650000	0.86243	ACG		0.542	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1		
FCRLB	127943	broad.mit.edu	37	1	161697383	161697383	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:161697383G>A	ENST00000367948.2	+	8	1427	c.1212G>A	c.(1210-1212)acG>acA	p.T404T	FCRLB_ENST00000495397.1_3'UTR|FCRLB_ENST00000367944.3_3'UTR|FCRLB_ENST00000367946.3_3'UTR|FCRLB_ENST00000392158.1_Silent_p.T404T|FCRLB_ENST00000367945.1_3'UTR|FCRLB_ENST00000336830.5_3'UTR			Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	404					negative regulation of immune response (GO:0050777)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)		p.T404T(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|skin(1)	17	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			TCAGGGGAACGCCCGAGACCC	0.637																																					p.T404T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1212A	1						.						28.0	34.0	32.0					1																	161697383		2202	4300	6502	159964007	SO:0001819	synonymous_variant	127943	exon6			AY670683	CCDS30927.1, CCDS72962.1, CCDS72963.1, CCDS72964.1, CCDS72965.1	1q23.3	2013-01-11	2006-09-26	2006-09-26	ENSG00000162746	ENSG00000162746		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26431	protein-coding gene	gene with protein product		609251	"""Fc receptor-like and mucin-like 2"""	FCRLM2		15676285	Standard	NM_001288829		Approved	FLJ31052, FCRL2, FREB-2, FCRLY	uc001gbi.3	Q6BAA4	OTTHUMG00000133629	ENST00000367948.2:c.1212G>A	1.37:g.161697383G>A		Somatic		Capture	Illumina HiSeq	Phase_I	159964007	NM_001002901	A2A3J5|A2A3J7|Q5VXA6|Q6BAA0|Q6BAA1|Q6BAA2|Q6BAA3|Q8IXZ7	Silent	SNP	ENST00000367948.2	37	CCDS30927.1																																																																																				0.637	FCRLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083585.1	NM_152378	
DUSP27	92235	broad.mit.edu	37	1	167095476	167095476	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:167095476G>A	ENST00000361200.2	+	6	1274	c.1108G>A	c.(1108-1110)Ggt>Agt	p.G370S	DUSP27_ENST00000485151.1_3'UTR|DUSP27_ENST00000271385.5_Missense_Mutation_p.G370S|DUSP27_ENST00000443333.1_Missense_Mutation_p.G370S			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	370					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.G370S(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						CCAGGATGGAGGTGGCTGGCG	0.627																																					p.G370S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1108A	1						.						34.0	33.0	33.0					1																	167095476		2200	4296	6496	165362100	SO:0001583	missense	92235	exon5			AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1108G>A	1.37:g.167095476G>A	ENSP00000354483:p.Gly370Ser	Somatic		Capture	Illumina HiSeq	Phase_I	165362100	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	G	3.479	-0.106207	0.06924	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.02974	4.09;4.09;4.09	4.53	-0.839	0.10759	.	993.011000	0.00166	N	0.000000	T	0.00412	0.0013	N	0.02011	-0.69	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.46789	-0.9166	10	0.12430	T	0.62	-0.0227	7.3335	0.26596	0.2255:0.3544:0.4201:0.0	.	370	Q5VZP5	DUS27_HUMAN	S	370	ENSP00000354483:G370S;ENSP00000271385:G370S;ENSP00000404874:G370S	ENSP00000271385:G370S	G	+	1	0	DUSP27	165362100	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.328000	0.19681	-0.032000	0.13758	0.643000	0.83706	GGT		0.627	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
DUSP27	92235	broad.mit.edu	37	1	167096069	167096069	+	Silent	SNP	C	C	T	rs372727539		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:167096069C>T	ENST00000361200.2	+	6	1867	c.1701C>T	c.(1699-1701)agC>agT	p.S567S	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Silent_p.S567S|DUSP27_ENST00000443333.1_Silent_p.S567S			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	567					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.S567S(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						GAGACAGCAGCGGTGAGCCCG	0.557																																					p.S567S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1701T	1						.	C		0,4406		0,0,2203	55.0	57.0	56.0		1701	3.4	0.6	1		56	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DUSP27	NM_001080426.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		567/1159	167096069	1,13005	2203	4300	6503	165362693	SO:0001819	synonymous_variant	92235	exon5			AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1701C>T	1.37:g.167096069C>T		Somatic		Capture	Illumina HiSeq	Phase_I	165362693	NM_001080426	A0AUM4|Q9C074	Silent	SNP	ENST00000361200.2	37	CCDS30932.1																																																																																				0.557	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
C1orf112	55732	broad.mit.edu	37	1	169822077	169822077	+	Silent	SNP	G	G	A	rs191037390		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:169822077G>A	ENST00000286031.6	+	24	3211	c.2511G>A	c.(2509-2511)gcG>gcA	p.A837A	C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000359326.4_Silent_p.A837A|SCYL3_ENST00000367772.4_3'UTR|SCYL3_ENST00000367771.6_3'UTR	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	837								p.A837A(2)		breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AAATGGAGGCGCTCCAAGAAA	0.458													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16720	0.0		0.0	False		,,,				2504	0.0				p.A837A												.	.	2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	c.G2511A	1						.						107.0	110.0	109.0					1																	169822077		2203	4300	6503	168088701	SO:0001819	synonymous_variant	55732	exon24			AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.2511G>A	1.37:g.169822077G>A		Somatic		Capture	Illumina HiSeq	Phase_I	168088701	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Silent	SNP	ENST00000286031.6	37	CCDS1285.1																																																																																				0.458	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186	
GORAB	92344	broad.mit.edu	37	1	170521360	170521360	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:170521360C>T	ENST00000367763.3	+	5	962	c.942C>T	c.(940-942)gtC>gtT	p.V314V		NM_152281.2	NP_689494.2	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting	314	Necessary for interaction with RCHY1.					cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.V314V(1)		endometrium(2)|large_intestine(3)|liver(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	17						AGGTGGAGGTCGAGAGATTGC	0.468																																					p.V314V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C942T	1						.						91.0	81.0	85.0					1																	170521360		2203	4300	6503	168787984	SO:0001819	synonymous_variant	92344	exon5			AK021814	CCDS1289.1, CCDS53428.1	1q24.2	2009-02-13	2009-02-13	2009-02-13	ENSG00000120370	ENSG00000120370			25676	protein-coding gene	gene with protein product	"""gerodermia osteodysplastica"""	607983	"""SCY1-like 1 binding protein 1"""	SCYL1BP1		12783284, 15781263, 18997784	Standard	NM_152281		Approved	FLJ11752, NTKL-BP1, GO	uc001gha.2	Q5T7V8	OTTHUMG00000035228	ENST00000367763.3:c.942C>T	1.37:g.170521360C>T		Somatic		Capture	Illumina HiSeq	Phase_I	168787984	NM_152281	Q49A22|Q6P1P9|Q9HAE6|Q9Y350	Silent	SNP	ENST00000367763.3	37	CCDS1289.1																																																																																				0.468	GORAB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085226.1	NM_152281	
FMO3	2328	broad.mit.edu	37	1	171086530	171086530	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:171086530A>G	ENST00000367755.4	+	9	1658	c.1547A>G	c.(1546-1548)aAg>aGg	p.K516R	FMO3_ENST00000538429.1_Missense_Mutation_p.K453R|FMO3_ENST00000392085.2_Missense_Mutation_p.K516R|FMO3_ENST00000542847.1_Missense_Mutation_p.K496R	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	516					drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)	p.K516R(1)		endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	CATTGGCTGAAGCTCTTTGCA	0.443																																					p.K516R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1547G	1						.						174.0	160.0	165.0					1																	171086530		2203	4300	6503	169353154	SO:0001583	missense	2328	exon9			BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.1547A>G	1.37:g.171086530A>G	ENSP00000356729:p.Lys516Arg	Somatic		Capture	Illumina HiSeq	Phase_I	169353154	NM_001002294	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	37	CCDS1292.1	.	.	.	.	.	.	.	.	.	.	A	11.54	1.668344	0.29604	.	.	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	4.55	0.268	0.15626	.	0.966296	0.08649	N	0.914303	T	0.18800	0.0451	L	0.28776	0.89	0.09310	N	1	B;B;B	0.29481	0.011;0.245;0.051	B;B;B	0.33339	0.019;0.162;0.068	T	0.34428	-0.9829	10	0.21540	T	0.41	-4.135	8.7902	0.34845	0.5358:0.0:0.4642:0.0	.	453;496;516	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	R	516;516;496;453	ENSP00000356729:K516R;ENSP00000375935:K516R;ENSP00000444073:K496R;ENSP00000439500:K453R	ENSP00000356729:K516R	K	+	2	0	FMO3	169353154	0.000000	0.05858	0.006000	0.13384	0.047000	0.14425	-0.414000	0.07114	-0.119000	0.11830	0.533000	0.62120	AAG		0.443	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894	
CROCC	9696	broad.mit.edu	37	1	17264166	17264166	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:17264166T>C	ENST00000375541.5	+	10	1293	c.1224T>C	c.(1222-1224)cgT>cgC	p.R408R	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin									p.R408R(1)		breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CAGTGAAGCGTCTTGAGAAGC	0.572																																					p.R408R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1224C	1						.						49.0	39.0	42.0					1																	17264166		2203	4300	6503	17136753	SO:0001819	synonymous_variant	9696	exon10			AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.1224T>C	1.37:g.17264166T>C		Somatic		Capture	Illumina HiSeq	Phase_I	17136753	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																				0.572	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
MYOC	4653	broad.mit.edu	37	1	171605240	171605240	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:171605240G>A	ENST00000037502.6	-	3	1411	c.1340C>T	c.(1339-1341)gCt>gTt	p.A447V		NM_000261.1	NP_000252.1	Q99972	MYOC_HUMAN	myocilin, trabecular meshwork inducible glucocorticoid response	447	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				bone development (GO:0060348)|clustering of voltage-gated sodium channels (GO:0045162)|ERBB2-ERBB3 signaling pathway (GO:0038133)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neuron projection development (GO:0031175)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of MAPK cascade (GO:0043408)|skeletal muscle hypertrophy (GO:0014734)	cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|node of Ranvier (GO:0033268)|proteinaceous extracellular matrix (GO:0005578)	fibronectin binding (GO:0001968)|frizzled binding (GO:0005109)|myosin light chain binding (GO:0032027)	p.A447V(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(1)|urinary_tract(2)	28	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					GTTGACGGTAGCATCTGCTGA	0.493																																					p.A447V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1340T	1						.						279.0	235.0	249.0					1																	171605240		2203	4300	6503	169871863	SO:0001583	missense	4653	exon3			BC029261	CCDS1297.1	1q23-q24	2008-02-05			ENSG00000034971	ENSG00000034971			7610	protein-coding gene	gene with protein product		601652		GLC1A		9169133, 9005853	Standard	NM_000261		Approved	TIGR, JOAG1	uc001ghu.3	Q99972	OTTHUMG00000034789	ENST00000037502.6:c.1340C>T	1.37:g.171605240G>A	ENSP00000037502:p.Ala447Val	Somatic		Capture	Illumina HiSeq	Phase_I	169871863	NM_000261	B2RD84|O00620|Q7Z6Q9	Missense_Mutation	SNP	ENST00000037502.6	37	CCDS1297.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.782648	0.49891	.	.	ENSG00000034971	ENST00000037502;ENST00000357746;ENST00000536591	D	0.89485	-2.52	5.17	5.17	0.71159	Olfactomedin-like (3);	0.099984	0.64402	D	0.000001	D	0.92273	0.7549	M	0.83953	2.67	0.38815	D	0.955508	P;D	0.55605	0.907;0.972	P;P	0.54460	0.753;0.622	D	0.93489	0.6834	10	0.87932	D	0	.	17.5936	0.88004	0.0:0.0:1.0:0.0	.	389;447	B4DV44;Q99972	.;MYOC_HUMAN	V	447;400;380	ENSP00000037502:A447V	ENSP00000037502:A447V	A	-	2	0	MYOC	169871863	0.999000	0.42202	0.102000	0.21198	0.004000	0.04260	7.829000	0.86735	2.556000	0.86216	0.555000	0.69702	GCT		0.493	MYOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084178.2	NM_000261	
TNR	7143	broad.mit.edu	37	1	175372450	175372450	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:175372450C>T	ENST00000367674.2	-	4	1510	c.802G>A	c.(802-804)Ggg>Agg	p.G268R	TNR_ENST00000263525.2_Missense_Mutation_p.G268R			Q92752	TENR_HUMAN	tenascin R	268	Cys-rich.				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.G268R(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)					GAACAGTCCCCAGGGCACCTC	0.632																																					p.G268R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G802A	1						.						121.0	81.0	95.0					1																	175372450		2203	4300	6503	173639073	SO:0001583	missense	7143	exon4			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.802G>A	1.37:g.175372450C>T	ENSP00000356646:p.Gly268Arg	Somatic		Capture	Illumina HiSeq	Phase_I	173639073	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	37	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.416635	0.42918	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.25749	1.78;1.78	6.17	5.27	0.74061	.	0.226096	0.46145	D	0.000320	T	0.16342	0.0393	N	0.16307	0.4	0.33473	D	0.586417	B;B	0.15930	0.015;0.001	B;B	0.15052	0.012;0.002	T	0.15492	-1.0435	10	0.28530	T	0.3	.	12.0162	0.53315	0.0:0.8122:0.1214:0.0664	.	268;268	B4DIX8;Q92752	.;TENR_HUMAN	R	268	ENSP00000356646:G268R;ENSP00000263525:G268R	ENSP00000263525:G268R	G	-	1	0	TNR	173639073	0.020000	0.18652	0.892000	0.35008	0.946000	0.59487	1.581000	0.36558	1.631000	0.50456	0.655000	0.94253	GGG		0.632	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
PAPPA2	60676	broad.mit.edu	37	1	176564651	176564651	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:176564651C>T	ENST00000367662.3	+	3	3075	c.1911C>T	c.(1909-1911)aaC>aaT	p.N637N	PAPPA2_ENST00000367661.3_Silent_p.N637N	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	637	Metalloprotease.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.N637N(1)		NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						ACATGCTGAACGACTTTGACG	0.597																																					p.N637N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1911T	1						.						71.0	76.0	75.0					1																	176564651		2168	4270	6438	174831274	SO:0001819	synonymous_variant	60676	exon3			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.1911C>T	1.37:g.176564651C>T		Somatic		Capture	Illumina HiSeq	Phase_I	174831274	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	37	CCDS41438.1																																																																																				0.597	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1		
TOR3A	64222	broad.mit.edu	37	1	179063290	179063290	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:179063290G>A	ENST00000367627.3	+	5	1633	c.881G>A	c.(880-882)cGg>cAg	p.R294Q	TOR3A_ENST00000352445.6_Missense_Mutation_p.R294Q	NM_022371.3	NP_071766.2	Q9H497	TOR3A_HUMAN	torsin family 3, member A	294					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R294Q(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|urinary_tract(1)	13						GGATGGTCCCGGGAAGAAATT	0.483																																					p.R294Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G881A	1						.						93.0	93.0	93.0					1																	179063290		2203	4300	6503	177329913	SO:0001583	missense	64222	exon5			BC001085	CCDS1329.1	1q25.2	2008-02-05	2003-04-02		ENSG00000186283	ENSG00000186283			11997	protein-coding gene	gene with protein product		607555	"""ATP-dependant interferon responsive"""	ADIR		10644435	Standard	NM_022371		Approved	FLJ22345, ADIR2	uc001gmd.3	Q9H497	OTTHUMG00000035077	ENST00000367627.3:c.881G>A	1.37:g.179063290G>A	ENSP00000356599:p.Arg294Gln	Somatic		Capture	Illumina HiSeq	Phase_I	177329913	NM_022371	B4DSY0|B7ZB65|Q5M7Y7|Q8WVA7|Q8WWM2|Q9H495|Q9H6E7	Missense_Mutation	SNP	ENST00000367627.3	37	CCDS1329.1	.	.	.	.	.	.	.	.	.	.	G	36	5.960824	0.97151	.	.	ENSG00000186283	ENST00000367627;ENST00000352445	T;T	0.31510	1.49;1.49	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.65903	0.2736	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.74589	-0.3615	10	0.87932	D	0	-39.6298	16.6603	0.85239	0.0:0.0:1.0:0.0	.	294	Q9H497	TOR3A_HUMAN	Q	294	ENSP00000356599:R294Q;ENSP00000335351:R294Q	ENSP00000335351:R294Q	R	+	2	0	TOR3A	177329913	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.024000	0.93689	2.607000	0.88179	0.561000	0.74099	CGG		0.483	TOR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084927.1	NM_022371	
CEP350	9857	broad.mit.edu	37	1	180056745	180056745	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:180056745C>T	ENST00000367607.3	+	32	6736	c.6318C>T	c.(6316-6318)gcC>gcT	p.A2106A	CEP350_ENST00000490141.1_3'UTR	NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	2106					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)		p.A2106A(1)		central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						AAACTGAAGCCGAGCTTAGCC	0.363																																					p.A2106A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C6318T	1						.						37.0	34.0	35.0					1																	180056745		2196	4268	6464	178323368	SO:0001819	synonymous_variant	9857	exon32			AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"""centrosome associated protein 350"""					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.6318C>T	1.37:g.180056745C>T		Somatic		Capture	Illumina HiSeq	Phase_I	178323368	NM_014810	O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	37	CCDS1336.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.433668	0.25813	.	.	ENSG00000135837	ENST00000429851	.	.	.	5.6	-11.2	0.00127	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.4525	0.07503	0.4189:0.0976:0.071:0.4125	.	.	.	.	X	281	.	.	R	+	1	2	CEP350	178323368	0.045000	0.20229	0.641000	0.29422	0.995000	0.86356	-0.766000	0.04725	-1.864000	0.01148	-0.136000	0.14681	CGA		0.363	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
CACNA1E	777	broad.mit.edu	37	1	181701631	181701631	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:181701631G>A	ENST00000367573.2	+	20	2409	c.2409G>A	c.(2407-2409)ccG>ccA	p.P803P	CACNA1E_ENST00000367567.4_Silent_p.P410P|CACNA1E_ENST00000360108.3_Silent_p.P784P|CACNA1E_ENST00000358338.5_Silent_p.P735P|CACNA1E_ENST00000367570.1_Silent_p.P803P|CACNA1E_ENST00000357570.5_Silent_p.P754P|CACNA1E_ENST00000526775.1_Silent_p.P784P	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	803					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.P803P(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						AGGAGGCGCCGACCATGaacc	0.657																																					p.P803P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2409A	1						.						39.0	58.0	51.0					1																	181701631		1768	3335	5103	179968254	SO:0001819	synonymous_variant	777	exon20			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.2409G>A	1.37:g.181701631G>A		Somatic		Capture	Illumina HiSeq	Phase_I	179968254	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																				0.657	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
CACNA1E	777	broad.mit.edu	37	1	181750627	181750627	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:181750627G>A	ENST00000367573.2	+	39	5332	c.5332G>A	c.(5332-5334)Ggc>Agc	p.G1778S	CACNA1E_ENST00000367567.4_Missense_Mutation_p.G1385S|CACNA1E_ENST00000360108.3_Missense_Mutation_p.G1759S|CACNA1E_ENST00000358338.5_Intron|CACNA1E_ENST00000367570.1_Missense_Mutation_p.G1778S|CACNA1E_ENST00000357570.5_Missense_Mutation_p.G1729S|CACNA1E_ENST00000526775.1_Missense_Mutation_p.G1759S	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1778					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.G1778S(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						GCTAGGCCTCGGCAAGAGATG	0.547																																					p.G1778S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5332A	1						.						34.0	33.0	34.0					1																	181750627		2040	4208	6248	180017250	SO:0001583	missense	777	exon39			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.5332G>A	1.37:g.181750627G>A	ENSP00000356545:p.Gly1778Ser	Somatic		Capture	Illumina HiSeq	Phase_I	180017250	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	35	5.459648	0.96240	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000367567;ENST00000360108;ENST00000367573	T;T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09;-0.09	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.84406	0.5465	M	0.90870	3.155	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	D	0.87313	0.2313	10	0.87932	D	0	.	19.4226	0.94727	0.0:0.0:1.0:0.0	.	1759;1778	Q15878-2;Q15878-3	.;.	S	1778;1759;1729;1385;1759;1778	ENSP00000356542:G1778S;ENSP00000434814:G1759S;ENSP00000350183:G1729S;ENSP00000356539:G1385S;ENSP00000353222:G1759S;ENSP00000356545:G1778S	ENSP00000350183:G1729S	G	+	1	0	CACNA1E	180017250	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	9.731000	0.98807	2.684000	0.91462	0.650000	0.86243	GGC		0.547	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
GLUL	2752	broad.mit.edu	37	1	182353767	182353767	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:182353767G>A	ENST00000331872.6	-	7	1435	c.895C>T	c.(895-897)Cgt>Tgt	p.R299C	GLUL_ENST00000491322.1_5'UTR|GLUL_ENST00000417584.2_Missense_Mutation_p.R299C|GLUL_ENST00000311223.5_Missense_Mutation_p.R299C|GLUL_ENST00000339526.4_Missense_Mutation_p.R299C	NM_001033044.2	NP_001028216.1	P15104	GLNA_HUMAN	glutamate-ammonia ligase	299					cell proliferation (GO:0008283)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to starvation (GO:0009267)|glutamate catabolic process (GO:0006538)|glutamine biosynthetic process (GO:0006542)|neurotransmitter uptake (GO:0001504)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of insulin secretion (GO:0032024)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein homooligomerization (GO:0051260)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glial cell projection (GO:0097386)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|glutamate-ammonia ligase activity (GO:0004356)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)	p.R299C(1)		endometrium(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	16					Ceftriaxone(DB01212)|Diazoxide(DB01119)|L-Glutamine(DB00130)|L-Methionine(DB00134)|Pegvisomant(DB00082)	CCAGTTAGACGTCGGGCATTG	0.532																																					p.R299C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C895T	1						.						110.0	102.0	105.0					1																	182353767		2203	4300	6503	180620390	SO:0001583	missense	2752	exon8			AL161952	CCDS1344.1	1q31	2010-05-04	2010-05-04		ENSG00000135821	ENSG00000135821	6.3.1.2		4341	protein-coding gene	gene with protein product	"""glutamine synthetase"""	138290	"""glutamate-ammonia ligase (glutamine synthase)"""	GLNS		1681907, 2888076	Standard	NM_002065		Approved		uc001gpa.2	P15104	OTTHUMG00000037407	ENST00000331872.6:c.895C>T	1.37:g.182353767G>A	ENSP00000356537:p.Arg299Cys	Somatic		Capture	Illumina HiSeq	Phase_I	180620390	NM_002065	Q499Y9|Q5T9Z1|Q7Z3W4|Q8IZ17	Missense_Mutation	SNP	ENST00000331872.6	37	CCDS1344.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.389969	0.82902	.	.	ENSG00000135821	ENST00000331872;ENST00000311223;ENST00000417584;ENST00000339526	D;D;D;D	0.99023	-5.34;-5.34;-5.34;-5.34	5.34	4.4	0.53042	Glutamine synthetase, catalytic domain (1);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99518	0.9828	H	0.98333	4.205	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.98300	1.0518	10	0.87932	D	0	-15.9646	9.6937	0.40145	0.0:0.1539:0.6867:0.1593	.	299	P15104	GLNA_HUMAN	C	299	ENSP00000356537:R299C;ENSP00000307900:R299C;ENSP00000398320:R299C;ENSP00000344958:R299C	ENSP00000307900:R299C	R	-	1	0	GLUL	180620390	1.000000	0.71417	0.991000	0.47740	0.983000	0.72400	7.294000	0.78760	1.178000	0.42870	0.563000	0.77884	CGT		0.532	GLUL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091043.1	NM_002065	
DHX9	1660	broad.mit.edu	37	1	182827934	182827934	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:182827934C>T	ENST00000367549.3	+	10	1077	c.967C>T	c.(967-969)Cga>Tga	p.R323*		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	323	Interaction with BRCA1.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)	p.R323*(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						ACCATCTCAGCGACAAAACCA	0.433																																					p.R323X	Colon(69;210 1162 3697 13559 39565)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C967T	1						.						111.0	100.0	103.0					1																	182827934		1902	4136	6038	181094557	SO:0001587	stop_gained	1660	exon10			L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"""DEAH-boxes"""	2750	protein-coding gene	gene with protein product	"""NDH II"", ""RNA helicase A"""	603115	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 9"""	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.967C>T	1.37:g.182827934C>T	ENSP00000356520:p.Arg323*	Somatic		Capture	Illumina HiSeq	Phase_I	181094557	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Nonsense_Mutation	SNP	ENST00000367549.3	37	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	C	39	7.406504	0.98265	.	.	ENSG00000135829	ENST00000399175;ENST00000367549	.	.	.	5.73	4.75	0.60458	.	0.221659	0.34002	N	0.004351	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	.	13.2709	0.60159	0.5261:0.4739:0.0:0.0	.	.	.	.	X	323	.	ENSP00000356520:R323X	R	+	1	2	DHX9	181094557	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	1.929000	0.40114	1.331000	0.45412	0.655000	0.94253	CGA		0.433	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588	
LAMC1	3915	broad.mit.edu	37	1	183086535	183086535	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:183086535G>A	ENST00000258341.4	+	9	1902	c.1645G>A	c.(1645-1647)Gtg>Atg	p.V549M		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	549	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.V549M(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						AGATATCGCCGTGATCTCAGA	0.512																																					p.V549M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1645A	1						.						146.0	122.0	130.0					1																	183086535		2203	4300	6503	181353158	SO:0001583	missense	3915	exon9			J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.1645G>A	1.37:g.183086535G>A	ENSP00000258341:p.Val549Met	Somatic		Capture	Illumina HiSeq	Phase_I	181353158	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.610912	0.66558	.	.	ENSG00000135862	ENST00000258341	T	0.31769	1.48	5.04	5.04	0.67666	Laminin B type IV (1);	0.200367	0.42172	D	0.000750	T	0.42585	0.1209	M	0.81497	2.545	0.58432	D	0.999996	P	0.52577	0.954	B	0.42827	0.399	T	0.56123	-0.8031	10	0.72032	D	0.01	.	18.3933	0.90490	0.0:0.0:1.0:0.0	.	549	P11047	LAMC1_HUMAN	M	549	ENSP00000258341:V549M	ENSP00000258341:V549M	V	+	1	0	LAMC1	181353158	1.000000	0.71417	0.836000	0.33094	0.694000	0.40290	3.742000	0.55097	2.338000	0.79540	0.591000	0.81541	GTG		0.512	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
NCF2	4688	broad.mit.edu	37	1	183556058	183556058	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:183556058G>A	ENST00000367535.3	-	2	480	c.229C>T	c.(229-231)Cga>Tga	p.R77*	NCF2_ENST00000367536.1_Nonsense_Mutation_p.R77*|NCF2_ENST00000413720.1_Nonsense_Mutation_p.R77*|NCF2_ENST00000418089.1_Nonsense_Mutation_p.R77*	NM_000433.3	NP_000424.2	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	77			R -> Q (in CGD2; dbSNP:rs119103275). {ECO:0000269|PubMed:10598813, ECO:0000269|PubMed:20167518}.		aging (GO:0007568)|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)|cellular defense response (GO:0006968)|cellular response to hormone stimulus (GO:0032870)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron apoptotic process (GO:0043525)|respiratory burst (GO:0045730)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hyperoxia (GO:0055093)|response to laminar fluid shear stress (GO:0034616)|response to lipopolysaccharide (GO:0032496)|response to progesterone (GO:0032570)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|NADPH oxidase complex (GO:0043020)|nucleolus (GO:0005730)|phagolysosome (GO:0032010)	electron carrier activity (GO:0009055)|protein C-terminus binding (GO:0008022)	p.R77*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30					Dextromethorphan(DB00514)	AGCATCCCTCGTTGGAAGTAA	0.512																																					p.R77X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C229T	1						.						196.0	163.0	174.0					1																	183556058		2203	4300	6503	181822681	SO:0001587	stop_gained	4688	exon2			BC001606	CCDS1356.1, CCDS53446.1, CCDS53447.1	1q25	2014-09-17	2008-07-31		ENSG00000116701	ENSG00000116701		"""Tetratricopeptide (TTC) repeat domain containing"""	7661	protein-coding gene	gene with protein product	"""NADPH oxidase activator 2"", ""chronic granulomatous disease, autosomal 2"""	608515	"""neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)"""				Standard	NM_000433		Approved	p67phox, NOXA2	uc001gqk.4	P19878	OTTHUMG00000035329	ENST00000367535.3:c.229C>T	1.37:g.183556058G>A	ENSP00000356505:p.Arg77*	Somatic		Capture	Illumina HiSeq	Phase_I	181822681	NM_001190794	B2R6Q1|B4DKQ7|B4DQA7|E9PHJ2|E9PHX3|Q2PP06|Q8NFC7|Q9BV51	Nonsense_Mutation	SNP	ENST00000367535.3	37	CCDS1356.1	.	.	.	.	.	.	.	.	.	.	G	37	6.296761	0.97453	.	.	ENSG00000116701	ENST00000367536;ENST00000392014;ENST00000413720;ENST00000418089;ENST00000367535	.	.	.	5.17	3.24	0.37175	.	0.108829	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-39.466	13.5056	0.61481	0.0:0.0:0.7019:0.2981	.	.	.	.	X	77;105;77;77;77	.	ENSP00000356505:R77X	R	-	1	2	NCF2	181822681	0.693000	0.27728	0.325000	0.25375	0.716000	0.41182	0.924000	0.28777	0.621000	0.30232	0.561000	0.74099	CGA		0.512	NCF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085483.1	NM_000433	
RGL1	23179	broad.mit.edu	37	1	183816808	183816808	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:183816808A>G	ENST00000360851.3	+	3	425	c.247A>G	c.(247-249)Aca>Gca	p.T83A	RGL1_ENST00000536277.1_Missense_Mutation_p.T81A|RGL1_ENST00000539189.1_Missense_Mutation_p.T83A|RGL1_ENST00000304685.4_Missense_Mutation_p.T118A			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	83	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				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.T118A(1)		breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						GAACCTGCTGACAGCTTTTGG	0.478																																					p.T118A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A352G	1						.						174.0	172.0	173.0					1																	183816808		2203	4300	6503	182083431	SO:0001583	missense	23179	exon4			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.247A>G	1.37:g.183816808A>G	ENSP00000354097:p.Thr83Ala	Somatic		Capture	Illumina HiSeq	Phase_I	182083431	NM_015149	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Missense_Mutation	SNP	ENST00000360851.3	37		.	.	.	.	.	.	.	.	.	.	A	18.85	3.712344	0.68730	.	.	ENSG00000143344	ENST00000304685;ENST00000367531;ENST00000536277;ENST00000360851;ENST00000539189	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.51	5.51	0.81932	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.40196	0.1107	L	0.42245	1.32	0.58432	D	0.999998	P;D;P;P	0.57899	0.94;0.981;0.877;0.952	P;P;P;P	0.58077	0.66;0.832;0.675;0.77	T	0.12319	-1.0552	10	0.40728	T	0.16	.	11.0745	0.48023	0.8617:0.0:0.0:0.1383	.	83;81;83;118	F5H6U6;B7Z2W5;Q9NZL6;Q5SXQ6	.;.;RGL1_HUMAN;.	A	118;118;81;83;83	ENSP00000303192:T118A;ENSP00000356501:T118A;ENSP00000438662:T81A;ENSP00000354097:T83A;ENSP00000437355:T83A	ENSP00000303192:T118A	T	+	1	0	RGL1	182083431	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	6.721000	0.74728	2.217000	0.71921	0.482000	0.46254	ACA		0.478	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149	
EDEM3	80267	broad.mit.edu	37	1	184677474	184677474	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:184677474G>A	ENST00000318130.8	-	17	2116	c.1850C>T	c.(1849-1851)gCt>gTt	p.A617V	EDEM3_ENST00000466392.1_Intron|EDEM3_ENST00000367512.3_Missense_Mutation_p.A574V	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	617					cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.A574V(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GATTGAACTAGCAGCCTATGA	0.393																																					p.A617V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1850T	1						.						64.0	60.0	62.0					1																	184677474		2203	4299	6502	182944097	SO:0001583	missense	80267	exon17			AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"""chromosome 1 open reading frame 22"""	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.1850C>T	1.37:g.184677474G>A	ENSP00000318147:p.Ala617Val	Somatic		Capture	Illumina HiSeq	Phase_I	182944097	NM_025191	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Missense_Mutation	SNP	ENST00000318130.8	37	CCDS1363.2	.	.	.	.	.	.	.	.	.	.	G	13.40	2.225681	0.39300	.	.	ENSG00000116406	ENST00000318130;ENST00000367512	T;T	0.72051	-0.62;-0.62	5.76	5.76	0.90799	.	0.051547	0.85682	D	0.000000	T	0.50667	0.1629	N	0.03324	-0.35	0.58432	D	0.999997	B	0.09022	0.002	B	0.06405	0.002	T	0.46345	-0.9198	10	0.19147	T	0.46	.	19.9759	0.97304	0.0:0.0:1.0:0.0	.	617	Q9BZQ6	EDEM3_HUMAN	V	617;574	ENSP00000318147:A617V;ENSP00000356482:A574V	ENSP00000318147:A617V	A	-	2	0	EDEM3	182944097	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.922000	0.70036	2.713000	0.92767	0.655000	0.94253	GCT		0.393	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191	
EDEM3	80267	broad.mit.edu	37	1	184706786	184706786	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:184706786G>A	ENST00000318130.8	-	3	530	c.264C>T	c.(262-264)ggC>ggT	p.G88G	EDEM3_ENST00000367512.3_Silent_p.G45G	NM_025191.3	NP_079467.3	Q9BZQ6	EDEM3_HUMAN	ER degradation enhancer, mannosidase alpha-like 3	88					cellular protein metabolic process (GO:0044267)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.G45G(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TTGGCTCTTGGCCTCTAACTC	0.453																																					p.G88G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C264T	1						.						130.0	113.0	119.0					1																	184706786		2203	4300	6503	182973409	SO:0001819	synonymous_variant	80267	exon3			AF288393	CCDS1363.2	1q25	2008-02-05	2006-03-31	2006-03-31	ENSG00000116406	ENSG00000116406			16787	protein-coding gene	gene with protein product		610214	"""chromosome 1 open reading frame 22"""	C1orf22		15537790, 15579471	Standard	NM_025191		Approved		uc010pok.2	Q9BZQ6	OTTHUMG00000035387	ENST00000318130.8:c.264C>T	1.37:g.184706786G>A		Somatic		Capture	Illumina HiSeq	Phase_I	182973409	NM_025191	B2RCH6|B7ZLZ2|Q0VGM5|Q5TEZ0|Q9HCW1|Q9UFV7	Silent	SNP	ENST00000318130.8	37	CCDS1363.2																																																																																				0.453	EDEM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085785.3	NM_025191	
HMCN1	83872	broad.mit.edu	37	1	185880862	185880862	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:185880862G>A	ENST00000271588.4	+	6	1079	c.850G>A	c.(850-852)Gcc>Acc	p.A284T	HMCN1_ENST00000367492.2_Missense_Mutation_p.A284T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	284					response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.A284T(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CCATAACTCTGCCAAAGTAGT	0.388																																					p.A284T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G850A	1						.						183.0	199.0	193.0					1																	185880862		2203	4300	6503	184147485	SO:0001583	missense	83872	exon6			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.850G>A	1.37:g.185880862G>A	ENSP00000271588:p.Ala284Thr	Somatic		Capture	Illumina HiSeq	Phase_I	184147485	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	35	5.449540	0.96205	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.64085	-0.07;-0.08	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.80879	0.4708	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.80362	-0.1414	10	0.51188	T	0.08	.	20.0429	0.97598	0.0:0.0:1.0:0.0	.	284	Q96RW7	HMCN1_HUMAN	T	284	ENSP00000271588:A284T;ENSP00000356462:A284T	ENSP00000271588:A284T	A	+	1	0	HMCN1	184147485	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.150000	0.94667	2.812000	0.96745	0.555000	0.69702	GCC		0.388	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
HMCN1	83872	broad.mit.edu	37	1	185985316	185985316	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:185985316C>T	ENST00000271588.4	+	32	5365	c.5136C>T	c.(5134-5136)tgC>tgT	p.C1712C	HMCN1_ENST00000367492.2_Silent_p.C1712C	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1712	Ig-like C2-type 14.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.C1712C(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AGTACATATGCGTGGCTACCA	0.433																																					p.C1712C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5136T	1						.						113.0	105.0	107.0					1																	185985316		2203	4300	6503	184251939	SO:0001819	synonymous_variant	83872	exon32			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.5136C>T	1.37:g.185985316C>T		Somatic		Capture	Illumina HiSeq	Phase_I	184251939	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																				0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
HMCN1	83872	broad.mit.edu	37	1	186135978	186135978	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:186135978G>A	ENST00000271588.4	+	100	15707	c.15478G>A	c.(15478-15480)Gct>Act	p.A5160T	HMCN1_ENST00000367492.2_Missense_Mutation_p.A5160T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5160	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.A5160T(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TACCTGCCACGCTGGTCAGGA	0.502																																					p.A5160T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G15478A	1						.						207.0	169.0	182.0					1																	186135978		2203	4300	6503	184402601	SO:0001583	missense	83872	exon100			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.15478G>A	1.37:g.186135978G>A	ENSP00000271588:p.Ala5160Thr	Somatic		Capture	Illumina HiSeq	Phase_I	184402601	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	9.519	1.107806	0.20714	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	D;D	0.92397	-3.03;-3.03	5.69	-1.16	0.09678	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);	0.731381	0.14313	N	0.327545	D	0.84147	0.5408	L	0.33753	1.03	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.69921	-0.5014	10	0.37606	T	0.19	.	6.4516	0.21906	0.3577:0.3138:0.3286:0.0	.	5160	Q96RW7	HMCN1_HUMAN	T	5160	ENSP00000271588:A5160T;ENSP00000356462:A5160T	ENSP00000271588:A5160T	A	+	1	0	HMCN1	184402601	0.000000	0.05858	0.000000	0.03702	0.930000	0.56654	0.540000	0.23191	-0.489000	0.06716	-0.150000	0.13652	GCT		0.502	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
HMCN1	83872	broad.mit.edu	37	1	186158913	186158913	+	Missense_Mutation	SNP	G	G	A	rs372803002		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:186158913G>A	ENST00000271588.4	+	107	17040	c.16811G>A	c.(16810-16812)cGc>cAc	p.R5604H	HMCN1_ENST00000367492.2_Missense_Mutation_p.R5487H	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5604					response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.R5604H(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GAGACCTACCGCATGAGGGTC	0.468													G|||	1	0.000199681	0.0	0.0014	5008	,	,		20093	0.0		0.0	False		,,,				2504	0.0				p.R5604H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G16811A	1						.						109.0	96.0	100.0					1																	186158913		2203	4300	6503	184425536	SO:0001583	missense	83872	exon107			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.16811G>A	1.37:g.186158913G>A	ENSP00000271588:p.Arg5604His	Somatic		Capture	Illumina HiSeq	Phase_I	184425536	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	32	5.146255	0.94603	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.64991	-0.12;-0.13	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.54775	0.1879	L	0.55743	1.74	0.34450	D	0.700538	B	0.33135	0.399	B	0.23275	0.045	T	0.64368	-0.6424	10	0.31617	T	0.26	.	15.43	0.75084	0.0678:0.0:0.9322:0.0	.	5604	Q96RW7	HMCN1_HUMAN	H	5604;5487	ENSP00000271588:R5604H;ENSP00000356462:R5487H	ENSP00000271588:R5604H	R	+	2	0	HMCN1	184425536	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.932000	0.87634	2.793000	0.96121	0.655000	0.94253	CGC		0.468	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
TPR	7175	broad.mit.edu	37	1	186324543	186324543	+	Splice_Site	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:186324543G>A	ENST00000367478.4	-	17	2466	c.2170C>T	c.(2170-2172)Cgt>Tgt	p.R724C	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	724					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.R725C(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)		AAAACTTACCGTTTAGAAGCA	0.279			T	NTRK1	papillary thyroid																																p.R724C			Dom	yes		1	1q25	7175	translocated promoter region		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2170T	1						.						106.0	97.0	100.0					1																	186324543		1790	4055	5845	184591166	SO:0001630	splice_region_variant	7175	exon17			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.2171+1C>T	1.37:g.186324543G>A		Somatic		Capture	Illumina HiSeq	Phase_I	184591166	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.219688	0.79464	.	.	ENSG00000047410	ENST00000367478	T	0.19250	2.16	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.51007	0.1649	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.53585	-0.8418	10	0.87932	D	0	.	19.5146	0.95157	0.0:0.0:1.0:0.0	.	724	P12270	TPR_HUMAN	C	724	ENSP00000356448:R724C	ENSP00000356448:R724C	R	-	1	0	TPR	184591166	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	3.978000	0.56881	2.690000	0.91761	0.655000	0.94253	CGT		0.279	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	Missense_Mutation
C1orf27	54953	broad.mit.edu	37	1	186375235	186375235	+	Missense_Mutation	SNP	G	G	A	rs145574882	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:186375235G>A	ENST00000287859.6	+	12	1146	c.1021G>A	c.(1021-1023)Gtc>Atc	p.V341I	C1orf27_ENST00000432021.3_Missense_Mutation_p.V318I|C1orf27_ENST00000367470.3_Missense_Mutation_p.V318I|C1orf27_ENST00000419367.3_Missense_Mutation_p.V309I	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	341						integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)	p.V341I(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	9						AGAGTTCCACGTCCTCCCTTA	0.353													G|||	21	0.00419329	0.0151	0.0014	5008	,	,		17010	0.0		0.0	False		,,,				2504	0.0				p.V309I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G925A	1						.	G	ILE/VAL,ILE/VAL,ILE/VAL	59,3633		0,59,1787	93.0	85.0	88.0		1021,925,952	1.0	1.0	1	dbSNP_134	88	0,8216		0,0,4108	yes	missense,missense,missense	C1orf27	NM_017847.5,NM_001164246.1,NM_001164245.1	29,29,29	0,59,5895	AA,AG,GG		0.0,1.598,0.4955	benign,benign,benign	341/455,309/423,318/432	186375235	59,11849	1846	4108	5954	184641858	SO:0001583	missense	54953	exon11			BC003397	CCDS53448.1, CCDS53449.1, CCDS53450.1	1q25	2012-06-25			ENSG00000157181	ENSG00000157181			24299	protein-coding gene	gene with protein product	"""transactivated by recombinant transforming growth factor beta"""	609335				12868032	Standard	NM_017847		Approved	FLJ20505, odr-4, TTG1	uc021pgj.1	Q5SWX8	OTTHUMG00000035579	ENST00000287859.6:c.1021G>A	1.37:g.186375235G>A	ENSP00000287859:p.Val341Ile	Somatic		Capture	Illumina HiSeq	Phase_I	184641858	NM_001164246	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Missense_Mutation	SNP	ENST00000287859.6	37	CCDS53448.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	11.15	1.555047	0.27739	0.01598	0.0	ENSG00000157181	ENST00000367470;ENST00000419367;ENST00000287859	T;T;T	0.40756	1.02;1.02;1.02	4.96	1.04	0.20106	.	1.046210	0.07408	N	0.891884	T	0.10680	0.0261	N	0.12182	0.205	0.09310	N	0.999998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.20107	-1.0285	10	0.37606	T	0.19	-3.9844	0.8917	0.01255	0.4468:0.1608:0.2362:0.1563	.	309;318;341	E9PFR7;Q5SWX8-2;Q5SWX8	.;.;ODR4_HUMAN	I	318;309;341	ENSP00000356440:V318I;ENSP00000395084:V309I;ENSP00000287859:V341I	ENSP00000287859:V341I	V	+	1	0	C1orf27	184641858	0.329000	0.24696	1.000000	0.80357	0.854000	0.48673	0.605000	0.24179	0.722000	0.32252	-0.339000	0.08088	GTC		0.353	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847	
ALDH4A1	8659	broad.mit.edu	37	1	19201067	19201067	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:19201067A>G	ENST00000375341.3	-	14	1726	c.1469T>C	c.(1468-1470)gTg>gCg	p.V490A	ALDH4A1_ENST00000538309.1_Missense_Mutation_p.V430A|ALDH4A1_ENST00000290597.5_Missense_Mutation_p.V490A|ALDH4A1_ENST00000538839.1_Missense_Mutation_p.V439A|RP13-279N23.2_ENST00000494072.3_3'UTR	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	490					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|proline biosynthetic process (GO:0006561)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|electron carrier activity (GO:0009055)|identical protein binding (GO:0042802)	p.V490A(1)		cervix(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GGCCTCCTGCACGACGTCCCT	0.617																																					p.V490A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1469C	1						.						167.0	135.0	146.0					1																	19201067		2203	4300	6503	19073654	SO:0001583	missense	8659	exon14			U24266	CCDS188.1, CCDS53272.1	1p36	2008-02-05			ENSG00000159423	ENSG00000159423	1.5.1.12	"""Aldehyde dehydrogenases"""	406	protein-coding gene	gene with protein product		606811		ALDH4		8621661	Standard	NM_003748		Approved	P5CDh	uc001bbc.3	P30038	OTTHUMG00000002443	ENST00000375341.3:c.1469T>C	1.37:g.19201067A>G	ENSP00000364490:p.Val490Ala	Somatic		Capture	Illumina HiSeq	Phase_I	19073654	NM_170726	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Missense_Mutation	SNP	ENST00000375341.3	37	CCDS188.1	.	.	.	.	.	.	.	.	.	.	A	16.15	3.040315	0.55003	.	.	ENSG00000159423	ENST00000290597;ENST00000375341;ENST00000538839;ENST00000538309	T;T;T;T	0.72394	-0.65;-0.65;1.84;-0.65	5.36	5.36	0.76844	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.501171	0.22322	N	0.061599	T	0.59824	0.2222	L	0.31294	0.92	0.18873	N	0.999988	B	0.09022	0.002	B	0.18263	0.021	T	0.52968	-0.8504	10	0.42905	T	0.14	-28.0718	12.7156	0.57113	1.0:0.0:0.0:0.0	.	490	P30038	AL4A1_HUMAN	A	490;490;439;430	ENSP00000290597:V490A;ENSP00000364490:V490A;ENSP00000446071:V439A;ENSP00000442988:V430A	ENSP00000290597:V490A	V	-	2	0	ALDH4A1	19073654	0.964000	0.33143	0.226000	0.23910	0.164000	0.22412	8.876000	0.92379	2.025000	0.59659	0.459000	0.35465	GTG		0.617	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1		
UBR4	23352	broad.mit.edu	37	1	19504038	19504038	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:19504038G>A	ENST00000375254.3	-	19	2581	c.2554C>T	c.(2554-2556)Ccg>Tcg	p.P852S	UBR4_ENST00000375226.2_Missense_Mutation_p.P852S|UBR4_ENST00000375217.2_Missense_Mutation_p.P852S|UBR4_ENST00000375267.2_Missense_Mutation_p.P852S	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	852					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P852S(1)		breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AAGATAAGCGGCACGAAGCGC	0.502																																					p.P852S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2554T	1						.						139.0	131.0	134.0					1																	19504038		2203	4300	6503	19376625	SO:0001583	missense	23352	exon19			AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.2554C>T	1.37:g.19504038G>A	ENSP00000364403:p.Pro852Ser	Somatic		Capture	Illumina HiSeq	Phase_I	19376625	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	18.65	3.668960	0.67814	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000419533	T;T;T;T	0.48522	0.81;0.81;0.81;0.81	5.73	4.81	0.61882	.	0.057672	0.64402	D	0.000001	T	0.41834	0.1176	L	0.40543	1.245	0.80722	D	1	B	0.27823	0.19	B	0.25759	0.063	T	0.34551	-0.9824	10	0.59425	D	0.04	.	15.8322	0.78764	0.0:0.0:0.8629:0.1371	.	852	Q5T4S7	UBR4_HUMAN	S	852;852;852;852;68	ENSP00000364403:P852S;ENSP00000364416:P852S;ENSP00000364365:P852S;ENSP00000364374:P852S	ENSP00000364365:P852S	P	-	1	0	UBR4	19376625	1.000000	0.71417	0.853000	0.33588	0.509000	0.34042	9.238000	0.95380	1.414000	0.47017	0.655000	0.94253	CCG		0.502	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
PQLC2	54896	broad.mit.edu	37	1	19653785	19653785	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:19653785C>T	ENST00000375153.3	+	7	1323	c.683C>T	c.(682-684)aCg>aTg	p.T228M	PQLC2_ENST00000375155.3_Missense_Mutation_p.T228M|PQLC2_ENST00000400548.2_Missense_Mutation_p.T163M	NM_001040125.1	NP_001035214.1	Q6ZP29	LAAT1_HUMAN	PQ loop repeat containing 2	228	PQ-loop 2.				amino acid homeostasis (GO:0080144)|arginine transport (GO:0015809)|lysine transport (GO:0015819)	integral component of organelle membrane (GO:0031301)|lysosomal membrane (GO:0005765)	arginine transmembrane transporter activity (GO:0015181)|basic amino acid transmembrane transporter activity (GO:0015174)|L-lysine transmembrane transporter activity (GO:0015189)	p.T228M(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(1)	10		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;1.89e-05)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00124)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGGGAACACGCTGTATGGG	0.642																																					p.T228M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C683T	1						.						80.0	74.0	76.0					1																	19653785		2203	4300	6503	19526372	SO:0001583	missense	54896	exon8			BC015324	CCDS195.2, CCDS30618.1	1p36.13	2013-10-11			ENSG00000040487	ENSG00000040487			26001	protein-coding gene	gene with protein product		614760				23169667	Standard	XM_005245915		Approved	FLJ20320	uc001bby.3	Q6ZP29	OTTHUMG00000002521	ENST00000375153.3:c.683C>T	1.37:g.19653785C>T	ENSP00000364295:p.Thr228Met	Somatic		Capture	Illumina HiSeq	Phase_I	19526372	NM_017765	B3KWQ5|Q6ZMJ3|Q6ZP27|Q9NXC7	Missense_Mutation	SNP	ENST00000375153.3	37	CCDS195.2	.	.	.	.	.	.	.	.	.	.	C	13.76	2.332894	0.41297	.	.	ENSG00000040487	ENST00000375155;ENST00000375153;ENST00000400548	D;D;D	0.98249	-4.82;-4.82;-4.82	5.16	3.26	0.37387	.	0.453258	0.26075	N	0.026485	D	0.95598	0.8569	L	0.50333	1.59	0.40686	D	0.982354	B	0.28128	0.201	B	0.26202	0.067	D	0.93594	0.6924	10	0.45353	T	0.12	-5.4157	7.5537	0.27812	0.0:0.6707:0.0:0.3293	.	228	Q6ZP29	PQLC2_HUMAN	M	228;228;163	ENSP00000364297:T228M;ENSP00000364295:T228M;ENSP00000383395:T163M	ENSP00000364295:T228M	T	+	2	0	PQLC2	19526372	0.121000	0.22262	1.000000	0.80357	0.961000	0.63080	0.355000	0.20163	1.182000	0.42928	0.484000	0.47621	ACG		0.642	PQLC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007255.1	NM_017765	
RGS21	431704	broad.mit.edu	37	1	192335065	192335065	+	Silent	SNP	C	C	T	rs551033145	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:192335065C>T	ENST00000417209.2	+	5	444	c.270C>T	c.(268-270)ttC>ttT	p.F90F		NM_001039152.3	NP_001034241.1	Q2M5E4	RGS21_HUMAN	regulator of G-protein signaling 21	90	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.F90F(1)		NS(1)|endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	15						ACATTGACTTCGGTACCAGAG	0.308													C|||	2	0.000399361	0.0	0.0	5008	,	,		16505	0.0		0.0	False		,,,				2504	0.002				p.F90F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C270T	1						.						91.0	89.0	90.0					1																	192335065		1829	4076	5905	190601688	SO:0001819	synonymous_variant	431704	exon5			AY643711	CCDS41448.1	1q31.2	2013-09-24	2007-08-14		ENSG00000253148	ENSG00000253148		"""Regulators of G-protein signaling"""	26839	protein-coding gene	gene with protein product		612407	"""regulator of G-protein signalling 21"""			15066150	Standard	NM_001039152		Approved		uc001gsh.3	Q2M5E4	OTTHUMG00000035594	ENST00000417209.2:c.270C>T	1.37:g.192335065C>T		Somatic		Capture	Illumina HiSeq	Phase_I	190601688	NM_001039152		Silent	SNP	ENST00000417209.2	37	CCDS41448.1																																																																																				0.308	RGS21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086387.2		
ASPM	259266	broad.mit.edu	37	1	197074072	197074072	+	Missense_Mutation	SNP	G	G	A	rs371861473		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:197074072G>A	ENST00000367409.4	-	18	4565	c.4309C>T	c.(4309-4311)Cgt>Tgt	p.R1437C	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1437					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.R1437C(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TGCATTTTACGTTGCTTCCAT	0.299																																					p.R1437C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4309T	1						.	G	,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	119.0	109.0	113.0		,4309	5.4	0.2	1		113	1,8595	1.2+/-3.3	0,1,4297	no	intron,missense	ASPM	NM_001206846.1,NM_018136.4	,180	0,2,6499	AA,AG,GG		0.0116,0.0227,0.0154	,probably-damaging	,1437/3478	197074072	2,13000	2203	4298	6501	195340695	SO:0001583	missense	259266	exon18			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.4309C>T	1.37:g.197074072G>A	ENSP00000356379:p.Arg1437Cys	Somatic		Capture	Illumina HiSeq	Phase_I	195340695	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.318046	0.23994	2.27E-4	1.16E-4	ENSG00000066279	ENST00000367409	T	0.68331	-0.32	5.39	5.39	0.77823	.	0.148798	0.46758	D	0.000266	T	0.79435	0.4445	M	0.70595	2.14	0.58432	D	0.999997	D	0.89917	1.0	D	0.69142	0.962	T	0.80432	-0.1385	10	0.59425	D	0.04	.	13.8186	0.63308	0.0763:0.0:0.9237:0.0	.	1437	Q8IZT6	ASPM_HUMAN	C	1437	ENSP00000356379:R1437C	ENSP00000356379:R1437C	R	-	1	0	ASPM	195340695	0.012000	0.17670	0.166000	0.22797	0.650000	0.38633	1.823000	0.39062	2.685000	0.91497	0.585000	0.79938	CGT		0.299	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
ZNF281	23528	broad.mit.edu	37	1	200376332	200376332	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:200376332C>T	ENST00000294740.3	-	2	2626	c.2502G>A	c.(2500-2502)gcG>gcA	p.A834A	ZNF281_ENST00000367352.3_Silent_p.A798A|ZNF281_ENST00000367353.1_Silent_p.A834A	NM_001281293.1|NM_001281294.1|NM_012482.4	NP_001268222.1|NP_001268223.1|NP_036614.1	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	834					embryonic body morphogenesis (GO:0010172)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|metal ion binding (GO:0046872)|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.A834A(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	27						GAGAACCAAACGCTTGTGCAA	0.443																																					p.A834A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2502A	1						.						104.0	106.0	105.0					1																	200376332		2203	4300	6503	198642955	SO:0001819	synonymous_variant	23528	exon2			AF125158	CCDS1402.1, CCDS60384.1	1q32.1	2012-08-08			ENSG00000162702	ENSG00000162702		"""Zinc fingers, C2H2-type"""	13075	protein-coding gene	gene with protein product						10448078	Standard	NM_012482		Approved	ZBP-99	uc001gve.3	Q9Y2X9	OTTHUMG00000035724	ENST00000294740.3:c.2502G>A	1.37:g.200376332C>T		Somatic		Capture	Illumina HiSeq	Phase_I	198642955	NM_012482	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Silent	SNP	ENST00000294740.3	37	CCDS1402.1																																																																																				0.443	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482	
KIF14	9928	broad.mit.edu	37	1	200529894	200529894	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:200529894G>A	ENST00000367350.4	-	26	4624	c.4186C>T	c.(4186-4188)Cta>Tta	p.L1396L		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1396	Required for CIT-binding.				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.L1396L(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						AGAAAATGTAGCTTGCTCCCT	0.378																																					p.L1396L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4186T	1						.						208.0	192.0	197.0					1																	200529894		2203	4300	6503	198796517	SO:0001819	synonymous_variant	9928	exon26			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.4186C>T	1.37:g.200529894G>A		Somatic		Capture	Illumina HiSeq	Phase_I	198796517	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Silent	SNP	ENST00000367350.4	37	CCDS30963.1																																																																																				0.378	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875	
KIF21B	23046	broad.mit.edu	37	1	200956173	200956173	+	Missense_Mutation	SNP	G	G	A	rs376964063		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:200956173G>A	ENST00000422435.2	-	25	3881	c.3565C>T	c.(3565-3567)Cgg>Tgg	p.R1189W	KIF21B_ENST00000360529.5_Missense_Mutation_p.R1189W|KIF21B_ENST00000461742.2_Missense_Mutation_p.R1189W|KIF21B_ENST00000332129.2_Missense_Mutation_p.R1189W	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	1189					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R1189W(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						ACCCTGTCCCGGTAATAGGGG	0.587																																					p.R1189W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3565T	1						.						90.0	90.0	90.0					1																	200956173		2203	4300	6503	199222796	SO:0001583	missense	23046	exon25			BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.3565C>T	1.37:g.200956173G>A	ENSP00000411831:p.Arg1189Trp	Somatic		Capture	Illumina HiSeq	Phase_I	199222796	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.194568	0.78902	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.73363	-0.41;-0.71;-0.74;-0.44	5.17	4.26	0.50523	.	0.061312	0.64402	D	0.000007	T	0.79639	0.4480	M	0.69823	2.125	0.41880	D	0.990316	D;D;D;D	0.71674	0.996;0.996;0.991;0.998	P;P;P;P	0.55965	0.619;0.727;0.518;0.788	T	0.80944	-0.1156	10	0.87932	D	0	.	8.3854	0.32497	0.0814:0.0:0.7254:0.1931	.	1189;1189;1189;1189	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	W	1189	ENSP00000328494:R1189W;ENSP00000353724:R1189W;ENSP00000433808:R1189W;ENSP00000411831:R1189W	ENSP00000328494:R1189W	R	-	1	2	KIF21B	199222796	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.925000	0.48884	1.191000	0.43056	0.655000	0.94253	CGG		0.587	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
KIF21B	23046	broad.mit.edu	37	1	200959286	200959286	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:200959286C>T	ENST00000422435.2	-	20	3326	c.3010G>A	c.(3010-3012)Gtg>Atg	p.V1004M	KIF21B_ENST00000360529.5_Missense_Mutation_p.V1004M|KIF21B_ENST00000461742.2_Missense_Mutation_p.V1004M|KIF21B_ENST00000332129.2_Missense_Mutation_p.V1004M	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	1004					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.V1004M(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						TCCAGCTGCACGATGGTGGCC	0.647																																					p.V1004M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3010A	1						.						84.0	82.0	83.0					1																	200959286		2203	4300	6503	199225909	SO:0001583	missense	23046	exon20			BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.3010G>A	1.37:g.200959286C>T	ENSP00000411831:p.Val1004Met	Somatic		Capture	Illumina HiSeq	Phase_I	199225909	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	C	3.365	-0.129705	0.06753	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.80653	-1.4;-1.4;-1.4;-1.4	5.2	1.22	0.21188	Prefoldin (1);	0.283299	0.34046	N	0.004317	T	0.55577	0.1929	N	0.11023	0.085	0.39848	D	0.973205	B;B;B;B	0.19200	0.034;0.01;0.01;0.017	B;B;B;B	0.12156	0.003;0.003;0.003;0.007	T	0.49862	-0.8894	10	0.02654	T	1	.	9.0974	0.36647	0.0:0.55:0.0:0.45	.	1004;1004;1004;1004	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	M	1004	ENSP00000328494:V1004M;ENSP00000353724:V1004M;ENSP00000433808:V1004M;ENSP00000411831:V1004M	ENSP00000328494:V1004M	V	-	1	0	KIF21B	199225909	0.126000	0.22350	0.982000	0.44146	0.990000	0.78478	0.154000	0.16343	-0.026000	0.13895	0.655000	0.94253	GTG		0.647	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
CACNA1S	779	broad.mit.edu	37	1	201009481	201009481	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:201009481T>C	ENST00000362061.3	-	43	5474	c.5248A>G	c.(5248-5250)Atg>Gtg	p.M1750V	CACNA1S_ENST00000367338.3_Missense_Mutation_p.M1731V|RP11-168O16.2_ENST00000415359.1_RNA	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1750					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.M1750V(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TCCTCAGGCATGGAGGACTCC	0.562																																					p.M1750V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A5248G	1						.						31.0	30.0	30.0					1																	201009481		2203	4300	6503	199276104	SO:0001583	missense	779	exon43			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.5248A>G	1.37:g.201009481T>C	ENSP00000355192:p.Met1750Val	Somatic		Capture	Illumina HiSeq	Phase_I	199276104	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	.	0.691	-0.794363	0.02862	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.95137	-3.62;-3.54	3.79	-2.85	0.05734	.	7739.210000	0.00166	N	0.000001	D	0.83825	0.5338	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.76451	-0.2954	10	0.15066	T	0.55	.	0.6848	0.00881	0.1537:0.2163:0.1995:0.4306	.	1750	Q13698	CAC1S_HUMAN	V	1750;1731	ENSP00000355192:M1750V;ENSP00000356307:M1731V	ENSP00000355192:M1750V	M	-	1	0	CACNA1S	199276104	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.533000	0.06157	-1.207000	0.02637	0.352000	0.21897	ATG		0.562	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
CACNA1S	779	broad.mit.edu	37	1	201047170	201047170	+	Silent	SNP	G	G	A	rs9333651		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:201047170G>A	ENST00000362061.3	-	11	1682	c.1456C>T	c.(1456-1458)Ctg>Ttg	p.L486L	CACNA1S_ENST00000367338.3_Silent_p.L486L	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	486					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.L486L(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CGCAGGCCCAGCCCGTACATC	0.577																																					p.L486L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1456T	1						.						144.0	126.0	132.0					1																	201047170		2203	4300	6503	199313793	SO:0001819	synonymous_variant	779	exon11			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.1456C>T	1.37:g.201047170G>A		Somatic		Capture	Illumina HiSeq	Phase_I	199313793	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																				0.577	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
CACNA1S	779	broad.mit.edu	37	1	201061169	201061169	+	Missense_Mutation	SNP	C	C	T	rs373218444		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:201061169C>T	ENST00000362061.3	-	4	698	c.472G>A	c.(472-474)Ggc>Agc	p.G158S	CACNA1S_ENST00000367338.3_Missense_Mutation_p.G158S	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	158					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.G158S(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ACATCCAAGCCGGCTCCTTTG	0.597																																					p.G158S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G472A	1						.	C	SER/GLY	0,4406		0,0,2203	94.0	89.0	91.0		472	4.5	0.9	1		91	1,8599	1.2+/-3.3	0,1,4299	no	missense	CACNA1S	NM_000069.2	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	158/1874	201061169	1,13005	2203	4300	6503	199327792	SO:0001583	missense	779	exon4			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.472G>A	1.37:g.201061169C>T	ENSP00000355192:p.Gly158Ser	Somatic		Capture	Illumina HiSeq	Phase_I	199327792	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.916150	0.92178	0.0	1.16E-4	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.97642	-4.47;-4.47	4.48	4.48	0.54585	Ion transport (1);	0.106709	0.64402	D	0.000004	D	0.97253	0.9102	L	0.41710	1.295	0.58432	D	0.999992	D	0.89917	1.0	D	0.87578	0.998	D	0.97559	1.0097	10	0.52906	T	0.07	.	14.9994	0.71459	0.0:1.0:0.0:0.0	.	158	Q13698	CAC1S_HUMAN	S	158	ENSP00000355192:G158S;ENSP00000356307:G158S	ENSP00000355192:G158S	G	-	1	0	CACNA1S	199327792	1.000000	0.71417	0.931000	0.37212	0.979000	0.70002	7.358000	0.79466	2.198000	0.70561	0.655000	0.94253	GGC		0.597	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
IGFN1	91156	broad.mit.edu	37	1	201196224	201196224	+	Silent	SNP	C	C	T	rs376488422		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:201196224C>T	ENST00000335211.4	+	23	11131	c.11001C>T	c.(10999-11001)ggC>ggT	p.G3667G	IGFN1_ENST00000295591.8_3'UTR	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	1210						nucleus (GO:0005634)|Z disc (GO:0030018)		p.G3667G(1)|p.G827G(1)		autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						ACCTGCTGGGCGTGTGCTCCC	0.662																																					p.G3667G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C11001T	1						.	C		0,4406		0,0,2203	69.0	45.0	53.0		11001	-2.6	1.0	1		53	4,8596	4.3+/-15.6	0,4,4296	no	coding-synonymous	IGFN1	NM_001164586.1		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		3667/3709	201196224	4,13002	2203	4300	6503	199462847	SO:0001819	synonymous_variant	91156	exon23			AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.11001C>T	1.37:g.201196224C>T		Somatic		Capture	Illumina HiSeq	Phase_I	199462847	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	C	2.769	-0.256053	0.05829	0.0	4.65E-4	ENSG00000163395	ENST00000412892	.	.	.	5.19	-2.59	0.06209	.	.	.	.	.	T	0.51584	0.1683	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45687	-0.9244	4	.	.	.	.	7.9239	0.29863	0.1169:0.2815:0.0:0.6016	.	.	.	.	C	1085	.	.	R	+	1	0	IGFN1	199462847	0.004000	0.15560	0.958000	0.39756	0.271000	0.26615	-1.570000	0.02140	-0.550000	0.06183	-0.136000	0.14681	CGT		0.662	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
TNNT2	7139	broad.mit.edu	37	1	201334425	201334425	+	Missense_Mutation	SNP	C	C	A	rs121964856		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:201334425C>A	ENST00000509001.1	-	9	561	c.275G>T	c.(274-276)cGg>cTg	p.R92L	TNNT2_ENST00000367320.2_Intron|TNNT2_ENST00000236918.7_Missense_Mutation_p.R97L|TNNT2_ENST00000367322.1_Missense_Mutation_p.R92L|TNNT2_ENST00000360372.4_Missense_Mutation_p.R87L|TNNT2_ENST00000460780.1_5'Flank|TNNT2_ENST00000421663.2_Missense_Mutation_p.R94L|TNNT2_ENST00000367315.2_Missense_Mutation_p.R92L|TNNT2_ENST00000458432.2_Missense_Mutation_p.R104L|TNNT2_ENST00000367318.5_Missense_Mutation_p.R92L|TNNT2_ENST00000367317.4_Missense_Mutation_p.R92L	NM_001276347.1	NP_001263276.1	P45379	TNNT2_HUMAN	troponin T type 2 (cardiac)	102					ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|muscle filament sliding (GO:0030049)|negative regulation of ATPase activity (GO:0032780)|positive regulation of ATPase activity (GO:0032781)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle thin filament (GO:0005865)|troponin complex (GO:0005861)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|tropomyosin binding (GO:0005523)|troponin C binding (GO:0030172)|troponin I binding (GO:0031013)	p.R92L(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(9)	20						CATGCGCTTCCGGTGGATGTC	0.577																																					p.R102L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G305T	1	GRCh37	CM951218|CM961373	TNNT2	M	rs121964856	.						140.0	132.0	135.0					1																	201334425		2203	4300	6503	199601048	SO:0001583	missense	7139	exon10			X74819	CCDS30968.1, CCDS30969.1, CCDS60390.1, CCDS73002.1, CCDS73003.1	1q32	2014-09-17	2005-09-12		ENSG00000118194	ENSG00000118194			11949	protein-coding gene	gene with protein product		191045	"""troponin T2, cardiac"", ""cardiomyopathy, hypertrophic 2"", ""cardiomyopathy, dilated 1D (autosomal dominant)"""	CMH2, CMD1D		8088824, 8205619, 9482583	Standard	NM_001001430		Approved	CMPD2	uc001gwf.4	P45379	OTTHUMG00000035733	ENST00000509001.1:c.275G>T	1.37:g.201334425C>A	ENSP00000422031:p.Arg92Leu	Somatic		Capture	Illumina HiSeq	Phase_I	199601048	NM_000364	A2TDB9|A8K3K6|O60214|Q99596|Q99597|Q9BUF6|Q9UM96	Missense_Mutation	SNP	ENST00000509001.1	37	CCDS30969.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.793525	0.90453	.	.	ENSG00000118194	ENST00000367322;ENST00000367318;ENST00000458432;ENST00000421663;ENST00000236918;ENST00000367317;ENST00000367315;ENST00000360372;ENST00000357848;ENST00000367319;ENST00000509001;ENST00000438742;ENST00000455702;ENST00000422165;ENST00000412633	D;D;D;D;D;D;D;D;D;D;D;D;D	0.99143	-5.48;-5.48;-5.48;-5.48;-5.48;-5.48;-5.48;-5.48;-5.48;-5.48;-5.48;-5.48;-5.48	5.02	5.02	0.67125	.	0.054356	0.64402	D	0.000001	D	0.98972	0.9650	L	0.49571	1.57	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0	D;D;D;D;D	0.87578	0.998;0.995;0.988;0.984;0.995	D	0.99920	1.1246	10	0.87932	D	0	-19.2546	18.347	0.90326	0.0:1.0:0.0:0.0	.	87;104;102;92;102	E7EPW4;F8WAF6;P45379;Q9BUF6;P45379-10	.;.;TNNT2_HUMAN;.;.	L	92;92;104;94;97;92;92;87;88;33;92;87;102;97;91	ENSP00000356291:R92L;ENSP00000356287:R92L;ENSP00000387874:R104L;ENSP00000404134:R94L;ENSP00000236918:R97L;ENSP00000356286:R92L;ENSP00000356284:R92L;ENSP00000353535:R87L;ENSP00000422031:R92L;ENSP00000414036:R87L;ENSP00000402238:R102L;ENSP00000395163:R97L;ENSP00000408731:R91L	ENSP00000236918:R97L	R	-	2	0	TNNT2	199601048	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.898000	0.63238	2.338000	0.79540	0.561000	0.74099	CGG		0.577	TNNT2-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360358.1	NM_000364	
IPO9	55705	broad.mit.edu	37	1	201843486	201843486	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:201843486C>T	ENST00000361565.4	+	21	2888	c.2819C>T	c.(2818-2820)gCa>gTa	p.A940V		NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	940					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)	p.A940V(1)		cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						GCCACTCCTGCAGAGTGGAGT	0.498																																					p.A940V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2819T	1						.						69.0	66.0	67.0					1																	201843486		2203	4300	6503	200110109	SO:0001583	missense	55705	exon21			AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700		"""Importins"""	19425	protein-coding gene	gene with protein product						11823430, 10574461	Standard	NM_018085		Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.2819C>T	1.37:g.201843486C>T	ENSP00000354742:p.Ala940Val	Somatic		Capture	Illumina HiSeq	Phase_I	200110109	NM_018085	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Missense_Mutation	SNP	ENST00000361565.4	37	CCDS1415.1	.	.	.	.	.	.	.	.	.	.	C	15.29	2.789529	0.50102	.	.	ENSG00000198700	ENST00000361565;ENST00000456707	T	0.67865	-0.29	5.95	5.02	0.67125	Armadillo-type fold (1);	0.199991	0.52532	D	0.000069	T	0.52240	0.1722	L	0.34521	1.04	0.49213	D	0.999766	B	0.14438	0.01	B	0.11329	0.006	T	0.45498	-0.9257	10	0.21540	T	0.41	.	9.7907	0.40704	0.1583:0.689:0.1527:0.0	.	940	Q96P70	IPO9_HUMAN	V	940;15	ENSP00000354742:A940V	ENSP00000354742:A940V	A	+	2	0	IPO9	200110109	0.996000	0.38824	0.991000	0.47740	0.997000	0.91878	3.497000	0.53295	1.465000	0.48006	0.655000	0.94253	GCA		0.498	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1	NM_018085	
GPR37L1	9283	broad.mit.edu	37	1	202097219	202097219	+	Silent	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:202097219C>A	ENST00000367282.5	+	2	1087	c.981C>A	c.(979-981)acC>acA	p.T327T		NM_004767.3	NP_004758.3	O60883	ETBR2_HUMAN	G protein-coupled receptor 37 like 1	327					negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.T325_C328>S(1)|p.T327T(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	18						TCACAGTCACCTGCCAGCTGG	0.607																																					p.T327T												.	.	2	Complex - deletion inframe(1)|Substitution - coding silent(1)	ovary(1)|large_intestine(1)	c.C981A	1						.						68.0	64.0	65.0					1																	202097219		2203	4300	6503	200363842	SO:0001819	synonymous_variant	9283	exon2			AJ310210	CCDS1420.1	1q32	2012-08-21	2006-02-15		ENSG00000170075	ENSG00000170075		"""GPCR / Class A : Orphans"""	14923	protein-coding gene	gene with protein product						9539149	Standard	NM_004767		Approved	ETBR-LP-2	uc001gxj.3	O60883	OTTHUMG00000035924	ENST00000367282.5:c.981C>A	1.37:g.202097219C>A		Somatic		Capture	Illumina HiSeq	Phase_I	200363842	NM_004767	B2R7M9|Q5SXP7|Q86VP7	Silent	SNP	ENST00000367282.5	37	CCDS1420.1																																																																																				0.607	GPR37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087496.2	NM_004767	
GPR37L1	9283	broad.mit.edu	37	1	202097367	202097367	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:202097367G>A	ENST00000367282.5	+	2	1235	c.1129G>A	c.(1129-1131)Gtc>Atc	p.V377I		NM_004767.3	NP_004758.3	O60883	ETBR2_HUMAN	G protein-coupled receptor 37 like 1	377					negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.V377I(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	18						CCCAGAGAACGTCTGCAACAT	0.627																																					p.V377I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1129A	1						.						162.0	143.0	150.0					1																	202097367		2203	4300	6503	200363990	SO:0001583	missense	9283	exon2			AJ310210	CCDS1420.1	1q32	2012-08-21	2006-02-15		ENSG00000170075	ENSG00000170075		"""GPCR / Class A : Orphans"""	14923	protein-coding gene	gene with protein product						9539149	Standard	NM_004767		Approved	ETBR-LP-2	uc001gxj.3	O60883	OTTHUMG00000035924	ENST00000367282.5:c.1129G>A	1.37:g.202097367G>A	ENSP00000356251:p.Val377Ile	Somatic		Capture	Illumina HiSeq	Phase_I	200363990	NM_004767	B2R7M9|Q5SXP7|Q86VP7	Missense_Mutation	SNP	ENST00000367282.5	37	CCDS1420.1	.	.	.	.	.	.	.	.	.	.	G	6.363	0.435049	0.12045	.	.	ENSG00000170075	ENST00000541334;ENST00000367282	T	0.69435	-0.4	5.18	4.27	0.50696	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.47284	0.1437	N	0.19112	0.55	0.52099	D	0.999945	B	0.17268	0.021	B	0.20577	0.03	T	0.40515	-0.9559	10	0.02654	T	1	-47.4735	13.6917	0.62550	0.0748:0.0:0.9252:0.0	.	377	O60883	ETBR2_HUMAN	I	244;377	ENSP00000356251:V377I	ENSP00000356251:V377I	V	+	1	0	GPR37L1	200363990	0.994000	0.37717	1.000000	0.80357	0.981000	0.71138	1.963000	0.40452	1.199000	0.43173	0.561000	0.74099	GTC		0.627	GPR37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087496.2	NM_004767	
OTUD3	23252	broad.mit.edu	37	1	20234129	20234129	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:20234129C>T	ENST00000375120.3	+	8	1088	c.1087C>T	c.(1087-1089)Cgc>Tgc	p.R363C		NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	363					protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)	p.R363C(1)		breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GGAGAGGCACCGCCACAAAGC	0.567																																					p.R363C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1087T	1						.						53.0	68.0	63.0					1																	20234129		2110	4216	6326	20106716	SO:0001583	missense	23252	exon8			AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"""OTU domain containing"""	29038	protein-coding gene	gene with protein product		611758	"""OTU domain containing 3"""			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.1087C>T	1.37:g.20234129C>T	ENSP00000364261:p.Arg363Cys	Somatic		Capture	Illumina HiSeq	Phase_I	20106716	NM_015207	O75047	Missense_Mutation	SNP	ENST00000375120.3	37	CCDS41279.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.598146	0.87055	.	.	ENSG00000169914	ENST00000375120	T	0.36340	1.26	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.46718	0.1407	L	0.61218	1.895	0.80722	D	1	D	0.63046	0.992	P	0.47134	0.539	T	0.48692	-0.9013	10	0.87932	D	0	.	18.9006	0.92440	0.0:1.0:0.0:0.0	.	363	Q5T2D3	OTUD3_HUMAN	C	363	ENSP00000364261:R363C	ENSP00000364261:R363C	R	+	1	0	OTUD3	20106716	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	3.374000	0.52402	2.805000	0.96524	0.655000	0.94253	CGC		0.567	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1		
KDM5B	10765	broad.mit.edu	37	1	202702660	202702660	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:202702660C>T	ENST00000367265.3	-	23	4942	c.3778G>A	c.(3778-3780)Gtg>Atg	p.V1260M	KDM5B_ENST00000367264.2_Missense_Mutation_p.V1296M	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	1260					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.V1260M(1)		breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						TGCCAGTTCACGGTTCTTTCA	0.498																																					p.V1260M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3778A	1						.						110.0	108.0	108.0					1																	202702660		2203	4300	6503	200969283	SO:0001583	missense	10765	exon23			AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.3778G>A	1.37:g.202702660C>T	ENSP00000356234:p.Val1260Met	Somatic		Capture	Illumina HiSeq	Phase_I	200969283	NM_006618	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.829068	0.32329	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	T;T;T	0.00949	5.51;5.51;5.51	6.09	6.09	0.99107	.	0.355854	0.31577	N	0.007415	T	0.02047	0.0064	N	0.17800	0.525	0.48975	D	0.999732	D;B	0.69078	0.997;0.038	D;B	0.64042	0.921;0.013	T	0.65813	-0.6077	10	0.02654	T	1	-16.3607	20.6935	0.99705	0.0:1.0:0.0:0.0	.	1296;1260	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	M	1260;1102;1296;1102	ENSP00000356234:V1260M;ENSP00000356233:V1296M;ENSP00000235790:V1102M	ENSP00000235790:V1102M	V	-	1	0	KDM5B	200969283	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.566000	0.60843	2.897000	0.99335	0.643000	0.83706	GTG		0.498	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	
PRELP	5549	broad.mit.edu	37	1	203455928	203455928	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:203455928G>A	ENST00000343110.2	+	3	1195	c.1068G>A	c.(1066-1068)cgG>cgA	p.R356R		NM_002725.3|NM_201348.1	NP_002716.1|NP_958505.1	P51888	PRELP_HUMAN	proline/arginine-rich end leucine-rich repeat protein	356					carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)	p.R356R(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			BRCA - Breast invasive adenocarcinoma(75;0.109)			GCTACCTGCGGCTGGATGGAA	0.597																																					p.R356R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1068A	1						.						95.0	78.0	84.0					1																	203455928		2203	4300	6503	201722551	SO:0001819	synonymous_variant	5549	exon3			BC032498	CCDS1438.1	1q32	2008-02-05	2005-07-24		ENSG00000188783	ENSG00000188783		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	9357	protein-coding gene	gene with protein product	"""prolargin proteoglycan"""	601914	"""proline arginine-rich end leucine-rich repeat protein"""				Standard	NM_002725		Approved	SLRR2A, prolargin	uc001gzt.3	P51888	OTTHUMG00000035911	ENST00000343110.2:c.1068G>A	1.37:g.203455928G>A		Somatic		Capture	Illumina HiSeq	Phase_I	201722551	NM_002725	Q6FG38	Silent	SNP	ENST00000343110.2	37	CCDS1438.1																																																																																				0.597	PRELP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087474.1	NM_002725	
SNRPE	6635	broad.mit.edu	37	1	203832833	203832833	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:203832833C>T	ENST00000414487.2	+	3	169	c.124C>T	c.(124-126)Cgg>Tgg	p.R42W	SNRPE_ENST00000483099.1_3'UTR|SNRPE_ENST00000367208.1_Missense_Mutation_p.R2W	NM_003094.2	NP_003085.1	P62304	RUXE_HUMAN	small nuclear ribonucleoprotein polypeptide E	42					gene expression (GO:0010467)|hair cycle (GO:0042633)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|methylosome (GO:0034709)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pICln-Sm protein complex (GO:0034715)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U12-type spliceosomal complex (GO:0005689)|U4 snRNP (GO:0005687)|U7 snRNP (GO:0005683)	RNA binding (GO:0003723)	p.R42W(1)		breast(1)|large_intestine(2)|lung(1)|skin(1)	5	all_cancers(21;0.103)		BRCA - Breast invasive adenocarcinoma(75;0.109)			AGTGAATATGCGGATAGAAGG	0.433																																					p.R42W	Ovarian(83;324 1318 17952 32395 39614)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C124T	1						.						127.0	128.0	127.0					1																	203832833		2203	4300	6503	202099456	SO:0001583	missense	6635	exon3			M37716	CCDS30979.1	1q32	2011-10-11			ENSG00000182004	ENSG00000182004			11161	protein-coding gene	gene with protein product		128260				1835977, 2143747	Standard	NM_003094		Approved	Sm-E	uc001hai.3	P62304	OTTHUMG00000035985	ENST00000414487.2:c.124C>T	1.37:g.203832833C>T	ENSP00000400591:p.Arg42Trp	Somatic		Capture	Illumina HiSeq	Phase_I	202099456	NM_003094	B2R5B9|P08578|Q15498|Q5BKT2	Missense_Mutation	SNP	ENST00000414487.2	37	CCDS30979.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.276540	0.59758	.	.	ENSG00000182004	ENST00000414487;ENST00000367208	T;T	0.45276	0.9;0.9	5.35	4.44	0.53790	Like-Sm ribonucleoprotein (LSM) domain, eukaryotic/archaea-type (1);Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.060085	0.64402	N	0.000002	T	0.37210	0.0995	.	.	.	0.80722	D	1	B	0.16802	0.019	B	0.17722	0.019	T	0.18272	-1.0342	9	0.52906	T	0.07	.	13.7069	0.62646	0.0:0.9252:0.0:0.0748	.	42	P62304	RUXE_HUMAN	W	42;2	ENSP00000400591:R42W;ENSP00000356176:R2W	ENSP00000356176:R2W	R	+	1	2	SNRPE	202099456	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	4.545000	0.60698	1.260000	0.44134	-0.145000	0.13849	CGG		0.433	SNRPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087703.1	NM_003094	
PIK3C2B	5287	broad.mit.edu	37	1	204433164	204433164	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:204433164C>T	ENST00000367187.3	-	6	1842	c.1286G>A	c.(1285-1287)tGc>tAc	p.C429Y	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.C429Y	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	429	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				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.C429Y(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)			CTCCAGCCCGCAGGGCTTTAG	0.547																																					p.C429Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1286A	1						.						131.0	129.0	130.0					1																	204433164		2203	4300	6503	202699787	SO:0001583	missense	5287	exon6			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.1286G>A	1.37:g.204433164C>T	ENSP00000356155:p.Cys429Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	202699787	NM_002646	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	37	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.015672	0.75161	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.61859	0.09;0.07	4.93	4.01	0.46588	Phosphoinositide 3-kinase, ras-binding (2);	0.203652	0.52532	D	0.000074	T	0.61198	0.2328	M	0.64404	1.975	0.43714	D	0.996188	P;P	0.47106	0.537;0.89	B;P	0.49047	0.412;0.599	T	0.60372	-0.7276	10	0.33141	T	0.24	.	12.7128	0.57100	0.1649:0.8351:0.0:0.0	.	429;429	F5GWN5;O00750	.;P3C2B_HUMAN	Y	429	ENSP00000356155:C429Y;ENSP00000400561:C429Y	ENSP00000356155:C429Y	C	-	2	0	PIK3C2B	202699787	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.960000	0.76036	1.272000	0.44329	0.655000	0.94253	TGC		0.547	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
LRRN2	10446	broad.mit.edu	37	1	204587181	204587181	+	Missense_Mutation	SNP	G	G	A	rs182204828	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:204587181G>A	ENST00000367175.1	-	1	4152	c.1940C>T	c.(1939-1941)gCg>gTg	p.A647V	LRRN2_ENST00000367176.3_Missense_Mutation_p.A647V|LRRN2_ENST00000496057.1_5'Flank|LRRN2_ENST00000367177.3_Missense_Mutation_p.A647V|RP11-430C7.4_ENST00000453895.1_RNA			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	647					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.A647V(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			AAGGTGGGCCGCTAGCCCAGC	0.657													G|||	2	0.000399361	0.0	0.0	5008	,	,		19385	0.002		0.0	False		,,,				2504	0.0				p.A647V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1940T	1						.						35.0	40.0	39.0					1																	204587181		2203	4300	6503	202853804	SO:0001583	missense	10446	exon2			AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.1940C>T	1.37:g.204587181G>A	ENSP00000356143:p.Ala647Val	Somatic		Capture	Illumina HiSeq	Phase_I	202853804	NM_201630	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	37	CCDS1448.1	5	0.0022893772893772895	2	0.0040650406504065045	0	0.0	2	0.0034965034965034965	1	0.0013192612137203166	G	9.691	1.151863	0.21371	.	.	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.59224	0.28;0.28;0.28	5.47	3.53	0.40419	.	0.204271	0.24124	N	0.041324	T	0.30727	0.0774	N	0.08118	0	0.21355	N	0.999715	B	0.06786	0.001	B	0.01281	0.0	T	0.15578	-1.0432	10	0.17369	T	0.5	.	6.3768	0.21511	0.3847:0.0:0.6153:0.0	.	647	O75325	LRRN2_HUMAN	V	647	ENSP00000356144:A647V;ENSP00000356145:A647V;ENSP00000356143:A647V	ENSP00000356143:A647V	A	-	2	0	LRRN2	202853804	0.000000	0.05858	0.115000	0.21578	0.985000	0.73830	0.263000	0.18478	0.603000	0.29913	0.561000	0.74099	GCG		0.657	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338	
NFASC	23114	broad.mit.edu	37	1	204937477	204937477	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:204937477C>T	ENST00000401399.1	+	8	1006	c.807C>T	c.(805-807)atC>atT	p.I269I	NFASC_ENST00000367171.4_Silent_p.I269I|NFASC_ENST00000539706.1_Silent_p.I280I|NFASC_ENST00000339876.6_Silent_p.I269I|NFASC_ENST00000513543.1_Silent_p.I280I|NFASC_ENST00000404076.1_Silent_p.I263I|NFASC_ENST00000367170.4_Silent_p.I269I|NFASC_ENST00000338586.6_Silent_p.I269I|NFASC_ENST00000403080.1_Silent_p.I269I|NFASC_ENST00000360049.4_Silent_p.I280I|NFASC_ENST00000338515.6_Silent_p.I269I|NFASC_ENST00000367169.4_Silent_p.I269I|NFASC_ENST00000367172.4_Silent_p.I269I|NFASC_ENST00000404907.1_Silent_p.I280I			O94856	NFASC_HUMAN	neurofascin	269	Ig-like C2-type 3.				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.I280I(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)			TGGAATGCATCGCCTCCGGGG	0.572																																					p.I280I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C840T	1						.						123.0	98.0	106.0					1																	204937477		2203	4300	6503	203204100	SO:0001819	synonymous_variant	23114	exon7			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.807C>T	1.37:g.204937477C>T		Somatic		Capture	Illumina HiSeq	Phase_I	203204100	NM_001160331	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000401399.1	37	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376461	0.24857	.	.	ENSG00000163531	ENST00000367173	.	.	.	4.93	3.04	0.35103	.	.	.	.	.	T	0.54951	0.1890	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46498	-0.9187	4	.	.	.	.	6.4371	0.21829	0.0:0.6355:0.0:0.3645	.	.	.	.	L	239	.	.	S	+	2	0	NFASC	203204100	0.818000	0.29161	1.000000	0.80357	0.990000	0.78478	-0.081000	0.11321	0.486000	0.27676	-0.141000	0.14075	TCG		0.572	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
TMCC2	9911	broad.mit.edu	37	1	205210700	205210700	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:205210700G>A	ENST00000358024.3	+	2	664	c.275G>A	c.(274-276)cGt>cAt	p.R92H	TMCC2_ENST00000545499.1_Missense_Mutation_p.R14H|TMCC2_ENST00000495538.1_3'UTR	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	92						integral component of membrane (GO:0016021)		p.R92H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(3)|pancreas(1)|skin(1)|urinary_tract(1)	20	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CACAGCCGCCGTCGGTCTCGG	0.582																																					p.R92H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G275A	1						.						68.0	60.0	63.0					1																	205210700		2203	4300	6503	203477323	SO:0001583	missense	9911	exon2			AB001596	CCDS30984.1, CCDS55676.1, CCDS73010.1	1q32.1	2008-02-05	2005-07-13		ENSG00000133069	ENSG00000133069		"""Transmembrane and coiled-coil domain containing"""	24239	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 2"""			9455484	Standard	NM_014858		Approved	HUCEP11, FLJ38497	uc021pia.1	O75069	OTTHUMG00000037195	ENST00000358024.3:c.275G>A	1.37:g.205210700G>A	ENSP00000350718:p.Arg92His	Somatic		Capture	Illumina HiSeq	Phase_I	203477323	NM_014858	A2RRH3|B7Z1P7|Q6ZN09	Missense_Mutation	SNP	ENST00000358024.3	37	CCDS30984.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.807778	0.90623	.	.	ENSG00000133069	ENST00000358024;ENST00000545499	T;T	0.45668	0.89;0.97	4.78	4.78	0.61160	.	0.376195	0.28859	N	0.013914	T	0.55970	0.1954	L	0.36672	1.1	0.48632	D	0.999685	D	0.76494	0.999	D	0.73380	0.98	T	0.60434	-0.7264	10	0.87932	D	0	.	17.7739	0.88501	0.0:0.0:1.0:0.0	.	92	O75069	TMCC2_HUMAN	H	92;14	ENSP00000350718:R92H;ENSP00000437943:R14H	ENSP00000350718:R92H	R	+	2	0	TMCC2	203477323	1.000000	0.71417	1.000000	0.80357	0.776000	0.43924	8.002000	0.88514	2.360000	0.80028	0.462000	0.41574	CGT		0.582	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	NM_014858	
AVPR1B	553	broad.mit.edu	37	1	206224525	206224525	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:206224525C>T	ENST00000367126.4	+	1	550	c.85C>T	c.(85-87)Cgg>Tgg	p.R29W	RP11-38J22.3_ENST00000425896.1_RNA	NM_000707.3	NP_000698.1	P47901	V1BR_HUMAN	arginine vasopressin receptor 1B	29					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.R29W(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)	CTGGCTGGGCCGGGATGAGGA	0.667																																					p.R29W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C85T	1						.						102.0	121.0	115.0					1																	206224525		2203	4300	6503	204391148	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.85C>T	1.37:g.206224525C>T	ENSP00000356094:p.Arg29Trp	Somatic		Capture	Illumina HiSeq	Phase_I	204391148	NM_000707	B0M0J6|Q5TZ00	Missense_Mutation	SNP	ENST00000367126.4	37	CCDS30994.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.659565	0.47467	.	.	ENSG00000198049	ENST00000367126	T	0.37752	1.18	5.05	3.09	0.35607	.	0.095148	0.42964	D	0.000627	T	0.64713	0.2623	M	0.89785	3.06	0.48288	D	0.999624	D	0.89917	1.0	D	0.97110	1.0	T	0.70883	-0.4751	10	0.72032	D	0.01	-33.0942	12.4384	0.55612	0.4557:0.5443:0.0:0.0	.	29	P47901	V1BR_HUMAN	W	29	ENSP00000356094:R29W	ENSP00000356094:R29W	R	+	1	2	AVPR1B	204391148	0.472000	0.25870	1.000000	0.80357	0.505000	0.33919	1.045000	0.30341	0.643000	0.30638	0.603000	0.83216	CGG		0.667	AVPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087996.1	NM_000707	
CTSE	1510	broad.mit.edu	37	1	206325372	206325372	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:206325372A>G	ENST00000358184.2	+	5	715	c.597A>G	c.(595-597)ccA>ccG	p.P199P	CTSE_ENST00000361052.3_Silent_p.P204P|CTSE_ENST00000432969.2_Silent_p.P124P|CTSE_ENST00000468617.1_3'UTR|CTSE_ENST00000360218.2_Silent_p.P199P	NM_001910.3	NP_001901.1	P14091	CATE_HUMAN	cathepsin E	204					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|digestion (GO:0007586)|protein autoprocessing (GO:0016540)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)	p.P199P(1)		endometrium(2)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(3)	16			BRCA - Breast invasive adenocarcinoma(75;0.0754)			GAGTGACTCCAGTATTTGACA	0.507																																					p.P199P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A597G	1						.						165.0	142.0	150.0					1																	206325372		2203	4300	6503	204491995	SO:0001819	synonymous_variant	1510	exon5			BC042537	CCDS73012.1, CCDS73013.1	1q32.1	2008-02-05			ENSG00000196188	ENSG00000196188	3.4.23.5	"""Cathepsins"""	2530	protein-coding gene	gene with protein product		116890				2369841, 2674141	Standard	NM_001910		Approved		uc001hdu.3	P14091	OTTHUMG00000036121	ENST00000358184.2:c.597A>G	1.37:g.206325372A>G		Somatic		Capture	Illumina HiSeq	Phase_I	204491995	NM_001910	Q5TZ01|Q5TZ02|Q9NY58|Q9UCE3|Q9UCE4	Silent	SNP	ENST00000358184.2	37	CCDS1462.1																																																																																				0.507	CTSE-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087998.1	NM_001910	
SRGAP2	23380	broad.mit.edu	37	1	206626583	206626583	+	Silent	SNP	C	C	T	rs139336071	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:206626583C>T	ENST00000414007.1	+	16	1797	c.1797C>T	c.(1795-1797)taC>taT	p.Y599Y	SRGAP2_ENST00000471256.1_3'UTR|SRGAP2_ENST00000419187.2_Silent_p.Y44Y			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	739	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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.Y599Y(1)		NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					AGTTTGACTACGTGGGCCGGA	0.557													C|||	3	0.000599042	0.0	0.0014	5008	,	,		18086	0.0		0.001	False		,,,				2504	0.001				p.R652C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1954T	1						.						41.0	38.0	39.0					1																	206626583		2035	4213	6248	204693206	SO:0001819	synonymous_variant	23380	exon17			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	ENST00000414007.1:c.1797C>T	1.37:g.206626583C>T		Somatic		Capture	Illumina HiSeq	Phase_I	204693206	NM_001170637		Silent	SNP	ENST00000414007.1	37		1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	10.15|10.15	1.271435|1.271435	0.23221|0.23221	.|.	.|.	ENSG00000163486|ENSG00000163486	ENST00000295713|ENST00000426388	.|.	.|.	.|.	5.62|5.62	0.552|0.552	0.17230|0.17230	.|.	.|.	.|.	.|.	.|.	T|T	0.48447|0.48447	0.1500|0.1500	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.55630|0.55630	-0.8111|-0.8111	3|3	.|.	.|.	.|.	.|.	9.8047|9.8047	0.40786|0.40786	0.0:0.6584:0.0:0.3416|0.0:0.6584:0.0:0.3416	.|.	.|.	.|.	.|.	C|M	653|22	.|.	.|.	R|T	+|+	1|2	0|0	SRGAP2|SRGAP2	204693206|204693206	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.996000|0.996000	0.88848|0.88848	2.168000|2.168000	0.42424|0.42424	0.068000|0.068000	0.16574|0.16574	-0.140000|-0.140000	0.14226|0.14226	CGT|ACG		0.557	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding		NM_015326	
IKBKE	9641	broad.mit.edu	37	1	206649567	206649567	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:206649567C>T	ENST00000367120.3	+	6	775	c.402C>T	c.(400-402)cgC>cgT	p.R134R	IKBKE_ENST00000537984.1_Silent_p.R49R	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	134	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.R134R(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)					TTGTGCATCGCGACATCAAGC	0.627																																					p.R134R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C402T	1						.						97.0	82.0	87.0					1																	206649567		2203	4300	6503	204716190	SO:0001819	synonymous_variant	9641	exon6			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.402C>T	1.37:g.206649567C>T		Somatic		Capture	Illumina HiSeq	Phase_I	204716190	NM_001193322	D3DT78|Q3B754|Q3KR43|Q5JTS6	Silent	SNP	ENST00000367120.3	37	CCDS30996.1																																																																																				0.627	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1		
EIF2D	1939	broad.mit.edu	37	1	206782796	206782796	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:206782796G>T	ENST00000271764.2	-	3	472	c.264C>A	c.(262-264)tcC>tcA	p.S88S	EIF2D_ENST00000367114.3_Silent_p.S88S	NM_006893.2	NP_008824.2	P41214	EIF2D_HUMAN	eukaryotic translation initiation factor 2D	88					formation of translation preinitiation complex (GO:0001731)|intracellular protein transport (GO:0006886)|IRES-dependent translational initiation (GO:0002192)|ribosome disassembly (GO:0032790)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	receptor activity (GO:0004872)|translation initiation factor activity (GO:0003743)	p.S88S(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						GATCAGGATAGGACCACAGCG	0.443																																					p.S88S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C264A	1						.						137.0	122.0	127.0					1																	206782796		2203	4300	6503	204849419	SO:0001819	synonymous_variant	1939	exon3			BC001585	CCDS1465.1, CCDS55680.1	1q32.1	2014-05-06	2011-01-19	2011-01-19	ENSG00000143486	ENSG00000143486			6583	protein-coding gene	gene with protein product		613709				20566627	Standard	NM_001201478		Approved	LGTN	uc001heh.2	P41214	OTTHUMG00000184619	ENST00000271764.2:c.264C>A	1.37:g.206782796G>T		Somatic		Capture	Illumina HiSeq	Phase_I	204849419	NM_006893	Q5SY40|Q8IXV3|Q96DG3|Q96TG7|Q9NR27|Q9NSN0|Q9NV18|Q9NZ21	Silent	SNP	ENST00000271764.2	37	CCDS1465.1																																																																																				0.443	EIF2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088475.1	NM_006893	
YOD1	55432	broad.mit.edu	37	1	207224147	207224147	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:207224147C>T	ENST00000315927.4	-	1	275	c.229G>A	c.(229-231)Gcc>Acc	p.A77T	PFKFB2_ENST00000367080.3_5'Flank|PFKFB2_ENST00000367079.2_5'Flank|YOD1_ENST00000391927.1_Missense_Mutation_p.A33T|YOD1_ENST00000367084.1_Missense_Mutation_p.A33T|PFKFB2_ENST00000411990.2_Intron	NM_018566.3	NP_061036.3	Q5VVQ6	OTU1_HUMAN	YOD1 deubiquitinase	77	UBX-like.				cellular amino acid metabolic process (GO:0006520)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein K11-linked deubiquitination (GO:0035871)|protein K27-linked deubiquitination (GO:1990167)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)		Lys48-specific deubiquitinase activity (GO:1990380)|metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)	p.A77T(1)		cervix(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(3)	11	Prostate(682;0.19)					GTGATGGCGGCAATTTGGCCC	0.642																																					p.A77T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G229A	1						.						36.0	41.0	40.0					1																	207224147		2202	4296	6498	205290770	SO:0001583	missense	55432	exon1				CCDS31002.1, CCDS60402.1	1q32.2	2013-06-04	2013-06-04		ENSG00000180667	ENSG00000180667		"""OTU domain containing"""	25035	protein-coding gene	gene with protein product		612023	"""YOD1 OTU deubiquinating enzyme 1 homolog ( yeast)"", ""YOD1 OTU deubiquinating enzyme 1 homolog (S. cerevisiae)"""				Standard	NM_001276320		Approved	DKFZp451J1719, OTUD2, DUBA8	uc001hfe.1	Q5VVQ6	OTTHUMG00000036032	ENST00000315927.4:c.229G>A	1.37:g.207224147C>T	ENSP00000326813:p.Ala77Thr	Somatic		Capture	Illumina HiSeq	Phase_I	205290770	NM_018566	B2RNX3|Q5VVQ5|Q6ZRS6|Q86T63|Q9P1L8	Missense_Mutation	SNP	ENST00000315927.4	37	CCDS31002.1	.	.	.	.	.	.	.	.	.	.	C	19.07	3.756449	0.69648	.	.	ENSG00000180667	ENST00000367084;ENST00000315927;ENST00000391927	.	.	.	5.69	5.69	0.88448	.	0.102851	0.64402	D	0.000003	T	0.54334	0.1852	L	0.53729	1.69	0.80722	D	1	P;P	0.49090	0.763;0.919	B;B	0.39339	0.173;0.297	T	0.56703	-0.7935	9	0.37606	T	0.19	-18.4248	18.3672	0.90396	0.0:1.0:0.0:0.0	.	33;77	Q5VVQ6-2;Q5VVQ6	.;OTU1_HUMAN	T	33;77;33	.	ENSP00000326813:A77T	A	-	1	0	YOD1	205290770	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	3.833000	0.55790	2.669000	0.90835	0.655000	0.94253	GCC		0.642	YOD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087837.1	NM_018566	
CR2	1380	broad.mit.edu	37	1	207646986	207646986	+	Intron	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:207646986C>A	ENST00000367058.3	+	11	2167				CR2_ENST00000367059.3_Intron|CR2_ENST00000458541.2_Intron|CR2_ENST00000367057.3_Missense_Mutation_p.P692H	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2						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.P692H(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						ACTTGTGACCCTGGCTATTTG	0.493																																					p.P692H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2075A	1						.						160.0	154.0	156.0					1																	207646986		2203	4300	6503	205713609	SO:0001627	intron_variant	1380	exon11			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.1979-160C>A	1.37:g.207646986C>A		Somatic		Capture	Illumina HiSeq	Phase_I	205713609	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.365835	0.61513	.	.	ENSG00000117322	ENST00000367057	T	0.67171	-0.25	5.11	3.24	0.37175	.	.	.	.	.	T	0.77219	0.4098	M	0.78049	2.395	0.80722	D	1	D	0.76494	0.999	D	0.65874	0.939	T	0.75360	-0.3345	9	0.49607	T	0.09	.	7.9467	0.29991	0.0:0.8092:0.0:0.1908	.	692	P20023-3	.	H	692	ENSP00000356024:P692H	ENSP00000356024:P692H	P	+	2	0	CR2	205713609	0.682000	0.27624	0.996000	0.52242	0.995000	0.86356	1.239000	0.32719	0.655000	0.30866	0.655000	0.94253	CCT		0.493	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
PLXNA2	5362	broad.mit.edu	37	1	208200607	208200607	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:208200607G>A	ENST00000367033.3	-	32	6423	c.5666C>T	c.(5665-5667)gCc>gTc	p.A1889V	PLXNA2_ENST00000483048.1_5'UTR	NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1889					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.A1889V(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)		AATGGACATGGCATTAATGAG	0.567																																					p.A1889V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5666T	1						.						105.0	98.0	101.0					1																	208200607		2203	4300	6503	206267230	SO:0001583	missense	5362	exon32			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.5666C>T	1.37:g.208200607G>A	ENSP00000356000:p.Ala1889Val	Somatic		Capture	Illumina HiSeq	Phase_I	206267230	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.305996	0.60305	.	.	ENSG00000076356	ENST00000367033	T	0.00949	5.51	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.01489	0.0048	M	0.62723	1.935	0.80722	D	1	B;P	0.35242	0.179;0.492	B;B	0.24974	0.057;0.032	T	0.68330	-0.5437	10	0.16896	T	0.51	.	18.9064	0.92464	0.0:0.0:1.0:0.0	.	1889;159	O75051;Q9HAE7	PLXA2_HUMAN;.	V	1889	ENSP00000356000:A1889V	ENSP00000356000:A1889V	A	-	2	0	PLXNA2	206267230	1.000000	0.71417	0.996000	0.52242	0.950000	0.60333	7.530000	0.81962	2.466000	0.83321	0.655000	0.94253	GCC		0.567	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
PLXNA2	5362	broad.mit.edu	37	1	208216530	208216530	+	Missense_Mutation	SNP	G	G	A	rs372372428		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:208216530G>A	ENST00000367033.3	-	21	4650	c.3893C>T	c.(3892-3894)aCg>aTg	p.T1298M		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1298					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.T1298M(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)		ATTGATATCCGTCTGGAGCTC	0.547																																					p.T1298M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3893T	1						.	G	MET/THR	0,4406		0,0,2203	81.0	78.0	79.0		3893	5.2	1.0	1		79	1,8599	1.2+/-3.3	0,1,4299	no	missense	PLXNA2	NM_025179.3	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	1298/1895	208216530	1,13005	2203	4300	6503	206283153	SO:0001583	missense	5362	exon21			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.3893C>T	1.37:g.208216530G>A	ENSP00000356000:p.Thr1298Met	Somatic		Capture	Illumina HiSeq	Phase_I	206283153	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.908472	0.92107	0.0	1.16E-4	ENSG00000076356	ENST00000367033	T	0.01215	5.16	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.09512	0.0234	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00733	-1.1589	10	0.87932	D	0	.	18.8715	0.92317	0.0:0.0:1.0:0.0	.	1298	O75051	PLXA2_HUMAN	M	1298	ENSP00000356000:T1298M	ENSP00000356000:T1298M	T	-	2	0	PLXNA2	206283153	1.000000	0.71417	0.992000	0.48379	0.950000	0.60333	9.398000	0.97281	2.460000	0.83146	0.650000	0.86243	ACG		0.547	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
KIF17	57576	broad.mit.edu	37	1	21031328	21031328	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:21031328C>T	ENST00000247986.2	-	5	1045	c.735G>A	c.(733-735)gaG>gaA	p.E245E	KIF17_ENST00000375044.1_Silent_p.E145E|KIF17_ENST00000400463.3_Silent_p.E245E			Q9P2E2	KIF17_HUMAN	kinesin family member 17	245	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)	p.E245E(1)		NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|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;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		TGGACTGCCGCTCGCTGCCCG	0.682																																					p.E245E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G735A	1						.						37.0	41.0	40.0					1																	21031328		2203	4298	6501	20903915	SO:0001819	synonymous_variant	57576	exon5			AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.735G>A	1.37:g.21031328C>T		Somatic		Capture	Illumina HiSeq	Phase_I	20903915	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	37	CCDS213.1																																																																																				0.682	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
SERTAD4	56256	broad.mit.edu	37	1	210414991	210414991	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:210414991G>A	ENST00000367012.3	+	4	610	c.380G>A	c.(379-381)cGa>cAa	p.R127Q	SERTAD4_ENST00000490620.1_3'UTR	NM_019605.3	NP_062551.1	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	127	SERTA. {ECO:0000255|PROSITE- ProRule:PRU00396}.					nucleus (GO:0005634)		p.R127Q(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)		GTGTACCTCCGAAGATCTGTC	0.398																																					p.R127Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G380A	1						.						96.0	101.0	99.0					1																	210414991		2203	4300	6503	208481614	SO:0001583	missense	56256	exon4			BC012083	CCDS1494.1	1q32.1-q41	2008-02-05			ENSG00000082497	ENSG00000082497			25236	protein-coding gene	gene with protein product						12477932	Standard	NM_019605		Approved	DJ667H12.2	uc001hhy.3	Q9NUC0	OTTHUMG00000036391	ENST00000367012.3:c.380G>A	1.37:g.210414991G>A	ENSP00000355979:p.Arg127Gln	Somatic		Capture	Illumina HiSeq	Phase_I	208481614	NM_019605	B2RD32	Missense_Mutation	SNP	ENST00000367012.3	37	CCDS1494.1	.	.	.	.	.	.	.	.	.	.	G	18.98	3.736830	0.69304	.	.	ENSG00000082497	ENST00000367012	.	.	.	5.66	4.75	0.60458	.	0.000000	0.64402	D	0.000003	T	0.58047	0.2095	L	0.55481	1.735	0.38702	D	0.953019	B	0.29253	0.239	B	0.24974	0.057	T	0.63051	-0.6723	9	0.72032	D	0.01	-6.6775	14.8004	0.69909	0.0694:0.0:0.9306:0.0	.	127	Q9NUC0	SRTD4_HUMAN	Q	127	.	ENSP00000355979:R127Q	R	+	2	0	SERTAD4	208481614	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.113000	0.71553	1.391000	0.46566	0.655000	0.94253	CGA		0.398	SERTAD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088577.1	NM_019605	
KCNH1	3756	broad.mit.edu	37	1	211093036	211093036	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:211093036C>T	ENST00000271751.4	-	7	1435	c.1408G>A	c.(1408-1410)Gcc>Acc	p.A470T	KCNH1_ENST00000367007.4_Missense_Mutation_p.A443T			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	470					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.A470T(1)|p.A470S(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)		GTGGATGGGGCGATGTTCCCA	0.507																																					p.A443T												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1327A	1						.						162.0	154.0	157.0					1																	211093036		2203	4300	6503	209159659	SO:0001583	missense	3756	exon7			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.1408G>A	1.37:g.211093036C>T	ENSP00000271751:p.Ala470Thr	Somatic		Capture	Illumina HiSeq	Phase_I	209159659	NM_002238	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.041835	0.93685	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.98419	-4.92;-4.92	5.57	5.57	0.84162	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98112	0.9377	L	0.35793	1.09	0.80722	D	1	D;D	0.69078	0.988;0.997	P;D	0.65874	0.901;0.939	D	0.99844	1.1064	10	0.87932	D	0	.	18.5224	0.90958	0.0:1.0:0.0:0.0	.	443;470	Q14CL3;O95259	.;KCNH1_HUMAN	T	470;443	ENSP00000271751:A470T;ENSP00000355974:A443T	ENSP00000271751:A470T	A	-	1	0	KCNH1	209159659	1.000000	0.71417	0.975000	0.42487	0.991000	0.79684	7.538000	0.82048	2.623000	0.88846	0.561000	0.74099	GCC		0.507	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238	
TRAF5	7188	broad.mit.edu	37	1	211538772	211538772	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:211538772C>T	ENST00000261464.5	+	8	805	c.751C>T	c.(751-753)Cgt>Tgt	p.R251C	TRAF5_ENST00000427925.2_Missense_Mutation_p.R145C|TRAF5_ENST00000462410.1_3'UTR|TRAF5_ENST00000336184.2_Missense_Mutation_p.R251C|TRAF5_ENST00000367004.3_Missense_Mutation_p.R251C	NM_001033910.2	NP_001029082.1	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	251					apoptotic process (GO:0006915)|positive regulation of cell proliferation (GO:0008284)|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)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	CD40 receptor complex (GO:0035631)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)	signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R251C(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		GGAGCACATGCGTTTGGTTTT	0.408																																					p.R251C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C751T	1						.						75.0	71.0	72.0					1																	211538772		2203	4300	6503	209605395	SO:0001583	missense	7188	exon8			AB000509	CCDS1497.1	1q32	2008-02-05			ENSG00000082512	ENSG00000082512		"""RING-type (C3HC4) zinc fingers"""	12035	protein-coding gene	gene with protein product		602356				9126477	Standard	NM_001033910		Approved	RNF84	uc001hii.3	O00463	OTTHUMG00000036997	ENST00000261464.5:c.751C>T	1.37:g.211538772C>T	ENSP00000261464:p.Arg251Cys	Somatic		Capture	Illumina HiSeq	Phase_I	209605395	NM_004619	B4DIS9|B4E0A2|Q6FHY1	Missense_Mutation	SNP	ENST00000261464.5	37	CCDS1497.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.334100	0.81801	.	.	ENSG00000082512	ENST00000336184;ENST00000427925;ENST00000261464;ENST00000367004	T;D;T;T	0.83250	1.94;-1.7;1.94;1.94	5.4	5.4	0.78164	TRAF-like (1);	0.140137	0.49305	D	0.000158	T	0.75287	0.3829	N	0.08118	0	0.54753	D	0.999987	D;D;P	0.61697	0.99;0.975;0.9	P;B;B	0.47744	0.556;0.316;0.238	T	0.80600	-0.1310	10	0.54805	T	0.06	-9.1022	18.1829	0.89783	0.0:1.0:0.0:0.0	.	145;262;251	F5H1P7;B4E0A2;O00463	.;.;TRAF5_HUMAN	C	251;145;251;251	ENSP00000336825:R251C;ENSP00000389891:R145C;ENSP00000261464:R251C;ENSP00000355971:R251C	ENSP00000261464:R251C	R	+	1	0	TRAF5	209605395	1.000000	0.71417	1.000000	0.80357	0.787000	0.44495	5.730000	0.68546	2.532000	0.85374	0.561000	0.74099	CGT		0.408	TRAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089825.1	NM_004619	
PPP2R5A	5525	broad.mit.edu	37	1	212521784	212521784	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:212521784T>C	ENST00000261461.2	+	7	1392	c.818T>C	c.(817-819)aTg>aCg	p.M273T	PPP2R5A_ENST00000537030.3_Missense_Mutation_p.M216T	NM_006243.3	NP_006234.1	Q15172	2A5A_HUMAN	protein phosphatase 2, regulatory subunit B', alpha	273					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of lipid kinase activity (GO:0090219)|positive regulation of protein dephosphorylation (GO:0035307)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|M band (GO:0031430)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)|Z disc (GO:0030018)	kinase binding (GO:0019900)|protein phosphatase type 2A regulator activity (GO:0008601)	p.M273T(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	16				OV - Ovarian serous cystadenocarcinoma(81;0.0125)|all cancers(67;0.029)|Epithelial(68;0.154)|GBM - Glioblastoma multiforme(131;0.155)		CAATTTCTAATGAAGGTTCTT	0.348																																					p.M216T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T647C	1						.						109.0	105.0	106.0					1																	212521784		2202	4300	6502	210588407	SO:0001583	missense	5525	exon7			BC022474	CCDS1503.1, CCDS55686.1	1q32.2-q32.3	2010-06-18	2010-04-14		ENSG00000066027	ENSG00000066027		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9309	protein-coding gene	gene with protein product		601643	"""protein phosphatase 2, regulatory subunit B (B56), alpha isoform"", ""protein phosphatase 2, regulatory subunit B', alpha isoform"""			7592815	Standard	NM_006243		Approved	PR61A, B56A	uc001hjb.3	Q15172	OTTHUMG00000036750	ENST00000261461.2:c.818T>C	1.37:g.212521784T>C	ENSP00000261461:p.Met273Thr	Somatic		Capture	Illumina HiSeq	Phase_I	210588407	NM_001199756	B2R6D2|B7Z7L2|D3DT99|Q2NL72|Q5VVB2|Q8TBI9	Missense_Mutation	SNP	ENST00000261461.2	37	CCDS1503.1	.	.	.	.	.	.	.	.	.	.	T	8.723	0.914767	0.17907	.	.	ENSG00000066027	ENST00000542178;ENST00000261461;ENST00000537030	.	.	.	5.93	4.8	0.61643	Armadillo-type fold (1);	0.033173	0.85682	N	0.000000	T	0.38904	0.1058	N	0.16130	0.375	0.51482	D	0.999923	B;B	0.06786	0.001;0.001	B;B	0.14023	0.01;0.01	T	0.13045	-1.0524	9	0.23302	T	0.38	-14.7139	11.8224	0.52247	0.0:0.0683:0.0:0.9317	.	216;273	B7Z7L2;Q15172	.;2A5A_HUMAN	T	273;273;216	.	ENSP00000261461:M273T	M	+	2	0	PPP2R5A	210588407	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.880000	0.87243	1.065000	0.40693	0.460000	0.39030	ATG		0.348	PPP2R5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089302.1	NM_006243	
RPS6KC1	26750	broad.mit.edu	37	1	213302894	213302894	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:213302894T>C	ENST00000366960.3	+	6	647	c.497T>C	c.(496-498)gTa>gCa	p.V166A	RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543354.1_Intron|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.V154A|RPS6KC1_ENST00000543470.1_5'UTR	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	166					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)	p.V166A(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		AGTGATCTGGTATCTCTTACT	0.353																																					p.V166A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T497C	1						.						126.0	128.0	127.0					1																	213302894		2203	4300	6503	211369517	SO:0001583	missense	26750	exon6			AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"""ribosomal protein S6 kinase, 52kD, polypeptide 1"""			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.497T>C	1.37:g.213302894T>C	ENSP00000355927:p.Val166Ala	Somatic		Capture	Illumina HiSeq	Phase_I	211369517	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	T	9.993	1.231409	0.22626	.	.	ENSG00000136643	ENST00000366960;ENST00000366959	T;T	0.28666	1.6;1.6	5.53	4.38	0.52667	.	0.499487	0.21933	N	0.066995	T	0.17746	0.0426	N	0.08118	0	0.80722	D	1	B;B	0.20671	0.047;0.027	B;B	0.15484	0.013;0.013	T	0.03619	-1.1019	10	0.72032	D	0.01	-32.7884	12.6282	0.56642	0.0:0.0:0.1383:0.8617	.	166;154	Q96S38;B1APS8	KS6C1_HUMAN;.	A	166;154	ENSP00000355927:V166A;ENSP00000355926:V154A	ENSP00000355926:V154A	V	+	2	0	RPS6KC1	211369517	0.382000	0.25148	0.401000	0.26359	0.995000	0.86356	3.142000	0.50601	0.897000	0.36392	0.477000	0.44152	GTA		0.353	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424	
PTPN14	5784	broad.mit.edu	37	1	214543010	214543010	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:214543010G>A	ENST00000366956.5	-	17	3255	c.3061C>T	c.(3061-3063)Cga>Tga	p.R1021*	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	1021	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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.R1021*(1)		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)		GGCCAGTATCGGTGGCTTTTG	0.443																																					p.R1021X	Colon(92;557 1424 24372 34121 40073)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C3061T	1						.						203.0	190.0	194.0					1																	214543010		2203	4300	6503	212609633	SO:0001587	stop_gained	5784	exon17			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.3061C>T	1.37:g.214543010G>A	ENSP00000355923:p.Arg1021*	Somatic		Capture	Illumina HiSeq	Phase_I	212609633	NM_005401	Q5VSI0	Nonsense_Mutation	SNP	ENST00000366956.5	37	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	G	43	10.338041	0.99385	.	.	ENSG00000152104	ENST00000366956	.	.	.	5.51	4.58	0.56647	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5368	0.76011	0.0:0.0:0.8608:0.1392	.	.	.	.	X	1021	.	ENSP00000355923:R1021X	R	-	1	2	PTPN14	212609633	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.759000	0.85235	1.263000	0.44181	0.650000	0.86243	CGA		0.443	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401	
PTPN14	5784	broad.mit.edu	37	1	214546073	214546073	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:214546073G>A	ENST00000366956.5	-	16	3211	c.3017C>T	c.(3016-3018)gCc>gTc	p.A1006V	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	1006	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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.A1006V(1)		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)		AGTGACCATGGCAATCACATT	0.582																																					p.A1006V	Colon(92;557 1424 24372 34121 40073)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3017T	1						.						152.0	135.0	141.0					1																	214546073		2203	4300	6503	212612696	SO:0001583	missense	5784	exon16			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.3017C>T	1.37:g.214546073G>A	ENSP00000355923:p.Ala1006Val	Somatic		Capture	Illumina HiSeq	Phase_I	212612696	NM_005401	Q5VSI0	Missense_Mutation	SNP	ENST00000366956.5	37	CCDS1514.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.219908	0.58560	.	.	ENSG00000152104	ENST00000366956	T	0.05139	3.49	5.4	5.4	0.78164	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.054957	0.64402	D	0.000001	T	0.04272	0.0118	N	0.00630	-1.315	0.80722	D	1	D	0.65815	0.995	P	0.56216	0.794	T	0.51545	-0.8692	10	0.02654	T	1	.	19.5343	0.95242	0.0:0.0:1.0:0.0	.	1006	Q15678	PTN14_HUMAN	V	1006	ENSP00000355923:A1006V	ENSP00000355923:A1006V	A	-	2	0	PTPN14	212612696	1.000000	0.71417	1.000000	0.80357	0.557000	0.35523	9.611000	0.98342	2.684000	0.91462	0.650000	0.86243	GCC		0.582	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401	
USH2A	7399	broad.mit.edu	37	1	215807955	215807955	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:215807955G>A	ENST00000307340.3	-	70	15529	c.15143C>T	c.(15142-15144)gCg>gTg	p.A5048V	USH2A_ENST00000366943.2_Missense_Mutation_p.A5048V	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	5048					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.A5048V(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)		GCCCAGCATCGCCATTAACAC	0.463										HNSCC(13;0.011)																											p.A5048V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C15143T	1						.						133.0	124.0	127.0					1																	215807955		2203	4300	6503	213874578	SO:0001583	missense	7399	exon70			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.15143C>T	1.37:g.215807955G>A	ENSP00000305941:p.Ala5048Val	Somatic		Capture	Illumina HiSeq	Phase_I	213874578	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.915574	0.52546	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.16457	2.34;2.36	5.88	5.88	0.94601	.	0.348186	0.20392	N	0.093230	T	0.12347	0.0300	L	0.41824	1.3	0.35959	D	0.834492	P	0.46952	0.887	B	0.30495	0.116	T	0.20773	-1.0265	10	0.34782	T	0.22	.	13.85	0.63489	0.0785:0.0:0.9215:0.0	.	5048	O75445	USH2A_HUMAN	V	5048	ENSP00000305941:A5048V;ENSP00000355910:A5048V	ENSP00000305941:A5048V	A	-	2	0	USH2A	213874578	1.000000	0.71417	0.960000	0.40013	0.618000	0.37518	5.806000	0.69150	2.785000	0.95823	0.655000	0.94253	GCG		0.463	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
USH2A	7399	broad.mit.edu	37	1	215901419	215901419	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:215901419C>T	ENST00000307340.3	-	61	12405	c.12019G>A	c.(12019-12021)Gac>Aac	p.D4007N	USH2A_ENST00000366943.2_Missense_Mutation_p.D4007N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4007	Fibronectin type-III 25. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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.D4007N(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)		GTAGGATCGTCGGGTCTCTCC	0.458										HNSCC(13;0.011)																											p.D4007N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G12019A	1						.						135.0	127.0	129.0					1																	215901419		2203	4300	6503	213968042	SO:0001583	missense	7399	exon61			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.12019G>A	1.37:g.215901419C>T	ENSP00000305941:p.Asp4007Asn	Somatic		Capture	Illumina HiSeq	Phase_I	213968042	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	6.551	0.469866	0.12461	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.54675	0.56;0.56	5.25	1.92	0.25849	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.703248	0.12269	N	0.483946	T	0.37461	0.1004	L	0.35542	1.07	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23655	-1.0182	10	0.18276	T	0.48	.	8.784	0.34809	0.0:0.6087:0.0:0.3913	.	4007	O75445	USH2A_HUMAN	N	4007	ENSP00000305941:D4007N;ENSP00000355910:D4007N	ENSP00000305941:D4007N	D	-	1	0	USH2A	213968042	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	1.161000	0.31773	0.229000	0.21039	-1.094000	0.02160	GAC		0.458	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
TGFB2	7042	broad.mit.edu	37	1	218520267	218520267	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:218520267G>T	ENST00000366930.4	+	1	691	c.224G>T	c.(223-225)aGg>aTg	p.R75M	TGFB2_ENST00000366929.4_Missense_Mutation_p.R75M|RP11-224O19.2_ENST00000414452.1_RNA	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	75					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)	p.R75M(2)		breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		AACAGCACCAGGGACTTGCTC	0.597																																					p.R75M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G224T	1						.						28.0	29.0	29.0					1																	218520267		2203	4300	6503	216586890	SO:0001583	missense	7042	exon1			M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"""Endogenous ligands"""	11768	protein-coding gene	gene with protein product	"""prepro-transforming growth factor beta-2"""	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.224G>T	1.37:g.218520267G>T	ENSP00000355897:p.Arg75Met	Somatic		Capture	Illumina HiSeq	Phase_I	216586890	NM_003238	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Missense_Mutation	SNP	ENST00000366930.4	37	CCDS1521.1	.	.	.	.	.	.	.	.	.	.	G	34	5.330252	0.95733	.	.	ENSG00000092969	ENST00000366930;ENST00000366929	T;T	0.65364	-0.15;-0.15	5.45	5.45	0.79879	Transforming growth factor-beta, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.79118	0.4392	M	0.67700	2.07	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.996;0.989;0.998	T	0.79988	-0.1571	10	0.87932	D	0	.	19.4714	0.94965	0.0:0.0:1.0:0.0	.	75;75;76	P61812-2;P61812;Q59EG9	.;TGFB2_HUMAN;.	M	75	ENSP00000355897:R75M;ENSP00000355896:R75M	ENSP00000355896:R75M	R	+	2	0	TGFB2	216586890	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.620000	0.98373	2.837000	0.97791	0.591000	0.81541	AGG		0.597	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238	
HSPG2	3339	broad.mit.edu	37	1	22182022	22182022	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:22182022C>T	ENST00000374695.3	-	46	5927	c.5848G>A	c.(5848-5850)Gtg>Atg	p.V1950M	HSPG2_ENST00000430507.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1950	Ig-like C2-type 4.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.V1950M(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TCACCATGCACGTGGAGCACA	0.697																																					p.V1950M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5848A	1						.						14.0	16.0	15.0					1																	22182022		2202	4296	6498	22054609	SO:0001583	missense	3339	exon46			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.5848G>A	1.37:g.22182022C>T	ENSP00000363827:p.Val1950Met	Somatic		Capture	Illumina HiSeq	Phase_I	22054609	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.438800	0.83885	.	.	ENSG00000142798	ENST00000374695	T	0.79141	-1.24	5.12	5.12	0.69794	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.000000	0.36066	N	0.002812	D	0.91516	0.7321	H	0.95187	3.635	0.53688	D	0.999979	D	0.89917	1.0	D	0.91635	0.999	D	0.93931	0.7214	10	0.87932	D	0	.	16.0425	0.80695	0.0:1.0:0.0:0.0	.	1950	P98160	PGBM_HUMAN	M	1950	ENSP00000363827:V1950M	ENSP00000363827:V1950M	V	-	1	0	HSPG2	22054609	0.997000	0.39634	0.995000	0.50966	0.906000	0.53458	3.740000	0.55082	2.399000	0.81585	0.462000	0.41574	GTG		0.697	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
HSPG2	3339	broad.mit.edu	37	1	22206927	22206927	+	Silent	SNP	G	G	A	rs139220302		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:22206927G>A	ENST00000374695.3	-	16	2203	c.2124C>T	c.(2122-2124)agC>agT	p.S708S		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	708	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.S708S(2)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TGGCGATGTCGCTAAGTCCCA	0.662																																					p.S708S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2124T	1						.	G		1,4405	2.1+/-5.4	0,1,2202	86.0	69.0	75.0		2124	-6.1	0.9	1	dbSNP_134	75	0,8600		0,0,4300	no	coding-synonymous	HSPG2	NM_005529.5		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		708/4392	22206927	1,13005	2203	4300	6503	22079514	SO:0001819	synonymous_variant	3339	exon16			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.2124C>T	1.37:g.22206927G>A		Somatic		Capture	Illumina HiSeq	Phase_I	22079514	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																				0.662	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
RAB3GAP2	25782	broad.mit.edu	37	1	220364615	220364615	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:220364615C>T	ENST00000358951.2	-	14	1398	c.1282G>A	c.(1282-1284)Gca>Aca	p.A428T		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	428					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)	p.A428T(2)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		CCAATTTGTGCGTCGCGGTAC	0.468																																					p.A428T												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G1282A	1						.						42.0	40.0	41.0					1																	220364615		2203	4300	6503	218431238	SO:0001583	missense	25782	exon14			AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.1282G>A	1.37:g.220364615C>T	ENSP00000351832:p.Ala428Thr	Somatic		Capture	Illumina HiSeq	Phase_I	218431238	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	37	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	C	19.84	3.901210	0.72754	.	.	ENSG00000118873	ENST00000358951	T	0.72942	-0.7	5.69	4.78	0.61160	.	0.047702	0.85682	N	0.000000	T	0.80259	0.4590	L	0.49778	1.585	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82275	-0.0538	10	0.87932	D	0	.	14.552	0.68073	0.0:0.9297:0.0:0.0703	.	428	Q9H2M9	RBGPR_HUMAN	T	428	ENSP00000351832:A428T	ENSP00000351832:A428T	A	-	1	0	RAB3GAP2	218431238	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	7.190000	0.77755	1.420000	0.47138	-0.218000	0.12543	GCA		0.468	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414	
MIA3	375056	broad.mit.edu	37	1	222801762	222801762	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:222801762G>A	ENST00000344922.5	+	4	1225	c.1200G>A	c.(1198-1200)acG>acA	p.T400T	MIA3_ENST00000344507.1_Silent_p.T400T|MIA3_ENST00000344441.6_Silent_p.T400T|MIA3_ENST00000470521.1_3'UTR	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	400					chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.T400T(1)		breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		CAAGAGATACGATGGATTTAG	0.418																																					p.T400T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1200A	1						.						95.0	89.0	91.0					1																	222801762		1901	4126	6027	220868385	SO:0001819	synonymous_variant	375056	exon4				CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.1200G>A	1.37:g.222801762G>A		Somatic		Capture	Illumina HiSeq	Phase_I	220868385	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Silent	SNP	ENST00000344922.5	37	CCDS41470.1																																																																																				0.418	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
CELA3B	23436	broad.mit.edu	37	1	22313062	22313062	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:22313062T>C	ENST00000337107.6	+	7	700	c.681T>C	c.(679-681)gaT>gaC	p.D227D	RNU6-1022P_ENST00000365049.1_RNA|RN7SL386P_ENST00000485776.2_RNA|CELA3B_ENST00000473526.1_3'UTR	NM_007352.2	NP_031378.1	P08861	CEL3B_HUMAN	chymotrypsin-like elastase family, member 3B	227	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cholesterol metabolic process (GO:0008203)|proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.D227D(1)		breast(2)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	8						CCACAGAGGATGGTGGCTGGC	0.587																																					p.D227D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T681C	1						.						76.0	68.0	71.0					1																	22313062		2203	4300	6503	22185649	SO:0001819	synonymous_variant	23436	exon7			M18692	CCDS219.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000219073	ENSG00000219073	3.4.21.70		15945	protein-coding gene	gene with protein product	"""proteinase E"", ""elastase 1"", ""cholesterol-binding pancreatic protease"", ""pancreatic endopeptidase E"""		"""elastase 3B, pancreatic"""	ELA3B		2826474, 2460440	Standard	NM_007352		Approved	CBPP	uc001bfk.3	P08861	OTTHUMG00000002758	ENST00000337107.6:c.681T>C	1.37:g.22313062T>C		Somatic		Capture	Illumina HiSeq	Phase_I	22185649	NM_007352	B2RE44|P11423|Q5VU28|Q5VU29|Q5VU30	Silent	SNP	ENST00000337107.6	37	CCDS219.1																																																																																				0.587	CELA3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007797.1	NM_007352	
DISP1	84976	broad.mit.edu	37	1	223176179	223176179	+	Silent	SNP	C	C	T	rs374203038	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:223176179C>T	ENST00000284476.6	+	8	1604	c.1440C>T	c.(1438-1440)ggC>ggT	p.G480G		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	480					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)	p.G480G(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		CTTCTGACGGCGTGACTACCA	0.423													C|||	5	0.000998403	0.0008	0.0	5008	,	,		22020	0.0		0.0	False		,,,				2504	0.0041				p.G480G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1440T	1						.	C		0,4406		0,0,2203	80.0	76.0	77.0		1440	-1.6	1.0	1		77	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DISP1	NM_032890.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		480/1525	223176179	1,13005	2203	4300	6503	221242802	SO:0001819	synonymous_variant	84976	exon8			AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.1440C>T	1.37:g.223176179C>T		Somatic		Capture	Illumina HiSeq	Phase_I	221242802	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Silent	SNP	ENST00000284476.6	37	CCDS1536.1																																																																																				0.423	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
PSEN2	5664	broad.mit.edu	37	1	227083168	227083168	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:227083168C>T	ENST00000366783.3	+	13	1671	c.1235C>T	c.(1234-1236)gCg>gTg	p.A412V	PSEN2_ENST00000422240.2_Missense_Mutation_p.A411V|PSEN2_ENST00000340188.4_Missense_Mutation_p.A379V|PSEN2_ENST00000472139.2_Missense_Mutation_p.A268V|PSEN2_ENST00000391872.2_Missense_Mutation_p.A445V|ADCK3_ENST00000366779.1_5'Flank|PSEN2_ENST00000471728.1_3'UTR|PSEN2_ENST00000366782.1_Missense_Mutation_p.A445V	NM_000447.2|NM_012486.2	NP_000438.2|NP_036618.2	P49810	PSN2_HUMAN	presenilin 2	412					amyloid precursor protein catabolic process (GO:0042987)|anagen (GO:0042640)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|brain morphogenesis (GO:0048854)|calcium ion transport (GO:0006816)|cardiac muscle contraction (GO:0060048)|cell fate specification (GO:0001708)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic limb morphogenesis (GO:0030326)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|forebrain development (GO:0030900)|hematopoietic progenitor cell differentiation (GO:0002244)|intracellular signal transduction (GO:0035556)|locomotion (GO:0040011)|lung alveolus development (GO:0048286)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|memory (GO:0007613)|myeloid leukocyte differentiation (GO:0002573)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of protein binding (GO:0032091)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of protein phosphorylation (GO:0001933)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|positive regulation of coagulation (GO:0050820)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein processing (GO:0016485)|protein transport (GO:0015031)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of synaptic plasticity (GO:0048167)|response to hypoxia (GO:0001666)|somitogenesis (GO:0001756)|T cell activation involved in immune response (GO:0002286)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cell cortex (GO:0005938)|cell surface (GO:0009986)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary rootlet (GO:0035253)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|kinetochore (GO:0000776)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nuclear inner membrane (GO:0005637)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Z disc (GO:0030018)	aspartic-type endopeptidase activity (GO:0004190)|endopeptidase activity (GO:0004175)	p.A412V(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(8)|urinary_tract(1)	20		Prostate(94;0.0771)				TTCAAGAAGGCGCTGCCCGCC	0.612																																					p.A412V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1235T	1						.						153.0	94.0	114.0					1																	227083168		2203	4300	6503	225149791	SO:0001583	missense	5664	exon13			BC006365	CCDS1556.1, CCDS44324.1	1q42.13	2014-09-17	2014-02-24		ENSG00000143801	ENSG00000143801			9509	protein-coding gene	gene with protein product		600759	"""Alzheimer disease 4"""	AD4		7638621	Standard	NM_000447		Approved	AD3L, STM2, PS2	uc009xeo.1	P49810	OTTHUMG00000037563	ENST00000366783.3:c.1235C>T	1.37:g.227083168C>T	ENSP00000355747:p.Ala412Val	Somatic		Capture	Illumina HiSeq	Phase_I	225149791	NM_000447	A8K8D4|B1AP21|Q96P32	Missense_Mutation	SNP	ENST00000366783.3	37	CCDS1556.1	.	.	.	.	.	.	.	.	.	.	C	36	5.869714	0.97049	.	.	ENSG00000143801	ENST00000366783;ENST00000340188;ENST00000422240;ENST00000366782;ENST00000391872;ENST00000472139	D;D;D;D;D;D	0.99730	-6.56;-6.56;-6.56;-6.56;-6.56;-6.56	5.78	5.78	0.91487	.	0.052300	0.85682	D	0.000000	D	0.99764	0.9904	M	0.88450	2.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.97637	1.0146	10	0.87932	D	0	.	20.0119	0.97458	0.0:1.0:0.0:0.0	.	411;412	A8K8D4;P49810	.;PSN2_HUMAN	V	412;379;411;445;445;268	ENSP00000355747:A412V;ENSP00000339860:A379V;ENSP00000403737:A411V;ENSP00000355746:A445V;ENSP00000375745:A445V;ENSP00000427806:A268V	ENSP00000339860:A379V	A	+	2	0	PSEN2	225149791	1.000000	0.71417	0.972000	0.41901	0.961000	0.63080	7.683000	0.84093	2.733000	0.93635	0.591000	0.81541	GCG		0.612	PSEN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091539.1	NM_000447	
CDC42BPA	8476	broad.mit.edu	37	1	227223191	227223191	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:227223191G>A	ENST00000366769.3	-	24	4503	c.3212C>T	c.(3211-3213)gCa>gTa	p.A1071V	CDC42BPA_ENST00000366767.3_Missense_Mutation_p.A990V|CDC42BPA_ENST00000366765.3_Missense_Mutation_p.A1084V|CDC42BPA_ENST00000366764.2_Missense_Mutation_p.A1043V|CDC42BPA_ENST00000334218.5_Missense_Mutation_p.A1071V|CDC42BPA_ENST00000535525.1_Missense_Mutation_p.A1051V|CDC42BPA_ENST00000366766.2_Missense_Mutation_p.A1106V	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)									p.A990V(1)|p.A1071V(1)		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)				ACCTTCATATGCTGTTCCTAT	0.363																																					p.A990V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2969T	1						.						119.0	119.0	119.0					1																	227223191		2203	4300	6503	225289814	SO:0001583	missense	8476	exon23			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.3212C>T	1.37:g.227223191G>A	ENSP00000355731:p.Ala1071Val	Somatic		Capture	Illumina HiSeq	Phase_I	225289814	NM_014826		Missense_Mutation	SNP	ENST00000366769.3	37	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.774387	0.90108	.	.	ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000366762;ENST00000535525;ENST00000366765	T;T;T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07;1.07;1.07	5.94	5.94	0.96194	.	0.097133	0.64402	N	0.000001	T	0.52565	0.1742	M	0.65320	2	0.80722	D	1	B;B;B;B;P;P;B	0.43788	0.096;0.406;0.185;0.286;0.817;0.817;0.034	B;B;B;B;P;P;B	0.46510	0.05;0.125;0.226;0.175;0.519;0.519;0.05	T	0.47724	-0.9095	10	0.45353	T	0.12	.	20.3736	0.98901	0.0:0.0:1.0:0.0	.	1051;1043;386;990;1071;1106;273	F5H5N0;Q5VT25-4;E9PEF7;Q5VT25-3;Q5VT25-5;Q5VT25-2;Q5T799	.;.;.;.;.;.;.	V	1071;990;1071;1106;1043;386;1051;1084	ENSP00000355731:A1071V;ENSP00000355729:A990V;ENSP00000335341:A1071V;ENSP00000355728:A1106V;ENSP00000355726:A1043V;ENSP00000443275:A1051V;ENSP00000355727:A1084V	ENSP00000335341:A1071V	A	-	2	0	CDC42BPA	225289814	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	6.535000	0.73838	2.820000	0.97059	0.650000	0.86243	GCA		0.363	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	
ZNF678	339500	broad.mit.edu	37	1	227842155	227842155	+	Silent	SNP	A	A	G	rs138801672		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:227842155A>G	ENST00000343776.5	+	4	549	c.204A>G	c.(202-204)aaA>aaG	p.K68K	ZNF678_ENST00000397097.3_Silent_p.K123K|ZNF678_ENST00000608949.1_Silent_p.K68K	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	68					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.K68K(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				ACTTAGTGAAAGACTGGAGAA	0.373																																					p.K123K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A369G	1						.						115.0	123.0	121.0					1																	227842155		2203	4300	6503	225908778	SO:0001819	synonymous_variant	339500	exon4			BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"""Zinc fingers, C2H2-type"", ""-"""	28652	protein-coding gene	gene with protein product	"""hypothetical protein MGC42493"""					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.204A>G	1.37:g.227842155A>G		Somatic		Capture	Illumina HiSeq	Phase_I	225908778	NM_178549	Q8IVQ9	Silent	SNP	ENST00000343776.5	37																																																																																					0.373	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549	
OBSCN	84033	broad.mit.edu	37	1	228475406	228475406	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:228475406C>T	ENST00000422127.1	+	36	9600	c.9556C>T	c.(9556-9558)Cgg>Tgg	p.R3186W	OBSCN_ENST00000570156.2_Missense_Mutation_p.R3615W|OBSCN_ENST00000359599.6_Missense_Mutation_p.R2033W|OBSCN_ENST00000366707.4_Missense_Mutation_p.R305W|OBSCN_ENST00000366709.4_Missense_Mutation_p.R305W|OBSCN_ENST00000284548.11_Missense_Mutation_p.R3186W	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3186	Ig-like 32.				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.R3469W(1)|p.R3240W(1)		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)				GCGGCCAGTGCGGTTCCAGGA	0.652																																					p.R3186W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C9556T	1						.						48.0	55.0	52.0					1																	228475406		2160	4259	6419	226542029	SO:0001583	missense	84033	exon36			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.9556C>T	1.37:g.228475406C>T	ENSP00000409493:p.Arg3186Trp	Somatic		Capture	Illumina HiSeq	Phase_I	226542029	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.711203	0.48517	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34;-0.34	5.06	1.6	0.23607	Immunoglobulin I-set (1);Immunoglobulin-like (1);	1.958180	0.02367	N	0.077433	D	0.83179	0.5198	M	0.91300	3.195	0.09310	N	1	B;D	0.89917	0.043;1.0	B;D	0.65010	0.023;0.931	T	0.52917	-0.8511	10	0.38643	T	0.18	.	5.2706	0.15622	0.1144:0.6037:0.1246:0.1573	.	3186;3186	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	W	3186;3186;305;305;2033	ENSP00000284548:R3186W;ENSP00000409493:R3186W;ENSP00000355668:R305W;ENSP00000355670:R305W;ENSP00000352613:R2033W	ENSP00000284548:R3186W	R	+	1	2	OBSCN	226542029	0.000000	0.05858	0.003000	0.11579	0.116000	0.19942	0.220000	0.17660	0.519000	0.28406	0.561000	0.74099	CGG		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
OBSCN	84033	broad.mit.edu	37	1	228482678	228482678	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:228482678G>A	ENST00000422127.1	+	43	11637	c.11593G>A	c.(11593-11595)Gca>Aca	p.A3865T	OBSCN_ENST00000570156.2_Missense_Mutation_p.A4294T|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000359599.6_Missense_Mutation_p.A2712T|OBSCN_ENST00000366707.4_Missense_Mutation_p.A984T|OBSCN_ENST00000366709.4_Missense_Mutation_p.A984T|OBSCN_ENST00000284548.11_Missense_Mutation_p.A3865T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3865	Ig-like 39.				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.A4148T(1)|p.A3919T(1)		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)				CCTGTCTGTGGCAGACACTGG	0.597																																					p.A3865T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G11593A	1						.						135.0	139.0	138.0					1																	228482678		2140	4229	6369	226549301	SO:0001583	missense	84033	exon43			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.11593G>A	1.37:g.228482678G>A	ENSP00000409493:p.Ala3865Thr	Somatic		Capture	Illumina HiSeq	Phase_I	226549301	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.015005	0.35511	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.04809	3.55;3.55;3.55;3.55;3.55	5.01	5.01	0.66863	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.029550	0.07676	N	0.936339	T	0.07908	0.0198	N	0.17082	0.46	0.09310	N	1	P;B	0.51653	0.947;0.203	P;B	0.56563	0.801;0.036	T	0.41088	-0.9528	10	0.22706	T	0.39	.	9.4942	0.38978	0.1268:0.0:0.8732:0.0	.	3865;3865	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	T	3865;3865;984;984;2712	ENSP00000284548:A3865T;ENSP00000409493:A3865T;ENSP00000355668:A984T;ENSP00000355670:A984T;ENSP00000352613:A2712T	ENSP00000284548:A3865T	A	+	1	0	OBSCN	226549301	0.000000	0.05858	0.011000	0.14972	0.012000	0.07955	-0.098000	0.11024	2.611000	0.88343	0.563000	0.77884	GCA		0.597	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
TRIM17	51127	broad.mit.edu	37	1	228598852	228598852	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:228598852C>T	ENST00000366697.2	-	3	1507	c.551G>A	c.(550-552)cGc>cAc	p.R184H	TRIM17_ENST00000456946.2_Missense_Mutation_p.R184H|TRIM17_ENST00000366698.2_Missense_Mutation_p.R184H|TRIM17_ENST00000295033.3_Missense_Mutation_p.R184H|RP11-245P10.4_ENST00000436779.1_RNA			Q9Y577	TRI17_HUMAN	tripartite motif containing 17	184					protein autoubiquitination (GO:0051865)	intracellular (GO:0005622)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R184H(1)		NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)	10		Prostate(94;0.0724)				CAGCACAATGCGTTCTCTCCG	0.597																																					p.R184H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G551A	1						.						101.0	103.0	102.0					1																	228598852		2203	4300	6503	226665475	SO:0001583	missense	51127	exon4			AF156271	CCDS1571.1, CCDS44327.1	1q42	2013-01-09	2011-01-25	2001-11-30	ENSG00000162931	ENSG00000162931		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	13430	protein-coding gene	gene with protein product	"""ring finger protein 16"", ""RING finger protein terf"", ""testis RING finger protein"""	606123	"""tripartite motif-containing 17"""	RNF16		9792805, 10894938	Standard	NM_016102		Approved	terf, RBCC	uc001hsv.3	Q9Y577	OTTHUMG00000039974	ENST00000366697.2:c.551G>A	1.37:g.228598852C>T	ENSP00000355658:p.Arg184His	Somatic		Capture	Illumina HiSeq	Phase_I	226665475	NM_016102	B4DVJ2|Q5VST8	Missense_Mutation	SNP	ENST00000366697.2	37	CCDS1571.1	.	.	.	.	.	.	.	.	.	.	c	7.490	0.650494	0.14516	.	.	ENSG00000162931	ENST00000366697;ENST00000366698;ENST00000295033;ENST00000456946;ENST00000479800	T;T;T;T;T	0.04706	3.57;3.57;3.57;3.57;3.57	4.08	3.16	0.36331	.	0.462902	0.15389	N	0.264918	T	0.04543	0.0124	L	0.52011	1.625	0.09310	N	0.999991	B;B	0.33755	0.424;0.167	B;B	0.24701	0.055;0.017	T	0.31081	-0.9956	10	0.35671	T	0.21	.	6.7881	0.23685	0.0:0.8754:0.0:0.1246	.	184;184	Q9Y577-2;Q9Y577	.;TRI17_HUMAN	H	184;184;184;184;157	ENSP00000355658:R184H;ENSP00000355659:R184H;ENSP00000295033:R184H;ENSP00000403312:R184H;ENSP00000430468:R157H	ENSP00000295033:R184H	R	-	2	0	TRIM17	226665475	0.000000	0.05858	0.177000	0.23020	0.016000	0.09150	-0.048000	0.11944	2.222000	0.72286	0.443000	0.29094	CGC		0.597	TRIM17-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096439.2	NM_016102	
ABCB10	23456	broad.mit.edu	37	1	229675314	229675314	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:229675314C>T	ENST00000344517.4	-	6	1270	c.1228G>A	c.(1228-1230)Gtg>Atg	p.V410M		NM_012089.2	NP_036221.2	Q9NRK6	ABCBA_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 10	410	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.V410M(1)		breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)	31	Breast(184;0.143)|Ovarian(103;0.249)	Prostate(94;0.167)				ACAGAAAGCACGATCAGGTTT	0.502																																					p.V410M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1228A	1						.						75.0	74.0	74.0					1																	229675314		2203	4300	6503	227741937	SO:0001583	missense	23456	exon6			U18237	CCDS1580.1	1q32	2012-03-14			ENSG00000135776	ENSG00000135776		"""ATP binding cassette transporters / subfamily B"""	41	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family B member 10, mitochondrial"", ""ATP-binding cassette transporter 10"", ""ABC transporter 10 protein"", ""mitochondrial ATP-binding cassette 2"""	605454				7766993	Standard	NM_012089		Approved	EST20237, M-ABC2, MTABC2	uc001htp.4	Q9NRK6	OTTHUMG00000039471	ENST00000344517.4:c.1228G>A	1.37:g.229675314C>T	ENSP00000355637:p.Val410Met	Somatic		Capture	Illumina HiSeq	Phase_I	227741937	NM_012089	Q13040|Q6P1Q8|Q9H3V0	Missense_Mutation	SNP	ENST00000344517.4	37	CCDS1580.1	.	.	.	.	.	.	.	.	.	.	C	13.32	2.202824	0.38905	.	.	ENSG00000135776	ENST00000344517	D	0.89617	-2.54	5.25	4.33	0.51752	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.053554	0.85682	D	0.000000	D	0.83580	0.5285	L	0.35644	1.08	0.53688	D	0.99997	B	0.29955	0.263	B	0.20384	0.029	T	0.81735	-0.0797	10	0.51188	T	0.08	-24.7377	16.2069	0.82134	0.0:0.8667:0.1333:0.0	.	410	Q9NRK6	ABCBA_HUMAN	M	410	ENSP00000355637:V410M	ENSP00000355637:V410M	V	-	1	0	ABCB10	227741937	1.000000	0.71417	0.891000	0.34965	0.910000	0.53928	4.529000	0.60588	1.329000	0.45376	0.655000	0.94253	GTG		0.502	ABCB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095240.1	NM_012089	
COG2	22796	broad.mit.edu	37	1	230820960	230820960	+	Missense_Mutation	SNP	G	G	A	rs372577276		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:230820960G>A	ENST00000366669.4	+	12	1473	c.1358G>A	c.(1357-1359)cGa>cAa	p.R453Q	COG2_ENST00000366668.3_Missense_Mutation_p.R453Q|COG2_ENST00000534989.1_Missense_Mutation_p.R394Q|COG2_ENST00000535166.1_Missense_Mutation_p.R337Q|COG2_ENST00000546013.1_Missense_Mutation_p.R142Q	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	453					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)	p.R453Q(1)		NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				ATTTTGGCACGATACTCTGTG	0.438																																					p.R453Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1358A	1						.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	207.0	188.0	194.0		1358,1358	5.6	0.1	1		194	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	COG2	NM_001145036.1,NM_007357.2	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	453/738,453/739	230820960	1,13005	2203	4300	6503	228887583	SO:0001583	missense	22796	exon12			Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"""Components of oligomeric golgi complex"""	6546	protein-coding gene	gene with protein product		606974	"""low density lipoprotein receptor defect C complementing"""	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.1358G>A	1.37:g.230820960G>A	ENSP00000355629:p.Arg453Gln	Somatic		Capture	Illumina HiSeq	Phase_I	228887583	NM_007357	Q86U99	Missense_Mutation	SNP	ENST00000366669.4	37	CCDS1584.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.039429	0.93630	0.0	1.16E-4	ENSG00000135775	ENST00000366669;ENST00000535166;ENST00000366668;ENST00000534989;ENST00000546013	T;T;T;T;T	0.64803	3.54;3.54;3.54;3.54;-0.12	5.6	5.6	0.85130	.	0.110324	0.64402	D	0.000008	D	0.83603	0.5290	M	0.90759	3.145	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.72338	0.962;0.977	D	0.86261	0.1655	10	0.66056	D	0.02	-17.0083	19.6087	0.95589	0.0:0.0:1.0:0.0	.	453;453	Q86U99;Q14746	.;COG2_HUMAN	Q	453;337;453;394;142	ENSP00000355629:R453Q;ENSP00000445724:R337Q;ENSP00000355628:R453Q;ENSP00000440349:R394Q;ENSP00000442147:R142Q	ENSP00000355628:R453Q	R	+	2	0	COG2	228887583	1.000000	0.71417	0.059000	0.19551	0.779000	0.44077	9.354000	0.97083	2.639000	0.89480	0.655000	0.94253	CGA		0.438	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357	
MORN1	79906	broad.mit.edu	37	1	2319720	2319720	+	Missense_Mutation	SNP	C	C	T	rs142433202		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:2319720C>T	ENST00000378531.3	-	3	378	c.205G>A	c.(205-207)Gga>Aga	p.G69R	MORN1_ENST00000606372.1_5'UTR|MORN1_ENST00000378529.3_Missense_Mutation_p.G69R	NM_024848.1	NP_079124.1	Q5T089	MORN1_HUMAN	MORN repeat containing 1	69								p.G69R(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(1)|ovary(2)	9	all_cancers(77;0.000194)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.3e-15)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;2.21e-37)|OV - Ovarian serous cystadenocarcinoma(86;5.01e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00137)|BRCA - Breast invasive adenocarcinoma(365;0.00488)|STAD - Stomach adenocarcinoma(132;0.00665)|KIRC - Kidney renal clear cell carcinoma(229;0.0203)|Lung(427;0.212)		GTGATCTCTCCGTCCACAAAC	0.537													C|||	1	0.000199681	0.0	0.0014	5008	,	,		15747	0.0		0.0	False		,,,				2504	0.0				p.G69R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G205A	1						.	C	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	144.0	132.0	136.0		205	5.0	0.9	1	dbSNP_134	136	1,8599	1.2+/-3.3	0,1,4299	no	missense	MORN1	NM_024848.1	125	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	69/498	2319720	2,13004	2203	4300	6503	2309580	SO:0001583	missense	79906	exon3			AK024003	CCDS40.1, CCDS72688.1	1p36.33-p36.32	2008-02-05			ENSG00000116151	ENSG00000116151			25852	protein-coding gene	gene with protein product						12477932	Standard	XM_005244798		Approved	FLJ13941	uc001ajb.1	Q5T089	OTTHUMG00000001402	ENST00000378531.3:c.205G>A	1.37:g.2319720C>T	ENSP00000367792:p.Gly69Arg	Somatic		Capture	Illumina HiSeq	Phase_I	2309580	NM_024848	A6NKZ6|Q8WW30|Q9H852	Missense_Mutation	SNP	ENST00000378531.3	37	CCDS40.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	16.48	3.133962	0.56828	2.27E-4	1.16E-4	ENSG00000116151	ENST00000378531;ENST00000378529;ENST00000378525	T;T;T	0.61980	0.37;0.37;0.06	5.03	5.03	0.67393	.	0.000000	0.56097	D	0.000031	D	0.84092	0.5396	M	0.93328	3.405	0.43292	D	0.995273	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;1.0	D	0.88403	0.3016	10	0.72032	D	0.01	.	15.8628	0.79038	0.0:1.0:0.0:0.0	.	45;69;69	B4DRE3;Q5T089-2;Q5T089	.;.;MORN1_HUMAN	R	69;69;45	ENSP00000367792:G69R;ENSP00000367790:G69R;ENSP00000367786:G45R	ENSP00000367786:G45R	G	-	1	0	MORN1	2309580	0.990000	0.36364	0.920000	0.36463	0.019000	0.09904	4.533000	0.60615	2.331000	0.79229	0.561000	0.74099	GGA		0.537	MORN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004055.1	NM_024848	
EPHB2	2048	broad.mit.edu	37	1	23191577	23191577	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:23191577G>A	ENST00000400191.3	+	5	1193	c.1175G>A	c.(1174-1176)cGc>cAc	p.R392H	EPHB2_ENST00000374632.3_Missense_Mutation_p.R392H|EPHB2_ENST00000465676.1_3'UTR|EPHB2_ENST00000374627.1_Missense_Mutation_p.R386H|EPHB2_ENST00000544305.1_Missense_Mutation_p.R392H|MIR4253_ENST00000581187.1_RNA|EPHB2_ENST00000374630.3_Missense_Mutation_p.R392H	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	392	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)	p.R392H(2)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		ACCGAGCCACGCATTTACATC	0.617																																					p.R392H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1175A	1						.						102.0	84.0	90.0					1																	23191577		2203	4300	6503	23064164	SO:0001583	missense	2048	exon5			AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3393	protein-coding gene	gene with protein product		600997	"""EphB2"""	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.1175G>A	1.37:g.23191577G>A	ENSP00000383053:p.Arg392His	Somatic		Capture	Illumina HiSeq	Phase_I	23064164	NM_017449	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Missense_Mutation	SNP	ENST00000400191.3	37		.	.	.	.	.	.	.	.	.	.	G	16.59	3.165010	0.57476	.	.	ENSG00000133216	ENST00000374625;ENST00000544305;ENST00000374630;ENST00000400191;ENST00000374632;ENST00000374627	T;T;T;T;T	0.58506	0.33;0.33;0.33;0.33;0.33	5.13	5.13	0.70059	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.063700	0.64402	D	0.000009	T	0.58552	0.2130	M	0.69463	2.115	0.43761	D	0.996279	B;B;B;B	0.24823	0.076;0.112;0.063;0.051	B;B;B;B	0.26969	0.02;0.075;0.052;0.031	T	0.56171	-0.8023	10	0.35671	T	0.21	.	17.313	0.87214	0.0:0.0:1.0:0.0	.	392;392;410;392	A6NJM0;P29323;Q4LE53;P29323-3	.;EPHB2_HUMAN;.;.	H	392;392;392;392;392;386	ENSP00000444174:R392H;ENSP00000363761:R392H;ENSP00000383053:R392H;ENSP00000363763:R392H;ENSP00000363758:R386H	ENSP00000363755:R392H	R	+	2	0	EPHB2	23064164	1.000000	0.71417	0.999000	0.59377	0.959000	0.62525	6.463000	0.73530	2.667000	0.90743	0.462000	0.41574	CGC		0.617	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449	
TRIM67	440730	broad.mit.edu	37	1	231342436	231342436	+	Silent	SNP	C	C	T	rs565486696		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:231342436C>T	ENST00000366653.5	+	7	1719	c.1719C>T	c.(1717-1719)gaC>gaT	p.D573D	TRIM67_ENST00000366652.2_Silent_p.D573D|TRIM67_ENST00000449018.3_Silent_p.D511D|TRIM67_ENST00000444294.3_Silent_p.D571D			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	573	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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.D573D(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)				GTACCATCGACGGTCTTCACT	0.498													C|||	1	0.000199681	0.0	0.0	5008	,	,		16509	0.0		0.0	False		,,,				2504	0.001				p.D573D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1719T	1						.						77.0	84.0	82.0					1																	231342436		2063	4221	6284	229409059	SO:0001819	synonymous_variant	440730	exon7			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.1719C>T	1.37:g.231342436C>T		Somatic		Capture	Illumina HiSeq	Phase_I	229409059	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Silent	SNP	ENST00000366653.5	37	CCDS44333.1																																																																																				0.498	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342	
PCNXL2	80003	broad.mit.edu	37	1	233136250	233136250	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:233136250T>C	ENST00000258229.9	-	30	5363	c.5129A>G	c.(5128-5130)gAc>gGc	p.D1710G	PCNXL2_ENST00000344698.2_Missense_Mutation_p.D362G	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1710						integral component of membrane (GO:0016021)		p.D1710G(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)				GACTGCTGGGTCTTCATACTC	0.612																																					p.D1710G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A5129G	1						.						62.0	65.0	64.0					1																	233136250		2028	4181	6209	231202873	SO:0001583	missense	80003	exon30			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.5129A>G	1.37:g.233136250T>C	ENSP00000258229:p.Asp1710Gly	Somatic		Capture	Illumina HiSeq	Phase_I	231202873	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	37	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	T	29.4	5.003710	0.93287	.	.	ENSG00000135749	ENST00000344698;ENST00000258229	T;T	0.50277	0.75;0.75	5.51	5.51	0.81932	.	0.043031	0.85682	D	0.000000	T	0.70605	0.3243	M	0.80982	2.52	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.77004	0.989;0.95	T	0.75419	-0.3324	10	0.87932	D	0	.	15.9243	0.79603	0.0:0.0:0.0:1.0	.	1710;362	A6NKB5;A6NKB5-3	PCX2_HUMAN;.	G	362;1710	ENSP00000340759:D362G;ENSP00000258229:D1710G	ENSP00000258229:D1710G	D	-	2	0	PCNXL2	231202873	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.698000	0.84413	2.222000	0.72286	0.528000	0.53228	GAC		0.612	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801	
KDM1A	23028	broad.mit.edu	37	1	23398678	23398678	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:23398678C>T	ENST00000356634.3	+	12	1687	c.1538C>T	c.(1537-1539)gCg>gTg	p.A513V	KDM1A_ENST00000542151.1_Missense_Mutation_p.A537V|KDM1A_ENST00000400181.4_Missense_Mutation_p.A537V|RP1-184J9.2_ENST00000427154.1_RNA	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	513	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.A537V(1)		breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						GAGTTGGAAGCGAATCCCCCA	0.373																																					p.A537V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1610T	1						.						37.0	38.0	38.0					1																	23398678		2203	4300	6503	23271265	SO:0001583	missense	23028	exon14			AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"""Chromatin-modifying enzymes / K-demethylases"""	29079	protein-coding gene	gene with protein product		609132	"""amine oxidase (flavin containing) domain 2"", ""lysine (K)-specific demethylase 1"""	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.1538C>T	1.37:g.23398678C>T	ENSP00000349049:p.Ala513Val	Somatic		Capture	Illumina HiSeq	Phase_I	23271265	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Missense_Mutation	SNP	ENST00000356634.3	37	CCDS30627.1	.	.	.	.	.	.	.	.	.	.	C	16.37	3.104328	0.56291	.	.	ENSG00000004487	ENST00000356634;ENST00000400181;ENST00000542151	T;T;T	0.10099	2.91;2.91;2.91	4.97	4.04	0.47022	Amine oxidase (1);	0.168382	0.53938	D	0.000045	T	0.09905	0.0243	L	0.57536	1.79	0.80722	D	1	P;D	0.53151	0.948;0.958	B;B	0.35114	0.124;0.196	T	0.18871	-1.0323	10	0.27785	T	0.31	-16.2674	13.0139	0.58746	0.0:0.9203:0.0:0.0797	.	537;513	O60341-2;O60341	.;KDM1A_HUMAN	V	513;537;537	ENSP00000349049:A513V;ENSP00000383042:A537V;ENSP00000439072:A537V	ENSP00000349049:A513V	A	+	2	0	KDM1A	23271265	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	7.029000	0.76477	2.596000	0.87737	0.650000	0.86243	GCG		0.373	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013	
LUZP1	7798	broad.mit.edu	37	1	23420436	23420436	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:23420436T>C	ENST00000302291.4	-	4	1120	c.319A>G	c.(319-321)Aaa>Gaa	p.K107E	LUZP1_ENST00000374623.3_Missense_Mutation_p.K107E|LUZP1_ENST00000314174.5_Missense_Mutation_p.K107E|LUZP1_ENST00000418342.1_Missense_Mutation_p.K107E			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	107					artery development (GO:0060840)|neural fold bending (GO:0021503)|ventricular septum development (GO:0003281)	membrane (GO:0016020)|nucleus (GO:0005634)		p.K107E(1)		NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(2)	31		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		ATCTCAGATTTCAGCTCCCGG	0.468																																					p.K107E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A319G	1						.						96.0	107.0	103.0					1																	23420436		2203	4300	6503	23293023	SO:0001583	missense	7798	exon4			BC051733	CCDS30628.1	1p36	2008-02-05			ENSG00000169641	ENSG00000169641			14985	protein-coding gene	gene with protein product		601422				8812416	Standard	NM_033631		Approved	LUZP	uc010odv.1	Q86V48	OTTHUMG00000003227	ENST00000302291.4:c.319A>G	1.37:g.23420436T>C	ENSP00000303758:p.Lys107Glu	Somatic		Capture	Illumina HiSeq	Phase_I	23293023	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	.	.	.	.	.	.	.	.	.	.	T	15.80	2.939631	0.52972	.	.	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174;ENST00000471849	T;T;T;T;T	0.47177	2.0;2.0;2.0;1.78;0.85	6.17	4.99	0.66335	.	0.000000	0.51477	D	0.000094	T	0.55114	0.1900	M	0.76574	2.34	0.33833	D	0.630546	D;D	0.55385	0.971;0.971	P;P	0.48270	0.572;0.572	T	0.73139	-0.4077	10	0.87932	D	0	.	12.5523	0.56233	0.0:0.0:0.1386:0.8614	.	107;107	Q86V48-2;Q86V48	.;LUZP1_HUMAN	E	107	ENSP00000393460:K107E;ENSP00000363752:K107E;ENSP00000303758:K107E;ENSP00000313705:K107E;ENSP00000428061:K107E	ENSP00000303758:K107E	K	-	1	0	LUZP1	23293023	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.919000	0.70005	2.371000	0.80710	0.533000	0.62120	AAA		0.468	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631	
PCNXL2	80003	broad.mit.edu	37	1	233394381	233394381	+	Silent	SNP	G	G	A	rs374743322	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:233394381G>A	ENST00000258229.9	-	5	1461	c.1227C>T	c.(1225-1227)gaC>gaT	p.D409D	PCNXL2_ENST00000430153.1_De_novo_Start_OutOfFrame	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	409						integral component of membrane (GO:0016021)		p.D409D(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)				TGGGCTCAGCGTCAGACTTTA	0.557													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18855	0.0		0.0	False		,,,				2504	0.0				p.D409D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1227T	1						.	G		5,3841		0,5,1918	75.0	78.0	77.0		1227	-7.4	0.0	1		77	0,8268		0,0,4134	no	coding-synonymous	PCNXL2	NM_014801.3		0,5,6052	AA,AG,GG		0.0,0.13,0.0413		409/2138	233394381	5,12109	1923	4134	6057	231461004	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.1227C>T	1.37:g.233394381G>A		Somatic		Capture	Illumina HiSeq	Phase_I	231461004	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Silent	SNP	ENST00000258229.9	37	CCDS44335.1																																																																																				0.557	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801	
NID1	4811	broad.mit.edu	37	1	236154319	236154319	+	Missense_Mutation	SNP	G	G	A	rs138322087	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:236154319G>A	ENST00000264187.6	-	14	2877	c.2795C>T	c.(2794-2796)gCg>gTg	p.A932V	NID1_ENST00000366595.3_Missense_Mutation_p.A799V	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	932					basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)	p.A932V(1)		breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	GGTAGGCACCGCAGGTCCTTG	0.607													G|||	5	0.000998403	0.0	0.0	5008	,	,		17339	0.0		0.005	False		,,,				2504	0.0				p.A932V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2795T	1						.	G	VAL/ALA	2,4404	2.1+/-5.4	0,2,2201	61.0	59.0	60.0		2795	-0.2	0.0	1	dbSNP_134	60	24,8576	17.3+/-56.4	0,24,4276	yes	missense	NID1	NM_002508.2	64	0,26,6477	AA,AG,GG		0.2791,0.0454,0.1999	benign	932/1248	236154319	26,12980	2203	4300	6503	234220942	SO:0001583	missense	4811	exon14			BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.2795C>T	1.37:g.236154319G>A	ENSP00000264187:p.Ala932Val	Somatic		Capture	Illumina HiSeq	Phase_I	234220942	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	37	CCDS1608.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	8.367	0.834347	0.16820	4.54E-4	0.002791	ENSG00000116962	ENST00000264187;ENST00000366595	D;D	0.87650	-1.66;-2.28	5.1	-0.233	0.13078	.	1.453140	0.03646	N	0.240209	T	0.72423	0.3458	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.61327	-0.7085	10	0.37606	T	0.19	.	10.7113	0.45984	0.2689:0.0:0.7311:0.0	.	799;932	P14543-2;P14543	.;NID1_HUMAN	V	932;799	ENSP00000264187:A932V;ENSP00000355554:A799V	ENSP00000264187:A932V	A	-	2	0	NID1	234220942	0.121000	0.22262	0.000000	0.03702	0.158000	0.22134	1.673000	0.37534	-0.218000	0.10018	0.491000	0.48974	GCG		0.607	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	
ACTN2	88	broad.mit.edu	37	1	236906324	236906324	+	Silent	SNP	G	G	A	rs143566058		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:236906324G>A	ENST00000366578.4	+	11	1402	c.1236G>A	c.(1234-1236)acG>acA	p.T412T	ACTN2_ENST00000542672.1_Silent_p.T412T|ACTN2_ENST00000492634.1_3'UTR|ACTN2_ENST00000546208.1_5'UTR	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	412					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)	p.T412T(1)		endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			AGGCCTCAACGCACGAGACTT	0.502																																					p.T412T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1236A	1						.	G		0,4406		0,0,2203	97.0	89.0	91.0		1236	-10.9	0.0	1	dbSNP_134	91	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ACTN2	NM_001103.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		412/895	236906324	1,13005	2203	4300	6503	234972947	SO:0001819	synonymous_variant	88	exon11			BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"""EF-hand domain containing"""	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.1236G>A	1.37:g.236906324G>A		Somatic		Capture	Illumina HiSeq	Phase_I	234972947	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Silent	SNP	ENST00000366578.4	37	CCDS1613.1																																																																																				0.502	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103	
RYR2	6262	broad.mit.edu	37	1	237729943	237729943	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:237729943G>T	ENST00000366574.2	+	28	3608	c.3291G>T	c.(3289-3291)aaG>aaT	p.K1097N	RYR2_ENST00000542537.1_Missense_Mutation_p.K1081N|RYR2_ENST00000360064.6_Missense_Mutation_p.K1095N	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	1097	4 X approximate repeats.|B30.2/SPRY 2. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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.K1095K(2)|p.K1095N(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)			ATGCAGTGAAGGCCGGACGGT	0.557																																					p.K1097N												.	.	3	Substitution - coding silent(2)|Substitution - Missense(1)	lung(2)|large_intestine(1)	c.G3291T	1						.						128.0	129.0	128.0					1																	237729943		1960	4144	6104	235796566	SO:0001583	missense	6262	exon28			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.3291G>T	1.37:g.237729943G>T	ENSP00000355533:p.Lys1097Asn	Somatic		Capture	Illumina HiSeq	Phase_I	235796566	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.434040	0.25813	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;T;T	0.59906	0.23;0.23;0.23	5.29	5.29	0.74685	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.077097	0.49305	D	0.000148	T	0.44456	0.1294	L	0.33624	1.015	0.44745	D	0.997747	B	0.09022	0.002	B	0.08055	0.003	T	0.38067	-0.9678	10	0.45353	T	0.12	.	9.0998	0.36662	0.2045:0.0:0.7955:0.0	.	1097	Q92736	RYR2_HUMAN	N	1097;1095;1081	ENSP00000355533:K1097N;ENSP00000353174:K1095N;ENSP00000443798:K1081N	ENSP00000353174:K1095N	K	+	3	2	RYR2	235796566	0.060000	0.20803	0.995000	0.50966	0.849000	0.48306	0.552000	0.23376	2.465000	0.83290	0.655000	0.94253	AAG		0.557	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
RYR2	6262	broad.mit.edu	37	1	237972271	237972271	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:237972271G>A	ENST00000366574.2	+	100	14686	c.14369G>A	c.(14368-14370)cGa>cAa	p.R4790Q	RYR2_ENST00000542537.1_Missense_Mutation_p.R4774Q|RYR2_ENST00000360064.6_Missense_Mutation_p.R4796Q	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4790					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.R4788Q(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)			AATTTTTTCCGAAAATTCTAC	0.353																																					p.R4790Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G14369A	1						.						255.0	250.0	251.0					1																	237972271		1845	4091	5936	236038894	SO:0001583	missense	6262	exon100			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.14369G>A	1.37:g.237972271G>A	ENSP00000355533:p.Arg4790Gln	Somatic		Capture	Illumina HiSeq	Phase_I	236038894	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	34	5.378021	0.95945	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537;ENST00000536033	D;D;D	0.92048	-2.96;-2.96;-2.96	4.88	4.88	0.63580	Ion transport (1);	0.000000	0.47852	U	0.000203	D	0.95010	0.8385	L	0.55743	1.74	0.54753	D	0.999989	D;D	0.71674	0.998;0.998	P;D	0.76575	0.866;0.988	D	0.95562	0.8630	10	0.87932	D	0	.	18.3877	0.90472	0.0:0.0:1.0:0.0	.	223;4790	F5H3C7;Q92736	.;RYR2_HUMAN	Q	4790;4796;4774;223	ENSP00000355533:R4790Q;ENSP00000353174:R4796Q;ENSP00000443798:R4774Q	ENSP00000353174:R4796Q	R	+	2	0	RYR2	236038894	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.781000	0.99029	2.412000	0.81896	0.563000	0.77884	CGA		0.353	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
ZP4	57829	broad.mit.edu	37	1	238053923	238053923	+	Missense_Mutation	SNP	G	G	A	rs371052672		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:238053923G>A	ENST00000366570.4	-	1	171	c.13C>T	c.(13-15)Cgg>Tgg	p.R5W	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	5					acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)	p.R5W(1)		breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			AAAACGCACCGCAGCAGCCAC	0.557													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17424	0.0		0.0	False		,,,				2504	0.0				p.R5W	NSCLC(166;160 2029 11600 18754 19936)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C13T	1						.	G	TRP/ARG	0,4406		0,0,2203	38.0	38.0	38.0		13	-2.1	0.0	1		38	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZP4	NM_021186.3	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	5/541	238053923	1,13005	2203	4300	6503	236120546	SO:0001583	missense	57829	exon1			U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"""Zona pellucida glycoproteins"""	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.13C>T	1.37:g.238053923G>A	ENSP00000355529:p.Arg5Trp	Somatic		Capture	Illumina HiSeq	Phase_I	236120546	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	.	.	.	.	.	.	.	.	.	.	G	11.11	1.543054	0.27563	0.0	1.16E-4	ENSG00000116996	ENST00000366570	T	0.75260	-0.92	3.64	-2.11	0.07187	.	2.841300	0.01275	N	0.009565	T	0.53690	0.1812	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46665	-0.9175	10	0.62326	D	0.03	5.1698	4.3134	0.10981	0.4909:0.1788:0.3303:0.0	.	5	Q12836	ZP4_HUMAN	W	5	ENSP00000355529:R5W	ENSP00000355529:R5W	R	-	1	2	ZP4	236120546	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.091000	0.11146	-0.416000	0.07473	0.563000	0.77884	CGG		0.557	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1		
CHRM3	1131	broad.mit.edu	37	1	240071532	240071532	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:240071532C>T	ENST00000255380.4	+	5	1560	c.781C>T	c.(781-783)Cgt>Tgt	p.R261C		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	261					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.R261C(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)	AACTGAAAAGCGTACCAAAGA	0.483																																					p.R261C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C781T	1						.						45.0	50.0	48.0					1																	240071532		2203	4300	6503	238138155	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.781C>T	1.37:g.240071532C>T	ENSP00000255380:p.Arg261Cys	Somatic		Capture	Illumina HiSeq	Phase_I	238138155	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	37	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.498465	0.64298	.	.	ENSG00000133019	ENST00000255380	T	0.38887	1.11	6.06	6.06	0.98353	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.72145	0.3424	M	0.86343	2.81	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74999	-0.3472	10	0.87932	D	0	-9.3032	20.6244	0.99512	0.0:1.0:0.0:0.0	.	261	P20309	ACM3_HUMAN	C	261	ENSP00000255380:R261C	ENSP00000255380:R261C	R	+	1	0	CHRM3	238138155	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.692000	0.61746	2.879000	0.98667	0.650000	0.86243	CGT		0.483	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740	
MYOM3	127294	broad.mit.edu	37	1	24406678	24406678	+	Missense_Mutation	SNP	G	G	A	rs202106386		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:24406678G>A	ENST00000374434.3	-	20	2576	c.2414C>T	c.(2413-2415)cCg>cTg	p.P805L	MYOM3_ENST00000330966.7_Missense_Mutation_p.P806L|MYOM3_ENST00000329601.7_Missense_Mutation_p.P805L|RP11-293P20.2_ENST00000439239.2_RNA|RP11-293P20.4_ENST00000429191.1_RNA|MYOM3_ENST00000475306.1_5'Flank	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	805	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.					M band (GO:0031430)	protein homodimerization activity (GO:0042803)	p.P805L(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		TACATCGTACGGGGGGCCTGT	0.607													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19223	0.0		0.0	False		,,,				2504	0.0				p.P805L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2414T	1						.						32.0	37.0	35.0					1																	24406678		2042	4185	6227	24279265	SO:0001583	missense	127294	exon20			AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.2414C>T	1.37:g.24406678G>A	ENSP00000363557:p.Pro805Leu	Somatic		Capture	Illumina HiSeq	Phase_I	24279265	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	17.37	3.371316	0.61624	.	.	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.71934	-0.61;-0.61;-0.61	5.38	5.38	0.77491	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.224830	0.47455	D	0.000226	D	0.91277	0.7250	H	0.98721	4.31	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.992;1.0	D	0.94727	0.7906	10	0.87932	D	0	.	19.1469	0.93472	0.0:0.0:1.0:0.0	.	805;805	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	L	805;806;805	ENSP00000363557:P805L;ENSP00000332670:P806L;ENSP00000328415:P805L	ENSP00000328415:P805L	P	-	2	0	MYOM3	24279265	1.000000	0.71417	0.953000	0.39169	0.154000	0.21943	8.175000	0.89684	2.531000	0.85337	0.563000	0.77884	CCG		0.607	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
MYOM3	127294	broad.mit.edu	37	1	24409192	24409192	+	Silent	SNP	G	G	A	rs367719400		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:24409192G>A	ENST00000374434.3	-	17	2145	c.1983C>T	c.(1981-1983)ccC>ccT	p.P661P	MYOM3_ENST00000330966.7_Silent_p.P662P|MYOM3_ENST00000329601.7_Silent_p.P661P|RP11-293P20.2_ENST00000439239.2_RNA|RP11-293P20.4_ENST00000429191.1_RNA|MYOM3_ENST00000475306.1_5'UTR	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	661	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.					M band (GO:0031430)	protein homodimerization activity (GO:0042803)	p.P661P(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		TCCTCAGCCCGGGAACTGTAA	0.542																																					p.P661P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1983T	1						.	G		2,4008		0,2,2003	53.0	56.0	55.0		1983	-10.8	0.2	1		55	1,8387		0,1,4193	no	coding-synonymous	MYOM3	NM_152372.3		0,3,6196	AA,AG,GG		0.0119,0.0499,0.0242		661/1438	24409192	3,12395	2005	4194	6199	24281779	SO:0001819	synonymous_variant	127294	exon17			AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.1983C>T	1.37:g.24409192G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24281779	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Silent	SNP	ENST00000374434.3	37	CCDS41281.1																																																																																				0.542	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
ZBTB18	10472	broad.mit.edu	37	1	244218284	244218284	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:244218284G>A	ENST00000358704.4	+	2	1357	c.1208G>A	c.(1207-1209)cGc>cAc	p.R403H		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	394	Interaction with DNMT3A.				cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|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)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R394H(1)									ACGCACTTCCGCGAGCAGGAC	0.627																																					p.R394H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1181A	1						.						47.0	47.0	47.0					1																	244218284		2203	4300	6503	242284907	SO:0001583	missense	10472	exon1			U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13030	protein-coding gene	gene with protein product		608433	"""zinc finger protein 238"""	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.1208G>A	1.37:g.244218284G>A	ENSP00000351539:p.Arg403His	Somatic		Capture	Illumina HiSeq	Phase_I	242284907	NM_006352	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Missense_Mutation	SNP	ENST00000358704.4	37	CCDS1622.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.201714	0.79015	.	.	ENSG00000179456	ENST00000366538;ENST00000358704	T	0.34275	1.37	5.84	5.84	0.93424	Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.50222	0.1603	L	0.32530	0.975	0.80722	D	1	D;D	0.76494	0.998;0.999	P;P	0.62885	0.811;0.908	T	0.46555	-0.9183	10	0.62326	D	0.03	.	20.1379	0.98040	0.0:0.0:1.0:0.0	.	394;403	Q99592;Q99592-2	ZN238_HUMAN;.	H	403	ENSP00000351539:R403H	ENSP00000351539:R403H	R	+	2	0	ZNF238	242284907	1.000000	0.71417	0.987000	0.45799	0.986000	0.74619	9.862000	0.99564	2.779000	0.95612	0.655000	0.94253	CGC		0.627	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768	
NLRP3	114548	broad.mit.edu	37	1	247599334	247599334	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:247599334G>T	ENST00000336119.3	+	6	3307	c.2561G>T	c.(2560-2562)aGc>aTc	p.S854I	NLRP3_ENST00000391828.3_Missense_Mutation_p.S854I|NLRP3_ENST00000366496.2_Intron|NLRP3_ENST00000348069.2_Intron|NLRP3_ENST00000391827.2_Missense_Mutation_p.S797I|NLRP3_ENST00000366497.2_Intron	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	854					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)	p.S854I(1)		NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			TTGAGCACCAGCCATTCCCTG	0.488																																					p.S854I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2561T	1						.						129.0	111.0	117.0					1																	247599334		2203	4300	6503	245665957	SO:0001583	missense	114548	exon6			AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"""Nucleotide-binding domain and leucine rich repeat containing"""	16400	protein-coding gene	gene with protein product	"""Cryopyrin"", ""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"""	606416	"""cold autoinflammatory syndrome 1"""	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.2561G>T	1.37:g.247599334G>T	ENSP00000337383:p.Ser854Ile	Somatic		Capture	Illumina HiSeq	Phase_I	245665957	NM_004895	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	37	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	g	11.28	1.591505	0.28357	.	.	ENSG00000162711	ENST00000391828;ENST00000336119;ENST00000391827	T;T;T	0.42900	0.96;0.96;0.96	3.78	-5.94	0.02247	.	0.737426	0.11108	N	0.598863	T	0.39253	0.1071	M	0.72353	2.195	0.45056	D	0.998071	P;B;P	0.39903	0.603;0.365;0.694	B;B;B	0.38106	0.136;0.265;0.244	T	0.52049	-0.8627	10	0.62326	D	0.03	.	12.9786	0.58552	0.8482:0.0:0.1518:0.0	.	834;797;854	B7ZKS9;Q96P20-4;Q96P20	.;.;NALP3_HUMAN	I	854;854;797	ENSP00000375704:S854I;ENSP00000337383:S854I;ENSP00000375703:S797I	ENSP00000337383:S854I	S	+	2	0	NLRP3	245665957	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.867000	0.04241	-1.423000	0.02002	-0.440000	0.05779	AGC		0.488	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895	
OR2G2	81470	broad.mit.edu	37	1	247752184	247752184	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:247752184C>T	ENST00000320065.1	+	1	523	c.523C>T	c.(523-525)Cgc>Tgc	p.R175C	RP11-978I15.10_ENST00000435333.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R175C(1)		endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			CTGTGGGCATCGCCAAGTGGA	0.557																																					p.R175C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C523T	1						.						184.0	171.0	175.0					1																	247752184		2203	4300	6503	245818807	SO:0001583	missense	81470	exon1			BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"""GPCR / Class A : Olfactory receptors"""	15007	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily G, member 2"", ""olfactory receptor, family 2, subfamily G, member 2 pseudogene"""				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.523C>T	1.37:g.247752184C>T	ENSP00000326349:p.Arg175Cys	Somatic		Capture	Illumina HiSeq	Phase_I	245818807	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.563482	0.45694	.	.	ENSG00000177489	ENST00000320065	T	0.00137	8.68	4.29	2.22	0.28083	GPCR, rhodopsin-like superfamily (1);	0.910260	0.08981	U	0.865762	T	0.00384	0.0012	M	0.80616	2.505	0.09310	N	1	D	0.76494	0.999	D	0.65140	0.932	T	0.49872	-0.8893	10	0.54805	T	0.06	.	3.3058	0.07000	0.2201:0.5548:0.0:0.2251	.	175	Q8NGZ5	OR2G2_HUMAN	C	175	ENSP00000326349:R175C	ENSP00000326349:R175C	R	+	1	0	OR2G2	245818807	0.025000	0.19082	0.764000	0.31436	0.987000	0.75469	2.319000	0.43788	1.013000	0.39391	0.591000	0.81541	CGC		0.557	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
OR6F1	343169	broad.mit.edu	37	1	247875850	247875850	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:247875850C>A	ENST00000302084.2	-	1	255	c.208G>T	c.(208-210)Gag>Tag	p.E70*	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	70						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E70*(1)		breast(1)|kidney(1)|large_intestine(5)|lung(34)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)	47	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.0168)			TACCAAATCTCCAGGAAGGAG	0.478																																					p.E70X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G208T	1						.						103.0	103.0	103.0					1																	247875850		2203	4300	6503	245942473	SO:0001587	stop_gained	343169	exon1			BK004460	CCDS31095.1	1q44	2012-08-09			ENSG00000169214	ENSG00000169214		"""GPCR / Class A : Olfactory receptors"""	15027	protein-coding gene	gene with protein product							Standard	NM_001005286		Approved	OST731	uc001idj.1	Q8NGZ6	OTTHUMG00000040213	ENST00000302084.2:c.208G>T	1.37:g.247875850C>A	ENSP00000305640:p.Glu70*	Somatic		Capture	Illumina HiSeq	Phase_I	245942473	NM_001005286	B2RNV6|Q6IF02|Q96R39	Nonsense_Mutation	SNP	ENST00000302084.2	37	CCDS31095.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.075337	0.55646	.	.	ENSG00000169214	ENST00000302084	.	.	.	3.99	3.06	0.35304	.	0.000000	0.44285	D	0.000466	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-29.6693	12.7081	0.57073	0.0:0.8327:0.1673:0.0	.	.	.	.	X	70	.	ENSP00000305640:E70X	E	-	1	0	OR6F1	245942473	1.000000	0.71417	0.990000	0.47175	0.025000	0.11179	6.378000	0.73150	0.999000	0.39023	0.591000	0.81541	GAG		0.478	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286	
OR14A16	284532	broad.mit.edu	37	1	247978618	247978618	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:247978618G>T	ENST00000357627.1	-	1	413	c.414C>A	c.(412-414)acC>acA	p.T138T		NM_001001966.1	NP_001001966.1	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A, member 16	138						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T138T(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(32)|skin(2)|stomach(1)	45						TTTGGACACAGGTGCTCCTGT	0.527																																					p.T138T	Ovarian(112;180 1586 15073 21914 33526)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C414A	1						.						126.0	116.0	120.0					1																	247978618		2203	4300	6503	246045241	SO:0001819	synonymous_variant	284532	exon1			BK004366	CCDS31097.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000196772	ENSG00000196772		"""GPCR / Class A : Olfactory receptors"""	15022	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily AT, member 1"""	OR5AT1			Standard	NM_001001966		Approved		uc001idm.1	Q8NHC5	OTTHUMG00000040199	ENST00000357627.1:c.414C>A	1.37:g.247978618G>T		Somatic		Capture	Illumina HiSeq	Phase_I	246045241	NM_001001966	Q6IF96	Silent	SNP	ENST00000357627.1	37	CCDS31097.1																																																																																				0.527	OR14A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096856.1	NM_001001966	
OR2L13	284521	broad.mit.edu	37	1	248263479	248263479	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:248263479G>A	ENST00000358120.2	+	2	947	c.802G>A	c.(802-804)Gct>Act	p.A268T	OR2L13_ENST00000366478.2_Missense_Mutation_p.A268T			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13	268						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A268T(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(32)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	59	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0132)			CCGCTCACCAGCTGAAGACAA	0.473																																					p.A268T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G802A	1						.						109.0	109.0	109.0					1																	248263479		2203	4300	6503	246330102	SO:0001583	missense	284521	exon3			BC028158	CCDS1637.1	1q44	2012-08-09			ENSG00000196071	ENSG00000196071		"""GPCR / Class A : Olfactory receptors"""	19578	protein-coding gene	gene with protein product				OR2L14			Standard	NM_175911		Approved		uc001ids.3	Q8N349	OTTHUMG00000040446	ENST00000358120.2:c.802G>A	1.37:g.248263479G>A	ENSP00000350836:p.Ala268Thr	Somatic		Capture	Illumina HiSeq	Phase_I	246330102	NM_175911	Q5VUR5	Missense_Mutation	SNP	ENST00000358120.2	37	CCDS1637.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.053155	0.00394	.	.	ENSG00000196071	ENST00000366478;ENST00000358120	T;T	0.00107	8.72;8.72	4.21	-2.55	0.06288	GPCR, rhodopsin-like superfamily (1);	0.685438	0.12675	N	0.448470	T	0.00039	0.0001	N	0.01134	-0.995	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.13548	-1.0505	10	0.12103	T	0.63	.	0.5173	0.00605	0.3184:0.1151:0.2158:0.3507	.	268	Q8N349	OR2LD_HUMAN	T	268	ENSP00000355434:A268T;ENSP00000350836:A268T	ENSP00000350836:A268T	A	+	1	0	OR2L13	246330102	0.000000	0.05858	0.001000	0.08648	0.047000	0.14425	-1.266000	0.02842	-0.460000	0.07003	-0.840000	0.03056	GCT		0.473	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	NM_175911	
SH3BP5L	80851	broad.mit.edu	37	1	249106372	249106372	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:249106372G>A	ENST00000366472.5	-	7	2138	c.909C>T	c.(907-909)gaC>gaT	p.D303D	SH3BP5L_ENST00000475978.1_5'UTR|SH3BP5L_ENST00000411742.2_Silent_p.D271D	NM_030645.1	NP_085148.1	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	303								p.D303D(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			CGCTGTCTCCGTCCTCCATGT	0.751																																					p.D303D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C909T	1						.						13.0	15.0	14.0					1																	249106372		2191	4280	6471	247072995	SO:0001819	synonymous_variant	80851	exon7			AB051507	CCDS31126.1	1q44	2008-02-05			ENSG00000175137	ENSG00000175137			29360	protein-coding gene	gene with protein product							Standard	NM_030645		Approved	KIAA1720	uc001iew.1	Q7L8J4	OTTHUMG00000040389	ENST00000366472.5:c.909C>T	1.37:g.249106372G>A		Somatic		Capture	Illumina HiSeq	Phase_I	247072995	NM_030645	B4DQ94|Q96FI5|Q9BQH8|Q9C0E3	Silent	SNP	ENST00000366472.5	37	CCDS31126.1																																																																																				0.751	SH3BP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097140.1	NM_030645	
FAM213B	127281	broad.mit.edu	37	1	2520399	2520399	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:2520399C>A	ENST00000378425.5	+	6	575	c.499C>A	c.(499-501)Cca>Aca	p.P167T	FAM213B_ENST00000537325.1_Missense_Mutation_p.P160T|FAM213B_ENST00000444521.2_Missense_Mutation_p.P185T|FAM213B_ENST00000419916.2_Missense_Mutation_p.P197T|FAM213B_ENST00000484099.1_3'UTR|FAM213B_ENST00000378424.4_Missense_Mutation_p.P204H			Q8TBF2	PGFS_HUMAN	family with sequence similarity 213, member B	167					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|myelin sheath (GO:0043209)	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|prostaglandin-F synthase activity (GO:0047017)	p.P167T(1)									CCAGAAGTCCCCAGGCGACTA	0.652																																					p.P160T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C478A	1						.						62.0	62.0	62.0					1																	2520399		2203	4300	6503	2510259	SO:0001583	missense	127281	exon5			AK075273	CCDS44.1, CCDS44.2, CCDS55564.1, CCDS72690.1, CCDS72691.1	1p36.32	2011-12-08	2011-11-24	2011-11-24	ENSG00000157870	ENSG00000157870	1.11.1.20		28390	protein-coding gene	gene with protein product	"""prostamide/prostaglandin F synthase"""		"""chromosome 1 open reading frame 93"""	C1orf93		18006499	Standard	NM_152371		Approved	MGC26818	uc001ajv.2	Q8TBF2	OTTHUMG00000000847	ENST00000378425.5:c.499C>A	1.37:g.2520399C>A	ENSP00000367682:p.Pro167Thr	Somatic		Capture	Illumina HiSeq	Phase_I	2510259	NM_001195741	A8K793|B3KPY3|B4DQR9|B4E0S5|B7ZAC8|B9DI90|B9DI92|J3KQD0|Q8N2H0	Missense_Mutation	SNP	ENST00000378425.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.20|14.20	2.465860|2.465860	0.43839|0.43839	.|.	.|.	ENSG00000157870|ENSG00000157870	ENST00000378424|ENST00000419916;ENST00000537325;ENST00000378425;ENST00000444521	T|T;T;T;T	0.51325|0.50813	0.71|1.09;0.73;1.1;0.97	4.44|4.44	4.44|4.44	0.53790|0.53790	.|.	1.149570|1.149570	0.06726|0.06726	N|N	0.775697|0.775697	T|T	0.64216|0.64216	0.2578|0.2578	.|.	.|.	.|.	0.51233|0.51233	D|D	0.999917|0.999917	P|D;D;D;D;D	0.48407|0.89917	0.91|1.0;0.998;1.0;1.0;0.999	B|D;D;D;D;D	0.43478|0.97110	0.421|1.0;0.919;0.992;0.992;0.947	T|T	0.48625|0.48625	-0.9019|-0.9019	9|9	0.52906|0.20046	T|T	0.07|0.44	-3.3791|-3.3791	12.413|12.413	0.55478|0.55478	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	156|160;131;193;185;167	Q8TBF2-2|Q8TBF2-5;Q8TBF2-4;Q8TBF2-6;Q8TBF2-3;Q8TBF2	.|.;.;.;.;PGFS_HUMAN	H|T	204|197;160;167;185	ENSP00000367681:P204H|ENSP00000394405:P197T;ENSP00000443605:P160T;ENSP00000367682:P167T;ENSP00000413218:P185T	ENSP00000367681:P204H|ENSP00000367682:P167T	P|P	+|+	2|1	0|0	C1orf93|C1orf93	2510259|2510259	0.975000|0.975000	0.34042|0.34042	0.701000|0.701000	0.30321|0.30321	0.011000|0.011000	0.07611|0.07611	5.228000|5.228000	0.65310|0.65310	2.301000|2.301000	0.77427|0.77427	0.313000|0.313000	0.20887|0.20887	CCC|CCA		0.652	FAM213B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152371	
PRDM16	63976	broad.mit.edu	37	1	3328009	3328009	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:3328009C>T	ENST00000270722.5	+	9	1297	c.1248C>T	c.(1246-1248)caC>caT	p.H416H	PRDM16_ENST00000378398.3_Silent_p.H417H|PRDM16_ENST00000511072.1_Silent_p.H417H|PRDM16_ENST00000514189.1_Silent_p.H417H|PRDM16_ENST00000441472.2_Silent_p.H416H|PRDM16_ENST00000378391.2_Silent_p.H416H|PRDM16_ENST00000442529.2_Silent_p.H416H|PRDM16_ENST00000512462.1_3'UTR			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	416					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.H416H(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)		AGCGGATGCACGCCGACTGCC	0.572			T	EVI1	"""MDS, AML"""																																p.H416H			Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1248T	1						.						65.0	70.0	68.0					1																	3328009		2180	4295	6475	3317869	SO:0001819	synonymous_variant	63976	exon9			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.1248C>T	1.37:g.3328009C>T		Somatic		Capture	Illumina HiSeq	Phase_I	3317869	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																				0.572	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
CHD5	26038	broad.mit.edu	37	1	6185218	6185218	+	Missense_Mutation	SNP	C	C	T	rs143075819	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:6185218C>T	ENST00000262450.3	-	29	4435	c.4336G>A	c.(4336-4338)Gcc>Acc	p.A1446T	CHD5_ENST00000378021.1_Missense_Mutation_p.A303T	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.A1446T(1)		breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		GAGTTGAAGGCGTCCTGCGGG	0.637																																					p.A1446T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4336A	1						.						36.0	40.0	39.0					1																	6185218		2203	4298	6501	6107805	SO:0001583	missense	26038	exon29			AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.4336G>A	1.37:g.6185218C>T	ENSP00000262450:p.Ala1446Thr	Somatic		Capture	Illumina HiSeq	Phase_I	6107805	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	37	CCDS57.1	.	.	.	.	.	.	.	.	.	.	C	33	5.220691	0.95139	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000378021;ENST00000536802;ENST00000538279;ENST00000377999	D;T	0.91631	-2.88;2.09	4.5	4.5	0.54988	Domain of unknown function DUF1086 (1);	0.000000	0.64402	D	0.000001	D	0.89733	0.6800	L	0.42245	1.32	0.58432	D	0.999993	B;P	0.42973	0.419;0.796	B;B	0.41691	0.039;0.364	D	0.90341	0.4359	10	0.46703	T	0.11	-24.4588	17.5764	0.87950	0.0:1.0:0.0:0.0	.	1446;303	Q8TDI0;Q5TG85	CHD5_HUMAN;.	T	1446;962;303;854;854;303	ENSP00000262450:A1446T;ENSP00000367260:A303T	ENSP00000262450:A1446T	A	-	1	0	CHD5	6107805	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.629000	0.67798	2.221000	0.72209	0.561000	0.74099	GCC		0.637	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
RPL22	6146	broad.mit.edu	37	1	6257785	6257785	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:6257785delT	ENST00000234875.4	-	2	82	c.44delA	c.(43-45)aagfs	p.K16fs	RPL22_ENST00000484532.1_5'UTR|RPL22_ENST00000497965.1_5'UTR	NM_000983.3	NP_000974.1	P35268	RL22_HUMAN	ribosomal protein L22	16					alpha-beta T cell differentiation (GO:0046632)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	heparin binding (GO:0008201)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.K15fs*5(1)		kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	Ovarian(185;0.0634)	all_cancers(23;2.78e-38)|all_epithelial(116;8.88e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.53e-38)|GBM - Glioblastoma multiforme(13;3.33e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.8e-19)|Colorectal(212;6.8e-08)|COAD - Colon adenocarcinoma(227;8.04e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00107)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		AACTTGCTTCTTTTTTTTGCC	0.398			T	RUNX1	"""AML, CML"""																																p.K15fs			Dom	yes		1	1p36.31	6146	ribosomal protein L22 (EAP)		L	.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.44delA	1						.						62.0	55.0	57.0					1																	6257785		2203	4300	6503	6180372	SO:0001589	frameshift_variant	6146	exon2			BC058887	CCDS58.1	1p36.31	2011-04-06			ENSG00000116251	ENSG00000116251		"""L ribosomal proteins"""	10315	protein-coding gene	gene with protein product		180474				8395054	Standard	NM_000983		Approved	EAP, L22	uc001amd.3	P35268	OTTHUMG00000000953	ENST00000234875.4:c.44delA	1.37:g.6257785delT	ENSP00000346088:p.Lys16fs	Somatic		Capture	Illumina HiSeq	Phase_I	6180372	NM_000983	B2R495|Q6IBD1	Frame_Shift_Del	DEL	ENST00000234875.4	37	CCDS58.1																																																																																				0.398	RPL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002830.1	NM_000983	
RNF207	388591	broad.mit.edu	37	1	6273195	6273195	+	Missense_Mutation	SNP	C	C	T	rs368780534		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:6273195C>T	ENST00000377939.4	+	16	1731	c.1604C>T	c.(1603-1605)aCg>aTg	p.T535M	RNF207_ENST00000483336.1_3'UTR|RNF207_ENST00000377948.2_3'UTR	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	535						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.T535M(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		AAGCAGATCACGCCCTACGTC	0.607																																					p.T535M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1604T	1						.	C	MET/THR	0,4062		0,0,2031	51.0	56.0	54.0		1604	1.9	1.0	1		54	1,8369		0,1,4184	no	missense	RNF207	NM_207396.2	81	0,1,6215	TT,TC,CC		0.0119,0.0,0.0080	probably-damaging	535/635	6273195	1,12431	2031	4185	6216	6195782	SO:0001583	missense	388591	exon16			AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.1604C>T	1.37:g.6273195C>T	ENSP00000367173:p.Thr535Met	Somatic		Capture	Illumina HiSeq	Phase_I	6195782	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Missense_Mutation	SNP	ENST00000377939.4	37	CCDS59.2	.	.	.	.	.	.	.	.	.	.	C	19.49	3.836814	0.71373	0.0	1.19E-4	ENSG00000158286	ENST00000377939	T	0.18810	2.19	4.89	1.92	0.25849	.	0.256239	0.39615	N	0.001307	T	0.33760	0.0874	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	P	0.60173	0.87	T	0.02574	-1.1139	10	0.59425	D	0.04	-8.1833	7.7807	0.29064	0.0:0.7168:0.1341:0.1491	.	535	Q6ZRF8	RN207_HUMAN	M	535	ENSP00000367173:T535M	ENSP00000367173:T535M	T	+	2	0	RNF207	6195782	0.998000	0.40836	0.968000	0.41197	0.991000	0.79684	3.302000	0.51849	0.113000	0.18004	0.462000	0.41574	ACG		0.607	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
RNF207	388591	broad.mit.edu	37	1	6278397	6278397	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:6278397C>T	ENST00000377939.4	+	17	1828	c.1701C>T	c.(1699-1701)caC>caT	p.H567H	RNF207_ENST00000483336.1_3'UTR|RNF207_ENST00000377948.2_3'UTR	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	567						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.H567H(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		AGAACACGCACGACGACAGCA	0.582																																					p.H567H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1701T	1						.						70.0	81.0	78.0					1																	6278397		2140	4254	6394	6200984	SO:0001819	synonymous_variant	388591	exon17			AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.1701C>T	1.37:g.6278397C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6200984	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Silent	SNP	ENST00000377939.4	37	CCDS59.2																																																																																				0.582	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
ACOT7	11332	broad.mit.edu	37	1	6324710	6324710	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:6324710G>A	ENST00000377855.2	-	9	1236	c.1090C>T	c.(1090-1092)Cgg>Tgg	p.R364W	ACOT7_ENST00000545482.1_Missense_Mutation_p.R249W|ACOT7_ENST00000377845.3_Missense_Mutation_p.R334W|ACOT7_ENST00000608083.1_Missense_Mutation_p.R322W|ACOT7_ENST00000377842.3_Missense_Mutation_p.R313W|ACOT7_ENST00000361521.4_Missense_Mutation_p.R354W	NM_181864.2	NP_863654.1	O00154	BACH_HUMAN	acyl-CoA thioesterase 7	364					coenzyme A biosynthetic process (GO:0015937)|fatty acid catabolic process (GO:0009062)|long-chain fatty-acyl-CoA catabolic process (GO:0036116)|medium-chain fatty acid biosynthetic process (GO:0051792)|medium-chain fatty-acyl-CoA catabolic process (GO:0036114)|palmitic acid biosynthetic process (GO:1900535)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)	carboxylic ester hydrolase activity (GO:0052689)|fatty-acyl-CoA binding (GO:0000062)|long-chain fatty acyl-CoA binding (GO:0036042)|palmitoyl-CoA hydrolase activity (GO:0016290)|protein homodimerization activity (GO:0042803)	p.R354W(1)		kidney(1)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	16	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		TGCAGGTACCGCCCTTTGCCT	0.627																																					p.R364W	GBM(74;673 1226 4974 11850 13190)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1090T	1						.						202.0	140.0	161.0					1																	6324710		2202	4300	6502	6247297	SO:0001583	missense	11332	exon9			AB074417	CCDS65.1, CCDS66.1, CCDS67.1, CCDS30573.1	1p36	2008-08-14			ENSG00000097021	ENSG00000097021		"""Acyl CoA thioesterases"""	24157	protein-coding gene	gene with protein product	"""brain acyl CoA hydrolase"""	602587				10578051, 16103133, 16940157	Standard	XM_005263427		Approved	BACH, ACH1, ACT, CTE-II, LACH1, MGC1126, hBACH	uc001amt.3	O00154	OTTHUMG00000001295	ENST00000377855.2:c.1090C>T	1.37:g.6324710G>A	ENSP00000367086:p.Arg364Trp	Somatic		Capture	Illumina HiSeq	Phase_I	6247297	NM_181864	A8K0K7|A8K232|A8K6B8|A8K837|B3KQ12|O43703|Q53Y78|Q5JYL2|Q5JYL3|Q5JYL4|Q5JYL5|Q5JYL6|Q5TGR4|Q9UJM9|Q9Y539|Q9Y540	Missense_Mutation	SNP	ENST00000377855.2	37	CCDS65.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.309114	0.81247	.	.	ENSG00000097021	ENST00000377855;ENST00000377845;ENST00000377842;ENST00000361521;ENST00000545482	T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59	5.61	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.78246	0.4253	H	0.95679	3.705	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;0.996;0.999	T	0.82772	-0.0292	10	0.87932	D	0	.	10.0614	0.42277	0.0:0.0:0.7511:0.2489	.	354;364;334;313	B3KQ12;O00154;O00154-5;O00154-6	.;BACH_HUMAN;.;.	W	364;334;313;354;249	ENSP00000367086:R364W;ENSP00000367076:R334W;ENSP00000367073:R313W;ENSP00000354615:R354W;ENSP00000439218:R249W	ENSP00000354615:R354W	R	-	1	2	ACOT7	6247297	0.988000	0.35896	0.991000	0.47740	0.991000	0.79684	1.082000	0.30803	2.647000	0.89833	0.563000	0.77884	CGG		0.627	ACOT7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003773.1	NM_007274	
DNAJC11	55735	broad.mit.edu	37	1	6761816	6761816	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:6761816A>G	ENST00000377577.5	-	1	168	c.45T>C	c.(43-45)taT>taC	p.Y15Y	DNAJC11_ENST00000294401.7_Silent_p.Y15Y|DNAJC11_ENST00000377573.5_5'UTR	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	15	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.					extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)		p.Y15Y(2)		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)		GCAACGAGTAATAGTCTTCAT	0.667																																					p.Y15Y												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T45C	1						.						128.0	90.0	103.0					1																	6761816		2203	4300	6503	6684403	SO:0001819	synonymous_variant	55735	exon1			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.45T>C	1.37:g.6761816A>G		Somatic		Capture	Illumina HiSeq	Phase_I	6684403	NM_018198	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Silent	SNP	ENST00000377577.5	37	CCDS87.1																																																																																				0.667	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198	
SLC2A7	155184	broad.mit.edu	37	1	9064868	9064868	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:9064868G>A	ENST00000400906.1	-	11	1262	c.1263C>T	c.(1261-1263)gaC>gaT	p.D421D		NM_207420.2	NP_997303.2	Q6PXP3	GTR7_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 7	421					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)	p.D421D(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(10)|lung(4)|prostate(2)|skin(2)	24	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		GCACTGCCCCGTCCACCATGA	0.652																																					p.D421D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1263T	1						.						76.0	68.0	71.0					1																	9064868		2203	4300	6503	8987455	SO:0001819	synonymous_variant	155184	exon11			AL356306	CCDS98.2	1p36.2	2013-05-22			ENSG00000197241	ENSG00000197241		"""Solute carriers"""	13445	protein-coding gene	gene with protein product	"""intestinal facilitative glucose transporter 7"""	610371				11780753	Standard	NM_207420		Approved	GLUT7	uc009vmo.1	Q6PXP3	OTTHUMG00000057499	ENST00000400906.1:c.1263C>T	1.37:g.9064868G>A		Somatic		Capture	Illumina HiSeq	Phase_I	8987455	NM_207420	A2A333	Silent	SNP	ENST00000400906.1	37	CCDS98.2																																																																																				0.652	SLC2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127768.3	NM_207420	
SLC2A7	155184	broad.mit.edu	37	1	9083095	9083095	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:9083095C>T	ENST00000400906.1	-	3	192	c.193G>A	c.(193-195)Gca>Aca	p.A65T		NM_207420.2	NP_997303.2	Q6PXP3	GTR7_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 7	65					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)	p.A65T(2)		NS(1)|breast(1)|endometrium(4)|large_intestine(10)|lung(4)|prostate(2)|skin(2)	24	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		ATGAATGTTGCGTGTCGCTCA	0.498																																					p.A65T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G193A	1						.						170.0	157.0	161.0					1																	9083095		2203	4300	6503	9005682	SO:0001583	missense	155184	exon3			AL356306	CCDS98.2	1p36.2	2013-05-22			ENSG00000197241	ENSG00000197241		"""Solute carriers"""	13445	protein-coding gene	gene with protein product	"""intestinal facilitative glucose transporter 7"""	610371				11780753	Standard	NM_207420		Approved	GLUT7	uc009vmo.1	Q6PXP3	OTTHUMG00000057499	ENST00000400906.1:c.193G>A	1.37:g.9083095C>T	ENSP00000383698:p.Ala65Thr	Somatic		Capture	Illumina HiSeq	Phase_I	9005682	NM_207420	A2A333	Missense_Mutation	SNP	ENST00000400906.1	37	CCDS98.2	.	.	.	.	.	.	.	.	.	.	C	15.72	2.917421	0.52546	.	.	ENSG00000197241	ENST00000400906	T	0.73789	-0.78	4.68	1.51	0.23008	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.305652	0.30210	N	0.010158	T	0.59500	0.2198	L	0.38175	1.15	0.09310	N	1	B	0.32188	0.359	B	0.31495	0.131	T	0.54695	-0.8255	10	0.72032	D	0.01	.	5.9715	0.19355	0.1497:0.6776:0.0:0.1726	.	65	Q6PXP3	GTR7_HUMAN	T	65	ENSP00000383698:A65T	ENSP00000383698:A65T	A	-	1	0	SLC2A7	9005682	0.000000	0.05858	0.002000	0.10522	0.306000	0.27790	0.526000	0.22971	0.537000	0.28751	0.556000	0.70494	GCA		0.498	SLC2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127768.3	NM_207420	
RCAN3	11123	broad.mit.edu	37	1	24857837	24857837	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:24857837G>A	ENST00000374395.4	+	3	638	c.325G>A	c.(325-327)Gaa>Aaa	p.E109K	RCAN3_ENST00000436717.2_Missense_Mutation_p.E109K|RN7SL857P_ENST00000580228.1_RNA|RCAN3_ENST00000374393.2_Intron|RCAN3_ENST00000412742.2_Missense_Mutation_p.E109K|RCAN3_ENST00000538532.1_Intron	NM_001251978.1|NM_001251979.1|NM_001251984.1	NP_001238907.1|NP_001238908.1|NP_001238913.1	Q9UKA8	RCAN3_HUMAN	RCAN family member 3	109					anatomical structure morphogenesis (GO:0009653)|calcium-mediated signaling (GO:0019722)		RNA binding (GO:0003723)|troponin I binding (GO:0031013)	p.E109K(1)		central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)	7		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14)		AGAACTCCACGAAACAGACTT	0.408																																					p.E109K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G325A	1						.						57.0	60.0	59.0					1																	24857837		2203	4300	6503	24730424	SO:0001583	missense	11123	exon3				CCDS254.1, CCDS57980.1, CCDS57981.1, CCDS57982.1, CCDS72730.1	1p35.3-p33	2008-02-05	2007-06-26	2007-06-26	ENSG00000117602	ENSG00000117602			3042	protein-coding gene	gene with protein product		605860	"""Down syndrome critical region gene 1-like 2"""	DSCR1L2		10756093	Standard	NM_001251984		Approved		uc001bjj.3	Q9UKA8	OTTHUMG00000003298	ENST00000374395.4:c.325G>A	1.37:g.24857837G>A	ENSP00000363516:p.Glu109Lys	Somatic		Capture	Illumina HiSeq	Phase_I	24730424	NM_013441	A4GU14|A4LA69|E3VWE2|E5L4P0|E5L4P7|E7ENV1|E7EWD8|G1FI66|G1FLF0|Q5ECL3|Q5TGC6|Q9NUC8|Q9UKA7	Missense_Mutation	SNP	ENST00000374395.4	37	CCDS254.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.585083	0.86748	.	.	ENSG00000117602	ENST00000374395;ENST00000436717;ENST00000412742	T;T	0.43688	0.97;0.94	5.84	5.84	0.93424	Nucleotide-binding, alpha-beta plait (1);	0.047529	0.85682	D	0.000000	T	0.34600	0.0903	N	0.20530	0.585	0.80722	D	1	P;P;D	0.55800	0.938;0.951;0.973	B;P;P	0.45946	0.218;0.498;0.479	T	0.05162	-1.0902	10	0.10636	T	0.68	-29.9114	20.1454	0.98074	0.0:0.0:1.0:0.0	.	109;109;109	E7ENV1;Q9UKA8-2;Q9UKA8	.;.;RCAN3_HUMAN	K	109	ENSP00000363516:E109K;ENSP00000414447:E109K	ENSP00000363516:E109K	E	+	1	0	RCAN3	24730424	1.000000	0.71417	0.839000	0.33178	0.993000	0.82548	9.171000	0.94802	2.748000	0.94277	0.650000	0.86243	GAA		0.408	RCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009176.2		
SRRM1	10250	broad.mit.edu	37	1	24995634	24995634	+	Missense_Mutation	SNP	G	G	A	rs147911034		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:24995634G>A	ENST00000323848.9	+	14	2075	c.1760G>A	c.(1759-1761)cGt>cAt	p.R587H	SRRM1_ENST00000374389.4_Missense_Mutation_p.R596H|snoU13_ENST00000459464.1_RNA|SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000447431.2_Missense_Mutation_p.R599H	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	587	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.R587H(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		CCTCCCCCACGTCGGCGCTCA	0.468													G|||	1	0.000199681	0.0	0.0	5008	,	,		17792	0.0		0.001	False		,,,				2504	0.0				p.R587H	Ovarian(68;897 1494 3282 17478)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1760A	1						.						43.0	45.0	45.0					1																	24995634		2203	4300	6503	24868221	SO:0001583	missense	10250	exon14			AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"""Ser/Arg-related nuclear matrix protein"", ""plenty of prolines 101-like"""	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.1760G>A	1.37:g.24995634G>A	ENSP00000326261:p.Arg587His	Somatic		Capture	Illumina HiSeq	Phase_I	24868221	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.82	3.482873	0.63962	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.37058	1.22;1.22;1.22	5.97	5.97	0.96955	.	0.000000	0.64402	D	0.000009	T	0.57066	0.2028	L	0.46157	1.445	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.78314	0.991;0.98	T	0.54649	-0.8262	10	0.72032	D	0.01	-0.9983	20.4387	0.99107	0.0:0.0:1.0:0.0	.	599;587	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	H	587;599;596	ENSP00000326261:R587H;ENSP00000391430:R599H;ENSP00000363510:R596H	ENSP00000326261:R587H	R	+	2	0	SRRM1	24868221	1.000000	0.71417	0.369000	0.25952	0.614000	0.37383	7.005000	0.76323	2.836000	0.97738	0.655000	0.94253	CGT		0.468	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839	
SRRM1	10250	broad.mit.edu	37	1	24995922	24995922	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:24995922C>T	ENST00000323848.9	+	14	2363	c.2048C>T	c.(2047-2049)tCg>tTg	p.S683L	SRRM1_ENST00000374389.4_Missense_Mutation_p.S692L|snoU13_ENST00000459464.1_RNA|SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000447431.2_Missense_Mutation_p.S695L	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	683	Arg-rich.|Necessary for speckles and matrix localization.|Pro-rich.|Ser-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.S683L(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	36		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0422)|OV - Ovarian serous cystadenocarcinoma(117;1.01e-24)|Colorectal(126;5.95e-08)|COAD - Colon adenocarcinoma(152;3.24e-06)|GBM - Glioblastoma multiforme(114;0.000148)|BRCA - Breast invasive adenocarcinoma(304;0.00177)|KIRC - Kidney renal clear cell carcinoma(1967;0.00348)|STAD - Stomach adenocarcinoma(196;0.00483)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		AAACGGCATTCGCCCTCACCA	0.577																																					p.S683L	Ovarian(68;897 1494 3282 17478)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2048T	1						.						76.0	72.0	73.0					1																	24995922		2203	4300	6503	24868509	SO:0001583	missense	10250	exon14			AF048977	CCDS255.1	1p36	2010-04-22			ENSG00000133226	ENSG00000133226			16638	protein-coding gene	gene with protein product	"""Ser/Arg-related nuclear matrix protein"", ""plenty of prolines 101-like"""	605975				9531537	Standard	NM_005839		Approved	SRM160, POP101, MGC39488	uc001bjm.3	Q8IYB3	OTTHUMG00000003320	ENST00000323848.9:c.2048C>T	1.37:g.24995922C>T	ENSP00000326261:p.Ser683Leu	Somatic		Capture	Illumina HiSeq	Phase_I	24868509	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520014	0.85495	.	.	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.58210	0.35;0.35;0.35	5.85	5.85	0.93711	.	0.000000	0.53938	D	0.000060	T	0.72269	0.3439	M	0.62723	1.935	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.75484	0.986;0.953	T	0.72633	-0.4234	10	0.72032	D	0.01	-0.8003	20.1542	0.98100	0.0:1.0:0.0:0.0	.	695;683	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	L	683;695;692	ENSP00000326261:S683L;ENSP00000391430:S695L;ENSP00000363510:S692L	ENSP00000326261:S683L	S	+	2	0	SRRM1	24868509	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.904000	0.75708	2.767000	0.95098	0.563000	0.77884	TCG		0.577	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839	
SLC9A1	6548	broad.mit.edu	37	1	27427700	27427700	+	Missense_Mutation	SNP	C	C	T	rs201478450		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:27427700C>T	ENST00000263980.3	-	11	2679	c.2104G>A	c.(2104-2106)Ggc>Agc	p.G702S	SLC9A1_ENST00000545949.1_Missense_Mutation_p.G363S|SLC9A1_ENST00000490329.1_5'Flank	NM_003047.4	NP_003038.2	P19634	SL9A1_HUMAN	solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1	702					carbohydrate metabolic process (GO:0005975)|cardiac muscle cell differentiation (GO:0055007)|cell growth (GO:0016049)|cellular response to acidic pH (GO:0071468)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|hydrogen ion transmembrane transport (GO:1902600)|ion transport (GO:0006811)|negative regulation of apoptotic process (GO:0043066)|neuron death (GO:0070997)|positive regulation of action potential (GO:0045760)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial membrane permeability (GO:0035794)|protein oligomerization (GO:0051259)|regulation of intracellular pH (GO:0051453)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of the force of heart contraction (GO:0002026)|response to acidic pH (GO:0010447)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|sodium ion export (GO:0071436)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium-dependent protein binding (GO:0048306)|sodium:proton antiporter activity (GO:0015385)|solute:proton antiporter activity (GO:0015299)	p.G702S(1)		central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27				UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;2.19e-50)|OV - Ovarian serous cystadenocarcinoma(117;1.8e-29)|Colorectal(126;7.61e-09)|COAD - Colon adenocarcinoma(152;9.32e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000521)|KIRC - Kidney renal clear cell carcinoma(1967;0.00079)|STAD - Stomach adenocarcinoma(196;0.00125)|READ - Rectum adenocarcinoma(331;0.046)	Amiloride(DB00594)	TTACCTGAGCCGATGCGGGCC	0.637													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18515	0.0		0.0	False		,,,				2504	0.0				p.G702S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2104A	1						.	C	SER/GLY	1,4405	2.1+/-5.4	0,1,2202	45.0	46.0	46.0		2104	4.3	1.0	1		46	1,8599	1.2+/-3.3	0,1,4299	no	missense	SLC9A1	NM_003047.3	56	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign	702/816	27427700	2,13004	2203	4300	6503	27300287	SO:0001583	missense	6548	exon11			M81768	CCDS295.1	1p36.1-p35	2014-06-13	2012-03-22		ENSG00000090020	ENSG00000090020		"""Solute carriers"""	11071	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 143"""	107310	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 1 (antiporter, Na+/H+, amiloride sensitive)"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 1"""	APNH, NHE1		8283968	Standard	NM_003047		Approved	PPP1R143	uc001bnm.4	P19634	OTTHUMG00000004271	ENST00000263980.3:c.2104G>A	1.37:g.27427700C>T	ENSP00000263980:p.Gly702Ser	Somatic		Capture	Illumina HiSeq	Phase_I	27300287	NM_003047	B1ALD6|D3DPL4|Q96EM2	Missense_Mutation	SNP	ENST00000263980.3	37	CCDS295.1	20	0.009157509157509158	7	0.014227642276422764	5	0.013812154696132596	4	0.006993006993006993	4	0.005277044854881266	C	17.24	3.338499	0.60963	2.27E-4	1.16E-4	ENSG00000090020	ENST00000263980;ENST00000374089;ENST00000545949;ENST00000447808	T;T	0.46063	0.88;1.49	5.28	4.35	0.52113	.	1.042870	0.07449	N	0.898644	T	0.22666	0.0547	N	0.19112	0.55	0.46586	D	0.999115	B	0.15473	0.013	B	0.11329	0.006	T	0.02208	-1.1195	10	0.09084	T	0.74	.	14.3553	0.66733	0.0:0.928:0.0:0.072	.	702	P19634	SL9A1_HUMAN	S	702;206;363;123	ENSP00000263980:G702S;ENSP00000445520:G363S	ENSP00000263980:G702S	G	-	1	0	SLC9A1	27300287	1.000000	0.71417	0.994000	0.49952	0.944000	0.59088	5.131000	0.64751	2.763000	0.94921	0.650000	0.86243	GGC		0.637	SLC9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012336.2	NM_003047	
FCN3	8547	broad.mit.edu	37	1	27695957	27695957	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:27695957T>C	ENST00000270879.4	-	8	675	c.670A>G	c.(670-672)Agc>Ggc	p.S224G	MAP3K6_ENST00000493901.1_5'Flank|MAP3K6_ENST00000357582.2_5'Flank|MAP3K6_ENST00000374040.3_5'Flank|FCN3_ENST00000354982.2_Missense_Mutation_p.S213G	NM_003665.2	NP_003656.2	O75636	FCN3_HUMAN	ficolin (collagen/fibrinogen domain containing) 3	224	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)	p.S224G(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	7		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;1.42e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		CTGTGGAGGCTCAGGGAATCC	0.562																																					p.S213G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A637G	1						.						65.0	62.0	63.0					1																	27695957		2203	4300	6503	27568544	SO:0001583	missense	8547	exon7			D88587	CCDS300.1, CCDS301.1	1p36.11	2014-09-17	2013-09-12		ENSG00000142748	ENSG00000142748		"""Fibrinogen C domain containing"""	3625	protein-coding gene	gene with protein product	"""Hakata antigen"""	604973	"""ficolin (collagen/fibrinogen domain-containing) 3 (Hakata antigen)"""			9694814, 10330454	Standard	NM_003665		Approved	FCNH, HAKA1	uc001boa.3	O75636	OTTHUMG00000005722	ENST00000270879.4:c.670A>G	1.37:g.27695957T>C	ENSP00000270879:p.Ser224Gly	Somatic		Capture	Illumina HiSeq	Phase_I	27568544	NM_173452	Q6IBJ5|Q8WW86	Missense_Mutation	SNP	ENST00000270879.4	37	CCDS300.1	.	.	.	.	.	.	.	.	.	.	T	13.62	2.290831	0.40494	.	.	ENSG00000142748	ENST00000270879;ENST00000354982	T;T	0.77489	-1.1;-1.1	5.0	5.0	0.66597	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.352632	0.22824	N	0.055188	T	0.72391	0.3454	L	0.42686	1.345	0.80722	D	1	B;B	0.20671	0.047;0.047	B;B	0.28305	0.035;0.088	T	0.70226	-0.4930	10	0.49607	T	0.09	.	12.7131	0.57100	0.0:0.0:0.0:1.0	.	213;224	Q6UXM4;O75636	.;FCN3_HUMAN	G	224;213	ENSP00000270879:S224G;ENSP00000347077:S213G	ENSP00000270879:S224G	S	-	1	0	FCN3	27568544	0.002000	0.14202	0.985000	0.45067	0.279000	0.26890	0.107000	0.15375	2.102000	0.63906	0.459000	0.35465	AGC		0.562	FCN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000015667.1		
AHDC1	27245	broad.mit.edu	37	1	27875813	27875813	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:27875813G>A	ENST00000247087.5	-	5	3410	c.2814C>T	c.(2812-2814)tgC>tgT	p.C938C	AHDC1_ENST00000374011.2_Silent_p.C938C			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	938							DNA binding (GO:0003677)	p.C938C(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)		CGGCTGCCCGGCAGTCTGAAG	0.682																																					p.C938C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2814T	1						.						44.0	52.0	49.0					1																	27875813		2203	4300	6503	27748400	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.2814C>T	1.37:g.27875813G>A		Somatic		Capture	Illumina HiSeq	Phase_I	27748400	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Silent	SNP	ENST00000247087.5	37	CCDS30652.1																																																																																				0.682	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3		
AHDC1	27245	broad.mit.edu	37	1	27876033	27876033	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:27876033C>T	ENST00000247087.5	-	5	3190	c.2594G>A	c.(2593-2595)cGg>cAg	p.R865Q	AHDC1_ENST00000374011.2_Missense_Mutation_p.R865Q			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	865							DNA binding (GO:0003677)	p.R865Q(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)		CGATGCCTTCCGGGACTCTGG	0.657																																					p.R865Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2594A	1						.						35.0	39.0	38.0					1																	27876033		2203	4299	6502	27748620	SO:0001583	missense	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.2594G>A	1.37:g.27876033C>T	ENSP00000247087:p.Arg865Gln	Somatic		Capture	Illumina HiSeq	Phase_I	27748620	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Missense_Mutation	SNP	ENST00000247087.5	37	CCDS30652.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.230465	0.79688	.	.	ENSG00000126705	ENST00000247087;ENST00000374011	T;T	0.55234	0.53;0.53	5.77	5.77	0.91146	.	0.196285	0.33075	N	0.005307	T	0.42314	0.1197	N	0.24115	0.695	0.48830	D	0.999718	P	0.42161	0.772	B	0.36922	0.236	T	0.47812	-0.9088	10	0.72032	D	0.01	-12.6484	18.7552	0.91830	0.0:1.0:0.0:0.0	.	865	Q5TGY3	AHDC1_HUMAN	Q	865	ENSP00000247087:R865Q;ENSP00000363123:R865Q	ENSP00000247087:R865Q	R	-	2	0	AHDC1	27748620	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.148000	0.58085	2.723000	0.93209	0.655000	0.94253	CGG		0.657	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3		
SMPDL3B	27293	broad.mit.edu	37	1	28285041	28285041	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:28285041C>T	ENST00000373894.3	+	8	1251	c.1060C>T	c.(1060-1062)Cgc>Tgc	p.R354C	RP11-460I13.2_ENST00000448015.1_RNA|SMPDL3B_ENST00000549094.1_Missense_Mutation_p.R306C|XKR8_ENST00000373884.5_5'Flank	NM_014474.2	NP_055289.2	Q92485	ASM3B_HUMAN	sphingomyelin phosphodiesterase, acid-like 3B	354					sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)	p.R354C(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	16		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000431)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;5.68e-24)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00587)|READ - Rectum adenocarcinoma(331;0.055)		GGGGACGCCGCGCTGGGAGCT	0.627																																					p.R354C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1060T	1						.						50.0	54.0	53.0					1																	28285041		2203	4300	6503	28157628	SO:0001583	missense	27293	exon8			Y08134	CCDS30655.1, CCDS30656.1	1p35.3	2008-02-05			ENSG00000130768	ENSG00000130768			21416	protein-coding gene	gene with protein product							Standard	NM_014474		Approved	ASML3B	uc001bpg.3	Q92485	OTTHUMG00000003910	ENST00000373894.3:c.1060C>T	1.37:g.28285041C>T	ENSP00000363001:p.Arg354Cys	Somatic		Capture	Illumina HiSeq	Phase_I	28157628	NM_014474	B7ZB35|Q5T0Z0|Q96CB7	Missense_Mutation	SNP	ENST00000373894.3	37	CCDS30655.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.028557	0.54790	.	.	ENSG00000130768	ENST00000373894;ENST00000549094;ENST00000412515	D;D	0.89810	-2.57;-2.57	5.09	-2.87	0.05700	.	0.885835	0.09827	N	0.750775	D	0.90508	0.7026	M	0.75447	2.3	0.09310	N	1	D;D	0.76494	0.999;0.999	P;P	0.59221	0.854;0.634	T	0.81638	-0.0842	10	0.56958	D	0.05	-0.411	5.4029	0.16306	0.5335:0.2756:0.117:0.0739	.	306;354	F8VWW8;Q92485	.;ASM3B_HUMAN	C	354;306;306	ENSP00000363001:R354C;ENSP00000449450:R306C	ENSP00000363001:R354C	R	+	1	0	SMPDL3B	28157628	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.185000	0.09684	-0.313000	0.08728	-0.221000	0.12465	CGC		0.627	SMPDL3B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011170.1	NM_014474	
RCC1	1104	broad.mit.edu	37	1	28861881	28861881	+	Missense_Mutation	SNP	G	G	A	rs528320406		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:28861881G>A	ENST00000373833.6	+	9	935	c.650G>A	c.(649-651)cGg>cAg	p.R217Q	RCC1_ENST00000429051.1_3'UTR|RCC1_ENST00000373832.1_Missense_Mutation_p.R217Q|RCC1_ENST00000398958.2_Missense_Mutation_p.R217Q|RCC1_ENST00000373831.3_Missense_Mutation_p.R248Q			P18754	RCC1_HUMAN	regulator of chromosome condensation 1	217					chromosome segregation (GO:0007059)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|positive regulation of Ran GTPase activity (GO:0032853)|regulation of mitosis (GO:0007088)|spindle assembly (GO:0051225)|viral process (GO:0016032)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosomal DNA binding (GO:0031492)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.R217Q(1)		breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000318)|all_lung(284;0.000434)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.00989)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)|Medulloblastoma(700;0.123)		Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|STAD - Stomach adenocarcinoma(196;0.00299)|KIRC - Kidney renal clear cell carcinoma(1967;0.0101)|BRCA - Breast invasive adenocarcinoma(304;0.022)|READ - Rectum adenocarcinoma(331;0.0649)		CGTGGTGGCCGGCAAGGCCTC	0.602																																					p.R217Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G650A	1						.						69.0	66.0	67.0					1																	28861881		2203	4300	6503	28734468	SO:0001583	missense	1104	exon6			X12654	CCDS323.1, CCDS41295.1	1p35.3	2008-08-18	2005-05-09	2005-05-09	ENSG00000180198	ENSG00000180198			1913	protein-coding gene	gene with protein product		179710	"""chromosome condensation 1"""	CHC1		7851910	Standard	NM_001048199		Approved		uc001bqf.2	P18754	OTTHUMG00000003645	ENST00000373833.6:c.650G>A	1.37:g.28861881G>A	ENSP00000362939:p.Arg217Gln	Somatic		Capture	Illumina HiSeq	Phase_I	28734468	NM_001269	Q16269|Q6NT97	Missense_Mutation	SNP	ENST00000373833.6	37	CCDS323.1	.	.	.	.	.	.	.	.	.	.	G	35	5.571770	0.96553	.	.	ENSG00000180198	ENST00000398958;ENST00000427469;ENST00000434290;ENST00000373833;ENST00000419074;ENST00000373832;ENST00000373831;ENST00000411533;ENST00000430407	D;D;D;D;D;D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87	5.56	5.56	0.83823	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.099752	0.64402	D	0.000003	D	0.93051	0.7788	M	0.85542	2.76	0.80722	D	1	D;D;D	0.89917	0.965;1.0;1.0	P;D;D	0.71870	0.495;0.975;0.949	D	0.93498	0.6842	10	0.87932	D	0	-19.5465	18.2548	0.90016	0.0:0.0:1.0:0.0	.	248;234;217	P18754-2;E9PAT9;P18754	.;.;RCC1_HUMAN	Q	217;217;253;217;217;217;248;234;217	ENSP00000381931:R217Q;ENSP00000402740:R217Q;ENSP00000405258:R253Q;ENSP00000362939:R217Q;ENSP00000402260:R217Q;ENSP00000362938:R217Q;ENSP00000362937:R248Q;ENSP00000413644:R234Q;ENSP00000394650:R217Q	ENSP00000362937:R248Q	R	+	2	0	RCC1	28734468	1.000000	0.71417	0.995000	0.50966	0.939000	0.58152	6.108000	0.71522	2.890000	0.99128	0.655000	0.94253	CGG		0.602	RCC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010323.3	NM_001269	
PTPRU	10076	broad.mit.edu	37	1	29630439	29630439	+	Missense_Mutation	SNP	G	G	A	rs200085066		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:29630439G>A	ENST00000345512.3	+	17	2708	c.2579G>A	c.(2578-2580)cGg>cAg	p.R860Q	PTPRU_ENST00000460170.2_Missense_Mutation_p.R850Q|PTPRU_ENST00000323874.8_Missense_Mutation_p.R850Q|PTPRU_ENST00000428026.2_Missense_Mutation_p.R850Q|PTPRU_ENST00000356870.3_Missense_Mutation_p.R850Q|PTPRU_ENST00000415600.2_3'UTR|PTPRU_ENST00000373779.3_Missense_Mutation_p.R850Q	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	860	Mediates interaction with CTNNB1. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R860Q(1)		breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		CCCTGTGGCCGGAAGGGCTCC	0.657													G|||	1	0.000199681	0.0	0.0014	5008	,	,		16927	0.0		0.0	False		,,,				2504	0.0				p.R860Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2579A	1						.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	41.0	46.0	44.0		2549,2579,2549,2549	4.1	1.0	1		44	1,8597		0,1,4298	no	missense,missense,missense,missense	PTPRU	NM_001195001.1,NM_005704.4,NM_133177.3,NM_133178.3	43,43,43,43	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign	850/1434,860/1447,850/1441,850/1437	29630439	1,13003	2203	4299	6502	29503026	SO:0001583	missense	10076	exon17			U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9683	protein-coding gene	gene with protein product	"""pi R-PTP-Psi"""	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.2579G>A	1.37:g.29630439G>A	ENSP00000334941:p.Arg860Gln	Somatic		Capture	Illumina HiSeq	Phase_I	29503026	NM_005704	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	37	CCDS334.1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.580136	0.65992	0.0	1.16E-4	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.32272	1.5;1.52;1.52;1.52;1.46;1.52	4.12	4.12	0.48240	.	0.000000	0.85682	D	0.000000	T	0.47135	0.1429	L	0.50333	1.59	0.49389	D	0.999786	D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0	D;D;D;P;P	0.64410	0.925;0.925;0.925;0.842;0.83	T	0.33954	-0.9848	9	.	.	.	.	16.6233	0.84935	0.0:0.0:1.0:0.0	.	850;850;850;850;860	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	Q	860;850;850;850;850;850	ENSP00000334941:R860Q;ENSP00000362884:R850Q;ENSP00000349333:R850Q;ENSP00000314987:R850Q;ENSP00000392332:R850Q;ENSP00000432906:R850Q	.	R	+	2	0	PTPRU	29503026	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.504000	0.97986	2.588000	0.87417	0.555000	0.69702	CGG		0.657	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1		
SDC3	9672	broad.mit.edu	37	1	31349607	31349607	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:31349607G>A	ENST00000339394.6	-	3	836	c.662C>T	c.(661-663)aCg>aTg	p.T221M	SDC3_ENST00000336798.7_Missense_Mutation_p.T163M|SDC3_ENST00000471567.1_5'Flank	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	221	Ser/Thr-rich (mucin-like).				carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.T221K(1)|p.T221M(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		GGCCCGTGCCGTAGCCACTGT	0.672																																					p.T221M												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C662T	1						.						19.0	23.0	22.0					1																	31349607		2201	4295	6496	31122194	SO:0001583	missense	9672	exon3			AF248634	CCDS30661.1	1p35.2	2013-09-19	2007-02-15		ENSG00000162512	ENSG00000162512		"""Proteoglycans / Cell Surface : Syndecans"""	10660	protein-coding gene	gene with protein product	"""syndecan proteoglycan 3"""	186357	"""syndecan 3 (N-syndecan)"""			1556152, 11527150	Standard	NM_014654		Approved	N-syndecan, SYND3	uc001bse.2	O75056	OTTHUMG00000043646	ENST00000339394.6:c.662C>T	1.37:g.31349607G>A	ENSP00000344468:p.Thr221Met	Somatic		Capture	Illumina HiSeq	Phase_I	31122194	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Missense_Mutation	SNP	ENST00000339394.6	37	CCDS30661.1	.	.	.	.	.	.	.	.	.	.	G	9.956	1.221430	0.22457	.	.	ENSG00000162512	ENST00000336798;ENST00000339394	T;T	0.39229	1.09;1.13	4.99	4.04	0.47022	.	0.086763	0.48767	D	0.000180	T	0.42966	0.1226	N	0.24115	0.695	0.32061	N	0.595669	D;D	0.76494	0.999;0.998	P;P	0.60345	0.873;0.807	T	0.53315	-0.8456	10	0.66056	D	0.02	-5.0362	9.009	0.36129	0.0:0.1436:0.5632:0.2931	.	221;163	O75056;D3DPN2	SDC3_HUMAN;.	M	163;221	ENSP00000338346:T163M;ENSP00000344468:T221M	ENSP00000338346:T163M	T	-	2	0	SDC3	31122194	0.997000	0.39634	0.750000	0.31169	0.013000	0.08279	2.632000	0.46511	1.047000	0.40274	0.462000	0.41574	ACG		0.672	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654	
BAI2	576	broad.mit.edu	37	1	32196501	32196501	+	Missense_Mutation	SNP	G	G	A	rs146789434		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:32196501G>A	ENST00000373658.3	-	29	4621	c.4280C>T	c.(4279-4281)cCg>cTg	p.P1427L	BAI2_ENST00000398547.1_Missense_Mutation_p.P1360L|BAI2_ENST00000398556.3_Missense_Mutation_p.P1342L|BAI2_ENST00000398538.1_Missense_Mutation_p.P1415L|BAI2_ENST00000373655.2_Missense_Mutation_p.P1427L|BAI2_ENST00000440175.2_Missense_Mutation_p.P1036L|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000527361.1_Missense_Mutation_p.P1394L|BAI2_ENST00000398542.1_Missense_Mutation_p.P1327L|BAI2_ENST00000257070.4_Missense_Mutation_p.P1394L	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1427	Poly-Pro.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P1427L(1)		breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GGGTGTCGGCGGTGGCGGTTG	0.677																																					p.P1427L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4280T	1						.						35.0	49.0	44.0					1																	32196501		2203	4300	6503	31969088	SO:0001583	missense	576	exon29			AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.4280C>T	1.37:g.32196501G>A	ENSP00000362762:p.Pro1427Leu	Somatic		Capture	Illumina HiSeq	Phase_I	31969088	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	.	.	.	.	.	.	.	.	.	.	G	15.19	2.760827	0.49468	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538	T;T;T;T;T;T;T;T;T	0.46063	1.55;1.76;0.92;0.92;1.93;0.88;0.88;1.58;0.95	4.69	3.76	0.43208	.	0.202043	0.25786	N	0.028304	T	0.56426	0.1984	L	0.52905	1.665	0.52501	D	0.999956	D;B;D;B;D;B;B	0.69078	0.997;0.443;0.968;0.248;0.981;0.315;0.023	D;B;B;B;P;B;B	0.64144	0.922;0.186;0.291;0.018;0.485;0.09;0.005	T	0.60786	-0.7194	10	0.66056	D	0.02	.	14.1982	0.65684	0.0:0.0:0.8491:0.1509	.	1394;1415;1036;1342;1427;1427;1415	O60241-4;O60241-3;B4DKC3;A2A3C6;O60241-2;O60241;A2A3C2	.;.;.;.;.;BAI2_HUMAN;.	L	1342;1360;1427;1427;1327;1394;1394;1036;1415	ENSP00000381564:P1342L;ENSP00000381555:P1360L;ENSP00000362762:P1427L;ENSP00000362759:P1427L;ENSP00000381550:P1327L;ENSP00000257070:P1394L;ENSP00000435397:P1394L;ENSP00000391071:P1036L;ENSP00000381548:P1415L	ENSP00000257070:P1394L	P	-	2	0	BAI2	31969088	0.984000	0.35163	0.866000	0.34008	0.781000	0.44180	1.914000	0.39966	1.305000	0.44909	0.655000	0.94253	CCG		0.677	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
BAI2	576	broad.mit.edu	37	1	32205597	32205597	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:32205597C>T	ENST00000373658.3	-	14	2438	c.2097G>A	c.(2095-2097)gaG>gaA	p.E699E	BAI2_ENST00000398547.1_Silent_p.E632E|BAI2_ENST00000398556.3_Silent_p.E647E|BAI2_ENST00000398538.1_Silent_p.E687E|BAI2_ENST00000373655.2_Silent_p.E699E|BAI2_ENST00000440175.2_Silent_p.E341E|BAI2_ENST00000527361.1_Silent_p.E699E|BAI2_ENST00000398542.1_Silent_p.E632E|BAI2_ENST00000257070.4_Silent_p.E699E	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	699					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.E699E(1)		breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GAATGAAGTCCTCCACGACAC	0.587																																					p.E699E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2097A	1						.						91.0	90.0	90.0					1																	32205597		2203	4300	6503	31978184	SO:0001819	synonymous_variant	576	exon14			AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.2097G>A	1.37:g.32205597C>T		Somatic		Capture	Illumina HiSeq	Phase_I	31978184	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Silent	SNP	ENST00000373658.3	37	CCDS346.2																																																																																				0.587	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
LCK	3932	broad.mit.edu	37	1	32742272	32742272	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:32742272C>T	ENST00000336890.5	+	9	987	c.849C>T	c.(847-849)gaC>gaT	p.D283D	LCK_ENST00000333070.4_Silent_p.D283D|LCK_ENST00000373564.3_Silent_p.D290D	NM_005356.3	NP_005347.3	P06239	LCK_HUMAN	LCK proto-oncogene, Src family tyrosine kinase	283	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			PDAFL -> AGRLP (in Ref. 1; CAA28691). {ECO:0000305}.	activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|aging (GO:0007568)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular zinc ion homeostasis (GO:0006882)|dephosphorylation (GO:0016311)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hemopoiesis (GO:0030097)|innate immune response (GO:0045087)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of gene expression (GO:0010628)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|positive regulation of uterine smooth muscle contraction (GO:0070474)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of defense response to virus by virus (GO:0050690)|regulation of lymphocyte activation (GO:0051249)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to zinc ion (GO:0010043)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|pericentriolar material (GO:0000242)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|ATP binding (GO:0005524)|ATPase binding (GO:0051117)|CD4 receptor binding (GO:0042609)|CD8 receptor binding (GO:0042610)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine kinase activity (GO:0004713)|SH2 domain binding (GO:0042169)	p.D283D(1)|p.D290D(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.212)			Dasatinib(DB01254)|Ponatinib(DB08901)	TGTCCCCGGACGCCTTCCTGG	0.622			T	TRB@	T-ALL																																p.D283D			Dom	yes		1	1p35-p34.3	3932	lymphocyte-specific protein tyrosine kinase		L	.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C849T	1						.						82.0	69.0	73.0					1																	32742272		2203	4300	6503	32514859	SO:0001819	synonymous_variant	3932	exon9			M36881	CCDS359.1	1p34.3	2014-09-17	2014-06-25		ENSG00000182866	ENSG00000182866	2.7.10.1	"""SH2 domain containing"""	6524	protein-coding gene	gene with protein product		153390	"""lymphocyte-specific protein tyrosine kinase"""			2787474	Standard	XM_005270862		Approved		uc001buy.3	P06239	OTTHUMG00000007463	ENST00000336890.5:c.849C>T	1.37:g.32742272C>T		Somatic		Capture	Illumina HiSeq	Phase_I	32514859	NM_001042771	D3DPP8|P07100|Q12850|Q13152|Q5TDH8|Q5TDH9|Q7RTZ3|Q96DW4|Q9NYT8	Silent	SNP	ENST00000336890.5	37	CCDS359.1																																																																																				0.622	LCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019616.4	NM_005356	
SYNC	81493	broad.mit.edu	37	1	33160506	33160506	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:33160506A>G	ENST00000409190.3	-	2	1651	c.1193T>C	c.(1192-1194)cTt>cCt	p.L398P	SYNC_ENST00000373484.3_Missense_Mutation_p.L398P	NM_030786.2	NP_110413	Q9H7C4	SYNCI_HUMAN	syncoilin, intermediate filament protein	398	Coil 2.				intermediate filament-based process (GO:0045103)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural molecule activity (GO:0005198)	p.L67P(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						TTGCCTCACAAGTGCGATCTG	0.552																																					p.L398P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1193C	1						.						267.0	269.0	269.0					1																	33160506		2203	4300	6503	32933093	SO:0001583	missense	81493	exon2			AK024707	CCDS367.2, CCDS53294.1	1p35.1	2013-01-16	2008-09-19	2008-09-19	ENSG00000162520	ENSG00000162520		"""Intermediate filaments type III"""	28897	protein-coding gene	gene with protein product		611750	"""syncoilin, intermediate filament 1"""	SYNC1		11053421	Standard	NM_030786		Approved	SYNCOILIN	uc001bvt.2	Q9H7C4	OTTHUMG00000008087	ENST00000409190.3:c.1193T>C	1.37:g.33160506A>G	ENSP00000386439:p.Leu398Pro	Somatic		Capture	Illumina HiSeq	Phase_I	32933093	NM_001161708	B4DNK8|B4DY58|C9IY41	Missense_Mutation	SNP	ENST00000409190.3	37	CCDS367.2	.	.	.	.	.	.	.	.	.	.	A	16.95	3.262936	0.59431	.	.	ENSG00000162520	ENST00000373484;ENST00000409190	D;D	0.88509	-2.39;-2.39	4.3	3.07	0.35406	Filament (1);	0.000000	0.64402	D	0.000001	D	0.88680	0.6502	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.991;0.993	D	0.87581	0.2484	10	0.49607	T	0.09	-3.971	9.1622	0.37030	0.8374:0.0:0.0:0.1626	.	398;398	Q9H7C4-2;Q9H7C4	.;SYNCI_HUMAN	P	398	ENSP00000362583:L398P;ENSP00000386439:L398P	ENSP00000362583:L398P	L	-	2	0	SYNC	32933093	0.999000	0.42202	0.840000	0.33206	0.989000	0.77384	4.488000	0.60300	1.732000	0.51606	0.402000	0.26972	CTT		0.552	SYNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022129.3	NM_030786	
KIAA1522	57648	broad.mit.edu	37	1	33236769	33236769	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:33236769C>T	ENST00000373480.1	+	6	1915	c.1812C>T	c.(1810-1812)caC>caT	p.H604H	KIAA1522_ENST00000373481.3_Silent_p.H615H|KIAA1522_ENST00000294521.3_Intron|KIAA1522_ENST00000401073.2_Silent_p.H663H	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	604	Pro-rich.							p.H663H(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				TACCTCCTCACCCCAAGGTGC	0.637																																					p.H604H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1812T	1						.						77.0	83.0	81.0					1																	33236769		1924	4120	6044	33009356	SO:0001819	synonymous_variant	57648	exon6			AL713671	CCDS41298.1, CCDS55588.1, CCDS55589.1	1p35.1	2009-02-18			ENSG00000162522	ENSG00000162522			29301	protein-coding gene	gene with protein product						10819331	Standard	NM_020888		Approved		uc001bvu.1	Q9P206	OTTHUMG00000008088	ENST00000373480.1:c.1812C>T	1.37:g.33236769C>T		Somatic		Capture	Illumina HiSeq	Phase_I	33009356	NM_001198972	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Silent	SNP	ENST00000373480.1	37	CCDS55588.1																																																																																				0.637	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1		
TMEM54	113452	broad.mit.edu	37	1	33363727	33363727	+	Splice_Site	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:33363727C>A	ENST00000373463.3	-	2	329	c.210G>T	c.(208-210)gtG>gtT	p.V70V	TMEM54_ENST00000329151.5_Splice_Site_p.V70V|TMEM54_ENST00000475208.1_5'UTR	NM_033504.2	NP_277039.1	Q969K7	TMM54_HUMAN	transmembrane protein 54	70						integral component of membrane (GO:0016021)		p.V70V(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CTGGCCATACCACGATGGCGG	0.612																																					p.V70V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G210T	1						.						86.0	65.0	72.0					1																	33363727		2203	4300	6503	33136314	SO:0001630	splice_region_variant	113452	exon2				CCDS371.1	1p35-p34	2008-02-05			ENSG00000121900	ENSG00000121900			24143	protein-coding gene	gene with protein product						9500206	Standard	NM_033504		Approved	CAC-1	uc001bwi.1	Q969K7	OTTHUMG00000004016	ENST00000373463.3:c.210+1G>T	1.37:g.33363727C>A		Somatic		Capture	Illumina HiSeq	Phase_I	33136314	NM_033504	Q6UV18|Q8IVD0|Q9UM12	Silent	SNP	ENST00000373463.3	37	CCDS371.1																																																																																				0.612	TMEM54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011474.1	NM_033504	Silent
CSMD2	114784	broad.mit.edu	37	1	34401390	34401390	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:34401390G>A	ENST00000373381.4	-	4	859	c.683C>T	c.(682-684)aCg>aTg	p.T228M		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	188	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T188M(2)		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)				GAAGTCCCACGTGGCGCTGTT	0.627																																					p.T188M												.	.	2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.C563T	1						.						65.0	59.0	61.0					1																	34401390		2203	4300	6503	34173977	SO:0001583	missense	114784	exon4			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.683C>T	1.37:g.34401390G>A	ENSP00000362479:p.Thr228Met	Somatic		Capture	Illumina HiSeq	Phase_I	34173977	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	37		.	.	.	.	.	.	.	.	.	.	G	15.57	2.873126	0.51695	.	.	ENSG00000121904	ENST00000373381	T	0.66280	-0.2	5.27	1.33	0.21861	Complement control module (2);Sushi/SCR/CCP (3);	0.332353	0.26855	N	0.022148	T	0.55065	0.1897	L	0.45581	1.43	0.80722	D	1	P;P	0.51653	0.947;0.947	P;B	0.45946	0.498;0.411	T	0.53358	-0.8450	10	0.54805	T	0.06	.	8.8781	0.35358	0.3043:0.0:0.6957:0.0	.	188;228	Q7Z408;E7EUA6	CSMD2_HUMAN;.	M	228	ENSP00000362479:T228M	ENSP00000241312:T188M	T	-	2	0	CSMD2	34173977	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	5.605000	0.67634	0.225000	0.20959	0.563000	0.77884	ACG		0.627	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
SMIM12	113444	broad.mit.edu	37	1	35320955	35320955	+	3'UTR	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:35320955G>A	ENST00000521580.2	-	0	768				SMIM12_ENST00000456842.1_3'UTR|SMIM12_ENST00000423898.1_3'UTR|SMIM12_ENST00000446026.1_3'UTR	NM_001164824.1|NM_001164825.1|NM_138428.5	NP_001158296.1|NP_001158297.1|NP_612437.3	Q96EX1	SIM12_HUMAN	small integral membrane protein 12							integral component of membrane (GO:0016021)		p.G109G(1)									TAAAGGCAACGCCCAAATCCC	0.502																																					.												.	.	1	Substitution - coding silent(1)	large_intestine(1)	.	1						.						74.0	65.0	68.0					1																	35320955		2203	4300	6503	35093542	SO:0001624	3_prime_UTR_variant	113444	.				CCDS53295.1	1p34.3	2012-12-03	2012-12-03	2012-12-03	ENSG00000163866	ENSG00000163866			25154	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 212"""	C1orf212		12477932	Standard	NM_138428		Approved	FLJ90372	uc001byb.3	Q96EX1	OTTHUMG00000004375	ENST00000521580.2:c.*345C>T	1.37:g.35320955G>A		Somatic		Capture	Illumina HiSeq	Phase_I	35093542	.	D3DPR5|Q49AP7|Q52LP9|Q8NCB4	Silent	SNP	ENST00000521580.2	37	CCDS53295.1																																																																																				0.502	SMIM12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012715.3	NM_138428	
ZMYM6	9204	broad.mit.edu	37	1	35453636	35453636	+	Missense_Mutation	SNP	C	C	T	rs558695693		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:35453636C>T	ENST00000357182.4	-	16	3274	c.3047G>A	c.(3046-3048)cGt>cAt	p.R1016H	RP11-244H3.1_ENST00000417456.1_RNA|ZMYM6_ENST00000487874.1_Intron|ZMYM6_ENST00000373340.2_Intron|ZMYM6NB_ENST00000373337.3_5'Flank|ZMYM6_ENST00000493328.1_5'UTR	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	1016					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R1016H(1)		breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				tgccactaaacgttcacggtg	0.353													C|||	1	0.000199681	0.0	0.0	5008	,	,		17929	0.0		0.001	False		,,,				2504	0.0				p.R1016H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3047A	1						.						22.0	20.0	20.0					1																	35453636		1219	2570	3789	35226223	SO:0001583	missense	9204	exon16			AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"""Zinc fingers, MYM type"", ""Zinc fingers, BED-type"""	13050	protein-coding gene	gene with protein product	"""zinc finger, BED-type containing 7"""	613567	"""zinc finger protein 258"", ""zinc finger, MYM-type containing 6"""	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.3047G>A	1.37:g.35453636C>T	ENSP00000349708:p.Arg1016His	Somatic		Capture	Illumina HiSeq	Phase_I	35226223	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Missense_Mutation	SNP	ENST00000357182.4	37	CCDS387.2	.	.	.	.	.	.	.	.	.	.	C	0.459	-0.889915	0.02511	.	.	ENSG00000163867	ENST00000357182	T	0.21932	1.98	4.2	-1.32	0.09201	Ribonuclease H-like (1);	0.789972	0.11683	N	0.539677	T	0.04048	0.0113	N	0.00483	-1.445	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39583	-0.9607	10	0.12766	T	0.61	-3.0317	3.3364	0.07102	0.1713:0.3011:0.0:0.5275	.	1016	O95789	ZMYM6_HUMAN	H	1016	ENSP00000349708:R1016H	ENSP00000349708:R1016H	R	-	2	0	ZMYM6	35226223	0.996000	0.38824	0.978000	0.43139	0.544000	0.35116	0.110000	0.15437	-0.176000	0.10707	-0.300000	0.09419	CGT		0.353	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167	
SH3D21	79729	broad.mit.edu	37	1	36785422	36785422	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:36785422A>G	ENST00000426732.2	+	13	1095	c.810A>G	c.(808-810)ccA>ccG	p.P270P	SH3D21_ENST00000505871.1_Silent_p.P275P|EVA1B_ENST00000490466.1_5'Flank|SH3D21_ENST00000312808.4_Silent_p.P32P|SH3D21_ENST00000453908.2_Silent_p.P386P			A4FU49	SH321_HUMAN	SH3 domain containing 21	270						extracellular vesicular exosome (GO:0070062)		p.P32P(1)|p.P386P(1)		endometrium(1)|large_intestine(6)|lung(4)|pancreas(1)	12						TCCCCTCCCCAGAGAAGACCC	0.627																																					p.P275P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A825G	1						.						46.0	56.0	52.0					1																	36785422		2203	4300	6503	36558009	SO:0001819	synonymous_variant	79729	exon11			AK056459	CCDS30674.1, CCDS30674.2	1p34.3	2011-02-21	2011-02-21	2011-02-21	ENSG00000214193	ENSG00000214193			26236	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 113"""	C1orf113		12477932	Standard	NM_024676		Approved	FLJ22938	uc010oia.1	A4FU49	OTTHUMG00000007868	ENST00000426732.2:c.810A>G	1.37:g.36785422A>G		Somatic		Capture	Illumina HiSeq	Phase_I	36558009	NM_024676	B4DLI6|D3DPS6|J3KQM5|Q5VTK7|Q86XZ6|Q8N445|Q96DN4|Q9H5W5	Silent	SNP	ENST00000426732.2	37																																																																																					0.627	SH3D21-202	KNOWN	basic	protein_coding	protein_coding		NM_024676	
STK40	83931	broad.mit.edu	37	1	36826926	36826926	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:36826926C>T	ENST00000373129.3	-	3	414	c.8G>A	c.(7-9)cGg>cAg	p.R3Q	STK40_ENST00000482458.1_5'UTR|STK40_ENST00000373130.3_Missense_Mutation_p.R3Q|STK40_ENST00000373132.3_Missense_Mutation_p.R3Q|STK40_ENST00000359297.2_Missense_Mutation_p.R3Q	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	3					glycogen metabolic process (GO:0005977)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|regulation of MAPK cascade (GO:0043408)|respiratory system process (GO:0003016)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R3Q(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)	13		Myeloproliferative disorder(586;0.0393)				TGATGCTCTCCGCTTCATTCT	0.517																																					p.R3Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G8A	1						.						135.0	130.0	132.0					1																	36826926		2203	4300	6503	36599513	SO:0001583	missense	83931	exon3			BC008344	CCDS407.1, CCDS60089.1	1p34.3	2008-02-05			ENSG00000196182	ENSG00000196182			21373	protein-coding gene	gene with protein product		609437					Standard	NM_032017		Approved	MGC4796, SgK495	uc001cak.1	Q8N2I9	OTTHUMG00000008238	ENST00000373129.3:c.8G>A	1.37:g.36826926C>T	ENSP00000362221:p.Arg3Gln	Somatic		Capture	Illumina HiSeq	Phase_I	36599513	NM_032017	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Missense_Mutation	SNP	ENST00000373129.3	37	CCDS407.1	.	.	.	.	.	.	.	.	.	.	C	32	5.136973	0.94517	.	.	ENSG00000196182	ENST00000373129;ENST00000359297;ENST00000373130;ENST00000373132	T;T;T;T	0.69685	-0.35;-0.42;-0.36;-0.35	5.67	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.66829	0.2829	N	0.24115	0.695	0.45035	D	0.998054	D;D;D	0.76494	0.999;0.992;0.986	P;P;B	0.57009	0.811;0.594;0.267	T	0.70981	-0.4724	10	0.59425	D	0.04	-24.0059	15.0477	0.71841	0.1431:0.8569:0.0:0.0	.	3;3;3	Q8N2I9-3;Q8N2I9-4;Q8N2I9	.;.;STK40_HUMAN	Q	3	ENSP00000362221:R3Q;ENSP00000352245:R3Q;ENSP00000362222:R3Q;ENSP00000362224:R3Q	ENSP00000352245:R3Q	R	-	2	0	STK40	36599513	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.125000	0.77193	1.368000	0.46115	0.561000	0.74099	CGG		0.517	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017	
OSCP1	127700	broad.mit.edu	37	1	36889029	36889029	+	Silent	SNP	G	G	A	rs369435790		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:36889029G>A	ENST00000356637.5	-	6	648	c.585C>T	c.(583-585)aaC>aaT	p.N195N	OSCP1_ENST00000495222.1_5'UTR|OSCP1_ENST00000315643.9_Silent_p.N195N|OSCP1_ENST00000433045.2_Silent_p.N140N|OSCP1_ENST00000235532.5_Silent_p.N185N			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1	195					transport (GO:0006810)	plasma membrane (GO:0005886)		p.N195N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	22						CAAAGCGACCGTTATTATTCT	0.398																																					p.N185N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C555T	1						.	G		0,4406		0,0,2203	84.0	88.0	87.0		555	-7.5	0.6	1		87	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OSCP1	NM_145047.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		185/380	36889029	1,13005	2203	4300	6503	36661616	SO:0001819	synonymous_variant	127700	exon5				CCDS409.1, CCDS410.1, CCDS409.2	1p34.3	2009-07-06	2009-07-06	2009-07-06	ENSG00000116885	ENSG00000116885			29971	protein-coding gene	gene with protein product	"""oxidored nitro domain containing protein"""	608854	"""chromosome 1 open reading frame 102"""	C1orf102		12477932	Standard	NM_145047		Approved	NOR1	uc001caq.3	Q8WVF1	OTTHUMG00000008139	ENST00000356637.5:c.585C>T	1.37:g.36889029G>A		Somatic		Capture	Illumina HiSeq	Phase_I	36661616	NM_145047	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Silent	SNP	ENST00000356637.5	37																																																																																					0.398	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047	
CSF3R	1441	broad.mit.edu	37	1	36941125	36941125	+	Missense_Mutation	SNP	C	C	T	rs375879178		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:36941125C>T	ENST00000373106.1	-	4	761	c.214G>A	c.(214-216)Ggg>Agg	p.G72R	CSF3R_ENST00000331941.5_Missense_Mutation_p.G72R|CSF3R_ENST00000361632.4_Missense_Mutation_p.G72R|CSF3R_ENST00000440588.2_Missense_Mutation_p.G72R|CSF3R_ENST00000373103.1_Missense_Mutation_p.G72R|CSF3R_ENST00000338937.5_Missense_Mutation_p.G72R|CSF3R_ENST00000418048.2_Missense_Mutation_p.G72R|CSF3R_ENST00000373104.1_Missense_Mutation_p.G72R	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	72	Ig-like C2-type.				cell adhesion (GO:0007155)|defense response (GO:0006952)|neutrophil chemotaxis (GO:0030593)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.G72R(2)		central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	TGCCTGCCCCCGGGCTGAAGC	0.602																																					p.G72R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G214A	1						.	C	ARG/GLY,ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	65.0	54.0	58.0		214,214,214	0.5	0.0	1		58	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	CSF3R	NM_000760.3,NM_156039.3,NM_172313.2	125,125,125	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign,benign,benign	72/837,72/864,72/784	36941125	2,13004	2203	4300	6503	36713712	SO:0001583	missense	1441	exon4			M59820	CCDS412.1, CCDS413.1, CCDS414.1	1p35-p34.3	2014-09-17			ENSG00000119535	ENSG00000119535		"""CD molecules"", ""Fibronectin type III domain containing"""	2439	protein-coding gene	gene with protein product		138971		CD114		1371413	Standard	NM_000760		Approved	GCSFR	uc001cax.2	Q99062	OTTHUMG00000008010	ENST00000373106.1:c.214G>A	1.37:g.36941125C>T	ENSP00000362198:p.Gly72Arg	Somatic		Capture	Illumina HiSeq	Phase_I	36713712	NM_172313		Missense_Mutation	SNP	ENST00000373106.1	37	CCDS413.1	.	.	.	.	.	.	.	.	.	.	C	6.318	0.426814	0.11987	2.27E-4	1.16E-4	ENSG00000119535	ENST00000373106;ENST00000373104;ENST00000373103;ENST00000361632;ENST00000331941;ENST00000418048;ENST00000338937;ENST00000440588	T;T;T;T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06	5.73	0.517	0.17025	Immunoglobulin C2-set-like, ligand-binding (1);Immunoglobulin-like fold (1);	1.239310	0.05162	N	0.498013	T	0.59702	0.2213	L	0.38838	1.175	0.09310	N	1	P;B;B;B	0.43024	0.798;0.212;0.252;0.138	B;B;B;B	0.30251	0.113;0.015;0.025;0.01	T	0.48387	-0.9040	10	0.16896	T	0.51	-5.8203	4.729	0.12955	0.2385:0.5494:0.0:0.212	.	72;72;72;72	E1B6W6;Q99062-3;Q99062;Q99062-4	.;.;CSF3R_HUMAN;.	R	72	ENSP00000362198:G72R;ENSP00000362196:G72R;ENSP00000362195:G72R;ENSP00000355406:G72R;ENSP00000332180:G72R;ENSP00000401588:G72R;ENSP00000345013:G72R;ENSP00000397568:G72R	ENSP00000332180:G72R	G	-	1	0	CSF3R	36713712	0.028000	0.19301	0.001000	0.08648	0.054000	0.15201	1.406000	0.34646	-0.066000	0.12998	0.555000	0.69702	GGG		0.602	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039	
GRIK3	2899	broad.mit.edu	37	1	37307466	37307466	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:37307466G>A	ENST00000373091.3	-	10	1417	c.1401C>T	c.(1399-1401)atC>atT	p.I467I	GRIK3_ENST00000373093.4_Silent_p.I467I	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	467					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)	p.I467I(1)		breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				TTAGCAGGTCGATGCAGTAGC	0.577																																					p.I467I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1401T	1						.						214.0	197.0	203.0					1																	37307466		2203	4300	6503	37080053	SO:0001819	synonymous_variant	2899	exon10			U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.1401C>T	1.37:g.37307466G>A		Somatic		Capture	Illumina HiSeq	Phase_I	37080053	NM_000831	A9Z1Z8|B1AMS6|Q13004|Q16136	Silent	SNP	ENST00000373091.3	37	CCDS416.1																																																																																				0.577	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831	
ZC3H12A	80149	broad.mit.edu	37	1	37948137	37948137	+	Silent	SNP	C	C	T	rs186794112	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:37948137C>T	ENST00000373087.6	+	5	1037	c.921C>T	c.(919-921)ccC>ccT	p.P307P		NM_025079.2	NP_079355.2			zinc finger CCCH-type containing 12A									p.P307P(1)		NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AGCCGTGTCCCTATGGTATGG	0.627													C|||	9	0.00179712	0.0	0.0	5008	,	,		17037	0.0079		0.0	False		,,,				2504	0.001				p.P307P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C921T	1						.	C		0,4406		0,0,2203	99.0	101.0	100.0		921	1.0	1.0	1		100	1,8599		0,1,4299	no	coding-synonymous	ZC3H12A	NM_025079.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		307/600	37948137	1,13005	2203	4300	6503	37720724	SO:0001819	synonymous_variant	80149	exon5				CCDS417.1	1p34.3	2012-07-05			ENSG00000163874	ENSG00000163874		"""Zinc fingers, CCCH-type domain containing"""	26259	protein-coding gene	gene with protein product	"""MCP induced protein 1"""	610562				18178554, 22055188	Standard	NM_025079		Approved	FLJ23231, MCPIP1	uc001cbb.4	Q5D1E8	OTTHUMG00000004221	ENST00000373087.6:c.921C>T	1.37:g.37948137C>T		Somatic		Capture	Illumina HiSeq	Phase_I	37720724	NM_025079		Missense_Mutation	SNP	ENST00000373087.6	37	CCDS417.1																																																																																				0.627	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079	
MACF1	23499	broad.mit.edu	37	1	39749844	39749844	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:39749844C>A	ENST00000372915.3	+	9	1124	c.1037C>A	c.(1036-1038)cCt>cAt	p.P346H	MACF1_ENST00000317713.7_Missense_Mutation_p.P346H|MACF1_ENST00000564288.1_Missense_Mutation_p.P341H|MACF1_ENST00000545844.1_Missense_Mutation_p.P346H|MACF1_ENST00000361689.2_Missense_Mutation_p.P346H|MACF1_ENST00000567887.1_Missense_Mutation_p.P378H|MACF1_ENST00000539005.1_Missense_Mutation_p.P346H			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	346					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.P346H(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)			CCCCAAAACCCTGTTGAACTA	0.423																																					p.P346H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1037A	1						.						82.0	83.0	82.0					1																	39749844		2203	4300	6503	39522431	SO:0001583	missense	23499	exon11			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.1037C>A	1.37:g.39749844C>A	ENSP00000362006:p.Pro346His	Somatic		Capture	Illumina HiSeq	Phase_I	39522431	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	22.1	4.237994	0.79800	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000404645;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262;ENST00000372900	D;D;D;D;D;D;D	0.94758	-3.51;-3.51;-3.51;-3.51;-3.51;-3.51;-3.51	5.5	5.5	0.81552	.	.	.	.	.	D	0.96926	0.8996	M	0.67953	2.075	0.80722	D	1	D;D	0.89917	0.993;1.0	P;D	0.80764	0.905;0.994	D	0.97186	0.9854	9	0.72032	D	0.01	.	19.4617	0.94920	0.0:1.0:0.0:0.0	.	346;311	F8W8Q1;Q9UPN3-3	.;.	H	346;346;346;362;346;346;304;495;506	ENSP00000439537:P346H;ENSP00000362006:P346H;ENSP00000354573:P346H;ENSP00000313438:P346H;ENSP00000444364:P346H;ENSP00000435070:P304H;ENSP00000437059:P495H	ENSP00000313438:P346H	P	+	2	0	MACF1	39522431	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.484000	0.81180	2.596000	0.87737	0.650000	0.86243	CCT		0.423	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
MACF1	23499	broad.mit.edu	37	1	39818813	39818813	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:39818813C>T	ENST00000372915.3	+	43	11436	c.11349C>T	c.(11347-11349)agC>agT	p.S3783S	MACF1_ENST00000317713.7_Silent_p.S1716S|MACF1_ENST00000564288.1_Silent_p.S3778S|MACF1_ENST00000545844.1_Silent_p.S1716S|MACF1_ENST00000289893.4_Silent_p.S2218S|MACF1_ENST00000361689.2_Silent_p.S1716S|MACF1_ENST00000567887.1_Silent_p.S3815S|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000539005.1_Silent_p.S1716S			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3783					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.S2218S(1)|p.S1716S(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)			CGGGAGCTAGCTTGGAGAAAG	0.512																																					p.S1716S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C5148T	1						.						110.0	103.0	105.0					1																	39818813		2203	4300	6503	39591400	SO:0001819	synonymous_variant	23499	exon40			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.11349C>T	1.37:g.39818813C>T		Somatic		Capture	Illumina HiSeq	Phase_I	39591400	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	0.015	-1.566233	0.00903	.	.	ENSG00000127603	ENST00000372925	.	.	.	5.35	-0.698	0.11280	.	.	.	.	.	T	0.20455	0.0492	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24190	-1.0167	4	.	.	.	.	1.7988	0.03067	0.1168:0.3601:0.1791:0.344	.	.	.	.	F	850	.	.	L	+	1	0	MACF1	39591400	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.178000	0.09782	-0.029000	0.13827	-2.110000	0.00354	CTT		0.512	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
MACF1	23499	broad.mit.edu	37	1	39854170	39854170	+	Missense_Mutation	SNP	G	G	A	rs371560140		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:39854170G>A	ENST00000372915.3	+	57	15758	c.15671G>A	c.(15670-15672)cGt>cAt	p.R5224H	MACF1_ENST00000317713.7_Missense_Mutation_p.R3157H|MACF1_ENST00000564288.1_Missense_Mutation_p.R5219H|MACF1_ENST00000545844.1_Missense_Mutation_p.R3157H|MACF1_ENST00000289893.4_Missense_Mutation_p.R3659H|MACF1_ENST00000361689.2_Missense_Mutation_p.R3157H|MACF1_ENST00000567887.1_Missense_Mutation_p.R5256H|MACF1_ENST00000539005.1_Missense_Mutation_p.R3136H			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	5224					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.R3157H(1)|p.R3659H(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)			GGGAAAGCTCGTCAGGAACAG	0.517																																					p.R3157H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G9470A	1						.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	59.0	60.0	60.0		9470,10976	5.8	1.0	1		60	4,8596	3.7+/-12.6	0,4,4296	no	missense,missense	MACF1	NM_012090.4,NM_033044.3	29,29	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging,probably-damaging	3157/5431,3659/5939	39854170	4,13002	2203	4300	6503	39626757	SO:0001583	missense	23499	exon54			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.15671G>A	1.37:g.39854170G>A	ENSP00000362006:p.Arg5224His	Somatic		Capture	Illumina HiSeq	Phase_I	39626757	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	G	19.30	3.800770	0.70567	0.0	4.65E-4	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76	5.78	5.78	0.91487	.	0.000000	0.64402	D	0.000006	T	0.69305	0.3096	M	0.69358	2.11	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.997;0.998	T	0.67937	-0.5541	10	0.51188	T	0.08	.	20.0211	0.97503	0.0:0.0:1.0:0.0	.	5224;3157;3101	Q9UPN3;F8W8Q1;Q9UPN3-3	MACF1_HUMAN;.;.	H	3157;5224;3157;3157;3136;3659	ENSP00000439537:R3157H;ENSP00000362006:R5224H;ENSP00000354573:R3157H;ENSP00000313438:R3157H;ENSP00000444364:R3136H;ENSP00000289893:R3659H	ENSP00000289893:R3659H	R	+	2	0	MACF1	39626757	1.000000	0.71417	0.985000	0.45067	0.994000	0.84299	6.463000	0.73530	2.722000	0.93159	0.563000	0.77884	CGT		0.517	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
MYCL	4610	broad.mit.edu	37	1	40363267	40363267	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:40363267C>T	ENST00000372816.2	-	2	1319	c.872G>A	c.(871-873)cGc>cAc	p.R291H	RP1-118J21.5_ENST00000418255.1_RNA|MYCL_ENST00000397332.2_Missense_Mutation_p.R321H			P12524	MYCL_HUMAN	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived homolog	291	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.					nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R321H(1)									CCGCCTCTTGCGCTCCAGGAA	0.577																																					p.R291H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G872A	1						.						91.0	89.0	89.0					1																	40363267		2203	4300	6503	40135854	SO:0001583	missense	4610	exon2				CCDS30682.1, CCDS44117.1, CCDS44117.2, CCDS53300.1	1p34.3	2013-07-09	2013-07-09	2013-07-09	ENSG00000116990	ENSG00000116990		"""Basic helix-loop-helix proteins"""	7555	protein-coding gene	gene with protein product	"""l-myc protein"", ""myc-related gene from lung cancer"", ""oncogene lmyc"""	164850	"""v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived"""	MYCL1		8978772	Standard	NM_001033082		Approved	LMYC, bHLHe38	uc001cer.2	P12524	OTTHUMG00000009243	ENST00000372816.2:c.872G>A	1.37:g.40363267C>T	ENSP00000361903:p.Arg291His	Somatic		Capture	Illumina HiSeq	Phase_I	40135854	NM_001033081	A2A2C9|B4DJH2|Q14897|Q5QPL0|Q5QPL1|Q9NUE9	Missense_Mutation	SNP	ENST00000372816.2	37	CCDS30682.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.421675	0.83559	.	.	ENSG00000116990	ENST00000397332;ENST00000372816	D;D	0.94000	-3.33;-3.33	5.75	5.75	0.90469	Helix-loop-helix DNA-binding (5);	0.123571	0.52532	D	0.000077	D	0.95971	0.8688	H	0.94734	3.575	0.80722	D	1	D	0.52996	0.957	B	0.44044	0.439	D	0.96917	0.9671	10	0.87932	D	0	-28.0447	19.9598	0.97242	0.0:1.0:0.0:0.0	.	291	P12524	MYCL1_HUMAN	H	321;291	ENSP00000380494:R321H;ENSP00000361903:R291H	ENSP00000361903:R291H	R	-	2	0	MYCL1	40135854	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.775000	0.85489	2.716000	0.92895	0.655000	0.94253	CGC		0.577	MYCL-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277004.1	NM_001033082	
MFSD2A	84879	broad.mit.edu	37	1	40424484	40424484	+	Missense_Mutation	SNP	C	C	T	rs556985300		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:40424484C>T	ENST00000372809.5	+	3	522	c.379C>T	c.(379-381)Cgc>Tgc	p.R127C	MFSD2A_ENST00000372811.5_Missense_Mutation_p.R114C|MFSD2A_ENST00000420632.2_Intron	NM_001136493.1	NP_001129965.1	Q8NA29	NLS1_HUMAN	major facilitator superfamily domain containing 2A	127					establishment of blood-brain barrier (GO:0060856)|fatty acid transport (GO:0015908)|lipid transport across blood brain barrier (GO:1990379)|transcytosis (GO:0045056)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phospholipid transporter activity (GO:0005548)|symporter activity (GO:0015293)	p.R114C(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						CTGCCTGGGTCGCCTTATGCC	0.587													C|||	1	0.000199681	0.0	0.0	5008	,	,		19612	0.001		0.0	False		,,,				2504	0.0				p.R127C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C379T	1						.						148.0	146.0	147.0					1																	40424484		2203	4300	6503	40197071	SO:0001583	missense	84879	exon3			AK093223	CCDS446.1, CCDS44118.1, CCDS72762.1	1p34.2	2009-09-08	2009-09-08	2009-09-08	ENSG00000168389	ENSG00000168389			25897	protein-coding gene	gene with protein product		614397	"""major facilitator superfamily domain containing 2"""	MFSD2		18694395	Standard	XM_005271285		Approved	FLJ14490	uc001cev.3	Q8NA29	OTTHUMG00000009293	ENST00000372809.5:c.379C>T	1.37:g.40424484C>T	ENSP00000361895:p.Arg127Cys	Somatic		Capture	Illumina HiSeq	Phase_I	40197071	NM_001136493	A8K675|Q6UWU5|Q96F59|Q9BRC8	Missense_Mutation	SNP	ENST00000372809.5	37	CCDS44118.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.660868	0.88154	.	.	ENSG00000168389	ENST00000372811;ENST00000434861;ENST00000372809	D;D;D	0.90069	-2.61;-2.61;-2.61	5.94	5.94	0.96194	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.95303	0.8476	M	0.84683	2.71	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.992	D	0.95279	0.8384	10	0.87932	D	0	-17.9597	19.3514	0.94389	0.0:1.0:0.0:0.0	.	77;127;114	B4DNN7;Q8NA29;Q8NA29-2	.;MFS2A_HUMAN;.	C	114;112;127	ENSP00000361898:R114C;ENSP00000407606:R112C;ENSP00000361895:R127C	ENSP00000361895:R127C	R	+	1	0	MFSD2A	40197071	1.000000	0.71417	1.000000	0.80357	0.695000	0.40330	3.385000	0.52485	2.826000	0.97356	0.561000	0.74099	CGC		0.587	MFSD2A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025756.1	NM_032793	
MFSD2A	84879	broad.mit.edu	37	1	40432509	40432509	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:40432509C>T	ENST00000372809.5	+	8	1014	c.871C>T	c.(871-873)Cca>Tca	p.P291S	MFSD2A_ENST00000480630.1_Intron|MFSD2A_ENST00000372811.5_Missense_Mutation_p.P278S|MFSD2A_ENST00000420632.2_Missense_Mutation_p.P122S	NM_001136493.1	NP_001129965.1	Q8NA29	NLS1_HUMAN	major facilitator superfamily domain containing 2A	291					establishment of blood-brain barrier (GO:0060856)|fatty acid transport (GO:0015908)|lipid transport across blood brain barrier (GO:1990379)|transcytosis (GO:0045056)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phospholipid transporter activity (GO:0005548)|symporter activity (GO:0015293)	p.P278S(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						GCAGTCTGAGCCAATCGCCTA	0.572																																					p.P291S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C871T	1						.						98.0	99.0	98.0					1																	40432509		2203	4300	6503	40205096	SO:0001583	missense	84879	exon8			AK093223	CCDS446.1, CCDS44118.1, CCDS72762.1	1p34.2	2009-09-08	2009-09-08	2009-09-08	ENSG00000168389	ENSG00000168389			25897	protein-coding gene	gene with protein product		614397	"""major facilitator superfamily domain containing 2"""	MFSD2		18694395	Standard	XM_005271285		Approved	FLJ14490	uc001cev.3	Q8NA29	OTTHUMG00000009293	ENST00000372809.5:c.871C>T	1.37:g.40432509C>T	ENSP00000361895:p.Pro291Ser	Somatic		Capture	Illumina HiSeq	Phase_I	40205096	NM_001136493	A8K675|Q6UWU5|Q96F59|Q9BRC8	Missense_Mutation	SNP	ENST00000372809.5	37	CCDS44118.1	.	.	.	.	.	.	.	.	.	.	C	0.128	-1.117171	0.01799	.	.	ENSG00000168389	ENST00000372811;ENST00000420632;ENST00000372809	D;D;D	0.86694	-2.16;-2.16;-2.16	5.64	2.33	0.28932	Major facilitator superfamily domain, general substrate transporter (1);	0.216684	0.49305	N	0.000158	T	0.76793	0.4037	L	0.40543	1.245	0.46499	D	0.999072	B;B;B	0.18013	0.025;0.011;0.005	B;B;B	0.19946	0.027;0.018;0.01	T	0.60596	-0.7232	10	0.10902	T	0.67	-2.6145	5.8286	0.18568	0.1469:0.6627:0.0:0.1903	.	239;291;278	B4DNN7;Q8NA29;Q8NA29-2	.;MFS2A_HUMAN;.	S	278;122;291	ENSP00000361898:P278S;ENSP00000391261:P122S;ENSP00000361895:P291S	ENSP00000361895:P291S	P	+	1	0	MFSD2A	40205096	1.000000	0.71417	0.050000	0.19076	0.065000	0.16274	2.963000	0.49184	0.245000	0.21373	0.563000	0.77884	CCA		0.572	MFSD2A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025756.1	NM_032793	
ZMPSTE24	10269	broad.mit.edu	37	1	40758148	40758148	+	Missense_Mutation	SNP	G	G	A	rs555007253		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:40758148G>A	ENST00000372759.3	+	10	1400	c.1235G>A	c.(1234-1236)cGc>cAc	p.R412H		NM_005857.4	NP_005848.2	O75844	FACE1_HUMAN	zinc metallopeptidase STE24	412					CAAX-box protein processing (GO:0071586)|nuclear envelope organization (GO:0006998)|prenylated protein catabolic process (GO:0030327)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metalloexopeptidase activity (GO:0008235)	p.R412H(1)		endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	16	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;6.3e-18)			GTCCTAAGCCGCAGATTTGAG	0.383																																					p.R412H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1235A	1						.						99.0	107.0	105.0					1																	40758148		2203	4300	6503	40530735	SO:0001583	missense	10269	exon10			Y13834	CCDS449.1	1p34	2014-09-17	2012-12-10		ENSG00000084073	ENSG00000084073	3.4.24.84		12877	protein-coding gene	gene with protein product	"""Hutchinson-Gilford progeria syndrome"", ""CAAX prenyl protease 1 homolog"""	606480	"""zinc metalloproteinase (STE24 homolog, yeast)"", ""zinc metallopeptidase (STE24 homolog, yeast)"", ""zinc metallopeptidase STE24 homolog (S. cerevisiae)"""			10373325, 9700155, 16671095	Standard	NM_005857		Approved	FACE-1, Ste24p, STE24, HGPS, PRO1	uc001cfg.4	O75844	OTTHUMG00000005762	ENST00000372759.3:c.1235G>A	1.37:g.40758148G>A	ENSP00000361845:p.Arg412His	Somatic		Capture	Illumina HiSeq	Phase_I	40530735	NM_005857	B3KQI7|D3DPU7|Q8NDZ8|Q9UBQ2	Missense_Mutation	SNP	ENST00000372759.3	37	CCDS449.1	.	.	.	.	.	.	.	.	.	.	G	32	5.180732	0.94846	.	.	ENSG00000084073	ENST00000372759	D	0.90197	-2.63	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.97133	0.9063	H	0.96547	3.84	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98168	1.0450	10	0.87932	D	0	-33.874	19.2762	0.94032	0.0:0.0:1.0:0.0	.	412	O75844	FACE1_HUMAN	H	412	ENSP00000361845:R412H	ENSP00000361845:R412H	R	+	2	0	ZMPSTE24	40530735	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.388000	0.97237	2.560000	0.86352	0.467000	0.42956	CGC		0.383	ZMPSTE24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015766.1		
RIMKLA	284716	broad.mit.edu	37	1	42875813	42875813	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:42875813C>T	ENST00000431473.3	+	4	769	c.640C>T	c.(640-642)Ctt>Ttt	p.L214F		NM_173642.3	NP_775913.2	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family member A	214	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)	p.L173F(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						AGGCTCTATGCTTCGCTGCTC	0.532																																					p.L214F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C640T	1						.						131.0	125.0	127.0					1																	42875813		2203	4300	6503	42648400	SO:0001583	missense	284716	exon4			BC039737	CCDS466.2	1p34.2	2011-09-21	2008-10-13	2008-10-13	ENSG00000177181	ENSG00000177181	6.3.2.N6		28725	protein-coding gene	gene with protein product	"""N-acetylaspartylglutamate synthetase II"""		"""family with sequence similarity 80, member A"""	FAM80A		20657015, 21454531	Standard	NM_173642		Approved	MGC47816, RP11-157D18.1, NAAGS-II	uc001chi.2	Q8IXN7	OTTHUMG00000007335	ENST00000431473.3:c.640C>T	1.37:g.42875813C>T	ENSP00000414330:p.Leu214Phe	Somatic		Capture	Illumina HiSeq	Phase_I	42648400	NM_173642	Q5VUS5	Missense_Mutation	SNP	ENST00000431473.3	37	CCDS466.2	.	.	.	.	.	.	.	.	.	.	C	23.1	4.378389	0.82682	.	.	ENSG00000177181	ENST00000410070;ENST00000431473	.	.	.	5.74	5.74	0.90152	ATP-grasp fold (1);ATP-grasp fold, RimK-type (1);ATP-grasp fold, subdomain 2 (1);	0.000000	0.85682	D	0.000000	T	0.76716	0.4026	M	0.78049	2.395	0.58432	D	0.999996	D	0.76494	0.999	D	0.77557	0.99	T	0.75744	-0.3210	9	0.37606	T	0.19	-17.5595	10.7996	0.46480	0.0:0.9148:0.0:0.0852	.	214	Q8IXN7	RIMKA_HUMAN	F	90;214	.	ENSP00000387064:L90F	L	+	1	0	RIMKLA	42648400	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.474000	0.66781	2.712000	0.92718	0.650000	0.86243	CTT		0.532	RIMKLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019174.3	NM_173642	
TMEM125	128218	broad.mit.edu	37	1	43738965	43738965	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:43738965G>A	ENST00000432792.2	+	4	1142	c.572G>A	c.(571-573)gGc>gAc	p.G191D	TMEM125_ENST00000439858.1_Missense_Mutation_p.G191D			Q96AQ2	TM125_HUMAN	transmembrane protein 125	191						integral component of membrane (GO:0016021)		p.G191D(1)		breast(1)|large_intestine(1)|lung(1)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				AGTGGCCATGGCGGCCATGGC	0.617																																					p.G191D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G572A	1						.						39.0	32.0	35.0					1																	43738965		2203	4300	6503	43511552	SO:0001583	missense	128218	exon4			BC016858	CCDS480.1	1p34.2	2006-02-16			ENSG00000179178	ENSG00000179178			28275	protein-coding gene	gene with protein product							Standard	NM_144626		Approved	MGC17299	uc021oml.1	Q96AQ2	OTTHUMG00000007288	ENST00000432792.2:c.572G>A	1.37:g.43738965G>A	ENSP00000429275:p.Gly191Asp	Somatic		Capture	Illumina HiSeq	Phase_I	43511552	NM_144626	D3DPX1	Missense_Mutation	SNP	ENST00000432792.2	37	CCDS480.1	.	.	.	.	.	.	.	.	.	.	G	4.693	0.128870	0.08981	.	.	ENSG00000179178	ENST00000439858;ENST00000432792	T;T	0.39787	1.06;1.06	4.89	1.77	0.24775	.	0.402221	0.24426	N	0.038634	T	0.18383	0.0441	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.24012	-1.0172	10	0.11794	T	0.64	.	8.507	0.33193	0.0:0.3368:0.4171:0.2461	.	191	Q96AQ2	TM125_HUMAN	D	191	ENSP00000429775:G191D;ENSP00000429275:G191D	ENSP00000429275:G191D	G	+	2	0	TMEM125	43511552	0.000000	0.05858	0.001000	0.08648	0.137000	0.21094	0.082000	0.14847	0.451000	0.26802	0.514000	0.50259	GGC		0.617	TMEM125-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019032.2	NM_144626	
SZT2	23334	broad.mit.edu	37	1	43891292	43891292	+	Silent	SNP	G	G	A	rs150658389		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:43891292G>A	ENST00000562955.1	+	19	2793	c.2793G>A	c.(2791-2793)acG>acA	p.T931T	SZT2_ENST00000372442.1_Silent_p.T89T	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	931					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)		p.T89T(2)		NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						AGGACCTGACGTATTCTGAGA	0.567																																					p.T89T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G267A	1						.						95.0	98.0	97.0					1																	43891292		2203	4300	6503	43663879	SO:0001819	synonymous_variant	23334	exon5			AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.2793G>A	1.37:g.43891292G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43663879	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	37	CCDS30694.2																																																																																				0.567	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	
CCDC24	149473	broad.mit.edu	37	1	44461628	44461628	+	Silent	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:44461628C>A	ENST00000372318.3	+	9	891	c.720C>A	c.(718-720)tcC>tcA	p.S240S	SLC6A9_ENST00000372307.3_Intron|SLC6A9_ENST00000372306.3_Intron|CCDC24_ENST00000479055.1_3'UTR	NM_152499.1	NP_689712.1	Q8N4L8	CCD24_HUMAN	coiled-coil domain containing 24	240								p.S240S(1)		endometrium(3)|large_intestine(2)|lung(3)|stomach(1)	9	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				CCTTGGGGTCCTCCACACAGG	0.622																																					p.S240S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C720A	1						.						99.0	105.0	103.0					1																	44461628		2203	4300	6503	44234215	SO:0001819	synonymous_variant	149473	exon9				CCDS507.1	1p34.1	2008-02-05			ENSG00000159214	ENSG00000159214			28688	protein-coding gene	gene with protein product						12477932	Standard	NM_152499		Approved	MGC45441	uc001clj.3	Q8N4L8	OTTHUMG00000008299	ENST00000372318.3:c.720C>A	1.37:g.44461628C>A		Somatic		Capture	Illumina HiSeq	Phase_I	44234215	NM_152499	Q6RWT2	Missense_Mutation	SNP	ENST00000372318.3	37	CCDS507.1																																																																																				0.622	CCDC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022865.1	NM_152499	
RNF220	55182	broad.mit.edu	37	1	45111052	45111052	+	Intron	SNP	G	G	A	rs368735304		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:45111052G>A	ENST00000355387.2	+	12	1816				TMEM53_ENST00000372242.3_Missense_Mutation_p.R180W|RNF220_ENST00000361799.2_Intron|TMEM53_ENST00000372244.3_Missense_Mutation_p.P49L|TMEM53_ENST00000372243.3_Missense_Mutation_p.R90W|RNF220_ENST00000372247.2_Intron|RNF220_ENST00000443020.2_Intron|RNF220_ENST00000480686.1_Intron			Q5VTB9	RN220_HUMAN	ring finger protein 220						protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R180W(1)		endometrium(6)|kidney(1)|large_intestine(3)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	29						CAGTCTGGCCGGAGTGTGAGT	0.592																																					.												.	.	1	Substitution - Missense(1)	large_intestine(1)	.	1						.	G		0,4406		0,0,2203	71.0	62.0	65.0			1.1	0.9	1		65	1,8599	1.2+/-3.3	0,1,4299	no	intron	RNF220	NM_018150.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077			45111052	1,13005	2203	4300	6503	44883639	SO:0001627	intron_variant	79639	.			AK056424	CCDS510.1	1p34.1	2008-06-13	2008-06-13	2008-06-13	ENSG00000187147	ENSG00000187147		"""RING-type (C3HC4) zinc fingers"""	25552	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 164"""	C1orf164		11042152	Standard	NM_018150		Approved	FLJ10597	uc001clv.1	Q5VTB9	OTTHUMG00000007697	ENST00000355387.2:c.1367-30G>A	1.37:g.45111052G>A		Somatic		Capture	Illumina HiSeq	Phase_I	44883639	.	B3KPJ3|B4DLZ9|E9PCS1|Q4KMX2|Q9NVP6	Missense_Mutation	SNP	ENST00000355387.2	37	CCDS510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.919|1.919	-0.448899|-0.448899	0.04572|0.04572	0.0|0.0	1.16E-4|1.16E-4	ENSG00000126106|ENSG00000126106	ENST00000372244|ENST00000372243;ENST00000372242	.|.	.|.	.|.	4.91|4.91	1.07|1.07	0.20283|0.20283	.|.	.|.	.|.	.|.	.|.	T|T	0.25195|0.25195	0.0612|0.0612	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.29792|0.29792	-1.0000|-1.0000	5|7	0.87932|0.66056	D|D	0|0.02	.|.	0.4565|0.4565	0.00509|0.00509	0.4103:0.182:0.2308:0.1769|0.4103:0.182:0.2308:0.1769	.|.	.|90	.|Q5TDE6	.|.	L|W	49|90;180	.|.	ENSP00000361318:P49L|ENSP00000361316:R180W	P|R	-|-	2|1	0|2	TMEM53|TMEM53	44883639|44883639	0.000000|0.000000	0.05858|0.05858	0.935000|0.935000	0.37517|0.37517	0.522000|0.522000	0.34438|0.34438	0.043000|0.043000	0.13971|0.13971	0.714000|0.714000	0.32081|0.32081	0.561000|0.561000	0.74099|0.74099	CCG|CGG		0.592	RNF220-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020683.4	NM_018150	
BEST4	266675	broad.mit.edu	37	1	45251766	45251766	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:45251766C>T	ENST00000372207.3	-	4	615	c.616G>A	c.(616-618)Gct>Act	p.A206T		NM_153274.2	NP_695006.1	Q8NFU0	BEST4_HUMAN	bestrophin 4	206						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)	p.A206T(1)		large_intestine(1)|lung(4)|ovary(1)|skin(1)	7	Acute lymphoblastic leukemia(166;0.155)					AGACAGAGAGCGATATCGTCA	0.512											OREG0013447	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A206T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G616A	1						.						86.0	96.0	93.0					1																	45251766		2203	4300	6503	45024353	SO:0001583	missense	266675	exon4			AF440757	CCDS514.1	1p33-p32.3	2012-09-26	2006-10-18	2006-10-18	ENSG00000142959	ENSG00000142959		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	17106	protein-coding gene	gene with protein product		607336	"""vitelliform macular dystrophy 2-like 2"""	VMD2L2		12032738, 16702355	Standard	NM_153274		Approved		uc001cmm.3	Q8NFU0	OTTHUMG00000008488	ENST00000372207.3:c.616G>A	1.37:g.45251766C>T	ENSP00000361281:p.Ala206Thr	Somatic	930	Capture	Illumina HiSeq	Phase_I	45024353	NM_153274	Q5JR93	Missense_Mutation	SNP	ENST00000372207.3	37	CCDS514.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220737	0.58560	.	.	ENSG00000142959	ENST00000372207	D	0.98633	-5.04	5.55	3.65	0.41850	.	0.000000	0.85682	D	0.000000	D	0.95971	0.8688	L	0.35723	1.085	0.48395	D	0.999644	B	0.18741	0.03	B	0.22753	0.041	D	0.93969	0.7247	10	0.22109	T	0.4	-7.5816	11.5489	0.50708	0.0:0.8507:0.0:0.1493	.	206	Q8NFU0	BEST4_HUMAN	T	206	ENSP00000361281:A206T	ENSP00000361281:A206T	A	-	1	0	BEST4	45024353	0.703000	0.27826	1.000000	0.80357	0.945000	0.59286	1.542000	0.36137	1.591000	0.50007	0.655000	0.94253	GCT		0.512	BEST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023425.1	NM_153274	
ZSWIM5	57643	broad.mit.edu	37	1	45506187	45506187	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:45506187G>A	ENST00000359600.5	-	7	1838	c.1633C>T	c.(1633-1635)Cga>Tga	p.R545*		NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5	545						extracellular space (GO:0005615)	zinc ion binding (GO:0008270)	p.R545*(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|liver(1)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					GCGTCAACTCGAGCACAGGCT	0.448																																					p.R545X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1633T	1						.						70.0	65.0	67.0					1																	45506187		1897	4108	6005	45278774	SO:0001587	stop_gained	57643	exon7			AB040944	CCDS41319.1	1p34.1	2010-06-16			ENSG00000162415	ENSG00000162415		"""Zinc fingers, SWIM-type"""	29299	protein-coding gene	gene with protein product						10819331	Standard	NM_020883		Approved	KIAA1511	uc001cnd.2	Q9P217	OTTHUMG00000008950	ENST00000359600.5:c.1633C>T	1.37:g.45506187G>A	ENSP00000352614:p.Arg545*	Somatic		Capture	Illumina HiSeq	Phase_I	45278774	NM_020883	Q5SXQ9	Nonsense_Mutation	SNP	ENST00000359600.5	37	CCDS41319.1	.	.	.	.	.	.	.	.	.	.	G	39	7.375405	0.98245	.	.	ENSG00000162415	ENST00000359600	.	.	.	4.64	4.64	0.57946	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.9502	18.4215	0.90592	0.0:0.0:1.0:0.0	.	.	.	.	X	545	.	ENSP00000352614:R545X	R	-	1	2	ZSWIM5	45278774	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.045000	0.64220	2.523000	0.85059	0.655000	0.94253	CGA		0.448	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024823.2	XM_046581	
MAST2	23139	broad.mit.edu	37	1	46500522	46500522	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:46500522C>T	ENST00000361297.2	+	29	4464	c.4181C>T	c.(4180-4182)gCg>gTg	p.A1394V	MAST2_ENST00000372009.2_Missense_Mutation_p.A1204V	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2									p.A1394V(1)		breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					CCCAAGAGTGCGGAGCCACCC	0.612																																					p.A1394V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4181T	1						.						86.0	92.0	90.0					1																	46500522		2051	4194	6245	46273109	SO:0001583	missense	23139	exon29			AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.4181C>T	1.37:g.46500522C>T	ENSP00000354671:p.Ala1394Val	Somatic		Capture	Illumina HiSeq	Phase_I	46273109	NM_015112		Missense_Mutation	SNP	ENST00000361297.2	37	CCDS41326.1	.	.	.	.	.	.	.	.	.	.	c	16.68	3.190044	0.58017	.	.	ENSG00000086015	ENST00000361297;ENST00000372009	T;T	0.39056	1.1;1.1	4.4	3.35	0.38373	.	0.174231	0.49305	N	0.000147	T	0.40886	0.1135	M	0.66297	2.02	0.36144	D	0.846961	B;B	0.27192	0.047;0.171	B;B	0.21546	0.005;0.035	T	0.53049	-0.8493	10	0.62326	D	0.03	-8.7512	12.3307	0.55038	0.0:0.91:0.0:0.09	.	1204;1394	E7ERL6;Q6P0Q8	.;MAST2_HUMAN	V	1394;1204	ENSP00000354671:A1394V;ENSP00000361079:A1204V	ENSP00000354671:A1394V	A	+	2	0	MAST2	46273109	1.000000	0.71417	0.919000	0.36401	0.992000	0.81027	4.805000	0.62561	1.032000	0.39892	0.558000	0.71614	GCG		0.612	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
CYP4A11	1579	broad.mit.edu	37	1	47398461	47398461	+	Missense_Mutation	SNP	C	C	T	rs556756716		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:47398461C>T	ENST00000310638.4	-	11	1367	c.1336G>A	c.(1336-1338)Gct>Act	p.A446T	CYP4A11_ENST00000371904.4_Missense_Mutation_p.A447T|CYP4A11_ENST00000371905.1_Missense_Mutation_p.A446T|CYP4A11_ENST00000462347.1_Missense_Mutation_p.A348T|CYP4A11_ENST00000496519.1_5'Flank	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	446					arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)	p.A446T(2)		endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	GGCAGGAAAGCGTGGCTGTGT	0.517													C|||	1	0.000199681	0.0	0.0	5008	,	,		20751	0.001		0.0	False		,,,				2504	0.0				p.A446T												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1336A	1						.						272.0	287.0	282.0					1																	47398461		2203	4300	6503	47171048	SO:0001583	missense	1579	exon11			L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"""Cytochrome P450s"""	2642	protein-coding gene	gene with protein product		601310	"""cytochrome P450, subfamily IVA, polypeptide 11"""	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.1336G>A	1.37:g.47398461C>T	ENSP00000311095:p.Ala446Thr	Somatic		Capture	Illumina HiSeq	Phase_I	47171048	NM_000778	Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Missense_Mutation	SNP	ENST00000310638.4	37	CCDS543.1	.	.	.	.	.	.	.	.	.	.	N	17.46	3.395295	0.62066	.	.	ENSG00000187048	ENST00000310638;ENST00000371904;ENST00000371905	T;T;T	0.71103	-0.54;-0.54;-0.54	5.11	3.06	0.35304	.	0.110897	0.64402	D	0.000009	T	0.69024	0.3065	N	0.17248	0.465	0.80722	D	1	D	0.76494	0.999	D	0.71870	0.975	T	0.69709	-0.5072	10	0.87932	D	0	.	8.7965	0.34883	0.1786:0.7411:0.0:0.0803	.	446	Q02928	CP4AB_HUMAN	T	446;447;446	ENSP00000311095:A446T;ENSP00000360971:A447T;ENSP00000360972:A446T	ENSP00000311095:A446T	A	-	1	0	CYP4A11	47171048	0.998000	0.40836	0.626000	0.29213	0.169000	0.22640	2.994000	0.49433	0.509000	0.28195	0.650000	0.86243	GCT		0.517	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778	
SPATA6	54558	broad.mit.edu	37	1	48825368	48825368	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:48825368C>T	ENST00000371847.3	-	10	1148	c.984G>A	c.(982-984)tcG>tcA	p.S328S	SPATA6_ENST00000396199.3_Silent_p.S256S|SPATA6_ENST00000371843.3_Silent_p.S328S	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	328					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)		p.S328S(1)		breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						GCTTACTACACGACCTTGGGC	0.438																																					p.S328S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G984A	1						.						96.0	91.0	92.0					1																	48825368		2203	4300	6503	48597955	SO:0001819	synonymous_variant	54558	exon10			AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122			18309	protein-coding gene	gene with protein product	"""spermatogenesis-related factor-1"""	613947					Standard	XM_005270948		Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.984G>A	1.37:g.48825368C>T		Somatic		Capture	Illumina HiSeq	Phase_I	48597955	NM_019073	Q5T3N7|Q8WUE6	Silent	SNP	ENST00000371847.3	37	CCDS551.1																																																																																				0.438	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073	
AGBL4	84871	broad.mit.edu	37	1	49052793	49052793	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:49052793G>A	ENST00000371839.1	-	11	1266	c.1150C>T	c.(1150-1152)Cgt>Tgt	p.R384C	AGBL4_ENST00000334103.7_Missense_Mutation_p.R117C	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	384					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.R384C(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		AGGAAGCGACGGCCAGTTCCT	0.547																																					p.R384C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1150T	1						.						34.0	37.0	36.0					1																	49052793		2017	4165	6182	48825380	SO:0001583	missense	84871	exon11			AK027348	CCDS44137.1	1p33	2014-06-23			ENSG00000186094	ENSG00000186094			25892	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 6"""					21074048	Standard	NM_032785		Approved	FLJ14442, CCP6	uc001cru.2	Q5VU57	OTTHUMG00000007793	ENST00000371839.1:c.1150C>T	1.37:g.49052793G>A	ENSP00000360905:p.Arg384Cys	Somatic		Capture	Illumina HiSeq	Phase_I	48825380	NM_032785	B3KT26|B4DG37	Missense_Mutation	SNP	ENST00000371839.1	37	CCDS44137.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.588579	0.86851	.	.	ENSG00000186094	ENST00000371839;ENST00000411952;ENST00000334103	T;T	0.11495	2.77;2.77	5.9	5.9	0.94986	Peptidase M14, carboxypeptidase A (1);	0.000000	0.85682	D	0.000000	T	0.45875	0.1364	M	0.92268	3.29	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	1.0;0.998;1.0;1.0;1.0	T	0.54516	-0.8282	9	.	.	.	-22.8004	19.2681	0.93997	0.0:0.0:1.0:0.0	.	199;396;117;229;384	A0AVJ2;Q5VU57-2;B4DGK1;B1AMW2;Q5VU57	.;.;.;.;CBPC6_HUMAN	C	384;378;117	ENSP00000360905:R384C;ENSP00000335516:R117C	.	R	-	1	0	AGBL4	48825380	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	5.934000	0.70138	2.804000	0.96469	0.549000	0.68633	CGT		0.547	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785	
BEND5	79656	broad.mit.edu	37	1	49224725	49224725	+	Missense_Mutation	SNP	G	G	A	rs201098567		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:49224725G>A	ENST00000371833.3	-	3	678	c.592C>T	c.(592-594)Cgc>Tgc	p.R198C	BEND5_ENST00000476096.1_5'UTR|AGBL4_ENST00000371839.1_Intron|AGBL4_ENST00000371838.1_Intron	NM_024603.2	NP_078879.2	Q7L4P6	BEND5_HUMAN	BEN domain containing 5	198						Golgi apparatus (GO:0005794)		p.R29C(2)		large_intestine(5)|lung(2)|skin(1)	8						TGGAGGTGGCGCATCTCTTCC	0.587																																					p.R198C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C592T	1						.	G	CYS/ARG,	0,4406		0,0,2203	98.0	92.0	94.0		592,	4.5	1.0	1		94	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron	BEND5,AGBL4	NM_024603.2,NM_032785.3	180,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,	198/422,	49224725	1,13005	2203	4300	6503	48997312	SO:0001583	missense	79656	exon3			BC007932	CCDS552.2	1p33	2012-11-22	2008-10-03	2008-10-03	ENSG00000162373	ENSG00000162373		"""BEN domain containing"""	25668	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 165"""	C1orf165		12477932	Standard	NM_024603		Approved	FLJ11588	uc001crx.4	Q7L4P6	OTTHUMG00000008153	ENST00000371833.3:c.592C>T	1.37:g.49224725G>A	ENSP00000360899:p.Arg198Cys	Somatic		Capture	Illumina HiSeq	Phase_I	48997312	NM_024603	D3DQ27|Q96A62|Q9HAI3	Missense_Mutation	SNP	ENST00000371833.3	37	CCDS552.2	.	.	.	.	.	.	.	.	.	.	G	19.23	3.788076	0.70337	0.0	1.16E-4	ENSG00000162373	ENST00000371833	.	.	.	5.4	4.47	0.54385	.	0.048307	0.85682	D	0.000000	T	0.42040	0.1185	L	0.29908	0.895	0.58432	D	0.999996	D	0.69078	0.997	B	0.44315	0.446	T	0.24941	-1.0146	8	.	.	.	-20.9454	12.2606	0.54649	0.0:0.0:0.5714:0.4286	.	198	Q7L4P6	BEND5_HUMAN	C	198	.	.	R	-	1	0	BEND5	48997312	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.206000	0.58473	1.376000	0.46267	0.655000	0.94253	CGC		0.587	BEND5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022323.1	NM_024603	
TTC39A	22996	broad.mit.edu	37	1	51755719	51755719	+	Missense_Mutation	SNP	C	C	T	rs368894146	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:51755719C>T	ENST00000447632.2	-	16	1607	c.1559G>A	c.(1558-1560)cGt>cAt	p.R520H	TTC39A_ENST00000451380.1_Missense_Mutation_p.R484H|TTC39A_ENST00000534098.1_5'UTR|TTC39A_ENST00000371750.5_Missense_Mutation_p.R485H|TTC39A_ENST00000413473.2_Missense_Mutation_p.R488H|TTC39A_ENST00000262675.7_Missense_Mutation_p.R457H|TTC39A_ENST00000530004.1_Missense_Mutation_p.R128H			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A	520								p.0?(2)|p.R520H(1)|p.R457H(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(2)|prostate(2)|skin(3)|urinary_tract(1)	17						CTCCTGGACACGGCCCAGGTA	0.498													C|||	3	0.000599042	0.0023	0.0	5008	,	,		20084	0.0		0.0	False		,,,				2504	0.0				p.R488H												.	.	4	Substitution - Missense(2)|Whole gene deletion(2)	large_intestine(2)|thyroid(1)|central_nervous_system(1)	c.G1463A	1						.	C	HIS/ARG,HIS/ARG	1,3765		0,1,1882	55.0	53.0	53.0		1463,1454	3.2	0.9	1		53	0,8242		0,0,4121	no	missense,missense	TTC39A	NM_001144832.1,NM_001080494.2	29,29	0,1,6003	TT,TC,CC		0.0,0.0266,0.0083	benign,benign	488/582,485/579	51755719	1,12007	1883	4121	6004	51528307	SO:0001583	missense	22996	exon16			AB007921	CCDS44143.1, CCDS44144.1, CCDS72789.1, CCDS72790.1	1p32.3	2013-01-11	2008-06-23	2008-06-23	ENSG00000085831	ENSG00000085831		"""Tetratricopeptide (TTC) repeat domain containing"""	18657	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 34"""	C1orf34		9455484, 9461476	Standard	XM_005270643		Approved	KIAA0452, DEME-6	uc010onf.2	Q5SRH9	OTTHUMG00000008193	ENST00000447632.2:c.1559G>A	1.37:g.51755719C>T	ENSP00000393952:p.Arg520His	Somatic		Capture	Illumina HiSeq	Phase_I	51528307	NM_001144832	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	Missense_Mutation	SNP	ENST00000447632.2	37		.	.	.	.	.	.	.	.	.	.	C	13.78	2.340615	0.41498	2.66E-4	0.0	ENSG00000085831	ENST00000530004;ENST00000447632;ENST00000413473;ENST00000262675;ENST00000451380;ENST00000371750	T;T;T;T;T;T	0.67171	-0.25;0.67;0.67;0.67;0.67;0.67	6.07	3.17	0.36434	Tetratricopeptide-like helical (1);	0.396223	0.32055	N	0.006660	T	0.49474	0.1559	L	0.28556	0.865	0.26689	N	0.971383	B;B;B;B;B	0.27286	0.019;0.011;0.109;0.011;0.174	B;B;B;B;B	0.23275	0.012;0.005;0.02;0.009;0.045	T	0.40627	-0.9553	10	0.34782	T	0.22	-9.0014	9.0428	0.36327	0.0:0.7227:0.0:0.2773	.	488;484;457;520;485	Q5SRH9-4;E7EQY9;D3DQ30;Q5SRH9;G3XAF8	.;.;.;TT39A_HUMAN;.	H	128;520;488;457;484;485	ENSP00000431228:R128H;ENSP00000393952:R520H;ENSP00000406144:R488H;ENSP00000262675:R457H;ENSP00000397207:R484H;ENSP00000360815:R485H	ENSP00000262675:R457H	R	-	2	0	TTC39A	51528307	0.505000	0.26131	0.907000	0.35723	0.787000	0.44495	0.909000	0.28558	1.567000	0.49668	0.655000	0.94253	CGT		0.498	TTC39A-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000022434.2		
EPS15	2060	broad.mit.edu	37	1	51871645	51871645	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:51871645C>A	ENST00000371733.3	-	16	1705	c.1609G>T	c.(1609-1611)Gcc>Tcc	p.A537S	EPS15_ENST00000493793.1_5'UTR|EPS15_ENST00000396122.4_Missense_Mutation_p.A214S|EPS15_ENST00000371730.2_Intron	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	537					cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(2)|p.A537S(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						TTAAGGTTGGCTGTTTCACTG	0.433			T	MLL	ALL																																p.A223S			Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	.	.	3	Whole gene deletion(2)|Substitution - Missense(1)	thyroid(1)|large_intestine(1)|central_nervous_system(1)	c.G667T	1						.						213.0	180.0	191.0					1																	51871645		2203	4300	6503	51644233	SO:0001583	missense	2060	exon4			BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"""EF-hand domain containing"""	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.1609G>T	1.37:g.51871645C>A	ENSP00000360798:p.Ala537Ser	Somatic		Capture	Illumina HiSeq	Phase_I	51644233	NM_001159969	B2R8J7|D3DPJ2|Q5SRH4	Missense_Mutation	SNP	ENST00000371733.3	37	CCDS557.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.678360	0.47886	.	.	ENSG00000085832	ENST00000371733;ENST00000396122	T;T	0.42900	2.29;0.96	5.4	4.49	0.54785	.	0.000000	0.32204	N	0.006421	T	0.32823	0.0842	L	0.44542	1.39	0.41587	D	0.988775	B;B	0.33940	0.433;0.155	B;B	0.30029	0.11;0.07	T	0.19778	-1.0295	10	0.49607	T	0.09	.	10.2315	0.43258	0.0:0.8509:0.0:0.1491	.	537;223	P42566;P42566-2	EPS15_HUMAN;.	S	537;214	ENSP00000360798:A537S;ENSP00000379428:A214S	ENSP00000360798:A537S	A	-	1	0	EPS15	51644233	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.956000	0.40382	1.521000	0.48983	0.563000	0.77884	GCC		0.433	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981	
CC2D1B	200014	broad.mit.edu	37	1	52825482	52825482	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:52825482C>T	ENST00000371586.2	-	8	975	c.837G>A	c.(835-837)ccG>ccA	p.P279P	CC2D1B_ENST00000438831.1_5'UTR|CC2D1B_ENST00000460261.1_5'UTR|CC2D1B_ENST00000284376.3_Silent_p.P279P	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	279	Pro-rich.					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)	p.P279P(1)		breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						GCAGGGCCCGCGGGTCTGGGT	0.592																																					p.P279P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G837A	1						.						27.0	26.0	27.0					1																	52825482		2203	4300	6503	52598070	SO:0001819	synonymous_variant	200014	exon8			AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.837G>A	1.37:g.52825482C>T		Somatic		Capture	Illumina HiSeq	Phase_I	52598070	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Silent	SNP	ENST00000371586.2	37	CCDS30714.1	.	.	.	.	.	.	.	.	.	.	C	1.197	-0.633551	0.03584	.	.	ENSG00000154222	ENST00000438021;ENST00000450942	.	.	.	5.02	-10.0	0.00425	.	.	.	.	.	T	0.33818	0.0876	.	.	.	0.40241	D	0.977956	.	.	.	.	.	.	T	0.39502	-0.9611	4	.	.	.	-3.9345	2.543	0.04730	0.197:0.2804:0.3729:0.1497	.	.	.	.	H	66;199	.	.	R	-	2	0	CC2D1B	52598070	0.000000	0.05858	0.001000	0.08648	0.364000	0.29643	-3.229000	0.00549	-2.038000	0.00918	-1.934000	0.00508	CGC		0.592	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449	
CC2D1B	200014	broad.mit.edu	37	1	52826803	52826803	+	Splice_Site	SNP	G	G	A	rs140457418		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:52826803G>A	ENST00000371586.2	-	5	458	c.320C>T	c.(319-321)aCg>aTg	p.T107M	CC2D1B_ENST00000438831.1_De_novo_Start_InFrame|CC2D1B_ENST00000460261.1_5'Flank|CC2D1B_ENST00000284376.3_Splice_Site_p.T107M	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	107	Glu-rich.					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)	p.T107M(1)		breast(1)|large_intestine(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						CTGCAGCTCCGTCTAGGGAGA	0.572													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17850	0.0		0.0	False		,,,				2504	0.0				p.T107M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C320T	1						.	G	MET/THR	4,4402	8.1+/-20.4	0,4,2199	57.0	56.0	57.0		320	2.7	1.0	1	dbSNP_134	57	0,8600		0,0,4300	yes	missense-near-splice	CC2D1B	NM_032449.2	81	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	probably-damaging	107/859	52826803	4,13002	2203	4300	6503	52599391	SO:0001630	splice_region_variant	200014	exon5			AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.319-1C>T	1.37:g.52826803G>A		Somatic		Capture	Illumina HiSeq	Phase_I	52599391	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	37	CCDS30714.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.925|9.925	1.213193|1.213193	0.22289|0.22289	9.08E-4|9.08E-4	0.0|0.0	ENSG00000154222|ENSG00000154222	ENST00000450942|ENST00000371586;ENST00000284376;ENST00000371573	.|T;T	.|0.24723	.|1.84;1.84	4.71|4.71	2.72|2.72	0.32119|0.32119	.|.	.|0.190042	.|0.44902	.|D	.|0.000417	T|T	0.24890|0.24890	0.0604|0.0604	L|L	0.51422|0.51422	1.61|1.61	0.80722|0.80722	D|D	1|1	.|D	.|0.57257	.|0.979	.|P	.|0.44477	.|0.451	T|T	0.02646|0.02646	-1.1129|-1.1129	5|10	.|0.59425	.|D	.|0.04	-5.4388|-5.4388	9.6852|9.6852	0.40094|0.40094	0.0:0.0:0.6213:0.3787|0.0:0.0:0.6213:0.3787	.|.	.|107	.|Q5T0F9	.|C2D1B_HUMAN	W|M	48|107;107;21	.|ENSP00000360642:T107M;ENSP00000284376:T107M	.|ENSP00000284376:T107M	R|T	-|-	1|2	2|0	CC2D1B|CC2D1B	52599391|52599391	0.923000|0.923000	0.31300|0.31300	0.999000|0.999000	0.59377|0.59377	0.187000|0.187000	0.23431|0.23431	0.447000|0.447000	0.21710|0.21710	0.639000|0.639000	0.30564|0.30564	0.655000|0.655000	0.94253|0.94253	CGG|ACG		0.572	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449	Missense_Mutation
ZYG11B	79699	broad.mit.edu	37	1	53279267	53279267	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:53279267C>G	ENST00000294353.6	+	11	1900	c.1755C>G	c.(1753-1755)gaC>gaG	p.D585E	ZYG11B_ENST00000443756.2_Missense_Mutation_p.D515E|ZYG11B_ENST00000545132.1_3'UTR	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	585								p.D585E(1)		breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						ATTTTATAGACCACATCAGTA	0.323																																					p.D585E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1755G	1						.						70.0	66.0	68.0					1																	53279267		2203	4300	6503	53051855	SO:0001583	missense	79699	exon11			AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"""ZYG11 cell cycle regulator family"""	25820	protein-coding gene	gene with protein product			"""zyg-11 homolog (C. elegans)"", ""zyg-11 homolog B (C. elegans)"""	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.1755C>G	1.37:g.53279267C>G	ENSP00000294353:p.Asp585Glu	Somatic		Capture	Illumina HiSeq	Phase_I	53051855	NM_024646	Q8N2X3|Q9H8L8	Missense_Mutation	SNP	ENST00000294353.6	37	CCDS30717.1	.	.	.	.	.	.	.	.	.	.	C	10.28	1.305375	0.23736	.	.	ENSG00000162378	ENST00000443756;ENST00000294353	T;T	0.47528	0.84;0.84	5.27	3.4	0.38934	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.26593	0.0650	N	0.19112	0.55	0.80722	D	1	B;B	0.21753	0.019;0.06	B;B	0.22753	0.041;0.023	T	0.05468	-1.0883	10	0.07325	T	0.83	.	8.532	0.33340	0.0:0.7668:0.0:0.2332	.	515;585	B4DK95;Q9C0D3	.;ZY11B_HUMAN	E	515;585	ENSP00000400522:D515E;ENSP00000294353:D585E	ENSP00000294353:D585E	D	+	3	2	ZYG11B	53051855	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.822000	0.39052	1.213000	0.43380	0.655000	0.94253	GAC		0.323	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646	
YIPF1	54432	broad.mit.edu	37	1	54337051	54337051	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:54337051G>A	ENST00000072644.1	-	7	811	c.475C>T	c.(475-477)Cga>Tga	p.R159*	YIPF1_ENST00000469457.1_5'UTR|YIPF1_ENST00000371399.1_5'UTR|YIPF1_ENST00000539954.1_Nonsense_Mutation_p.R184*	NM_018982.4	NP_061855.1	Q9Y548	YIPF1_HUMAN	Yip1 domain family, member 1	159						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)		p.R159*(2)		endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|skin(1)|urinary_tract(2)	19						CAACCTTTTCGGAATTCGGGC	0.453																																					p.R159X												YIPF1,large_intestine,colon,Substitution - Missense,0 	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C475T	1						.						134.0	120.0	125.0					1																	54337051		2203	4300	6503	54109639	SO:0001587	stop_gained	54432	exon7			BC009674	CCDS584.1	1p33-p32.1	2008-02-05			ENSG00000058799	ENSG00000058799		"""Yip1 domain family"""	25231	protein-coding gene	gene with protein product						12477932	Standard	NM_018982		Approved	DJ167A19.1, FinGER1	uc001cvu.3	Q9Y548	OTTHUMG00000008074	ENST00000072644.1:c.475C>T	1.37:g.54337051G>A	ENSP00000072644:p.Arg159*	Somatic		Capture	Illumina HiSeq	Phase_I	54109639	NM_018982	B2RCM7|D3DQ40|Q9NWJ1	Nonsense_Mutation	SNP	ENST00000072644.1	37	CCDS584.1	.	.	.	.	.	.	.	.	.	.	G	39	7.499856	0.98322	.	.	ENSG00000058799	ENST00000072644;ENST00000539954;ENST00000412288	.	.	.	5.55	5.55	0.83447	.	0.163795	0.52532	D	0.000071	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	-19.221	13.5214	0.61569	0.0:0.0:0.7391:0.2609	.	.	.	.	X	159;184;159	.	ENSP00000072644:R159X	R	-	1	2	YIPF1	54109639	0.991000	0.36638	1.000000	0.80357	0.981000	0.71138	1.244000	0.32778	2.604000	0.88044	0.555000	0.69702	CGA		0.453	YIPF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022103.5	NM_018982	
MRPL37	51253	broad.mit.edu	37	1	54681856	54681856	+	Missense_Mutation	SNP	G	G	A	rs369065705		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:54681856G>A	ENST00000360840.5	+	6	1110	c.1033G>A	c.(1033-1035)Gtg>Atg	p.V345M	MRPL37_ENST00000605337.1_Missense_Mutation_p.V345M|MRPL37_ENST00000336230.6_Missense_Mutation_p.V214M	NM_016491.3	NP_057575.2	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37	345					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.V345M(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(4)|skin(2)	19						GGTGCAGAGCGTGGGCACGGA	0.517																																					p.V345M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1033A	1						.	G	MET/VAL	0,4406		0,0,2203	176.0	155.0	162.0		1033	3.3	1.0	1		162	1,8599	1.2+/-3.3	0,1,4299	no	missense	MRPL37	NM_016491.3	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	345/424	54681856	1,13005	2203	4300	6503	54454444	SO:0001583	missense	51253	exon6			AB051344	CCDS589.1	1p32.1	2012-09-13			ENSG00000116221	ENSG00000116221		"""Mitochondrial ribosomal proteins / large subunits"""	14034	protein-coding gene	gene with protein product		611843				10600119	Standard	NM_016491		Approved	RPML2, MRP-L2	uc001cxa.4	Q9BZE1	OTTHUMG00000008118	ENST00000360840.5:c.1033G>A	1.37:g.54681856G>A	ENSP00000354086:p.Val345Met	Somatic		Capture	Illumina HiSeq	Phase_I	54454444	NM_016491	Q96Q67|Q9BWR1|Q9P0P3	Missense_Mutation	SNP	ENST00000360840.5	37	CCDS589.1	.	.	.	.	.	.	.	.	.	.	G	11.02	1.514810	0.27123	0.0	1.16E-4	ENSG00000116221	ENST00000360840;ENST00000329505;ENST00000336230	T;T	0.32753	1.44;1.44	5.23	3.33	0.38152	.	0.118458	0.64402	D	0.000020	T	0.49047	0.1534	M	0.77820	2.39	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.991	P;P;P	0.60886	0.88;0.854;0.771	T	0.53034	-0.8495	10	0.87932	D	0	-14.5998	9.371	0.38254	0.2227:0.0:0.7773:0.0	.	214;282;345	A6NHR2;E9PB99;Q9BZE1	.;.;RM37_HUMAN	M	345;282;214	ENSP00000354086:V345M;ENSP00000338526:V214M	ENSP00000328799:V282M	V	+	1	0	MRPL37	54454444	0.989000	0.36119	0.963000	0.40424	0.057000	0.15508	2.009000	0.40903	1.204000	0.43247	-0.391000	0.06502	GTG		0.517	MRPL37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022224.1	NM_016491	
C1orf177	163747	broad.mit.edu	37	1	55282733	55282733	+	Silent	SNP	A	A	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:55282733A>T	ENST00000371273.3	+	9	1137	c.1122A>T	c.(1120-1122)cgA>cgT	p.R374R	C1orf177_ENST00000358193.3_Silent_p.R374R	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	374								p.R374R(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						AGCGATATCGATCCCTATTCC	0.597																																					p.R374R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1122T	1						.						118.0	88.0	98.0					1																	55282733		2203	4300	6503	55055321	SO:0001819	synonymous_variant	163747	exon9			AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.1122A>T	1.37:g.55282733A>T		Somatic		Capture	Illumina HiSeq	Phase_I	55055321	NM_001110533	B7WPL2|Q8N7Y9	Silent	SNP	ENST00000371273.3	37	CCDS44153.1																																																																																				0.597	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607	
PCSK9	255738	broad.mit.edu	37	1	55524309	55524309	+	Missense_Mutation	SNP	G	G	A	rs145468572	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:55524309G>A	ENST00000302118.5	+	9	1782	c.1492G>A	c.(1492-1494)Gag>Aag	p.E498K	PCSK9_ENST00000543384.1_3'UTR|PCSK9_ENST00000490692.1_3'UTR	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	498	C-terminal domain.				apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.E498K(1)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						GCGGCGGGGCGAGCGCATGGA	0.637																																					p.E498K	Pancreas(137;1454 1827 5886 22361 42375)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1492A	1						.	G	LYS/GLU	0,4406		0,0,2203	22.0	20.0	21.0		1492	3.4	0.2	1	dbSNP_134	21	4,8592	3.7+/-12.6	0,4,4294	yes	missense	PCSK9	NM_174936.3	56	0,4,6497	AA,AG,GG		0.0465,0.0,0.0308	possibly-damaging	498/693	55524309	4,12998	2203	4298	6501	55296897	SO:0001583	missense	255738	exon9			AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.1492G>A	1.37:g.55524309G>A	ENSP00000303208:p.Glu498Lys	Somatic		Capture	Illumina HiSeq	Phase_I	55296897	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Missense_Mutation	SNP	ENST00000302118.5	37	CCDS603.1	.	.	.	.	.	.	.	.	.	.	G	19.05	3.752033	0.69533	0.0	4.65E-4	ENSG00000169174	ENST00000302118	T	0.72725	-0.68	4.35	3.43	0.39272	.	0.071954	0.51477	D	0.000090	T	0.67924	0.2945	M	0.61703	1.905	0.80722	D	1	D	0.62365	0.991	B	0.43809	0.432	T	0.70561	-0.4838	10	0.62326	D	0.03	-15.1672	11.8615	0.52469	0.0879:0.0:0.9121:0.0	.	498	Q8NBP7	PCSK9_HUMAN	K	498	ENSP00000303208:E498K	ENSP00000303208:E498K	E	+	1	0	PCSK9	55296897	1.000000	0.71417	0.231000	0.23993	0.588000	0.36517	5.092000	0.64511	0.793000	0.33875	0.313000	0.20887	GAG		0.637	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
C1orf168	199920	broad.mit.edu	37	1	57257913	57257913	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:57257913G>A	ENST00000343433.6	-	2	653	c.573C>T	c.(571-573)gcC>gcT	p.A191A	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	191								p.A191A(1)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						GAAGAGTCTGGGCTCCTTTTG	0.463																																					p.A191A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C573T	1						.						102.0	104.0	103.0					1																	57257913		2203	4300	6503	57030501	SO:0001819	synonymous_variant	199920	exon2			BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.573C>T	1.37:g.57257913G>A		Somatic		Capture	Illumina HiSeq	Phase_I	57030501	NM_001004303	Q63HM3|Q6ZUY6	Silent	SNP	ENST00000343433.6	37	CCDS30729.1																																																																																				0.463	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303	
EFCAB7	84455	broad.mit.edu	37	1	64022857	64022857	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:64022857delT	ENST00000371088.4	+	10	1533	c.1287delT	c.(1285-1287)aatfs	p.N429fs	EFCAB7_ENST00000461039.1_3'UTR	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	429	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)	p.F431fs*3(1)		breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						AAGAATATAATTTTTTTGAAT	0.294																																					p.N429fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1287delT	1						.						70.0	80.0	77.0					1																	64022857		2203	4298	6501	63795445	SO:0001589	frameshift_variant	84455	exon10			BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.1287delT	1.37:g.64022857delT	ENSP00000360129:p.Asn429fs	Somatic		Capture	Illumina HiSeq	Phase_I	63795445	NM_032437	Q658P0|Q96B95|Q96JM6	Frame_Shift_Del	DEL	ENST00000371088.4	37	CCDS30737.1																																																																																				0.294	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
UBE2U	148581	broad.mit.edu	37	1	64672525	64672525	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:64672525C>T	ENST00000371076.3	+	3	471	c.227C>T	c.(226-228)cCg>cTg	p.P76L		NM_152489.1	NP_689702.1	Q5VVX9	UBE2U_HUMAN	ubiquitin-conjugating enzyme E2U (putative)	76					protein ubiquitination (GO:0016567)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)	p.P76L(1)		large_intestine(3)|lung(2)|skin(1)	6						ATAACAATTCCGTTTCATCCA	0.294																																					p.P76L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C227T	1						.						46.0	47.0	47.0					1																	64672525		2201	4293	6494	64445113	SO:0001583	missense	148581	exon3			BC029895	CCDS627.1	1p31.3	2008-02-05			ENSG00000177414	ENSG00000177414		"""Ubiquitin-conjugating enzymes E2"""	28559	protein-coding gene	gene with protein product						12477932	Standard	NM_152489		Approved	MGC35130	uc001dbn.1	Q5VVX9	OTTHUMG00000009023	ENST00000371076.3:c.227C>T	1.37:g.64672525C>T	ENSP00000360116:p.Pro76Leu	Somatic		Capture	Illumina HiSeq	Phase_I	64445113	NM_152489	Q8N1D4	Missense_Mutation	SNP	ENST00000371076.3	37	CCDS627.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.151028	0.57151	.	.	ENSG00000177414	ENST00000371077;ENST00000371076	T;T	0.34667	1.35;1.35	5.87	5.87	0.94306	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.64402	D	0.000009	T	0.31136	0.0787	L	0.33710	1.025	0.58432	D	0.999995	D	0.89917	1.0	D	0.97110	1.0	T	0.09271	-1.0682	10	0.02654	T	1	.	15.7051	0.77573	0.0:1.0:0.0:0.0	.	76	Q5VVX9	UBE2U_HUMAN	L	76	ENSP00000360117:P76L;ENSP00000360116:P76L	ENSP00000360116:P76L	P	+	2	0	UBE2U	64445113	1.000000	0.71417	1.000000	0.80357	0.288000	0.27193	3.824000	0.55723	2.777000	0.95525	0.591000	0.81541	CCG		0.294	UBE2U-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025005.1	NM_152489	
CACHD1	57685	broad.mit.edu	37	1	65068576	65068576	+	Silent	SNP	A	A	G	rs369437288		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:65068576A>G	ENST00000371073.2	+	4	498	c.498A>G	c.(496-498)ccA>ccG	p.P166P	CACHD1_ENST00000290039.5_Silent_p.P115P|CACHD1_ENST00000495994.1_3'UTR			Q5VU97	CAHD1_HUMAN	cache domain containing 1	166					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)		p.P115P(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						CCTTCAATCCAGGACGAGACT	0.348													A|||	1	0.000199681	0.0	0.0	5008	,	,		14292	0.001		0.0	False		,,,				2504	0.0				p.P115P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A345G	1						.	A		0,3662		0,0,1831	117.0	104.0	108.0		345	3.1	1.0	1		108	1,8169		0,1,4084	no	coding-synonymous	CACHD1	NM_020925.2		0,1,5915	GG,GA,AA		0.0122,0.0,0.0085		115/1224	65068576	1,11831	1831	4085	5916	64841164	SO:0001819	synonymous_variant	57685	exon4			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"""von Willebrand factor type A and cache domain containing 1"""	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.498A>G	1.37:g.65068576A>G		Somatic		Capture	Illumina HiSeq	Phase_I	64841164	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Silent	SNP	ENST00000371073.2	37																																																																																					0.348	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925	
CACHD1	57685	broad.mit.edu	37	1	65130209	65130209	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:65130209C>A	ENST00000371073.2	+	15	2123	c.2123C>A	c.(2122-2124)aCc>aAc	p.T708N	CACHD1_ENST00000290039.5_Missense_Mutation_p.T657N|CACHD1_ENST00000495994.1_3'UTR			Q5VU97	CAHD1_HUMAN	cache domain containing 1	708					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)		p.T657N(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GTAATGGCTACCAGCCACGTC	0.463																																					p.T657N												.	.	1	Substitution - Missense(1)	prostate(1)	c.C1970A	1						.						117.0	104.0	109.0					1																	65130209		2203	4300	6503	64902797	SO:0001583	missense	57685	exon15			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"""von Willebrand factor type A and cache domain containing 1"""	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.2123C>A	1.37:g.65130209C>A	ENSP00000360113:p.Thr708Asn	None		Capture	Illumina HiSeq	Phase_I	64902797	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Missense_Mutation	SNP	ENST00000371073.2	37		.	.	.	.	.	.	.	.	.	.	C	29.1	4.977496	0.92982	.	.	ENSG00000158966	ENST00000371073;ENST00000290039	T;T	0.26810	1.71;1.72	6.17	6.17	0.99709	.	0.041943	0.85682	D	0.000000	T	0.17408	0.0418	L	0.40543	1.245	0.80722	D	1	B	0.23891	0.093	B	0.29785	0.107	T	0.02966	-1.1088	10	0.33940	T	0.23	-30.9607	20.8794	0.99867	0.0:1.0:0.0:0.0	.	708	Q5VU97	CAHD1_HUMAN	N	708;657	ENSP00000360113:T708N;ENSP00000290039:T657N	ENSP00000290039:T657N	T	+	2	0	CACHD1	64902797	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.487000	0.81328	2.941000	0.99782	0.655000	0.94253	ACC		0.463	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925	
LEPR	3953	broad.mit.edu	37	1	66074506	66074506	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:66074506G>A	ENST00000349533.6	+	12	1859	c.1674G>A	c.(1672-1674)tgG>tgA	p.W558*	LEPR_ENST00000406510.3_Intron|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000371060.3_Nonsense_Mutation_p.W558*|LEPR_ENST00000344610.8_Nonsense_Mutation_p.W558*|LEPR_ENST00000371059.3_Nonsense_Mutation_p.W558*|LEPR_ENST00000371058.1_Nonsense_Mutation_p.W558*	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.W558*(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)		AAATATCTTGGGAAAAGCCAG	0.343																																					p.W558X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1674A	1						.						60.0	63.0	62.0					1																	66074506		2203	4296	6499	65847094	SO:0001587	stop_gained	3953	exon12			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.1674G>A	1.37:g.66074506G>A	ENSP00000330393:p.Trp558*	Somatic		Capture	Illumina HiSeq	Phase_I	65847094	NM_001003679	Q6FHL5	Nonsense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	.	.	.	.	.	.	.	.	.	.	G	39	7.641610	0.98406	.	.	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	.	.	.	5.45	5.45	0.79879	.	0.107310	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.9234	19.357	0.94418	0.0:0.0:1.0:0.0	.	.	.	.	X	558	.	ENSP00000340884:W558X	W	+	3	0	LEPR	65847094	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.130000	0.77235	2.583000	0.87209	0.650000	0.86243	TGG		0.343	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
ZRANB2	9406	broad.mit.edu	37	1	71536547	71536547	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:71536547G>A	ENST00000370920.3	-	7	947	c.646C>T	c.(646-648)Cgc>Tgc	p.R216C	ZRANB2_ENST00000254821.6_Missense_Mutation_p.R216C	NM_203350.2	NP_976225.1	O95218	ZRAB2_HUMAN	zinc finger, RAN-binding domain containing 2	216	Arg/Ser-rich.|Required for nuclear targeting.				mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R216C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|stomach(1)	15						GAGGATGAGCGTGATGAAGAT	0.388																																					p.R216C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C646T	1						.						276.0	258.0	264.0					1																	71536547		2203	4300	6503	71309135	SO:0001583	missense	9406	exon7			AF065391	CCDS659.1, CCDS660.1	1p31	2008-02-05	2006-06-28	2006-06-28	ENSG00000132485	ENSG00000132485		"""Zinc fingers, RAN-binding domain containing"""	13058	protein-coding gene	gene with protein product		604347	"""zinc finger protein 265"""	ZNF265		9931435	Standard	NM_005455		Approved	ZIS, ZIS1, ZIS2	uc001dft.3	O95218	OTTHUMG00000009660	ENST00000370920.3:c.646C>T	1.37:g.71536547G>A	ENSP00000359958:p.Arg216Cys	Somatic		Capture	Illumina HiSeq	Phase_I	71309135	NM_005455	D3DQ75|Q53GS3|Q59F92|Q5VV33|Q5VV34|Q8IXN6|Q9UP63	Missense_Mutation	SNP	ENST00000370920.3	37	CCDS659.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.015985	0.75161	.	.	ENSG00000132485	ENST00000370920;ENST00000254821	T;T	0.68765	-0.35;-0.35	6.06	6.06	0.98353	.	0.093739	0.85682	D	0.000000	T	0.70290	0.3207	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.973;0.988	T	0.72537	-0.4263	10	0.66056	D	0.02	.	20.6397	0.99537	0.0:0.0:1.0:0.0	.	216;216	O95218;O95218-2	ZRAB2_HUMAN;.	C	216	ENSP00000359958:R216C;ENSP00000254821:R216C	ENSP00000254821:R216C	R	-	1	0	ZRANB2	71309135	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.617000	0.83032	2.880000	0.98712	0.650000	0.86243	CGC		0.388	ZRANB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026636.1	NM_203350	
RABGGTB	5876	broad.mit.edu	37	1	76257984	76257984	+	Missense_Mutation	SNP	C	C	T	rs138598204		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:76257984C>T	ENST00000319942.3	+	7	769	c.698C>T	c.(697-699)cCg>cTg	p.P233L	SNORD45B_ENST00000364617.1_RNA|RABGGTB_ENST00000496055.1_3'UTR|RABGGTB_ENST00000535300.1_Missense_Mutation_p.P59L	NM_004582.3	NP_004573.2	P53611	PGTB2_HUMAN	Rab geranylgeranyltransferase, beta subunit	233	Geranylgeranyl diphosphate binding. {ECO:0000250}.				cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)	p.P233L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)	19						AATGGAAGGCCGGAGAAGGTA	0.423													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16250	0.0		0.0	False		,,,				2504	0.0				p.P233L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C698T	1						.	C	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	88.0	92.0	91.0		698	4.7	1.0	1	dbSNP_134	91	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RABGGTB	NM_004582.2	98	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	233/332	76257984	2,13004	2203	4300	6503	76030572	SO:0001583	missense	5876	exon7			U49245	CCDS669.1	1p31	2008-02-05			ENSG00000137955	ENSG00000137955			9796	protein-coding gene	gene with protein product		179080				8706741, 8954794	Standard	NM_004582		Approved		uc001dgy.2	P53611	OTTHUMG00000009786	ENST00000319942.3:c.698C>T	1.37:g.76257984C>T	ENSP00000317473:p.Pro233Leu	Somatic		Capture	Illumina HiSeq	Phase_I	76030572	NM_004582	Q92697	Missense_Mutation	SNP	ENST00000319942.3	37	CCDS669.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.949448	0.92660	2.27E-4	1.16E-4	ENSG00000137955	ENST00000535300;ENST00000319942;ENST00000370824	T;T	0.24908	1.83;1.83	5.58	4.67	0.58626	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.050356	0.85682	N	0.000000	T	0.57373	0.2049	H	0.96916	3.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.74106	-0.3772	10	0.66056	D	0.02	-19.7191	14.406	0.67083	0.0:0.929:0.0:0.071	.	233;233	Q59GT6;P53611	.;PGTB2_HUMAN	L	59;233;233	ENSP00000440452:P59L;ENSP00000317473:P233L	ENSP00000317473:P233L	P	+	2	0	RABGGTB	76030572	1.000000	0.71417	0.993000	0.49108	0.944000	0.59088	7.792000	0.85828	1.360000	0.45960	0.561000	0.74099	CCG		0.423	RABGGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026972.1	NM_004582	
PIGK	10026	broad.mit.edu	37	1	77672403	77672403	+	Missense_Mutation	SNP	C	C	T	rs146489857		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:77672403C>T	ENST00000370812.3	-	3	184	c.161G>A	c.(160-162)cGa>cAa	p.R54Q	PIGK_ENST00000370813.5_Intron|PIGK_ENST00000359130.1_Missense_Mutation_p.R54Q|PIGK_ENST00000445065.1_Intron|PIGK_ENST00000478391.1_Intron	NM_005482.2	NP_005473.1	Q92643	GPI8_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class K	54					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	cysteine-type endopeptidase activity (GO:0004197)|GPI-anchor transamidase activity (GO:0003923)|protein disulfide isomerase activity (GO:0003756)	p.R54Q(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	19						AAACCAGAATCGGGATGTACA	0.363																																					p.R54Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G161A	1						.	C	GLN/ARG	0,4406		0,0,2203	112.0	110.0	111.0		161	5.0	1.0	1	dbSNP_134	111	2,8598	2.2+/-6.3	0,2,4298	no	missense	PIGK	NM_005482.2	43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	54/396	77672403	2,13004	2203	4300	6503	77444991	SO:0001583	missense	10026	exon3			AF022913	CCDS674.1	1p31.1	2013-02-26	2006-06-28		ENSG00000142892	ENSG00000142892		"""Phosphatidylinositol glycan anchor biosynthesis"""	8965	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	605087	"""phosphatidylinositol glycan, class K"""			9356492	Standard	NM_005482		Approved	hGPI8, GPI8	uc001dhk.3	Q92643	OTTHUMG00000009686	ENST00000370812.3:c.161G>A	1.37:g.77672403C>T	ENSP00000359848:p.Arg54Gln	Somatic		Capture	Illumina HiSeq	Phase_I	77444991	NM_005482	B2R7K3|B4E2M3|O14822|Q5TG77	Missense_Mutation	SNP	ENST00000370812.3	37	CCDS674.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.931390	0.92389	0.0	2.33E-4	ENSG00000142892	ENST00000370812;ENST00000359130	T;T	0.52057	0.68;0.71	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.74876	0.3774	H	0.95365	3.66	0.80722	D	1	D;D	0.71674	0.996;0.998	D;D	0.77557	0.99;0.99	T	0.83148	-0.0105	10	0.72032	D	0.01	-9.9363	17.4531	0.87597	0.0:1.0:0.0:0.0	.	54;54	A6NEM5;Q92643	.;GPI8_HUMAN	Q	54	ENSP00000359848:R54Q;ENSP00000352041:R54Q	ENSP00000352041:R54Q	R	-	2	0	PIGK	77444991	1.000000	0.71417	0.998000	0.56505	0.822000	0.46500	7.086000	0.76885	2.468000	0.83385	0.655000	0.94253	CGA		0.363	PIGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026687.1	NM_005482	
ELTD1	64123	broad.mit.edu	37	1	79387315	79387315	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:79387315A>C	ENST00000370742.3	-	9	1303	c.1240T>G	c.(1240-1242)Tcc>Gcc	p.S414A		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	414	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				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.S414A(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)		GGACCAGAGGACATCAAAATT	0.388																																					p.S414A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1240G	1						.						149.0	140.0	143.0					1																	79387315		1951	4143	6094	79159903	SO:0001583	missense	64123	exon9			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.1240T>G	1.37:g.79387315A>C	ENSP00000359778:p.Ser414Ala	Somatic		Capture	Illumina HiSeq	Phase_I	79159903	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	CCDS41352.1	.	.	.	.	.	.	.	.	.	.	A	6.769	0.510696	0.12883	.	.	ENSG00000162618	ENST00000370742	T	0.36520	1.25	5.32	5.32	0.75619	GPS domain (2);	0.000000	0.85682	D	0.000000	T	0.10252	0.0251	N	0.03304	-0.355	0.52099	D	0.999947	B	0.29988	0.264	B	0.36885	0.235	T	0.21075	-1.0256	9	.	.	.	.	15.5771	0.76400	1.0:0.0:0.0:0.0	.	414	Q9HBW9	ELTD1_HUMAN	A	414	ENSP00000359778:S414A	.	S	-	1	0	ELTD1	79159903	1.000000	0.71417	1.000000	0.80357	0.506000	0.33950	5.750000	0.68712	2.130000	0.65690	0.477000	0.44152	TCC		0.388	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	
CYR61	3491	broad.mit.edu	37	1	86048471	86048471	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:86048471T>C	ENST00000451137.2	+	5	1116	c.892T>C	c.(892-894)Ttt>Ctt	p.F298L		NM_001554.4	NP_001545.2	O00622	CYR61_HUMAN	cysteine-rich, angiogenic inducer, 61	298	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.|Heparin-binding. {ECO:0000250}.				anatomical structure morphogenesis (GO:0009653)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|cell proliferation (GO:0008283)|chemotaxis (GO:0006935)|chondroblast differentiation (GO:0060591)|chorio-allantoic fusion (GO:0060710)|extracellular matrix organization (GO:0030198)|intussusceptive angiogenesis (GO:0002041)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of apoptotic process (GO:0043066)|osteoblast differentiation (GO:0001649)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|reactive oxygen species metabolic process (GO:0072593)|regulation of cell growth (GO:0001558)|regulation of ERK1 and ERK2 cascade (GO:0070372)|ventricular septum development (GO:0003281)|wound healing, spreading of cells (GO:0044319)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)	p.F298L(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|prostate(1)	5				all cancers(265;0.0216)|Epithelial(280;0.0441)		ACCAGTCAGGTTTACTTACGC	0.507											OREG0013583	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F298L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T892C	1						.						49.0	47.0	48.0					1																	86048471		2203	4300	6503	85821059	SO:0001583	missense	3491	exon5			AF031385	CCDS706.1	1p22.3	2008-02-05			ENSG00000142871	ENSG00000142871			2654	protein-coding gene	gene with protein product		602369		IGFBP10		9135077	Standard	NM_001554		Approved	GIG1, CCN1	uc001dle.3	O00622	OTTHUMG00000010577	ENST00000451137.2:c.892T>C	1.37:g.86048471T>C	ENSP00000398736:p.Phe298Leu	Somatic	1241	Capture	Illumina HiSeq	Phase_I	85821059	NM_001554	O14934|O43775|Q9BZL7	Missense_Mutation	SNP	ENST00000451137.2	37	CCDS706.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.152461	0.38021	.	.	ENSG00000142871	ENST00000451137;ENST00000536321;ENST00000360431	D	0.90504	-2.68	5.67	5.67	0.87782	Cystine knot (1);Cystine knot, C-terminal (2);	0.091326	0.85682	D	0.000000	T	0.79563	0.4467	N	0.25485	0.75	0.80722	D	1	B	0.06786	0.001	B	0.11329	0.006	T	0.76438	-0.2959	10	0.44086	T	0.13	-8.9903	15.9132	0.79488	0.0:0.0:0.0:1.0	.	298	O00622	CYR61_HUMAN	L	298;274;298	ENSP00000398736:F298L	ENSP00000353612:F298L	F	+	1	0	CYR61	85821059	1.000000	0.71417	0.994000	0.49952	0.612000	0.37316	6.176000	0.71955	2.148000	0.66965	0.533000	0.62120	TTT		0.507	CYR61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029187.1	NM_001554	
CLCA4	22802	broad.mit.edu	37	1	87025637	87025637	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:87025637C>T	ENST00000370563.3	+	2	224	c.182C>T	c.(181-183)aCg>aTg	p.T61M	CLCA4_ENST00000263723.5_5'UTR	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	61	Metalloprotease domain. {ECO:0000250|UniProtKB:A8K7I4}.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)	p.T61M(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		ACAGCTTCTACGTACCTGTTT	0.343																																					p.T61M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C182T	1						.						138.0	124.0	128.0					1																	87025637		1820	4083	5903	86798225	SO:0001583	missense	22802	exon2			AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.182C>T	1.37:g.87025637C>T	ENSP00000359594:p.Thr61Met	Somatic		Capture	Illumina HiSeq	Phase_I	86798225	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	De_novo_Start_OutOfFrame	SNP	ENST00000370563.3	37	CCDS41355.1	.	.	.	.	.	.	.	.	.	.	C	13.66	2.303901	0.40795	.	.	ENSG00000016602	ENST00000370563	T	0.12465	2.68	5.82	2.79	0.32731	Chloride channel calcium-activated (1);	0.957600	0.08747	N	0.899695	T	0.10380	0.0254	M	0.72894	2.215	0.18873	N	0.999986	P	0.42483	0.781	P	0.48571	0.582	T	0.30357	-0.9981	10	0.33940	T	0.23	-4.8939	6.2731	0.20965	0.2637:0.5996:0.0:0.1366	.	61	Q14CN2	CLCA4_HUMAN	M	61	ENSP00000359594:T61M	ENSP00000359594:T61M	T	+	2	0	CLCA4	86798225	0.000000	0.05858	0.161000	0.22692	0.786000	0.44442	0.637000	0.24659	0.768000	0.33290	0.655000	0.94253	ACG		0.343	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
HS2ST1	9653	broad.mit.edu	37	1	87563588	87563588	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:87563588C>T	ENST00000370550.5	+	5	1019	c.656C>T	c.(655-657)cCg>cTg	p.P219L	HS2ST1_ENST00000370551.4_Missense_Mutation_p.P219L|RP5-1052I5.2_ENST00000370548.2_Missense_Mutation_p.P193L|HS2ST1_ENST00000356813.4_Missense_Mutation_p.P193L	NM_012262.3	NP_036394.1	Q7LGA3	HS2ST_HUMAN	heparan sulfate 2-O-sulfotransferase 1	219					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	sulfotransferase activity (GO:0008146)	p.P219L(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)	9		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)		CTTCAAATCCCGTTCTTCTGT	0.453																																					p.P219L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C656T	1						.						152.0	144.0	147.0					1																	87563588		2203	4300	6503	87336176	SO:0001583	missense	9653	exon5			AB007917	CCDS711.1, CCDS44171.1	1p22.3	2008-02-05			ENSG00000153936	ENSG00000153936		"""Sulfotransferases, membrane-bound"""	5193	protein-coding gene	gene with protein product		604844				9455484	Standard	NM_012262		Approved	KIAA0448	uc010osk.2	Q7LGA3	OTTHUMG00000010255	ENST00000370550.5:c.656C>T	1.37:g.87563588C>T	ENSP00000359581:p.Pro219Leu	Somatic		Capture	Illumina HiSeq	Phase_I	87336176	NM_001134492	D3DT22|O75036|Q32NB5|Q8TAC5|Q9H441|Q9NUJ9	Missense_Mutation	SNP	ENST00000370550.5	37	CCDS711.1	.	.	.	.	.	.	.	.	.	.	C	35	5.560970	0.96527	.	.	ENSG00000153936	ENST00000370551;ENST00000370550;ENST00000370548;ENST00000356813	T;T;T	0.80653	-1.4;-1.4;-1.4	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.84170	0.5413	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.986	T	0.80313	-0.1435	10	0.29301	T	0.29	-34.4699	19.6092	0.95599	0.0:1.0:0.0:0.0	.	219;193	Q7LGA3;Q7LGA3-2	HS2ST_HUMAN;.	L	219;219;193;193	ENSP00000359581:P219L;ENSP00000359579:P193L;ENSP00000349268:P193L	ENSP00000349268:P193L	P	+	2	0	HS2ST1	87336176	1.000000	0.71417	0.983000	0.44433	0.964000	0.63967	7.776000	0.85560	2.693000	0.91896	0.655000	0.94253	CCG		0.453	HS2ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028279.2	NM_012262	
LMO4	8543	broad.mit.edu	37	1	87805290	87805290	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:87805290C>T	ENST00000370544.5	+	3	1088	c.308C>T	c.(307-309)gCg>gTg	p.A103V	LMO4_ENST00000489303.1_3'UTR|LMO4_ENST00000370542.1_Missense_Mutation_p.A103V	NM_006769.3	NP_006760.1	P61968	LMO4_HUMAN	LIM domain only 4	103	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of protein complex assembly (GO:0031333)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell activation (GO:0050865)|regulation of cell fate specification (GO:0042659)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron differentiation (GO:0021522)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)|ventral spinal cord interneuron differentiation (GO:0021514)|ventricular septum development (GO:0003281)	transcription factor complex (GO:0005667)	enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.A103V(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(1)	9		Lung NSC(277;0.179)		all cancers(265;0.00456)|Epithelial(280;0.0148)|BRCA - Breast invasive adenocarcinoma(282;0.153)		GTCATGAGGGCGCAAGGCAAT	0.423																																					p.A103V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C308T	1						.						100.0	98.0	99.0					1																	87805290		2203	4300	6503	87577878	SO:0001583	missense	8543	exon3			U24576	CCDS713.1	1p22.3	2008-02-05			ENSG00000143013	ENSG00000143013			6644	protein-coding gene	gene with protein product		603129					Standard	NM_006769		Approved		uc001dmi.3	P61968	OTTHUMG00000010248	ENST00000370544.5:c.308C>T	1.37:g.87805290C>T	ENSP00000359575:p.Ala103Val	Somatic		Capture	Illumina HiSeq	Phase_I	87577878	NM_006769	D3DT23|O00158|O88894	Missense_Mutation	SNP	ENST00000370544.5	37	CCDS713.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.650274	0.87958	.	.	ENSG00000143013	ENST00000370544;ENST00000370542	T;T	0.51071	0.72;0.72	5.93	5.93	0.95920	Zinc finger, LIM-type (5);	0.046304	0.85682	D	0.000000	T	0.29093	0.0723	L	0.47190	1.495	0.80722	D	1	P	0.41265	0.744	B	0.26969	0.075	T	0.34825	-0.9813	10	0.62326	D	0.03	.	20.3312	0.98718	0.0:1.0:0.0:0.0	.	103	P61968	LMO4_HUMAN	V	103	ENSP00000359575:A103V;ENSP00000359573:A103V	ENSP00000359573:A103V	A	+	2	0	LMO4	87577878	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.816000	0.86201	2.797000	0.96272	0.655000	0.94253	GCG		0.423	LMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028264.2	NM_006769	
GBP7	388646	broad.mit.edu	37	1	89615094	89615094	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:89615094G>A	ENST00000294671.2	-	7	1171	c.1033C>T	c.(1033-1035)Ccc>Tcc	p.P345S		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	345						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.P345S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		GTGTCTGTGGGGAATCTCACT	0.547																																					p.P345S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1033T	1						.						124.0	112.0	116.0					1																	89615094		2203	4300	6503	89387682	SO:0001583	missense	388646	exon7			AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1033C>T	1.37:g.89615094G>A	ENSP00000294671:p.Pro345Ser	Somatic		Capture	Illumina HiSeq	Phase_I	89387682	NM_207398		Missense_Mutation	SNP	ENST00000294671.2	37	CCDS720.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.357873	0.41801	.	.	ENSG00000213512	ENST00000294671	T	0.03920	3.76	3.54	3.54	0.40534	Guanylate-binding protein, C-terminal (3);	0.059742	0.64402	D	0.000002	T	0.17195	0.0413	M	0.92268	3.29	0.37636	D	0.921851	D	0.71674	0.998	D	0.66084	0.941	T	0.07673	-1.0760	10	0.72032	D	0.01	.	12.621	0.56603	0.0:0.0:1.0:0.0	.	345	Q8N8V2	GBP7_HUMAN	S	345	ENSP00000294671:P345S	ENSP00000294671:P345S	P	-	1	0	GBP7	89387682	1.000000	0.71417	0.988000	0.46212	0.254000	0.26022	6.105000	0.71505	1.819000	0.53055	0.523000	0.50628	CCC		0.547	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
ABCA4	24	broad.mit.edu	37	1	94466432	94466432	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:94466432C>T	ENST00000370225.3	-	47	6525	c.6439G>A	c.(6439-6441)Gcc>Acc	p.A2147T	ABCA4_ENST00000536513.1_Missense_Mutation_p.A417T|ABCA4_ENST00000465352.1_5'Flank|ABCA4_ENST00000535881.1_Missense_Mutation_p.A266T	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	2147	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)	p.A2147T(1)		NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CATCGAAAGGCGCCCTTTACC	0.572																																					p.A2147T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6439A	1						.						160.0	124.0	137.0					1																	94466432		2203	4300	6503	94239020	SO:0001583	missense	24	exon47			U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.6439G>A	1.37:g.94466432C>T	ENSP00000359245:p.Ala2147Thr	Somatic		Capture	Illumina HiSeq	Phase_I	94239020	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.660814	0.29515	.	.	ENSG00000198691	ENST00000546054;ENST00000370225;ENST00000536513;ENST00000535881	D;D;D	0.97906	-4.6;-4.6;-4.6	5.84	-4.57	0.03421	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.561946	0.19638	N	0.109504	T	0.81555	0.4847	N	0.03115	-0.41	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.61422	-0.7066	10	0.25106	T	0.35	.	7.5559	0.27824	0.1017:0.3774:0.0:0.5209	.	2147	P78363	ABCA4_HUMAN	T	939;2147;417;266	ENSP00000359245:A2147T;ENSP00000439707:A417T;ENSP00000443203:A266T	ENSP00000359245:A2147T	A	-	1	0	ABCA4	94239020	0.000000	0.05858	0.636000	0.29352	0.895000	0.52256	-1.660000	0.01974	-1.153000	0.02829	-0.345000	0.07892	GCC		0.572	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
ABCA4	24	broad.mit.edu	37	1	94497436	94497436	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:94497436C>T	ENST00000370225.3	-	27	4112	c.4026G>A	c.(4024-4026)ccG>ccA	p.P1342P		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1342					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)	p.P1342P(1)		NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TGTTGAGCTGCGGGCCTGGGC	0.662																																					p.P1342P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4026A	1						.						58.0	62.0	61.0					1																	94497436		2203	4300	6503	94270024	SO:0001819	synonymous_variant	24	exon27			U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.4026G>A	1.37:g.94497436C>T		Somatic		Capture	Illumina HiSeq	Phase_I	94270024	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																				0.662	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
LPPR4	9890	broad.mit.edu	37	1	99767376	99767376	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:99767376C>T	ENST00000370185.3	+	6	1386	c.889C>T	c.(889-891)Cgg>Tgg	p.R297W	LPPR4_ENST00000370184.1_Missense_Mutation_p.R139W|LPPR4_ENST00000457765.1_Intron	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		297					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)	p.R297W(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		CGGGCTAACACGGATAACTCA	0.373																																					p.R297W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C889T	1						.						150.0	144.0	146.0					1																	99767376		2203	4300	6503	99539964	SO:0001583	missense	9890	exon6																														ENST00000370185.3:c.889C>T	1.37:g.99767376C>T	ENSP00000359204:p.Arg297Trp	Somatic		Capture	Illumina HiSeq	Phase_I	99539964	NM_014839	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Missense_Mutation	SNP	ENST00000370185.3	37	CCDS757.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.134698	0.77662	.	.	ENSG00000117600	ENST00000370185;ENST00000263178;ENST00000370184	D;D	0.94046	-3.34;-3.34	5.11	3.16	0.36331	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.128581	0.52532	D	0.000071	D	0.96426	0.8834	M	0.91920	3.255	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	D	0.96713	0.9527	10	0.87932	D	0	-16.7263	13.7648	0.62988	0.2804:0.7196:0.0:0.0	.	297	Q7Z2D5	LPPR4_HUMAN	W	297;297;139	ENSP00000359204:R297W;ENSP00000359203:R139W	ENSP00000263178:R297W	R	+	1	2	RP4-788L13.1	99539964	0.984000	0.35163	1.000000	0.80357	0.994000	0.84299	1.809000	0.38922	0.495000	0.27882	0.491000	0.48974	CGG		0.373	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2		
PALMD	54873	broad.mit.edu	37	1	100127911	100127911	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:100127911C>T	ENST00000263174.4	+	2	457	c.82C>T	c.(82-84)Cgt>Tgt	p.R28C	PALMD_ENST00000605497.1_Missense_Mutation_p.R28C	NM_017734.4	NP_060204.1	Q9NP74	PALMD_HUMAN	palmdelphin	28					regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)		p.R28C(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)		CTCACAGAAGCGTCTGAAAAT	0.279																																					p.R28C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C82T	1						.						64.0	72.0	70.0					1																	100127911		2202	4297	6499	99900499	SO:0001583	missense	54873	exon2			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.82C>T	1.37:g.100127911C>T	ENSP00000263174:p.Arg28Cys	Somatic		Capture	Illumina HiSeq	Phase_I	99900499	NM_017734	Q9H7E6|Q9NPM5|Q9NPM6|Q9NPS0	Missense_Mutation	SNP	ENST00000263174.4	37	CCDS758.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.646472	0.67358	.	.	ENSG00000099260	ENST00000263174	T	0.39997	1.05	5.56	4.63	0.57726	.	0.054019	0.64402	D	0.000001	T	0.56891	0.2016	M	0.80982	2.52	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	T	0.65380	-0.6182	10	0.87932	D	0	-7.8768	12.837	0.57780	0.1639:0.8361:0.0:0.0	.	28	Q9NP74	PALMD_HUMAN	C	28	ENSP00000263174:R28C	ENSP00000263174:R28C	R	+	1	0	PALMD	99900499	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.792000	0.47837	1.305000	0.44909	0.563000	0.77884	CGT		0.279	PALMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029672.1	NM_017734	
FRRS1	391059	broad.mit.edu	37	1	100176425	100176425	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:100176425C>T	ENST00000414213.1	-	15	2162	c.1561G>A	c.(1561-1563)Gta>Ata	p.V521I	FRRS1_ENST00000492943.1_5'Flank|FRRS1_ENST00000287474.5_Missense_Mutation_p.V521I			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	521	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.					integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)	p.V521I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		TGCCAGGCTACGAATCCGGTC	0.448																																					p.V521I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1561A	1						.						98.0	85.0	90.0					1																	100176425		2203	4300	6503	99949013	SO:0001583	missense	391059	exon15			AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"""stromal cell derived factor receptor 2 homolog (mouse)"""	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.1561G>A	1.37:g.100176425C>T	ENSP00000393884:p.Val521Ile	Somatic		Capture	Illumina HiSeq	Phase_I	99949013	NM_001013660	A6NLN7	Missense_Mutation	SNP	ENST00000414213.1	37		.	.	.	.	.	.	.	.	.	.	C	26.0	4.698681	0.88830	.	.	ENSG00000156869	ENST00000414213;ENST00000287474	.	.	.	5.61	5.61	0.85477	.	0.302981	0.29587	N	0.011729	T	0.67702	0.2921	M	0.68593	2.085	0.80722	D	1	D	0.69078	0.997	P	0.59424	0.857	T	0.60520	-0.7247	9	0.17832	T	0.49	-26.8416	19.5966	0.95541	0.0:1.0:0.0:0.0	.	521	Q6ZNA5-2	.	I	521	.	ENSP00000287474:V521I	V	-	1	0	FRRS1	99949013	1.000000	0.71417	1.000000	0.80357	0.538000	0.34931	2.104000	0.41815	2.802000	0.96397	0.655000	0.94253	GTA		0.448	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660	
FRRS1	391059	broad.mit.edu	37	1	100206462	100206462	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:100206462C>T	ENST00000414213.1	-	6	1064	c.463G>A	c.(463-465)Gtg>Atg	p.V155M	FRRS1_ENST00000287474.5_Missense_Mutation_p.V155M			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	155	Reelin. {ECO:0000255|PROSITE- ProRule:PRU00363}.					integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)	p.V155M(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		GGAATCTTCACCCAGTAGATT	0.393																																					p.V155M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G463A	1						.						189.0	188.0	188.0					1																	100206462		2203	4300	6503	99979050	SO:0001583	missense	391059	exon6			AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"""stromal cell derived factor receptor 2 homolog (mouse)"""	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.463G>A	1.37:g.100206462C>T	ENSP00000393884:p.Val155Met	Somatic		Capture	Illumina HiSeq	Phase_I	99979050	NM_001013660	A6NLN7	Missense_Mutation	SNP	ENST00000414213.1	37		.	.	.	.	.	.	.	.	.	.	C	25.4	4.637848	0.87760	.	.	ENSG00000156869	ENST00000414213;ENST00000287474	.	.	.	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.77164	0.4090	M	0.84433	2.695	0.80722	D	1	P	0.41265	0.744	P	0.51415	0.669	T	0.79308	-0.1857	9	0.59425	D	0.04	-20.3025	19.5689	0.95404	0.0:1.0:0.0:0.0	.	155	Q6ZNA5-2	.	M	155	.	ENSP00000287474:V155M	V	-	1	0	FRRS1	99979050	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.960000	0.70348	2.626000	0.88956	0.655000	0.94253	GTG		0.393	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660	
PROX1	5629	broad.mit.edu	37	1	214169999	214169999	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:214169999delT	ENST00000366958.4	+	2	729	c.121delT	c.(121-123)tttfs	p.F42fs	PROX1_ENST00000261454.4_Frame_Shift_Del_p.F42fs|PROX1_ENST00000498508.2_Frame_Shift_Del_p.F42fs|PROX1_ENST00000435016.1_Frame_Shift_Del_p.F42fs	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	42					aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.F42fs*4(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		AAGAGCAACGTTTTTTAGTGC	0.478																																					p.F41fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.121delT	1						.						124.0	111.0	116.0					1																	214169999		2203	4300	6503	212236622	SO:0001589	frameshift_variant	5629	exon2			U44060	CCDS31021.1	1q41	2011-06-20	2007-06-01		ENSG00000117707	ENSG00000117707		"""Homeoboxes / PROS class"""	9459	protein-coding gene	gene with protein product		601546	"""prospero-related homeobox 1"""			8812486	Standard	NM_002763		Approved		uc001hkg.2	Q92786	OTTHUMG00000036946	ENST00000366958.4:c.121delT	1.37:g.214169999delT	ENSP00000355925:p.Phe42fs	Somatic		Capture	Illumina HiSeq	Phase_I	212236622	NM_002763	A6NK29|A8K2B1|Q5SW76|Q8TB91	Frame_Shift_Del	DEL	ENST00000366958.4	37	CCDS31021.1																																																																																				0.478	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763	
AGT	183	broad.mit.edu	37	1	230839031	230839032	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	CT	CT	CT	-	CT	CT	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:230839031_230839032delCT	ENST00000366667.4	-	5	1527_1528	c.1313_1314delAG	c.(1312-1314)gagfs	p.E438fs		NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	438					activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)	p.E438fs*9(1)		endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		ACTCTGTGGGCTCTCTCTCATC	0.54																																					p.438_438del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1313_1314del	1						.																																			228905655	SO:0001589	frameshift_variant	183	exon5			K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"""Serine (or cysteine) peptidase inhibitors"", ""Endogenous ligands"""	333	protein-coding gene	gene with protein product	"""alpha-1 antiproteinase, antitrypsin"""	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.1313_1314delAG	1.37:g.230839037_230839038delCT	ENSP00000355627:p.Glu438fs	Somatic		Capture	Illumina HiSeq	Phase_I	228905654	NM_000029	Q16358|Q16359|Q96F91	Frame_Shift_Del	DEL	ENST00000366667.4	37	CCDS1585.1																																																																																				0.540	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029	
ZNF692	55657	broad.mit.edu	37	1	249144659	249144659	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr1:249144659C>T	ENST00000306601.4	-	12	1476	c.1310G>A	c.(1309-1311)cGc>cAc	p.R437H	ZNF692_ENST00000366471.3_Missense_Mutation_p.R392H|ZNF692_ENST00000451251.1_Missense_Mutation_p.R442H|ZNF692_ENST00000366469.5_Missense_Mutation_p.R436H|ZNF692_ENST00000427146.1_Missense_Mutation_p.R392H	NM_017865.3	NP_060335.2	Q9BU19	ZN692_HUMAN	zinc finger protein 692	437					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.R437H(1)		endometrium(3)|large_intestine(6)|lung(7)|stomach(1)	17	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			TGCATGCTTGCGCTGGTGCCA	0.582																																					p.R392H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1175A	1						.						59.0	58.0	58.0					1																	249144659		2203	4300	6503	247111282	SO:0001583	missense	55657	exon11			BC002948	CCDS31127.1, CCDS44348.1, CCDS53487.1	1q44	2013-01-08			ENSG00000171163	ENSG00000171163		"""Zinc fingers, C2H2-type"""	26049	protein-coding gene	gene with protein product						12477932	Standard	NM_001136036		Approved	FLJ20531, Zfp692	uc001ifc.2	Q9BU19	OTTHUMG00000040423	ENST00000306601.4:c.1310G>A	1.37:g.249144659C>T	ENSP00000305483:p.Arg437His	Somatic		Capture	Illumina HiSeq	Phase_I	247111282	NM_001193328	B4DXZ0|Q5SRA5|Q5SRA6|Q9HBC9|Q9NW93|Q9NWY6|Q9UF97	Missense_Mutation	SNP	ENST00000306601.4	37	CCDS31127.1	.	.	.	.	.	.	.	.	.	.	C	19.94	3.919035	0.73098	.	.	ENSG00000171163	ENST00000306601;ENST00000427146;ENST00000366470;ENST00000366471;ENST00000366469;ENST00000451251	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	4.39	4.39	0.52855	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.149049	0.30410	N	0.009697	T	0.39200	0.1069	M	0.63843	1.955	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;0.999;1.0;1.0	D;D;D;D;D	0.75484	0.986;0.973;0.973;0.986;0.976	T	0.16778	-1.0391	10	0.87932	D	0	-29.5862	8.4377	0.32797	0.0:0.8947:0.0:0.1053	.	442;392;265;437;170	B4DXZ0;Q9BU19-2;Q9BU19-3;Q9BU19;Q59EV5	.;.;.;ZN692_HUMAN;.	H	437;392;265;392;436;442	ENSP00000305483:R437H;ENSP00000390044:R392H;ENSP00000355427:R392H;ENSP00000355425:R436H;ENSP00000391200:R442H	ENSP00000305483:R437H	R	-	2	0	ZNF692	247111282	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	1.668000	0.37481	2.443000	0.82685	0.491000	0.48974	CGC		0.582	ZNF692-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097298.1	NM_017865	
SPTLC3	55304	broad.mit.edu	37	20	13053053	13053053	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:13053053G>A	ENST00000399002.2	+	3	727	c.453G>A	c.(451-453)acG>acA	p.T151T	SPTLC3_ENST00000378194.4_Silent_p.T151T	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	151					small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)	p.T124T(1)|p.T151T(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						ATAACTGGACGTTTAGGTGAG	0.458																																					p.T151T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G453A	20						.						180.0	184.0	183.0					20																	13053053		1839	4089	5928	13001053	SO:0001819	synonymous_variant	55304	exon3			AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	"""chromosome 20 open reading frame 38"", ""serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)"""	C20orf38, SPTLC2L		17023427	Standard	NM_018327		Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.453G>A	20.37:g.13053053G>A		Somatic		Capture	Illumina HiSeq	Phase_I	13001053	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Silent	SNP	ENST00000399002.2	37	CCDS13115.2																																																																																				0.458	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327	
NSFL1C	55968	broad.mit.edu	37	20	1433207	1433207	+	Missense_Mutation	SNP	C	C	T	rs371393612		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:1433207C>T	ENST00000216879.4	-	7	1583	c.716G>A	c.(715-717)cGg>cAg	p.R239Q	NSFL1C_ENST00000381658.4_Missense_Mutation_p.R128Q|NSFL1C_ENST00000461211.1_5'UTR|NSFL1C_ENST00000476071.1_Missense_Mutation_p.R241Q|NSFL1C_ENST00000353088.2_Missense_Mutation_p.R208Q|NSFL1C_ENST00000350991.4_Missense_Mutation_p.R241Q	NM_016143.4	NP_057227.2	Q9UNZ2	NSF1C_HUMAN	NSFL1 (p97) cofactor (p47)	239	SEP. {ECO:0000255|PROSITE- ProRule:PRU00732}.					chromosome (GO:0005694)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.R239Q(1)		breast(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	16						GTCCTCGTCCCGATGGTCCTC	0.572																																					p.R239Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G716A	20						.	C	GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	179.0	159.0	166.0		722,716,623	5.1	1.0	20		166	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	NSFL1C	NM_001206736.1,NM_016143.4,NM_018839.4	43,43,43	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	probably-damaging,probably-damaging,probably-damaging	241/373,239/371,208/340	1433207	3,13003	2203	4300	6503	1381207	SO:0001583	missense	55968	exon7			AF112211	CCDS13015.1, CCDS13016.1, CCDS56175.1	20p13	2011-06-28			ENSG00000088833	ENSG00000088833		"""UBX domain containing"""	15912	protein-coding gene	gene with protein product	"""SHP1 homolog (S. cerevisiae)"", ""UBX domain protein 2C"""	606610				11042152	Standard	NM_016143		Approved	dJ776F14.1, p47, UBXD10, UBX1, UBXN2C	uc002wfc.3	Q9UNZ2	OTTHUMG00000031665	ENST00000216879.4:c.716G>A	20.37:g.1433207C>T	ENSP00000216879:p.Arg239Gln	Somatic		Capture	Illumina HiSeq	Phase_I	1381207	NM_016143	A2A2L1|B2RD74|Q5JXA4|Q5JXA5|Q7Z533|Q9H102|Q9NVL9|Q9UI06	Missense_Mutation	SNP	ENST00000216879.4	37	CCDS13015.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.723872	0.68959	2.27E-4	2.33E-4	ENSG00000088833	ENST00000353088;ENST00000476071;ENST00000216879;ENST00000381658;ENST00000350991	T;T;T;T;T	0.49432	0.78;0.79;0.8;0.79;0.8	5.13	5.13	0.70059	SEP domain (4);	0.000000	0.85682	D	0.000000	T	0.61464	0.2349	L	0.46819	1.47	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.998	D;D;D	0.77557	0.986;0.983;0.99	T	0.53158	-0.8478	10	0.27082	T	0.32	-15.8878	17.2951	0.87168	0.0:1.0:0.0:0.0	.	208;128;239	Q9UNZ2-4;Q9UNZ2-6;Q9UNZ2	.;.;NSF1C_HUMAN	Q	208;241;239;128;241	ENSP00000338643:R208Q;ENSP00000418529:R241Q;ENSP00000216879:R239Q;ENSP00000371074:R128Q;ENSP00000202584:R241Q	ENSP00000216879:R239Q	R	-	2	0	NSFL1C	1381207	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.754000	0.62191	2.824000	0.97209	0.655000	0.94253	CGG		0.572	NSFL1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077525.2	NM_016143	
TASP1	55617	broad.mit.edu	37	20	13415764	13415764	+	Silent	SNP	G	G	A	rs146597003	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:13415764G>A	ENST00000337743.4	-	12	1143	c.1023C>T	c.(1021-1023)ggC>ggT	p.G341G	TASP1_ENST00000480436.1_5'UTR|TASP1_ENST00000539805.1_Missense_Mutation_p.A144V	NM_017714.2	NP_060184.2	Q9H6P5	TASP1_HUMAN	taspase, threonine aspartase, 1	341					positive regulation of transcription, DNA-templated (GO:0045893)		threonine-type endopeptidase activity (GO:0004298)	p.G341G(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(11)|liver(1)|lung(11)|stomach(2)|urinary_tract(2)	31						CAATCACTCCGCCAAGCACGC	0.418																																					p.G341G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1023T	20						.	G		0,4406		0,0,2203	64.0	55.0	58.0		1023	-4.1	1.0	20	dbSNP_134	58	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	TASP1	NM_017714.2		0,11,6492	AA,AG,GG		0.1279,0.0,0.0846		341/421	13415764	11,12995	2203	4300	6503	13363764	SO:0001819	synonymous_variant	55617	exon12			AK000219	CCDS13116.1	20p12	2005-10-15	2005-10-15	2005-10-15	ENSG00000089123	ENSG00000089123	3.4.25.-		15859	protein-coding gene	gene with protein product		608270	"""chromosome 20 open reading frame 13"""	C20orf13		14636557	Standard	XR_430268		Approved	FLJ20212, dJ585I14.2	uc002woi.3	Q9H6P5	OTTHUMG00000031904	ENST00000337743.4:c.1023C>T	20.37:g.13415764G>A		Somatic		Capture	Illumina HiSeq	Phase_I	13363764	NM_017714	B7Z690|B7Z963|Q5TDU9|Q9BQN0|Q9NQ08|Q9NTS6|Q9NXJ2	Silent	SNP	ENST00000337743.4	37	CCDS13116.1	.	.	.	.	.	.	.	.	.	.	G	10.60	1.396886	0.25205	0.0	0.001279	ENSG00000089123	ENST00000539805	.	.	.	5.84	-4.07	0.03975	.	.	.	.	.	T	0.53498	0.1800	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58171	-0.7683	5	0.87932	D	0	-13.7059	3.1132	0.06365	0.2288:0.084:0.4396:0.2476	.	.	.	.	V	144	.	ENSP00000444062:A144V	A	-	2	0	TASP1	13363764	0.869000	0.29996	0.982000	0.44146	0.505000	0.33919	-0.216000	0.09266	-0.641000	0.05487	-0.302000	0.09304	GCG		0.418	TASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078041.2	NM_017714	
MACROD2	140733	broad.mit.edu	37	20	13982936	13982936	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:13982936C>T	ENST00000310348.4	+	2	49	c.49C>T	c.(49-51)Cgt>Tgt	p.R17C	MACROD2_ENST00000217246.4_Missense_Mutation_p.R17C			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	17					brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)	p.R17C(1)		breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				TTTGCAAGAACGTTTATTGAA	0.333																																					p.R17C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C49T	20						.						71.0	71.0	71.0					20																	13982936		2203	4300	6503	13930936	SO:0001583	missense	140733	exon2			BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"""chromosome 20 open reading frame 133"""	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.49C>T	20.37:g.13982936C>T	ENSP00000309809:p.Arg17Cys	Somatic		Capture	Illumina HiSeq	Phase_I	13930936	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	37	CCDS13120.2	.	.	.	.	.	.	.	.	.	.	C	21.1	4.095256	0.76870	.	.	ENSG00000172264	ENST00000217246;ENST00000310348	T;T	0.46819	0.86;0.86	6.02	5.08	0.68730	.	0.000000	0.64402	D	0.000001	T	0.47248	0.1435	M	0.66939	2.045	0.80722	D	1	B;B	0.28439	0.135;0.212	B;B	0.22880	0.019;0.042	T	0.50432	-0.8829	10	0.87932	D	0	-7.2058	14.0442	0.64695	0.0:0.9274:0.0:0.0726	.	17;17	A1Z1Q3;A1Z1Q3-2	MACD2_HUMAN;.	C	17	ENSP00000217246:R17C;ENSP00000309809:R17C	ENSP00000217246:R17C	R	+	1	0	MACROD2	13930936	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.054000	0.64275	1.555000	0.49500	0.650000	0.86243	CGT		0.333	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676	
FLRT3	23767	broad.mit.edu	37	20	14307657	14307657	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:14307657G>T	ENST00000378053.3	-	2	752	c.496C>A	c.(496-498)Ctt>Att	p.L166I	FLRT3_ENST00000341420.4_Missense_Mutation_p.L166I|MACROD2_ENST00000310348.4_Intron|FLRT3_ENST00000462077.1_5'Flank|MACROD2_ENST00000217246.4_Intron	NM_013281.3	NP_037413.1	Q9NZU0	FLRT3_HUMAN	fibronectin leucine rich transmembrane protein 3	166					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.L166I(1)		breast(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Colorectal(1;0.0464)	COAD - Colon adenocarcinoma(2;0.129)	Colorectal(1;0.0393)		ATTGTGCTAAGGTGATTACGG	0.448																																					p.L166I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C496A	20						.						106.0	103.0	104.0					20																	14307657		2203	4300	6503	14255657	SO:0001583	missense	23767	exon3			AF169677	CCDS13121.1	20p11	2013-02-11			ENSG00000125848	ENSG00000125848		"""Fibronectin type III domain containing"""	3762	protein-coding gene	gene with protein product		604808				10644439	Standard	NM_198391		Approved		uc002wow.2	Q9NZU0	OTTHUMG00000031914	ENST00000378053.3:c.496C>A	20.37:g.14307657G>T	ENSP00000367292:p.Leu166Ile	Somatic		Capture	Illumina HiSeq	Phase_I	14255657	NM_198391	D3DW20|Q542Z9|Q96K39|Q96K42|Q96KB1|Q9P259	Missense_Mutation	SNP	ENST00000378053.3	37	CCDS13121.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.909324	0.52439	.	.	ENSG00000125848	ENST00000378053;ENST00000341420;ENST00000541882	T;T	0.62639	0.01;0.01	6.06	6.06	0.98353	.	0.000000	0.64402	D	0.000001	T	0.66886	0.2835	N	0.17564	0.495	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.60541	-0.7243	10	0.16896	T	0.51	-10.4222	20.6208	0.99490	0.0:0.0:1.0:0.0	.	166	Q9NZU0	FLRT3_HUMAN	I	166	ENSP00000367292:L166I;ENSP00000339912:L166I	ENSP00000339912:L166I	L	-	1	0	FLRT3	14255657	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.922000	0.63404	2.882000	0.98803	0.655000	0.94253	CTT		0.448	FLRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078075.1	NM_013281	
KIF16B	55614	broad.mit.edu	37	20	16337084	16337084	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:16337084C>T	ENST00000354981.2	-	23	3669	c.3512G>A	c.(3511-3513)cGc>cAc	p.R1171H	KIF16B_ENST00000378003.2_Intron|KIF16B_ENST00000355755.3_Missense_Mutation_p.R1171H	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	1171					ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)	p.R1171H(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						GCCCAAAGAGCGAGAAACCAT	0.483																																					p.R1171H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3512A	20						.						85.0	76.0	79.0					20																	16337084		2203	4300	6503	16285084	SO:0001583	missense	55614	exon23			AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.3512G>A	20.37:g.16337084C>T	ENSP00000347076:p.Arg1171His	Somatic		Capture	Illumina HiSeq	Phase_I	16285084	NM_024704	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	37	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.652688	0.88056	.	.	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997	T;T	0.75704	-0.68;-0.96	5.9	5.9	0.94986	Phox homologous domain (1);	.	.	.	.	D	0.82848	0.5126	L	0.58101	1.795	0.80722	D	1	D	0.67145	0.996	P	0.57846	0.828	T	0.83190	-0.0084	9	0.66056	D	0.02	.	20.2806	0.98513	0.0:1.0:0.0:0.0	.	1171	Q96L93	KI16B_HUMAN	H	1171;1171;1015	ENSP00000347076:R1171H;ENSP00000347995:R1171H	ENSP00000347076:R1171H	R	-	2	0	KIF16B	16285084	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.212000	0.65225	2.795000	0.96236	0.643000	0.83706	CGC		0.483	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
BFSP1	631	broad.mit.edu	37	20	17479551	17479551	+	Silent	SNP	G	G	A	rs199579980		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:17479551G>A	ENST00000377873.3	-	6	909	c.870C>T	c.(868-870)taC>taT	p.Y290Y	BFSP1_ENST00000544874.1_Silent_p.Y151Y|BFSP1_ENST00000377868.2_Silent_p.Y165Y|BFSP1_ENST00000536626.1_Silent_p.Y151Y	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	290	Coil 2.|Rod.				cell maturation (GO:0048469)|lens fiber cell development (GO:0070307)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)	p.Y290Y(1)		central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1)	18						GCCGGCAGTCGTAAGAAGACT	0.527													G|||	1	0.000199681	0.0	0.0	5008	,	,		19141	0.001		0.0	False		,,,				2504	0.0				p.Y165Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C495T	20						.						101.0	88.0	92.0					20																	17479551		2203	4300	6503	17427551	SO:0001819	synonymous_variant	631	exon6			Y16717	CCDS13126.1, CCDS54448.1, CCDS63229.1	20p12.1	2014-06-05			ENSG00000125864	ENSG00000125864		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1040	protein-coding gene	gene with protein product		603307				9787085	Standard	NM_001161705		Approved	CP94, CP115, LIFL-H, filensin	uc002wpo.3	Q12934	OTTHUMG00000031940	ENST00000377873.3:c.870C>T	20.37:g.17479551G>A		Somatic		Capture	Illumina HiSeq	Phase_I	17427551	NM_001161705	F5H0G1|O43595|O76034|O95676|Q8IVZ6|Q9HBX4	Silent	SNP	ENST00000377873.3	37	CCDS13126.1																																																																																				0.527	BFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078119.6	NM_001195	
SLC24A3	57419	broad.mit.edu	37	20	19679316	19679316	+	Missense_Mutation	SNP	G	G	A	rs143870319		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:19679316G>A	ENST00000328041.6	+	15	1908	c.1711G>A	c.(1711-1713)Gga>Aga	p.G571R	RP4-718D20.3_ENST00000600889.1_RNA|RP4-718D20.3_ENST00000435992.2_RNA|RP4-718D20.3_ENST00000609846.1_RNA|RP4-718D20.3_ENST00000598694.1_RNA|RP4-718D20.3_ENST00000593770.1_RNA	NM_020689.3	NP_065740.2	Q9HC58	NCKX3_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	571					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)	p.G571R(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TGTGGATTACGGATCCTACGT	0.547													G|||	1	0.000199681	0.0	0.0	5008	,	,		18752	0.0		0.001	False		,,,				2504	0.0				p.G571R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1711A	20						.	G	ARG/GLY	1,4405		0,1,2202	90.0	69.0	76.0		1711	4.8	1.0	20	dbSNP_134	76	1,8597		0,1,4298	no	missense	SLC24A3	NM_020689.3	125	0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	571/645	19679316	2,13002	2203	4299	6502	19627316	SO:0001583	missense	57419	exon15			AF169257	CCDS13140.1	20p13	2013-05-22			ENSG00000185052	ENSG00000185052		"""Solute carriers"""	10977	protein-coding gene	gene with protein product		609839					Standard	NM_020689		Approved		uc002wrl.3	Q9HC58	OTTHUMG00000031993	ENST00000328041.6:c.1711G>A	20.37:g.19679316G>A	ENSP00000333519:p.Gly571Arg	Somatic		Capture	Illumina HiSeq	Phase_I	19627316	NM_020689	B1AKV7|Q9BQJ9|Q9BQL7|Q9BQY3|Q9H519	Missense_Mutation	SNP	ENST00000328041.6	37	CCDS13140.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.29	3.082652	0.55861	2.27E-4	1.16E-4	ENSG00000185052	ENST00000328041	T	0.67698	-0.28	5.8	4.85	0.62838	Sodium/calcium exchanger membrane region (1);	0.093976	0.64402	D	0.000001	T	0.72669	0.3489	M	0.80422	2.495	0.80722	D	1	P	0.50819	0.939	P	0.50352	0.638	T	0.74598	-0.3612	9	.	.	.	.	9.3981	0.38415	0.0785:0.1472:0.7744:0.0	.	571	Q9HC58	NCKX3_HUMAN	R	571	ENSP00000333519:G571R	.	G	+	1	0	SLC24A3	19627316	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.699000	0.74613	2.758000	0.94735	0.561000	0.74099	GGA		0.547	SLC24A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078207.4	NM_020689	
CRNKL1	51340	broad.mit.edu	37	20	20023134	20023134	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:20023134C>T	ENST00000377340.2	-	9	1513	c.1482G>A	c.(1480-1482)tgG>tgA	p.W494*	CRNKL1_ENST00000536226.1_Nonsense_Mutation_p.W333*|CRNKL1_ENST00000377327.4_Nonsense_Mutation_p.W482*	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	494	Mediates interaction with HSP90. {ECO:0000250|UniProtKB:P63154}.				mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.W494*(1)		breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						AGTAATCAAACCATGCATCAT	0.428																																					p.W494X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1482A	20						.						126.0	117.0	120.0					20																	20023134		2203	4300	6503	19971134	SO:0001587	stop_gained	51340	exon9			AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"""SYF3 pre-mRNA-splicing factor"""	610952	"""crooked neck (Drosophila Crn homolog)-like 1"", ""Crn, crooked neck-like 1 (Drosophila)"", ""crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"""				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.1482G>A	20.37:g.20023134C>T	ENSP00000366557:p.Trp494*	Somatic		Capture	Illumina HiSeq	Phase_I	19971134	NM_016652	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Nonsense_Mutation	SNP	ENST00000377340.2	37	CCDS33446.1	.	.	.	.	.	.	.	.	.	.	C	39	7.459333	0.98296	.	.	ENSG00000101343	ENST00000377327;ENST00000377340;ENST00000536226	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.0224	20.3312	0.98718	0.0:1.0:0.0:0.0	.	.	.	.	X	482;494;333	.	ENSP00000366544:W482X	W	-	3	0	CRNKL1	19971134	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.818000	0.86416	2.797000	0.96272	0.655000	0.94253	TGG		0.428	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1		
CFAP61	26074	broad.mit.edu	37	20	20269304	20269304	+	Missense_Mutation	SNP	C	C	A	rs187562153	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:20269304C>A	ENST00000245957.5	+	23	2924	c.2848C>A	c.(2848-2850)Ctc>Atc	p.L950I	C20orf26_ENST00000377309.2_Intron	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		950								p.L950I(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		GTTTAAAGCCCTCAATGATGC	0.403																																					p.L950I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2848A	20						.						216.0	205.0	209.0					20																	20269304		2203	4300	6503	20217304	SO:0001583	missense	26074	exon23																														ENST00000245957.5:c.2848C>A	20.37:g.20269304C>A	ENSP00000245957:p.Leu950Ile	Somatic		Capture	Illumina HiSeq	Phase_I	20217304	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	37	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	C	0.158	-1.084134	0.01888	.	.	ENSG00000089101	ENST00000343997;ENST00000389655;ENST00000245957	T	0.50001	0.76	5.75	-4.69	0.03299	.	0.279929	0.26840	N	0.022227	T	0.13927	0.0337	N	0.04705	-0.18	0.47476	D	0.99943	B	0.06786	0.001	B	0.08055	0.003	T	0.32745	-0.9895	10	0.06625	T	0.88	.	1.6929	0.02856	0.2442:0.2613:0.0827:0.4117	.	950	Q8NHU2	CT026_HUMAN	I	890;916;950	ENSP00000245957:L950I	ENSP00000245957:L950I	L	+	1	0	C20orf26	20217304	0.001000	0.12720	0.029000	0.17559	0.620000	0.37586	-0.084000	0.11268	-1.165000	0.02786	-0.355000	0.07637	CTC		0.403	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
KIZ-AS1	101929591	broad.mit.edu	37	20	21142689	21142689	+	RNA	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:21142689C>T	ENST00000591761.1	-	0	5142				PLK1S1_ENST00000457464.1_RNA|RP5-872K7.7_ENST00000425746.2_RNA																							ACATTCACACCGACAGACAGC	0.448																																					p.R92X												.	.	0			c.C274T	20						.						68.0	68.0	68.0					20																	21142689		1982	4171	6153	21090689			55857	exon4																															20.37:g.21142689C>T		Somatic		Capture	Illumina HiSeq	Phase_I	21090689	NM_001163022		Nonsense_Mutation	SNP	ENST00000591761.1	37																																																																																					0.448	RP4-777D9.2-002	KNOWN	basic	antisense	antisense	OTTHUMT00000078258.2		
ZNF343	79175	broad.mit.edu	37	20	2463857	2463857	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:2463857G>A	ENST00000278772.4	-	6	2237	c.1750C>T	c.(1750-1752)Cga>Tga	p.R584*	RP4-734P14.4_ENST00000461548.1_Intron	NM_001282495.1|NM_001282496.1|NM_024325.4	NP_001269424.1|NP_001269425.1|NP_077301.4	Q6P1L6	ZN343_HUMAN	zinc finger protein 343	584					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.R584*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|skin(4)|upper_aerodigestive_tract(1)	25						CTAAAGCCTCGCCCACACTCC	0.522																																					p.R584X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1750T	20						.						101.0	83.0	89.0					20																	2463857		2203	4300	6503	2411857	SO:0001587	stop_gained	79175	exon6			AK096911	CCDS13028.1, CCDS74692.1, CCDS74693.1, CCDS74694.1	20p13	2013-01-08			ENSG00000088876	ENSG00000088876		"""Zinc fingers, C2H2-type"", ""-"""	16017	protein-coding gene	gene with protein product							Standard	NM_001282498		Approved	MGC10715	uc002wge.1	Q6P1L6	OTTHUMG00000031701	ENST00000278772.4:c.1750C>T	20.37:g.2463857G>A	ENSP00000278772:p.Arg584*	Somatic		Capture	Illumina HiSeq	Phase_I	2411857	NM_024325	Q5JXU8|Q5JXU9|Q8N8F2|Q96EX8|Q96NA5|Q9BQB0	Nonsense_Mutation	SNP	ENST00000278772.4	37	CCDS13028.1	.	.	.	.	.	.	.	.	.	.	G	38	7.002011	0.97994	.	.	ENSG00000088876	ENST00000278772	.	.	.	2.65	0.578	0.17391	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	.	2.4345	0.04479	0.2901:0.0:0.4746:0.2353	.	.	.	.	X	584	.	ENSP00000278772:R584X	R	-	1	2	ZNF343	2411857	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-0.504000	0.06375	0.035000	0.15519	0.591000	0.81541	CGA		0.522	ZNF343-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077617.1	NM_024325	
CST8	10047	broad.mit.edu	37	20	23472318	23472318	+	Missense_Mutation	SNP	G	G	A	rs372735686		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:23472318G>A	ENST00000246012.1	+	2	371	c.14G>A	c.(13-15)cGg>cAg	p.R5Q		NM_005492.2	NP_005483.1	O60676	CST8_HUMAN	cystatin 8 (cystatin-related epididymal specific)	5					negative regulation of endopeptidase activity (GO:0010951)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.R5Q(2)		breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(9)|skin(2)	16	Colorectal(13;0.0431)|Lung NSC(19;0.235)					CCCAGGTGCCGGTGGCTCTCC	0.607																																					p.R5Q												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G14A	20						.	G	GLN/ARG	0,4406		0,0,2203	122.0	108.0	113.0		14	-3.7	0.0	20		113	1,8599	1.2+/-3.3	0,1,4299	no	missense	CST8	NM_005492.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	5/143	23472318	1,13005	2203	4300	6503	23420318	SO:0001583	missense	10047	exon2			AF059244	CCDS13156.1	20p11.21	2012-08-14			ENSG00000125815	ENSG00000125815			2480	protein-coding gene	gene with protein product		608683				7619504, 20565543	Standard	NM_005492		Approved	CRES, CTES5	uc002wth.1	O60676	OTTHUMG00000032071	ENST00000246012.1:c.14G>A	20.37:g.23472318G>A	ENSP00000246012:p.Arg5Gln	Somatic		Capture	Illumina HiSeq	Phase_I	23420318	NM_005492	Q2M2X6	Missense_Mutation	SNP	ENST00000246012.1	37	CCDS13156.1	.	.	.	.	.	.	.	.	.	.	G	9.284	1.048993	0.19827	0.0	1.16E-4	ENSG00000125815	ENST00000449810;ENST00000246012	T;T	0.11277	2.79;3.06	4.05	-3.68	0.04463	.	1.656980	0.02557	N	0.096283	T	0.06781	0.0173	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.31586	-0.9938	10	0.28530	T	0.3	-6.3079	3.5424	0.07816	0.4549:0.0:0.2324:0.3127	.	5	O60676	CST8_HUMAN	Q	5	ENSP00000399144:R5Q;ENSP00000246012:R5Q	ENSP00000246012:R5Q	R	+	2	0	CST8	23420318	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	-0.098000	0.11024	-0.723000	0.04915	-0.136000	0.14681	CGG		0.607	CST8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078336.1		
ACSS1	84532	broad.mit.edu	37	20	25004117	25004117	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:25004117G>A	ENST00000323482.4	-	4	871	c.792C>T	c.(790-792)gaC>gaT	p.D264D	ACSS1_ENST00000542618.1_Silent_p.D143D|ACSS1_ENST00000432802.2_Silent_p.D264D|ACSS1_ENST00000537502.1_Silent_p.D181D	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	264					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.D264D(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)	CCAGCGGGACGTCCAGATCCC	0.547																																					p.D264D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C792T	20						.						117.0	87.0	97.0					20																	25004117		2203	4300	6503	24952117	SO:0001819	synonymous_variant	84532	exon4				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.792C>T	20.37:g.25004117G>A		Somatic		Capture	Illumina HiSeq	Phase_I	24952117	NM_032501	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	37	CCDS13167.1																																																																																				0.547	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
PYGB	5834	broad.mit.edu	37	20	25273100	25273100	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:25273100C>T	ENST00000216962.4	+	17	2138	c.2028C>T	c.(2026-2028)ggC>ggT	p.G676G		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	676					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)	p.G676G(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						AGGCCTCAGGCACAGGCAACA	0.657																																					p.G676G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2028T	20						.						96.0	89.0	91.0					20																	25273100		2203	4300	6503	25221100	SO:0001819	synonymous_variant	5834	exon17				CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.2028C>T	20.37:g.25273100C>T		Somatic		Capture	Illumina HiSeq	Phase_I	25221100	NM_002862	Q96AK1|Q9NPX8	Silent	SNP	ENST00000216962.4	37	CCDS13171.1	.	.	.	.	.	.	.	.	.	.	C	10.18	1.279816	0.23392	.	.	ENSG00000100994	ENST00000428458	.	.	.	4.28	3.32	0.38043	.	.	.	.	.	T	0.52500	0.1738	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47736	-0.9094	4	.	.	.	-35.3326	4.7289	0.12955	0.1574:0.6043:0.1524:0.0859	.	.	.	.	V	95	.	.	A	+	2	0	PYGB	25221100	0.957000	0.32711	0.995000	0.50966	0.989000	0.77384	0.107000	0.15375	1.124000	0.41980	0.462000	0.41574	GCA		0.657	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
CPXM1	56265	broad.mit.edu	37	20	2779113	2779113	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:2779113G>T	ENST00000380605.2	-	3	475	c.411C>A	c.(409-411)tcC>tcA	p.S137S		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	137	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.S137S(1)		endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						CAAGACCAAAGGACTGGCTGC	0.597																																					p.S137S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C411A	20						.						69.0	65.0	67.0					20																	2779113		2203	4300	6503	2727113	SO:0001819	synonymous_variant	56265	exon3			AL035460	CCDS13033.1	20p13	2012-02-10	2006-08-24	2006-08-24	ENSG00000088882	ENSG00000088882			15771	protein-coding gene	gene with protein product	"""carboxypeptidase-like protein X1"""	609555	"""carboxypeptidase X (M14 family)"""	CPXM		14702039	Standard	NM_019609		Approved	CPX-1, CPX1	uc002wgu.3	Q96SM3	OTTHUMG00000031706	ENST00000380605.2:c.411C>A	20.37:g.2779113G>T		Somatic		Capture	Illumina HiSeq	Phase_I	2727113	NM_001184699	Q6P4G8|Q6UW65|Q9NUB5	Silent	SNP	ENST00000380605.2	37	CCDS13033.1																																																																																				0.597	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609	
PTPRA	5786	broad.mit.edu	37	20	2945773	2945773	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:2945773A>G	ENST00000216877.6	+	5	740	c.340A>G	c.(340-342)Acg>Gcg	p.T114A	PTPRA_ENST00000318266.5_Missense_Mutation_p.T114A|PTPRA_ENST00000358719.4_5'UTR|PTPRA_ENST00000356147.3_Missense_Mutation_p.T114A|PTPRA_ENST00000399903.2_Missense_Mutation_p.T114A|PTPRA_ENST00000425918.2_Missense_Mutation_p.T125A|PTPRA_ENST00000380393.3_Missense_Mutation_p.T114A	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	114				T -> M (in Ref. 4; CAA38662). {ECO:0000305}.	axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.T114A(1)		NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TAACCAGTTCACGGATGCCAG	0.473																																					p.T114A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A340G	20						.						99.0	106.0	103.0					20																	2945773		2203	4300	6503	2893773	SO:0001583	missense	5786	exon5				CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.340A>G	20.37:g.2945773A>G	ENSP00000216877:p.Thr114Ala	Somatic		Capture	Illumina HiSeq	Phase_I	2893773	NM_080840	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Missense_Mutation	SNP	ENST00000216877.6	37	CCDS13039.1	.	.	.	.	.	.	.	.	.	.	A	10.83	1.462116	0.26248	.	.	ENSG00000132670	ENST00000380393;ENST00000455631;ENST00000216877;ENST00000399903;ENST00000431048;ENST00000418580;ENST00000425918;ENST00000318266;ENST00000430705;ENST00000356147	T;T;T;T;T;T;T;T;T	0.47528	3.96;0.91;3.98;3.96;0.9;3.96;3.98;0.84;3.98	5.52	3.11	0.35812	.	0.317773	0.29165	U	0.012959	T	0.25494	0.0620	N	0.14661	0.345	0.20403	N	0.999909	B;B	0.13594	0.008;0.0	B;B	0.12156	0.007;0.001	T	0.09122	-1.0689	10	0.36615	T	0.2	.	4.4995	0.11856	0.738:0.0:0.0912:0.1708	.	125;114	B7Z2A4;P18433-4	.;.	A	114;114;114;114;114;114;125;114;114;114	ENSP00000369756:T114A;ENSP00000414089:T114A;ENSP00000216877:T114A;ENSP00000382787:T114A;ENSP00000390775:T114A;ENSP00000393553:T125A;ENSP00000314568:T114A;ENSP00000394132:T114A;ENSP00000348468:T114A	ENSP00000216877:T114A	T	+	1	0	PTPRA	2893773	0.300000	0.24435	0.452000	0.26994	0.991000	0.79684	1.364000	0.34171	1.028000	0.39785	0.533000	0.62120	ACG		0.473	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3		
ZNF337	26152	broad.mit.edu	37	20	25657536	25657536	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:25657536T>C	ENST00000376436.1	-	4	927	c.388A>G	c.(388-390)Atg>Gtg	p.M130V	RP4-694B14.5_ENST00000414393.1_RNA|ZNF337_ENST00000252979.5_Missense_Mutation_p.M130V|ZNF337_ENST00000538750.1_Missense_Mutation_p.M98V|RP4-694B14.5_ENST00000439498.1_RNA|ZNF337_ENST00000481610.1_5'Flank|RP4-694B14.5_ENST00000455791.1_RNA|RP4-694B14.5_ENST00000421829.1_RNA|RP4-694B14.5_ENST00000428254.1_RNA			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	130					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.M130V(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						GAAAATGCCATGGGCTTAGTG	0.463																																					p.M130V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A388G	20						.						169.0	159.0	163.0					20																	25657536		2203	4300	6503	25605536	SO:0001583	missense	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.388A>G	20.37:g.25657536T>C	ENSP00000365619:p.Met130Val	Somatic		Capture	Illumina HiSeq	Phase_I	25605536	NM_015655	B4DSM2|Q9Y3Y5	Missense_Mutation	SNP	ENST00000376436.1	37	CCDS13174.1	.	.	.	.	.	.	.	.	.	.	.	2.161	-0.392292	0.04932	.	.	ENSG00000130684	ENST00000376436;ENST00000252979;ENST00000376412;ENST00000538750	T;T;T	0.05447	3.53;3.53;3.44	1.13	-2.27	0.06846	.	.	.	.	.	T	0.02047	0.0064	N	0.03608	-0.345	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.01281	0.0;0.0	T	0.45175	-0.9279	9	0.13108	T	0.6	.	2.3318	0.04238	0.3438:0.1868:0.0:0.4695	.	98;130	B4DSM2;Q9Y3M9	.;ZN337_HUMAN	V	130;130;130;98	ENSP00000365619:M130V;ENSP00000252979:M130V;ENSP00000442181:M98V	ENSP00000252979:M130V	M	-	1	0	ZNF337	25605536	0.624000	0.27102	0.005000	0.12908	0.639000	0.38242	1.926000	0.40084	-1.238000	0.02535	0.254000	0.18369	ATG		0.463	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1		
COX4I2	84701	broad.mit.edu	37	20	30226843	30226843	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:30226843G>A	ENST00000376075.3	+	2	98	c.23G>A	c.(22-24)aGc>aAc	p.S8N	COX4I2_ENST00000490030.1_3'UTR	NM_032609.2	NP_115998.2	Q96KJ9	COX42_HUMAN	cytochrome c oxidase subunit IV isoform 2 (lung)	8					cellular respiration (GO:0045333)|generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)	mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)	p.S8N(1)		breast(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	11	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.01e-05)|all cancers(5;9.46e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00121)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			GCTGCCTGGAGCTTGGTGCTG	0.582																																					p.S8N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G23A	20						.						98.0	78.0	85.0					20																	30226843		2203	4300	6503	29690504	SO:0001583	missense	84701	exon2			AF257180	CCDS13187.1	20q11.21	2011-07-04	2004-08-11		ENSG00000131055	ENSG00000131055		"""Mitochondrial respiratory chain complex / Complex IV"""	16232	protein-coding gene	gene with protein product	"""cytochrome c oxidase subunit IV-like 2"""	607976	"""cytochrome c oxidase subunit IV isoform 2"""	COX4L2		11311561, 17937768	Standard	NM_032609		Approved	COXIV-2, COX4B, dJ857M17.2, COX4-2	uc002wwj.1	Q96KJ9	OTTHUMG00000032180	ENST00000376075.3:c.23G>A	20.37:g.30226843G>A	ENSP00000365243:p.Ser8Asn	Somatic		Capture	Illumina HiSeq	Phase_I	29690504	NM_032609	Q6GTF4|Q9H0Z4	Missense_Mutation	SNP	ENST00000376075.3	37	CCDS13187.1	.	.	.	.	.	.	.	.	.	.	G	11.10	1.540632	0.27563	.	.	ENSG00000131055	ENST00000376075	T	0.64085	-0.08	4.21	2.24	0.28232	.	0.307263	0.34088	N	0.004274	T	0.43567	0.1253	L	0.27053	0.805	0.23550	N	0.997432	B	0.09022	0.002	B	0.06405	0.002	T	0.30822	-0.9965	10	0.45353	T	0.12	-10.8192	6.5771	0.22573	0.2183:0.0:0.7817:0.0	.	8	Q96KJ9	COX42_HUMAN	N	8	ENSP00000365243:S8N	ENSP00000365243:S8N	S	+	2	0	COX4I2	29690504	0.698000	0.27777	0.682000	0.30024	0.482000	0.33219	0.586000	0.23894	0.712000	0.32039	0.561000	0.74099	AGC		0.582	COX4I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078548.1	NM_032609	
COX4I2	84701	broad.mit.edu	37	20	30232628	30232628	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:30232628G>A	ENST00000376075.3	+	5	512	c.437G>A	c.(436-438)cGc>cAc	p.R146H	COX4I2_ENST00000490030.1_3'UTR	NM_032609.2	NP_115998.2	Q96KJ9	COX42_HUMAN	cytochrome c oxidase subunit IV isoform 2 (lung)	146					cellular respiration (GO:0045333)|generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)	mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)	p.R146H(1)		breast(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	11	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.01e-05)|all cancers(5;9.46e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00121)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			CAGCTGCAGCGCATGCTGGAC	0.577																																					p.R146H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G437A	20						.						91.0	75.0	80.0					20																	30232628		2203	4300	6503	29696289	SO:0001583	missense	84701	exon5			AF257180	CCDS13187.1	20q11.21	2011-07-04	2004-08-11		ENSG00000131055	ENSG00000131055		"""Mitochondrial respiratory chain complex / Complex IV"""	16232	protein-coding gene	gene with protein product	"""cytochrome c oxidase subunit IV-like 2"""	607976	"""cytochrome c oxidase subunit IV isoform 2"""	COX4L2		11311561, 17937768	Standard	NM_032609		Approved	COXIV-2, COX4B, dJ857M17.2, COX4-2	uc002wwj.1	Q96KJ9	OTTHUMG00000032180	ENST00000376075.3:c.437G>A	20.37:g.30232628G>A	ENSP00000365243:p.Arg146His	Somatic		Capture	Illumina HiSeq	Phase_I	29696289	NM_032609	Q6GTF4|Q9H0Z4	Missense_Mutation	SNP	ENST00000376075.3	37	CCDS13187.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.444854	0.83993	.	.	ENSG00000131055	ENST00000376075	T	0.58060	0.36	4.38	4.38	0.52667	.	0.000000	0.85682	D	0.000000	T	0.70859	0.3272	M	0.78456	2.415	0.58432	D	0.999994	D	0.89917	1.0	D	0.97110	1.0	T	0.73802	-0.3868	10	0.56958	D	0.05	-3.8229	12.2862	0.54793	0.0:0.0:1.0:0.0	.	146	Q96KJ9	COX42_HUMAN	H	146	ENSP00000365243:R146H	ENSP00000365243:R146H	R	+	2	0	COX4I2	29696289	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	6.277000	0.72608	2.271000	0.75665	0.313000	0.20887	CGC		0.577	COX4I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078548.1	NM_032609	
ASXL1	171023	broad.mit.edu	37	20	31024504	31024504	+	Missense_Mutation	SNP	C	C	A	rs201002256		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:31024504C>A	ENST00000375687.4	+	13	4413	c.3989C>A	c.(3988-3990)cCt>cAt	p.P1330H	ASXL1_ENST00000306058.5_Missense_Mutation_p.P1325H	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1330					bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.P1330H(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						GCTGAGATCCCTCCAGTTTTT	0.567			"""F, N, Mis"""		"""MDS, CMML"""																																p.P1330H			Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3989A	20						.						42.0	45.0	44.0					20																	31024504		2203	4300	6503	30488165	SO:0001583	missense	171023	exon12			AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"""additional sex combs like 1 (Drosophila)"""			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.3989C>A	20.37:g.31024504C>A	ENSP00000364839:p.Pro1330His	Somatic		Capture	Illumina HiSeq	Phase_I	30488165	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	.	.	.	.	.	.	.	.	.	.	C	14.16	2.452308	0.43531	.	.	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	T;T	0.15487	2.42;2.42	4.56	4.56	0.56223	.	0.244954	0.36268	N	0.002697	T	0.30665	0.0772	L	0.36672	1.1	0.33311	D	0.566107	D;D	0.76494	0.999;0.999	D;P	0.64042	0.921;0.894	T	0.24048	-1.0171	10	0.72032	D	0.01	-14.7772	16.7751	0.85549	0.0:1.0:0.0:0.0	.	1325;1330	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	H	1330;1330;1330;1251;1325	ENSP00000364839:P1330H;ENSP00000305119:P1325H	ENSP00000305119:P1325H	P	+	2	0	ASXL1	30488165	0.445000	0.25657	0.993000	0.49108	0.519000	0.34347	0.918000	0.28678	2.826000	0.97356	0.561000	0.74099	CCT		0.567	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338	
FASTKD5	60493	broad.mit.edu	37	20	3127474	3127474	+	Missense_Mutation	SNP	C	C	T	rs376790179		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:3127474C>T	ENST00000380266.3	-	2	2564	c.2243G>A	c.(2242-2244)cGc>cAc	p.R748H	UBOX5_ENST00000348031.2_Intron|UBOX5_ENST00000217173.2_Intron|UBOX5-AS1_ENST00000446537.1_RNA	NM_021826.4	NP_068598.1	Q7L8L6	FAKD5_HUMAN	FAST kinase domains 5	748	RAP. {ECO:0000255|PROSITE- ProRule:PRU00619}.				cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)	p.R748H(1)		breast(2)|endometrium(2)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(2)	19						CTTTTCTAAGCGAGTTCGTTT	0.478																																					p.R748H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2243A	20						.						119.0	117.0	118.0					20																	3127474		2203	4300	6503	3075474	SO:0001583	missense	60493	exon2			BC007413	CCDS13048.1	20p13	2006-07-07			ENSG00000215251	ENSG00000215251			25790	protein-coding gene	gene with protein product		614272				11347906	Standard	NM_021826		Approved	FLJ13149	uc002whz.4	Q7L8L6	OTTHUMG00000031727	ENST00000380266.3:c.2243G>A	20.37:g.3127474C>T	ENSP00000369618:p.Arg748His	Somatic		Capture	Illumina HiSeq	Phase_I	3075474	NM_021826	Q96JN3|Q9H5D1|Q9H8Y3	Missense_Mutation	SNP	ENST00000380266.3	37	CCDS13048.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.136110	0.77662	.	.	ENSG00000215251	ENST00000380266	T	0.17054	2.3	5.83	5.83	0.93111	RAP domain (3);	0.107358	0.39759	N	0.001280	T	0.44371	0.1290	M	0.66939	2.045	0.44677	D	0.997669	D	0.89917	1.0	D	0.87578	0.998	T	0.21415	-1.0246	10	0.72032	D	0.01	.	20.1152	0.97926	0.0:1.0:0.0:0.0	.	748	Q7L8L6	FAKD5_HUMAN	H	748	ENSP00000369618:R748H	ENSP00000369618:R748H	R	-	2	0	FASTKD5	3075474	0.987000	0.35691	0.999000	0.59377	0.987000	0.75469	2.735000	0.47377	2.750000	0.94351	0.655000	0.94253	CGC		0.478	FASTKD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077701.2	NM_021826	
NOL4L	140688	broad.mit.edu	37	20	31040798	31040798	+	Silent	SNP	C	C	T	rs373854304		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:31040798C>T	ENST00000359676.5	-	6	919	c.777G>A	c.(775-777)acG>acA	p.T259T	C20orf112_ENST00000475781.1_5'UTR|RP5-1184F4.5_ENST00000442179.1_RNA	NM_001256798.1|NM_080616.4	NP_001243727.1|NP_542183.2	Q96MY1	NOL4L_HUMAN		259						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.T259T(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(5)	15						GATGGGGTGGCGTGGGTCTGG	0.642																																					p.T259T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G777A	20						.	C		1,4405	2.1+/-5.4	0,1,2202	72.0	71.0	71.0		777	-8.9	0.4	20		71	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C20orf112	NM_080616.3		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		259/437	31040798	2,13004	2203	4300	6503	30504459	SO:0001819	synonymous_variant	140688	exon6																														ENST00000359676.5:c.777G>A	20.37:g.31040798C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30504459	NM_080616	Q5JYB7|Q6P0Y4|Q9BR34|Q9NQF6	Silent	SNP	ENST00000359676.5	37	CCDS13202.1																																																																																				0.642	C20orf112-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078628.2		
CBFA2T2	9139	broad.mit.edu	37	20	32232208	32232208	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:32232208C>T	ENST00000346541.3	+	12	2108	c.1571C>T	c.(1570-1572)gCg>gTg	p.A524V	CBFA2T2_ENST00000397800.1_Missense_Mutation_p.A495V|CBFA2T2_ENST00000375279.2_Missense_Mutation_p.A524V|CBFA2T2_ENST00000359606.3_Missense_Mutation_p.A534V|CBFA2T2_ENST00000543126.1_Missense_Mutation_p.A72V|CBFA2T2_ENST00000342704.6_Missense_Mutation_p.A515V|CBFA2T2_ENST00000492345.1_Missense_Mutation_p.A495V	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	524					epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.A524V(1)		breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						TGCAATATCGCGCGATACTGT	0.617																																					p.A515V	Esophageal Squamous(174;142 1955 14837 21276 28041)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1544T	20						.						76.0	71.0	73.0					20																	32232208		2203	4300	6503	31695869	SO:0001583	missense	9139	exon11			AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"""Zinc fingers, MYND-type"""	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.1571C>T	20.37:g.32232208C>T	ENSP00000262653:p.Ala524Val	Somatic		Capture	Illumina HiSeq	Phase_I	31695869	NM_001032999	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Missense_Mutation	SNP	ENST00000346541.3	37	CCDS13221.1	.	.	.	.	.	.	.	.	.	.	C	32	5.193315	0.94960	.	.	ENSG00000078699	ENST00000397803;ENST00000375279;ENST00000342704;ENST00000346541;ENST00000397800;ENST00000359606;ENST00000543126	T;T;T;T;T	0.49139	0.79;0.8;0.79;0.8;1.38	5.79	5.79	0.91817	Zinc finger, MYND-type (3);	0.000000	0.85682	D	0.000000	T	0.58708	0.2141	N	0.25201	0.72	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.994	T	0.60682	-0.7215	10	0.56958	D	0.05	0.0382	20.0222	0.97508	0.0:1.0:0.0:0.0	.	524;515	O43439;F8W6D7	MTG8R_HUMAN;.	V	298;524;515;524;495;534;72	ENSP00000364428:A524V;ENSP00000345810:A515V;ENSP00000262653:A524V;ENSP00000380902:A495V;ENSP00000352622:A534V	ENSP00000345810:A515V	A	+	2	0	CBFA2T2	31695869	1.000000	0.71417	0.956000	0.39512	0.721000	0.41392	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	GCG		0.617	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999	
GGT7	2686	broad.mit.edu	37	20	33437795	33437795	+	Silent	SNP	C	C	T	rs375464567		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:33437795C>T	ENST00000336431.5	-	14	1838	c.1794G>A	c.(1792-1794)ccG>ccA	p.P598P	GGT7_ENST00000469018.1_5'UTR	NM_178026.2	NP_821158.2	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7	598					glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.P598P(2)		NS(2)|breast(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	20						ACTGCAGGTCCGGGTGTAGGC	0.607																																					p.P598P												.	.	2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	c.G1794A	20						.	C		0,3860		0,0,1930	31.0	35.0	33.0		1794	-9.4	0.9	20		33	1,8261		0,1,4130	no	coding-synonymous	GGT7	NM_178026.2		0,1,6060	TT,TC,CC		0.0121,0.0,0.0082		598/663	33437795	1,12121	1930	4131	6061	32901456	SO:0001819	synonymous_variant	2686	exon14			AL049709	CCDS13242.2	20q11.22	2008-11-24	2008-03-10	2008-03-10	ENSG00000131067	ENSG00000131067		"""Gamma-glutamyltransferases"""	4259	protein-coding gene	gene with protein product		612342	"""gamma-glutamyltransferase-like 3"""	GGTL5, GGTL3		8104871, 18357469	Standard	NM_178026		Approved	D20S101, dJ18C9.2	uc002xay.3	Q9UJ14	OTTHUMG00000032314	ENST00000336431.5:c.1794G>A	20.37:g.33437795C>T		Somatic		Capture	Illumina HiSeq	Phase_I	32901456	NM_178026	Q8N899|Q8NF66|Q9BYP5|Q9BYP6	Silent	SNP	ENST00000336431.5	37	CCDS13242.2																																																																																				0.607	GGT7-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078816.2	NM_178026	
MYH7B	57644	broad.mit.edu	37	20	33584895	33584895	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:33584895C>T	ENST00000262873.7	+	29	3494	c.3402C>T	c.(3400-3402)tcC>tcT	p.S1134S		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1092						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.S1134S(1)		NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GGAAGGACTCCGAGCTGAGCC	0.662																																					p.S1134S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3402T	20						.						13.0	16.0	15.0					20																	33584895		1678	3569	5247	33048556	SO:0001819	synonymous_variant	57644	exon31			AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.3402C>T	20.37:g.33584895C>T		Somatic		Capture	Illumina HiSeq	Phase_I	33048556	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																				0.662	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
UQCC1	55245	broad.mit.edu	37	20	33902528	33902528	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:33902528G>A	ENST00000374385.5	-	8	791	c.614C>T	c.(613-615)aCa>aTa	p.T205I	UQCC1_ENST00000374377.5_Missense_Mutation_p.T93I|UQCC1_ENST00000542501.1_3'UTR|UQCC1_ENST00000359226.2_Missense_Mutation_p.T125I|UQCC1_ENST00000540457.1_Missense_Mutation_p.T50I|UQCC1_ENST00000374380.2_Missense_Mutation_p.T137I|UQCC1_ENST00000349714.5_Missense_Mutation_p.T178I|UQCC1_ENST00000374384.2_Intron|UQCC1_ENST00000407996.2_Intron|UQCC1_ENST00000397556.3_Missense_Mutation_p.T106I	NM_018244.4	NP_060714.3	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1	205						cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)		p.T205I(1)									GAAATGATTTGTCATGAGGAT	0.403																																					p.T205I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C614T	20						.						122.0	108.0	113.0					20																	33902528		2203	4300	6503	33365942	SO:0001583	missense	55245	exon8			AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019		"""Mitochondrial respiratory chain complex assembly factors"""	15891	protein-coding gene	gene with protein product	"""Basic FGF-repressed Zic-binding protein"", ""cytochrome B protein synthesis 3 homolog (S. cerevisiae)"""	611797	"""chromosome 20 open reading frame 44"", ""ubiquinol-cytochrome c reductase complex chaperone"""	C20orf44, UQCC			Standard	NM_018244		Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374385.5:c.614C>T	20.37:g.33902528G>A	ENSP00000363506:p.Thr205Ile	Somatic		Capture	Illumina HiSeq	Phase_I	33365942	NM_018244	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	Missense_Mutation	SNP	ENST00000374385.5	37	CCDS13252.1	.	.	.	.	.	.	.	.	.	.	G	18.22	3.575776	0.65878	.	.	ENSG00000101019	ENST00000349714;ENST00000359226;ENST00000374380;ENST00000374385;ENST00000374377;ENST00000397556;ENST00000540457;ENST00000424405;ENST00000438533	T;T;T;T;T	0.44083	1.52;1.5;1.49;0.93;1.47	5.0	5.0	0.66597	.	0.122950	0.50627	D	0.000103	T	0.44393	0.1291	M	0.63428	1.95	0.80722	D	1	P;B;B;P;B	0.41345	0.746;0.213;0.32;0.687;0.367	B;B;B;B;B	0.43251	0.346;0.067;0.117;0.413;0.173	T	0.46498	-0.9187	10	0.72032	D	0.01	-18.8636	11.0547	0.47911	0.0938:0.0:0.9062:0.0	.	137;90;106;178;205	B1AKV5;Q9NVA1-3;B7Z314;B7ZBG4;Q9NVA1	.;.;.;.;UQCC_HUMAN	I	178;125;137;205;93;106;50;173;219	ENSP00000335364:T178I;ENSP00000352161:T125I;ENSP00000363506:T205I;ENSP00000399713:T173I;ENSP00000398531:T219I	ENSP00000335364:T178I	T	-	2	0	UQCC	33365942	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.994000	0.63901	2.769000	0.95229	0.650000	0.86243	ACA		0.403	UQCC1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078866.1	NM_018244	
CPNE1	8904	broad.mit.edu	37	20	34220487	34220487	+	Silent	SNP	C	C	T	rs375260288		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:34220487C>T	ENST00000317619.3	-	5	655	c.261G>A	c.(259-261)gaG>gaA	p.E87E	CPNE1_ENST00000397442.1_Silent_p.E87E|CPNE1_ENST00000397443.1_Silent_p.E87E|CPNE1_ENST00000397446.1_Silent_p.E87E|RP1-309K20.6_ENST00000541176.2_3'UTR|CPNE1_ENST00000397445.1_Silent_p.E87E|CPNE1_ENST00000352393.4_Silent_p.E87E|CPNE1_ENST00000317677.5_Silent_p.E92E			Q99829	CPNE1_HUMAN	copine I	87	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid metabolic process (GO:0006629)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)	p.E87E(1)		breast(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			CATCCCTCAGCTCTGGCGTCT	0.512																																					p.E87E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G261A	20						.	C	,,,,,	1,4405	2.1+/-5.4	0,1,2202	178.0	154.0	162.0		261,276,261,261,261,261	2.1	1.0	20		162	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CPNE1	NM_001198863.1,NM_003915.5,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	,,,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,,,	87/537,92/543,87/538,87/538,87/538,87/538	34220487	1,13005	2203	4300	6503	33683901	SO:0001819	synonymous_variant	8904	exon4			U83246	CCDS13260.1, CCDS46595.1	20q11.22	2009-06-01			ENSG00000214078	ENSG00000214078			2314	protein-coding gene	gene with protein product		604205				9430674	Standard	NM_152925		Approved	CPN1	uc002xdm.3	Q99829	OTTHUMG00000032356	ENST00000317619.3:c.261G>A	20.37:g.34220487C>T		Somatic		Capture	Illumina HiSeq	Phase_I	33683901	NM_152927	E1P5Q4|Q6IBL3|Q9H243|Q9NTZ7	Silent	SNP	ENST00000317619.3	37	CCDS13260.1																																																																																				0.512	CPNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078909.3	NM_152930	
AAR2	25980	broad.mit.edu	37	20	34828308	34828308	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:34828308G>A	ENST00000373932.3	+	2	864	c.518G>A	c.(517-519)cGc>cAc	p.R173H	AAR2_ENST00000320849.4_Missense_Mutation_p.R173H|AAR2_ENST00000397286.3_Missense_Mutation_p.R173H	NM_015511.3	NP_056326.2	Q9Y312	AAR2_HUMAN	AAR2 splicing factor homolog (S. cerevisiae)	173								p.R173H(1)									ACCAAGGACCGCGTGGGGCAG	0.577																																					p.R173H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G518A	20						.						98.0	96.0	96.0					20																	34828308		2203	4300	6503	34291722	SO:0001583	missense	25980	exon2				CCDS13273.1	20q11.23	2012-07-20	2012-07-20	2012-07-20	ENSG00000131043	ENSG00000131043			15886	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 4"""	C20orf4			Standard	NM_015511		Approved	bA234K24.2	uc002xfc.3	Q9Y312	OTTHUMG00000032380	ENST00000373932.3:c.518G>A	20.37:g.34828308G>A	ENSP00000363043:p.Arg173His	Somatic		Capture	Illumina HiSeq	Phase_I	34291722	NM_015511	E1P5S7|Q9H4F9|Q9P1P3|Q9UFK9	Missense_Mutation	SNP	ENST00000373932.3	37	CCDS13273.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.747323	0.89663	.	.	ENSG00000131043	ENST00000397286;ENST00000320849;ENST00000373932	T;T;T	0.46063	0.88;0.88;0.88	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.67031	0.2850	M	0.80746	2.51	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.991;0.995	T	0.69628	-0.5094	10	0.56958	D	0.05	.	17.4533	0.87599	0.0:0.0:1.0:0.0	.	173;173	A2A2Q9;Q9Y312	.;CT004_HUMAN	H	173	ENSP00000380455:R173H;ENSP00000313674:R173H;ENSP00000363043:R173H	ENSP00000313674:R173H	R	+	2	0	C20orf4	34291722	1.000000	0.71417	0.976000	0.42696	0.958000	0.62258	8.889000	0.92470	2.770000	0.95276	0.650000	0.86243	CGC		0.577	AAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079001.2	NM_015511	
GFRA4	64096	broad.mit.edu	37	20	3640864	3640864	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:3640864G>A	ENST00000319242.3	-	4	759	c.760C>T	c.(760-762)Ccc>Tcc	p.P254S	GFRA4_ENST00000290417.2_Missense_Mutation_p.P224S			Q9GZZ7	GFRA4_HUMAN	GDNF family receptor alpha 4	254					negative regulation of ossification (GO:0030279)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)	p.P254S(1)		large_intestine(1)|lung(2)	3						AGGACTGGGGGCCACCCGCTG	0.662																																					p.P224S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C670T	20						.						14.0	15.0	15.0					20																	3640864		2198	4274	6472	3588864	SO:0001583	missense	64096	exon5			AF253318	CCDS13055.1, CCDS13056.1	20p13-p12	2008-07-16			ENSG00000125861	ENSG00000125861			13821	protein-coding gene	gene with protein product	"""persephin receptor"""					10958791, 15225646	Standard	XM_005260793		Approved		uc002win.3	Q9GZZ7	OTTHUMG00000031748	ENST00000319242.3:c.760C>T	20.37:g.3640864G>A	ENSP00000313423:p.Pro254Ser	Somatic		Capture	Illumina HiSeq	Phase_I	3588864	NM_022139	Q5JT74|Q9H191|Q9H192	Missense_Mutation	SNP	ENST00000319242.3	37	CCDS13056.1	.	.	.	.	.	.	.	.	.	.	G	8.979	0.974874	0.18736	.	.	ENSG00000125861	ENST00000290417;ENST00000319242	.	.	.	5.17	0.929	0.19449	.	0.624753	0.15423	N	0.263142	T	0.24812	0.0602	L	0.32530	0.975	0.09310	N	1	B;B	0.19331	0.004;0.035	B;B	0.16289	0.005;0.015	T	0.27020	-1.0086	9	0.09338	T	0.73	-4.1356	7.1718	0.25722	0.4011:0.0:0.5989:0.0	.	254;224	Q9GZZ7;Q9GZZ7-2	GFRA4_HUMAN;.	S	224;254	.	ENSP00000290417:P224S	P	-	1	0	GFRA4	3588864	0.006000	0.16342	0.002000	0.10522	0.087000	0.18053	0.539000	0.23175	0.092000	0.17331	0.650000	0.86243	CCC		0.662	GFRA4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077744.1	NM_145762	
TGIF2	60436	broad.mit.edu	37	20	35207263	35207263	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:35207263C>T	ENST00000373874.2	+	2	285	c.86C>T	c.(85-87)tCg>tTg	p.S29L	TGIF2_ENST00000373872.4_Missense_Mutation_p.S29L|RP5-977B1.11_ENST00000561134.1_RNA|TGIF2-C20orf24_ENST00000558530.1_Missense_Mutation_p.S29L	NM_001199514.1|NM_001199515.1	NP_001186443.1|NP_001186444.1	Q9GZN2	TGIF2_HUMAN	TGFB-induced factor homeobox 2	29					gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nodal signaling pathway (GO:0038092)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S29L(1)		cervix(3)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				CCCAAGGAGTCGGTGAAGATC	0.602																																					p.S29L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C86T	20						.						125.0	109.0	115.0					20																	35207263		2203	4300	6503	34640677	SO:0001583	missense	60436	exon2			AB042646	CCDS13278.1	20q11.23	2012-12-12	2007-02-07		ENSG00000118707	ENSG00000118707		"""Homeoboxes / TALE class"""	15764	protein-coding gene	gene with protein product		607294	"""TGFB-induced factor 2 (TALE family homeobox)"""			11006116	Standard	NM_021809		Approved		uc021wcv.1	Q9GZN2	OTTHUMG00000172332	ENST00000373874.2:c.86C>T	20.37:g.35207263C>T	ENSP00000362981:p.Ser29Leu	Somatic		Capture	Illumina HiSeq	Phase_I	34640677	NM_001199535	B2R9U3|E1P5T9|H0YNI0	Missense_Mutation	SNP	ENST00000373874.2	37	CCDS13278.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.993107	0.93167	.	.	ENSG00000118707	ENST00000373874;ENST00000373872	D;D	0.83673	-1.75;-1.75	5.01	5.01	0.66863	Homeodomain-related (1);Homeobox (2);Homeodomain-like (1);	0.071257	0.64402	D	0.000020	D	0.86997	0.6068	L	0.41492	1.28	0.29479	N	0.856462	D	0.89917	1.0	D	0.69307	0.963	D	0.84025	0.0356	10	0.87932	D	0	-11.9919	15.8254	0.78703	0.0:1.0:0.0:0.0	.	29	Q9GZN2	TGIF2_HUMAN	L	29	ENSP00000362981:S29L;ENSP00000362979:S29L	ENSP00000362979:S29L	S	+	2	0	TGIF2	34640677	1.000000	0.71417	0.929000	0.37066	0.951000	0.60555	7.374000	0.79633	2.316000	0.78162	0.561000	0.74099	TCG		0.602	TGIF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079004.2	NM_021809	
TGM2	7052	broad.mit.edu	37	20	36759572	36759572	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:36759572C>T	ENST00000361475.2	-	12	2009	c.1836G>A	c.(1834-1836)ccG>ccA	p.P612P	TGM2_ENST00000536724.1_Silent_p.P552P|TGM2_ENST00000536701.1_Silent_p.P531P	NM_004613.2|NM_198951.1	NP_004604.2|NP_945189.1	P21980	TGM2_HUMAN	transglutaminase 2	612					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|branching involved in salivary gland morphogenesis (GO:0060445)|isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein homooligomerization (GO:0051260)|salivary gland cavitation (GO:0060662)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.P612P(1)		endometrium(2)|large_intestine(11)|liver(1)|lung(7)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)	CCACAGGGAGCGGGTTCTGCA	0.617																																					p.P612P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1836A	20						.						86.0	80.0	82.0					20																	36759572		2203	4300	6503	36192986	SO:0001819	synonymous_variant	7052	exon12			M98478	CCDS13302.1	20q12	2013-05-02	2013-05-02		ENSG00000198959	ENSG00000198959	2.3.2.13	"""Transglutaminases"""	11778	protein-coding gene	gene with protein product	"""C polypeptide, protein-glutamine-gamma-glutamyltransferase"""	190196	"""transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)"""			7912692, 11390390	Standard	NM_004613		Approved	TGC	uc002xhr.3	P21980	OTTHUMG00000032437	ENST00000361475.2:c.1836G>A	20.37:g.36759572C>T		Somatic		Capture	Illumina HiSeq	Phase_I	36192986	NM_004613	E1P5V9|Q16436|Q6B838|Q9BTN7|Q9UH35	Silent	SNP	ENST00000361475.2	37	CCDS13302.1																																																																																				0.617	TGM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079151.2	NM_198951	
PPP1R16B	26051	broad.mit.edu	37	20	37536775	37536775	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:37536775G>A	ENST00000299824.1	+	10	1322	c.1133G>A	c.(1132-1134)cGg>cAg	p.R378Q	PPP1R16B_ENST00000373331.2_Missense_Mutation_p.R336Q	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	378					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)	p.R378Q(1)		biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				GAGGATCAGCGGACCTCCACC	0.612																																					p.R336Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1007A	20						.						112.0	97.0	102.0					20																	37536775		2203	4300	6503	36970189	SO:0001583	missense	26051	exon9			AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	15850	protein-coding gene	gene with protein product	"""TGF-beta-inhibited membrane-associated protein"", ""ankyrin repeat domain protein 4"""	613275	"""protein phosphatase 1, regulatory (inhibitor) subunit 16B"""			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1133G>A	20.37:g.37536775G>A	ENSP00000299824:p.Arg378Gln	Somatic		Capture	Illumina HiSeq	Phase_I	36970189	NM_001172735	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Missense_Mutation	SNP	ENST00000299824.1	37	CCDS13309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	31|31	5.059193|5.059193	0.93846|0.93846	.|.	.|.	ENSG00000101445|ENSG00000101445	ENST00000438192|ENST00000299824;ENST00000373331	.|T;T	.|0.70282	.|-0.26;-0.47	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|0.280948	.|0.38111	.|N	.|0.001816	T|T	0.75895|0.75895	0.3912|0.3912	N|N	0.22421|0.22421	0.69|0.69	0.38900|0.38900	D|D	0.957303|0.957303	.|D;P	.|0.69078	.|0.997;0.911	.|D;B	.|0.67725	.|0.953;0.262	T|T	0.76753|0.76753	-0.2843|-0.2843	5|10	.|0.44086	.|T	.|0.13	.|.	20.0987|20.0987	0.97860|0.97860	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|336;378	.|E9PFS8;Q96T49	.|.;PP16B_HUMAN	R|Q	279|378;336	.|ENSP00000299824:R378Q;ENSP00000362428:R336Q	.|ENSP00000299824:R378Q	G|R	+|+	1|2	0|0	PPP1R16B|PPP1R16B	36970189|36970189	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.890000|0.890000	0.51754|0.51754	6.211000|6.211000	0.72182|0.72182	2.771000|2.771000	0.95319|0.95319	0.644000|0.644000	0.83932|0.83932	GGA|CGG		0.612	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568	
PPP1R16B	26051	broad.mit.edu	37	20	37546918	37546918	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:37546918C>T	ENST00000299824.1	+	11	1502	c.1313C>T	c.(1312-1314)gCg>gTg	p.A438V	PPP1R16B_ENST00000373331.2_Missense_Mutation_p.A396V	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	438					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)	p.A438V(2)		biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				TACCAGTATGCGCTGGCCAAC	0.622																																					p.A396V												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.C1187T	20						.						157.0	150.0	152.0					20																	37546918		2203	4300	6503	36980332	SO:0001583	missense	26051	exon10			AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	15850	protein-coding gene	gene with protein product	"""TGF-beta-inhibited membrane-associated protein"", ""ankyrin repeat domain protein 4"""	613275	"""protein phosphatase 1, regulatory (inhibitor) subunit 16B"""			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1313C>T	20.37:g.37546918C>T	ENSP00000299824:p.Ala438Val	Somatic		Capture	Illumina HiSeq	Phase_I	36980332	NM_001172735	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Missense_Mutation	SNP	ENST00000299824.1	37	CCDS13309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.22|17.22	3.335057|3.335057	0.60853|0.60853	.|.	.|.	ENSG00000101445|ENSG00000101445	ENST00000299824;ENST00000373331|ENST00000438192	T;T|.	0.71698|.	-0.4;-0.59|.	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	0.265483|.	0.37809|.	N|.	0.001934|.	T|T	0.30355|0.30355	0.0762|0.0762	N|N	0.08118|0.08118	0|0	0.27868|0.27868	N|N	0.94016|0.94016	P;B|.	0.35872|.	0.525;0.024|.	B;B|.	0.27380|.	0.079;0.002|.	T|T	0.19289|0.19289	-1.0310|-1.0310	10|5	0.59425|.	D|.	0.04|.	.|.	17.1291|17.1291	0.86722|0.86722	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	396;438|.	E9PFS8;Q96T49|.	.;PP16B_HUMAN|.	V|C	438;396|339	ENSP00000299824:A438V;ENSP00000362428:A396V|.	ENSP00000299824:A438V|.	A|R	+|+	2|1	0|0	PPP1R16B|PPP1R16B	36980332|36980332	0.684000|0.684000	0.27642|0.27642	0.997000|0.997000	0.53966|0.53966	0.890000|0.890000	0.51754|0.51754	2.638000|2.638000	0.46562|0.46562	2.474000|2.474000	0.83562|0.83562	0.655000|0.655000	0.94253|0.94253	GCG|CGC		0.622	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568	
PPP1R16B	26051	broad.mit.edu	37	20	37547131	37547131	+	Missense_Mutation	SNP	C	C	T	rs368927917		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:37547131C>T	ENST00000299824.1	+	11	1715	c.1526C>T	c.(1525-1527)aCg>aTg	p.T509M	PPP1R16B_ENST00000373331.2_Missense_Mutation_p.T467M	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	509					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)	p.T509M(1)		biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				ATGGCCAGGACGGGCGAGAGT	0.617																																					p.T467M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1400T	20						.	C	MET/THR,MET/THR	0,4406		0,0,2203	65.0	54.0	58.0		1400,1526	-0.9	0.2	20		58	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	PPP1R16B	NM_001172735.1,NM_015568.2	81,81	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	467/526,509/568	37547131	2,13004	2203	4300	6503	36980545	SO:0001583	missense	26051	exon10			AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	15850	protein-coding gene	gene with protein product	"""TGF-beta-inhibited membrane-associated protein"", ""ankyrin repeat domain protein 4"""	613275	"""protein phosphatase 1, regulatory (inhibitor) subunit 16B"""			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.1526C>T	20.37:g.37547131C>T	ENSP00000299824:p.Thr509Met	Somatic		Capture	Illumina HiSeq	Phase_I	36980545	NM_001172735	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Missense_Mutation	SNP	ENST00000299824.1	37	CCDS13309.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.32|12.32	1.903515|1.903515	0.33628|0.33628	0.0|0.0	2.33E-4|2.33E-4	ENSG00000101445|ENSG00000101445	ENST00000438192|ENST00000299824;ENST00000373331	.|T;T	.|0.70986	.|-0.33;-0.53	5.35|5.35	-0.874|-0.874	0.10631|0.10631	.|.	.|0.954445	.|0.08815	.|N	.|0.889639	T|T	0.39226|0.39226	0.1070|0.1070	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|P;P	.|0.47106	.|0.89;0.713	.|B;B	.|0.34873	.|0.191;0.143	T|T	0.37934|0.37934	-0.9684|-0.9684	5|10	.|0.48119	.|T	.|0.1	.|.	1.7937|1.7937	0.03057|0.03057	0.1418:0.3702:0.2795:0.2085|0.1418:0.3702:0.2795:0.2085	.|.	.|467;509	.|E9PFS8;Q96T49	.|.;PP16B_HUMAN	W|M	410|509;467	.|ENSP00000299824:T509M;ENSP00000362428:T467M	.|ENSP00000299824:T509M	R|T	+|+	1|2	2|0	PPP1R16B|PPP1R16B	36980545|36980545	0.007000|0.007000	0.16637|0.16637	0.166000|0.166000	0.22797|0.22797	0.997000|0.997000	0.91878|0.91878	0.221000|0.221000	0.17680|0.17680	0.206000|0.206000	0.20587|0.20587	0.655000|0.655000	0.94253|0.94253	CGG|ACG		0.617	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568	
FAM83D	81610	broad.mit.edu	37	20	37580472	37580472	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:37580472C>T	ENST00000217429.4	+	4	1198	c.1157C>T	c.(1156-1158)gCa>gTa	p.A386V		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	356					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.A386V(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)|stomach(1)	28		Myeloproliferative disorder(115;0.00878)				GAGGGCAAGGCAGAGCGCAAG	0.607																																					p.A386V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1157T	20						.						47.0	54.0	52.0					20																	37580472		2083	4204	6287	37013886	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.1157C>T	20.37:g.37580472C>T	ENSP00000217429:p.Ala386Val	Somatic		Capture	Illumina HiSeq	Phase_I	37013886	NM_030919	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Missense_Mutation	SNP	ENST00000217429.4	37	CCDS42872.1	.	.	.	.	.	.	.	.	.	.	C	8.108	0.778130	0.16120	.	.	ENSG00000101447	ENST00000217429;ENST00000424027	T	0.12147	2.71	5.69	-2.06	0.07298	.	0.930893	0.09186	N	0.836762	T	0.12092	0.0294	M	0.70595	2.14	0.09310	N	1	P	0.35077	0.483	B	0.27887	0.084	T	0.25433	-1.0132	10	0.35671	T	0.21	.	5.4545	0.16582	0.4263:0.3966:0.1059:0.0712	.	356	Q9H4H8	FA83D_HUMAN	V	386;340	ENSP00000217429:A386V	ENSP00000217429:A386V	A	+	2	0	FAM83D	37013886	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.061000	0.11693	0.019000	0.15079	0.655000	0.94253	GCA		0.607	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1		
TOP1	7150	broad.mit.edu	37	20	39713142	39713142	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:39713142A>C	ENST00000361337.2	+	8	798	c.548A>C	c.(547-549)aAa>aCa	p.K183T		NM_003286.2	NP_003277.1	P11387	TOP1_HUMAN	topoisomerase (DNA) I	183	Lys-rich.				chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|DNA topological change (GO:0006265)|embryonic cleavage (GO:0040016)|phosphorylation (GO:0016310)|programmed cell death (GO:0012501)|response to drug (GO:0042493)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|replication fork protection complex (GO:0031298)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|poly(A) RNA binding (GO:0044822)	p.K183T(1)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Sodium stibogluconate(DB05630)|Topotecan(DB01030)	GATAAAGATAAAAAAGTTCCT	0.373			T	NUP98	AML*																																p.K183T			Dom	yes		20	20q12-q13.1	7150	topoisomerase (DNA) I		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A548C	20						.						55.0	52.0	53.0					20																	39713142		2200	4297	6497	39146556	SO:0001583	missense	7150	exon8				CCDS13312.1	20q12-q13.1	1990-06-22			ENSG00000198900	ENSG00000198900	5.99.1.2		11986	protein-coding gene	gene with protein product		126420					Standard	NM_003286		Approved		uc010ggd.1	P11387	OTTHUMG00000033057	ENST00000361337.2:c.548A>C	20.37:g.39713142A>C	ENSP00000354522:p.Lys183Thr	Somatic		Capture	Illumina HiSeq	Phase_I	39146556	NM_003286	A8KA78|E1P5W3|O43256|Q12855|Q12856|Q15610|Q5TFY3|Q9UJN0	Missense_Mutation	SNP	ENST00000361337.2	37	CCDS13312.1	.	.	.	.	.	.	.	.	.	.	A	18.14	3.557710	0.65425	.	.	ENSG00000198900	ENST00000361337	T	0.25579	1.79	4.12	4.12	0.48240	.	0.084250	0.50627	D	0.000101	T	0.15825	0.0381	L	0.29908	0.895	0.47905	D	0.999543	B	0.33694	0.421	B	0.27608	0.081	T	0.06267	-1.0836	10	0.31617	T	0.26	-14.4205	9.8094	0.40812	1.0:0.0:0.0:0.0	.	183	P11387	TOP1_HUMAN	T	183	ENSP00000354522:K183T	ENSP00000354522:K183T	K	+	2	0	TOP1	39146556	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.623000	0.61247	2.097000	0.63578	0.482000	0.46254	AAA		0.373	TOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080397.2		
PLCG1	5335	broad.mit.edu	37	20	39802799	39802799	+	Silent	SNP	G	G	A	rs140172118	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:39802799G>A	ENST00000373271.1	+	31	4083	c.3678G>A	c.(3676-3678)acG>acA	p.T1226T	PLCG1_ENST00000608689.1_3'UTR|PLCG1_ENST00000244007.3_Silent_p.T1227T|PLCG1_ENST00000373272.2_Silent_p.T1227T	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	1226					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.T1227T(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)				TCAGTGGTACGTCCCTGCGGG	0.597																																					p.T1227T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3681A	20						.	G	,	4,4402	8.1+/-20.4	0,4,2199	71.0	75.0	74.0		3681,3678	-11.0	0.0	20	dbSNP_134	74	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PLCG1	NM_002660.2,NM_182811.1	,	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	,	1227/1292,1226/1291	39802799	4,13002	2203	4300	6503	39236213	SO:0001819	synonymous_variant	5335	exon31			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.3678G>A	20.37:g.39802799G>A		Somatic		Capture	Illumina HiSeq	Phase_I	39236213	NM_002660	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Silent	SNP	ENST00000373271.1	37	CCDS13314.1																																																																																				0.597	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811	
PLCG1	5335	broad.mit.edu	37	20	39802903	39802903	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:39802903G>A	ENST00000373271.1	+	31	4187	c.3782G>A	c.(3781-3783)cGc>cAc	p.R1261H	PLCG1_ENST00000608689.1_3'UTR|PLCG1_ENST00000244007.3_Missense_Mutation_p.R1262H|PLCG1_ENST00000373272.2_Missense_Mutation_p.R1262H	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	1261					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.R1262H(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)				GAGGACTTCCGCATCTCCCAG	0.607																																					p.R1262H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3785A	20						.						61.0	64.0	63.0					20																	39802903		2203	4300	6503	39236317	SO:0001583	missense	5335	exon31			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.3782G>A	20.37:g.39802903G>A	ENSP00000362368:p.Arg1261His	Somatic		Capture	Illumina HiSeq	Phase_I	39236317	NM_002660	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Missense_Mutation	SNP	ENST00000373271.1	37	CCDS13314.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.171993	0.78452	.	.	ENSG00000124181	ENST00000244007;ENST00000373271;ENST00000373272	T;T;T	0.61510	0.1;0.1;0.1	5.35	3.1	0.35709	.	0.063422	0.64402	N	0.000006	T	0.64875	0.2638	L	0.46157	1.445	0.58432	D	0.999996	D;D;D	0.89917	1.0;0.999;0.999	D;P;D	0.70016	0.967;0.846;0.927	T	0.61422	-0.7066	10	0.48119	T	0.1	.	8.7424	0.34564	0.0998:0.1433:0.757:0.0	.	1262;1261;1262	P19174-2;P19174;A2A284	.;PLCG1_HUMAN;.	H	1262;1261;1262	ENSP00000244007:R1262H;ENSP00000362368:R1261H;ENSP00000362369:R1262H	ENSP00000244007:R1262H	R	+	2	0	PLCG1	39236317	1.000000	0.71417	0.998000	0.56505	0.944000	0.59088	7.261000	0.78400	0.438000	0.26450	0.455000	0.32223	CGC		0.607	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811	
ZHX3	23051	broad.mit.edu	37	20	39832133	39832133	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:39832133G>A	ENST00000309060.3	-	4	1839	c.1424C>T	c.(1423-1425)gCg>gTg	p.A475V	ZHX3_ENST00000540170.1_Missense_Mutation_p.A475V|ZHX3_ENST00000432768.2_Missense_Mutation_p.A475V|ZHX3_ENST00000544979.2_Missense_Mutation_p.A475V|ZHX3_ENST00000558993.1_Intron|ZHX3_ENST00000557816.1_Intron|ZHX3_ENST00000560361.1_Missense_Mutation_p.A475V|ZHX3_ENST00000559234.1_Missense_Mutation_p.A475V			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	475	Required for homodimerization and interaction with NFYA.|Required for repressor activity.				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.A475V(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)				CGACTGGGCCGCATTGACCAC	0.537																																					p.A475V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1424T	20						.						72.0	58.0	62.0					20																	39832133		2203	4300	6503	39265547	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.1424C>T	20.37:g.39832133G>A	ENSP00000312222:p.Ala475Val	Somatic		Capture	Illumina HiSeq	Phase_I	39265547	NM_015035	E1P5W5|F5H820|O43145|Q6NUJ7	Missense_Mutation	SNP	ENST00000309060.3	37	CCDS13315.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.997092	0.35226	.	.	ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000373262;ENST00000432768	T;T;T;T;T	0.34859	1.34;2.8;2.8;2.59;1.34	5.93	5.93	0.95920	.	0.242897	0.40469	N	0.001094	T	0.32645	0.0836	L	0.40543	1.245	0.18873	N	0.999981	P;B;P	0.41673	0.532;0.348;0.759	B;B;B	0.37480	0.251;0.102;0.176	T	0.38394	-0.9663	10	0.72032	D	0.01	-9.9771	16.3863	0.83505	0.0:0.1314:0.8686:0.0	.	475;475;475	A8K8Q0;Q9H4I2;F5H820	.;ZHX3_HUMAN;.	V	475;475;475;475;253;475	ENSP00000312222:A475V;ENSP00000362360:A475V;ENSP00000442290:A475V;ENSP00000443783:A475V;ENSP00000415498:A475V	ENSP00000312222:A475V	A	-	2	0	ZHX3	39265547	0.534000	0.26362	0.181000	0.23098	0.707000	0.40811	2.718000	0.47236	2.815000	0.96918	0.561000	0.74099	GCG		0.537	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035	
ZHX3	23051	broad.mit.edu	37	20	39833352	39833352	+	Missense_Mutation	SNP	G	G	A	rs139157503		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:39833352G>A	ENST00000309060.3	-	4	620	c.205C>T	c.(205-207)Cgg>Tgg	p.R69W	ZHX3_ENST00000540170.1_Missense_Mutation_p.R69W|ZHX3_ENST00000432768.2_Missense_Mutation_p.R69W|ZHX3_ENST00000544979.2_Missense_Mutation_p.R69W|ZHX3_ENST00000558993.1_Missense_Mutation_p.R69W|ZHX3_ENST00000557816.1_Missense_Mutation_p.R69W|ZHX3_ENST00000560361.1_Missense_Mutation_p.R69W|ZHX3_ENST00000559234.1_Missense_Mutation_p.R69W			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	69	Required for nuclear localization.				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.R69W(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)				AAAGTGCTCCGATGCCCATTG	0.507																																					p.R69W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C205T	20						.	G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	121.0	118.0	119.0		205	3.9	0.9	20	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZHX3	NM_015035.3	101	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	69/957	39833352	2,13004	2203	4300	6503	39266766	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.205C>T	20.37:g.39833352G>A	ENSP00000312222:p.Arg69Trp	Somatic		Capture	Illumina HiSeq	Phase_I	39266766	NM_015035	E1P5W5|F5H820|O43145|Q6NUJ7	Missense_Mutation	SNP	ENST00000309060.3	37	CCDS13315.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.101546	0.56183	2.27E-4	1.16E-4	ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000432768;ENST00000441102;ENST00000419740;ENST00000373261;ENST00000436440	T;T;T;T;T	0.34472	1.36;2.75;2.75;2.54;1.36	5.83	3.89	0.44902	.	0.571686	0.18968	N	0.126211	T	0.43500	0.1250	L	0.57536	1.79	0.09310	N	1	D;D;D;D	0.71674	0.991;0.977;0.998;0.995	P;P;P;B	0.56916	0.462;0.462;0.809;0.409	T	0.37526	-0.9702	10	0.66056	D	0.02	-10.4593	3.6565	0.08222	0.1426:0.1332:0.5864:0.1378	.	69;69;69;69	A8K8Q0;Q9H4I2;F5H820;F6R4Q5	.;ZHX3_HUMAN;.;.	W	69	ENSP00000312222:R69W;ENSP00000362360:R69W;ENSP00000442290:R69W;ENSP00000443783:R69W;ENSP00000415498:R69W	ENSP00000312222:R69W	R	-	1	2	ZHX3	39266766	0.035000	0.19736	0.950000	0.38849	0.954000	0.61252	2.034000	0.41145	1.488000	0.48433	-0.136000	0.14681	CGG		0.507	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035	
EMILIN3	90187	broad.mit.edu	37	20	39992390	39992390	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:39992390C>T	ENST00000332312.3	-	3	594	c.402G>A	c.(400-402)acG>acA	p.T134T		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	134						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)		p.T134T(1)		biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				CCCCATGGTCCGTGAGGTGCT	0.627																																					p.T134T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G402A	20						.						97.0	82.0	87.0					20																	39992390		2203	4300	6503	39425804	SO:0001819	synonymous_variant	90187	exon3			AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.402G>A	20.37:g.39992390C>T		Somatic		Capture	Illumina HiSeq	Phase_I	39425804	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																				0.627	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
CHD6	84181	broad.mit.edu	37	20	40126083	40126083	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:40126083C>T	ENST00000373233.3	-	8	1210	c.1033G>A	c.(1033-1035)Gca>Aca	p.A345T	CHD6_ENST00000309279.7_Missense_Mutation_p.A345T|CHD6_ENST00000373222.3_3'UTR	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	345	Required for DNA-dependent ATPase activity.				ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)	p.A345T(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				ATCTTCTGTGCGATGCGAGGA	0.408																																					p.A345T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1033A	20						.						159.0	134.0	143.0					20																	40126083		2203	4300	6503	39559497	SO:0001583	missense	84181	exon8			AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.1033G>A	20.37:g.40126083C>T	ENSP00000362330:p.Ala345Thr	Somatic		Capture	Illumina HiSeq	Phase_I	39559497	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	C	15.93	2.977552	0.53720	.	.	ENSG00000124177	ENST00000373233;ENST00000309279	T;T	0.73047	-0.71;-0.71	5.48	4.48	0.54585	Chromo domain (1);Chromo domain-like (1);Chromo domain/shadow (1);	0.118493	0.38005	N	0.001859	T	0.55986	0.1955	L	0.34521	1.04	0.42593	D	0.993252	P	0.34662	0.462	B	0.33568	0.166	T	0.53920	-0.8370	10	0.25751	T	0.34	-13.0567	9.7581	0.40515	0.206:0.6828:0.1112:0.0	.	345	Q8TD26	CHD6_HUMAN	T	345	ENSP00000362330:A345T;ENSP00000308684:A345T	ENSP00000308684:A345T	A	-	1	0	CHD6	39559497	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.137000	0.50562	2.572000	0.86782	0.655000	0.94253	GCA		0.408	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1		
CSNK2A1	1457	broad.mit.edu	37	20	464627	464627	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:464627G>T	ENST00000217244.3	-	14	1529	c.1154C>A	c.(1153-1155)gCt>gAt	p.A385D	CSNK2A1_ENST00000400217.2_Missense_Mutation_p.A249D|CSNK2A1_ENST00000400227.3_Intron|CSNK2A1_ENST00000349736.5_Missense_Mutation_p.A385D	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	385					axon guidance (GO:0007411)|chaperone-mediated protein folding (GO:0061077)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|plasma membrane (GO:0005886)|Sin3 complex (GO:0016580)	ATP binding (GO:0005524)|Hsp90 protein binding (GO:0051879)|protein N-terminus binding (GO:0047485)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)	p.A385D(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.0969)			GCCAGCGGCAGCTGGAACAGG	0.617																																					p.A385D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1154A	20						.						32.0	31.0	31.0					20																	464627		2200	4294	6494	412627	SO:0001583	missense	1457	exon13			M55265	CCDS13003.1, CCDS13004.1	20p13	2013-01-17			ENSG00000101266	ENSG00000101266			2457	protein-coding gene	gene with protein product		115440				2174700, 1766873	Standard	NM_177559		Approved		uc002wdx.1	P68400	OTTHUMG00000031636	ENST00000217244.3:c.1154C>A	20.37:g.464627G>T	ENSP00000217244:p.Ala385Asp	Somatic		Capture	Illumina HiSeq	Phase_I	412627	NM_001895	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Missense_Mutation	SNP	ENST00000217244.3	37	CCDS13003.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.78|15.78	2.935407|2.935407	0.52866|0.52866	.|.	.|.	ENSG00000101266|ENSG00000101266	ENST00000349736;ENST00000217244;ENST00000400217|ENST00000381973	T;T;T|.	0.64260|.	0.3;0.3;-0.09|.	5.44|5.44	5.44|5.44	0.79542|0.79542	.|.	.|0.655433	.|0.16069	.|N	.|0.231091	T|T	0.50000|0.50000	0.1590|0.1590	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	B|.	0.29085|.	0.232|.	B|.	0.24848|.	0.056|.	T|T	0.32268|0.32268	-0.9913|-0.9913	9|7	0.87932|0.08837	D|T	0|0.75	-11.3441|-11.3441	18.4312|18.4312	0.90625|0.90625	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	385|.	P68400|.	CSK21_HUMAN|.	D|M	385;385;249|385	ENSP00000339247:A385D;ENSP00000217244:A385D;ENSP00000383076:A249D|.	ENSP00000217244:A385D|ENSP00000371400:L385M	A|L	-|-	2|1	0|2	CSNK2A1|CSNK2A1	412627|412627	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.298000|8.298000	0.89944|0.89944	2.829000|2.829000	0.97493|0.97493	0.655000|0.655000	0.94253|0.94253	GCT|CTG		0.617	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895	
SMOX	54498	broad.mit.edu	37	20	4162550	4162550	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:4162550G>A	ENST00000305958.4	+	4	761	c.536G>A	c.(535-537)cGc>cAc	p.R179H	SMOX_ENST00000379460.2_Missense_Mutation_p.R179H|SMOX_ENST00000339123.6_Missense_Mutation_p.R179H|SMOX_ENST00000484515.1_3'UTR|SMOX_ENST00000346595.2_Intron|SMOX_ENST00000278795.3_Missense_Mutation_p.R179H	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase	179					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity (GO:0052895)|norspermine:oxygen oxidoreductase activity (GO:0052894)|polyamine oxidase activity (GO:0046592)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)	p.R179H(2)		breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(7)|lung(5)|skin(2)|urinary_tract(1)	26					Spermine(DB00127)	GTGCGTAACCGCATCAGGAAT	0.537																																					p.R179H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G536A	20						.						86.0	86.0	86.0					20																	4162550		2203	4300	6503	4110550	SO:0001583	missense	54498	exon4			AK000753	CCDS13075.1, CCDS13076.1, CCDS13077.1, CCDS13078.1, CCDS74702.1	20p13	2003-10-15	2003-10-15	2003-10-15	ENSG00000088826	ENSG00000088826			15862	protein-coding gene	gene with protein product		615854	"""chromosome 20 open reading frame 16"""	C20orf16		11454677, 12398765	Standard	NM_175839		Approved	FLJ20746, dJ779E11.1, PAO, PAOh1, MGC1010, SMO	uc002wkp.3	Q9NWM0	OTTHUMG00000031777	ENST00000305958.4:c.536G>A	20.37:g.4162550G>A	ENSP00000307252:p.Arg179His	Somatic		Capture	Illumina HiSeq	Phase_I	4110550	NM_175840	A2A2P5|A2A2P6|A8BE87|D3DVZ4|Q5TE26|Q5TE27|Q6UY28|Q8IX00|Q96LC3|Q96LC4|Q96QT3|Q9BW38|Q9H6H1|Q9NP51|Q9NPY1|Q9NPY2	Missense_Mutation	SNP	ENST00000305958.4	37	CCDS13075.1	.	.	.	.	.	.	.	.	.	.	G	14.97	2.694183	0.48202	.	.	ENSG00000088826	ENST00000339123;ENST00000305958;ENST00000278795;ENST00000379460;ENST00000457205	T;T;T;T;T	0.31769	2.98;2.98;2.98;2.98;1.48	5.44	5.44	0.79542	Amine oxidase (1);	0.806408	0.11832	N	0.525167	T	0.41650	0.1168	L	0.28649	0.875	0.46954	D	0.999269	D;D;D;D;P	0.76494	0.998;0.998;0.999;0.994;0.571	P;P;D;P;B	0.65773	0.841;0.899;0.938;0.669;0.05	T	0.03268	-1.1054	10	0.10902	T	0.67	-18.8399	16.8098	0.85716	0.0:0.0:1.0:0.0	.	156;179;179;179;179	B4DE63;Q9NWM0-6;Q9NWM0;Q9NWM0-2;Q9NWM0-4	.;.;SMOX_HUMAN;.;.	H	179;179;179;179;36	ENSP00000344595:R179H;ENSP00000307252:R179H;ENSP00000278795:R179H;ENSP00000368773:R179H;ENSP00000407269:R36H	ENSP00000278795:R179H	R	+	2	0	SMOX	4110550	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.439000	0.66556	2.576000	0.86940	0.558000	0.71614	CGC		0.537	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077806.1	NM_175842	
PTPRT	11122	broad.mit.edu	37	20	41306639	41306639	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:41306639G>A	ENST00000373187.1	-	7	1019	c.1020C>T	c.(1018-1020)gtC>gtT	p.V340V	PTPRT_ENST00000373190.1_Silent_p.V340V|PTPRT_ENST00000373193.3_Silent_p.V340V|PTPRT_ENST00000373198.4_Silent_p.V340V|PTPRT_ENST00000373184.1_Silent_p.V340V|PTPRT_ENST00000356100.2_Silent_p.V340V|PTPRT_ENST00000373201.1_Silent_p.V340V			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	340	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)	p.V340V(1)		NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				TGGGAGAGTCGACTATGTGGG	0.572																																					p.V340V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1020T	20						.						148.0	154.0	152.0					20																	41306639		2033	4182	6215	40740053	SO:0001819	synonymous_variant	11122	exon7			AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.1020C>T	20.37:g.41306639G>A		Somatic		Capture	Illumina HiSeq	Phase_I	40740053	NM_133170	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	37	CCDS42874.1																																																																																				0.572	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1		
L3MBTL1	26013	broad.mit.edu	37	20	42169452	42169452	+	Silent	SNP	C	C	T	rs377279389		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:42169452C>T	ENST00000427442.2	+	21	2484	c.2325C>T	c.(2323-2325)gaC>gaT	p.D775D	L3MBTL1_ENST00000418998.1_Silent_p.D775D|L3MBTL1_ENST00000444063.1_Silent_p.D707D|L3MBTL1_ENST00000373135.3_Silent_p.D707D|L3MBTL1_ENST00000373134.1_Silent_p.D712D			Q9Y468	LMBL1_HUMAN	l(3)mbt-like 1 (Drosophila)	707					chromatin modification (GO:0016568)|hemopoiesis (GO:0030097)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of mitosis (GO:0007088)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|condensed chromosome (GO:0000793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|identical protein binding (GO:0042802)|methylated histone binding (GO:0035064)|nucleosomal histone binding (GO:0031493)|nucleosome binding (GO:0031491)|SAM domain binding (GO:0032093)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.D707D(1)		breast(1)|large_intestine(3)|ovary(1)|skin(2)	7						TCTTCAAAGACGAGGTAAGGT	0.557													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20875	0.0		0.0	False		,,,				2504	0.0				p.D775D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2325T	20						.	C	,	2,4404	4.2+/-10.8	0,2,2201	93.0	74.0	81.0		2121,2325	1.2	1.0	20		81	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	L3MBTL1	NM_015478.6,NM_032107.4	,	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	,	707/773,775/841	42169452	3,13003	2203	4300	6503	41602866	SO:0001819	synonymous_variant	10110	exon21			U89358	CCDS13319.1, CCDS46602.1, CCDS46602.2	20q13.12	2013-01-10	2010-09-03	2010-09-03	ENSG00000185513	ENSG00000185513		"""Zinc fingers, C2HC-type containing"", ""Sterile alpha motif (SAM) domain containing"""	15905	protein-coding gene	gene with protein product	"""lethal (3) malignant brain tumor l(3)"""	608802	"""l(3)mbt (Drosophila)-like"", ""l(3)mbt-like (Drosophila)"""	L3MBTL		10445843, 17540172	Standard	NM_032107		Approved	ZC2HC3, dJ138B7.3, DKFZp586P1522, KIAA0681	uc010zwh.2	Q9Y468	OTTHUMG00000032503	ENST00000427442.2:c.2325C>T	20.37:g.42169452C>T		Somatic		Capture	Illumina HiSeq	Phase_I	41602866	NM_032107	B4DRC9|E1P5W7|Q5H8Y8|Q5H8Y9|Q8IUV7|Q9H1E6|Q9H1G5|Q9UG06|Q9UJB9|Q9Y4C9	De_novo_Start_OutOfFrame	SNP	ENST00000427442.2	37	CCDS46602.2																																																																																				0.557	L3MBTL1-007	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079300.3	NM_032107	
IFT52	51098	broad.mit.edu	37	20	42271225	42271225	+	Silent	SNP	C	C	T	rs185383168		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:42271225C>T	ENST00000373030.3	+	13	1357	c.1227C>T	c.(1225-1227)caC>caT	p.H409H	IFT52_ENST00000373039.4_Silent_p.H409H|IFT52_ENST00000471199.1_3'UTR	NM_016004.2	NP_057088.2	Q9Y366	IFT52_HUMAN	intraflagellar transport 52	409					cilium morphogenesis (GO:0060271)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|intraciliary transport (GO:0042073)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube formation (GO:0001841)|regulation of protein processing (GO:0070613)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|dendrite terminus (GO:0044292)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)	protein C-terminus binding (GO:0008022)	p.H409H(1)		endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TCCTTGAGCACGTCTTCTTCC	0.458													C|||	1	0.000199681	0.0	0.0	5008	,	,		21053	0.0		0.001	False		,,,				2504	0.0				p.H409H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1227T	20						.						140.0	121.0	128.0					20																	42271225		2203	4300	6503	41704639	SO:0001819	synonymous_variant	51098	exon13			AF151811	CCDS33470.1	20q12-q13.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000101052	ENSG00000101052		"""Intraflagellar transport homologs"""	15901	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 9"", ""intraflagellar transport 52 homolog (Chlamydomonas)"""	C20orf9		10810093	Standard	NM_016004		Approved	CGI-53, NGD5, dJ1028D15.1, NGD2	uc002xkw.3	Q9Y366	OTTHUMG00000032513	ENST00000373030.3:c.1227C>T	20.37:g.42271225C>T		Somatic		Capture	Illumina HiSeq	Phase_I	41704639	NM_016004	B3KMA1|E1P5W9|Q5H8Z0|Q9H1G3|Q9H1G4|Q9H1H2	Silent	SNP	ENST00000373030.3	37	CCDS33470.1																																																																																				0.458	IFT52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079317.1	NM_016004	
HNF4A	3172	broad.mit.edu	37	20	43034785	43034785	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:43034785C>T	ENST00000316099.4	+	2	292	c.203C>T	c.(202-204)aCg>aTg	p.T68M	HNF4A_ENST00000457232.1_Missense_Mutation_p.T46M|HNF4A_ENST00000443598.2_Missense_Mutation_p.T68M|HNF4A_ENST00000609795.1_Missense_Mutation_p.T46M|MIR3646_ENST00000578301.1_RNA|HNF4A_ENST00000316673.4_Missense_Mutation_p.T46M|HNF4A_ENST00000415691.2_Missense_Mutation_p.T68M	NM_000457.4|NM_001258355.1|NM_178849.2	NP_000448.3|NP_001245284.1|NP_849180.1	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	68					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|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 distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|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.T46M(1)|p.T68M(1)		endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			GACCGGGCCACGGGCAAACAC	0.642																																					p.T46M	Colon(79;2 1269 8820 14841 52347)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C137T	20						.						86.0	85.0	85.0					20																	43034785		2203	4300	6503	42468199	SO:0001583	missense	3172	exon2			X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"""Nuclear hormone receptors"""	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316099.4:c.203C>T	20.37:g.43034785C>T	ENSP00000312987:p.Thr68Met	Somatic		Capture	Illumina HiSeq	Phase_I	42468199	NM_001030003	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Missense_Mutation	SNP	ENST00000316099.4	37	CCDS13330.1	.	.	.	.	.	.	.	.	.	.	c	31	5.067151	0.93898	.	.	ENSG00000101076	ENST00000316673;ENST00000457232;ENST00000316099;ENST00000443598;ENST00000338692;ENST00000415691	D;D;D;D;D	0.97505	-4.41;-4.41;-4.41;-4.41;-4.41	5.17	5.17	0.71159	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.147487	0.64402	D	0.000010	D	0.98748	0.9579	M	0.90369	3.11	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	0.91635	0.999;0.992;0.986;0.994;0.999;0.998;0.998	D	0.99790	1.1031	10	0.87932	D	0	.	18.7348	0.91750	0.0:1.0:0.0:0.0	.	61;68;68;68;46;46;46	Q5QPB7;P41235;F1D8S2;P41235-3;F1D8T0;P41235-6;P41235-7	.;HNF4A_HUMAN;.;.;.;.;.	M	46;46;68;68;98;68	ENSP00000315180:T46M;ENSP00000396216:T46M;ENSP00000312987:T68M;ENSP00000410911:T68M;ENSP00000412111:T68M	ENSP00000312987:T68M	T	+	2	0	HNF4A	42468199	1.000000	0.71417	0.948000	0.38648	0.975000	0.68041	7.753000	0.85153	2.414000	0.81942	0.645000	0.84053	ACG		0.642	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3		
ADA	100	broad.mit.edu	37	20	43251496	43251496	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:43251496G>T	ENST00000372874.4	-	8	888	c.754C>A	c.(754-756)Ctg>Atg	p.L252M	PKIG_ENST00000372882.3_Intron|PKIG_ENST00000372887.1_Intron|ADA_ENST00000464097.1_5'UTR|ADA_ENST00000537820.1_Missense_Mutation_p.L228M	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	252					adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)	p.L252M(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	TCCTGCCGCAGCCTGTTATAA	0.567									Adenosine Deaminase Deficiency																												p.L252M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C754A	20						.						120.0	126.0	124.0					20																	43251496		2203	4300	6503	42684910	SO:0001583	missense	100	exon8	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.754C>A	20.37:g.43251496G>T	ENSP00000361965:p.Leu252Met	Somatic		Capture	Illumina HiSeq	Phase_I	42684910	NM_000022	Q53F92|Q6LA59	Missense_Mutation	SNP	ENST00000372874.4	37	CCDS13335.1	.	.	.	.	.	.	.	.	.	.	g	17.64	3.439012	0.63067	.	.	ENSG00000196839	ENST00000372874;ENST00000537820	D;D	0.97352	-4.35;-4.35	5.18	2.87	0.33458	Adenosine/AMP deaminase (1);	0.069900	0.64402	D	0.000015	D	0.98160	0.9392	M	0.86097	2.795	0.52501	D	0.999958	D	0.71674	0.998	D	0.77557	0.99	D	0.98372	1.0554	10	0.72032	D	0.01	-14.5831	11.4591	0.50199	0.0803:0.13:0.7897:0.0	.	252	P00813	ADA_HUMAN	M	252;228	ENSP00000361965:L252M;ENSP00000441818:L228M	ENSP00000361965:L252M	L	-	1	2	ADA	42684910	1.000000	0.71417	0.772000	0.31596	0.786000	0.44442	3.107000	0.50329	1.203000	0.43233	-0.358000	0.07595	CTG		0.567	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022	
ADA	100	broad.mit.edu	37	20	43252921	43252921	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:43252921G>A	ENST00000372874.4	-	6	662	c.528C>T	c.(526-528)acC>acT	p.T176T	ADA_ENST00000464097.1_5'UTR|ADA_ENST00000537820.1_Silent_p.T176T	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	176					adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)	p.T176T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	TGGCTACCACGGTCTGCTGCT	0.597									Adenosine Deaminase Deficiency																												p.T176T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C528T	20						.						103.0	84.0	90.0					20																	43252921		2203	4300	6503	42686335	SO:0001819	synonymous_variant	100	exon6	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.528C>T	20.37:g.43252921G>A		Somatic		Capture	Illumina HiSeq	Phase_I	42686335	NM_000022	Q53F92|Q6LA59	Silent	SNP	ENST00000372874.4	37	CCDS13335.1																																																																																				0.597	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022	
DNTTIP1	116092	broad.mit.edu	37	20	44424008	44424008	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:44424008G>A	ENST00000372622.3	+	4	366	c.298G>A	c.(298-300)Gtg>Atg	p.V100M		NM_052951.2	NP_443183.1	Q9H147	TDIF1_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 1	100						nucleolus (GO:0005730)|nucleus (GO:0005634)		p.V100M(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)	9		Myeloproliferative disorder(115;0.0122)				AGCACTGAACGTGCGAGACAA	0.522																																					p.V100M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G298A	20						.						55.0	39.0	44.0					20																	44424008		2203	4300	6503	43857415	SO:0001583	missense	116092	exon4			AB035676	CCDS13369.1	20q13.12	2003-09-10	2003-09-10	2003-09-12	ENSG00000101457	ENSG00000101457			16160	protein-coding gene	gene with protein product	"""novel protein similar to synaptotagmin 1 (SYT1, P65) (isoform 1)"", ""TdT binding protein"""	611388	"""chromosome 20 open reading frame 167"""	C20orf167		11473582	Standard	NM_052951		Approved	dJ447F3.4, Tdif1	uc002xpk.3	Q9H147	OTTHUMG00000032610	ENST00000372622.3:c.298G>A	20.37:g.44424008G>A	ENSP00000361705:p.Val100Met	Somatic		Capture	Illumina HiSeq	Phase_I	43857415	NM_052951	B2RA18|Q96DE3|Q9BQP2|Q9H148	Missense_Mutation	SNP	ENST00000372622.3	37	CCDS13369.1	.	.	.	.	.	.	.	.	.	.	-	28.3	4.905653	0.92107	.	.	ENSG00000101457	ENST00000372622;ENST00000449078;ENST00000415790	T;T	0.57107	0.54;0.42	5.47	5.47	0.80525	.	0.106801	0.64402	D	0.000005	T	0.69833	0.3155	M	0.66939	2.045	0.51767	D	0.999934	D	0.76494	0.999	D	0.63597	0.916	T	0.69881	-0.5025	10	0.54805	T	0.06	-24.6843	18.0826	0.89445	0.0:0.0:1.0:0.0	.	100	Q9H147	TDIF1_HUMAN	M	100;95;60	ENSP00000361705:V100M;ENSP00000392509:V60M	ENSP00000361705:V100M	V	+	1	0	DNTTIP1	43857415	1.000000	0.71417	0.920000	0.36463	0.994000	0.84299	7.669000	0.83911	2.857000	0.98124	0.645000	0.84053	GTG		0.522	DNTTIP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079502.1	NM_052951	
ACOT8	10005	broad.mit.edu	37	20	44472331	44472331	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:44472331C>T	ENST00000217455.4	-	5	766	c.676G>A	c.(676-678)Gtg>Atg	p.V226M		NM_005469.3	NP_005460.2	O14734	ACOT8_HUMAN	acyl-CoA thioesterase 8	226					acyl-CoA metabolic process (GO:0006637)|alpha-linolenic acid metabolic process (GO:0036109)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|dicarboxylic acid catabolic process (GO:0043649)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|peroxisome fission (GO:0016559)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|viral process (GO:0016032)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|choloyl-CoA hydrolase activity (GO:0033882)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)	p.V226M(1)		kidney(2)|large_intestine(3)|lung(4)|skin(1)	10		Myeloproliferative disorder(115;0.0122)				TAGGCGGCCACGCAGCAGTGC	0.602																																					p.V226M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G676A	20						.						67.0	57.0	61.0					20																	44472331		2203	4300	6503	43905738	SO:0001583	missense	10005	exon5			AF014404	CCDS13378.1	20q13.12	2012-05-16	2005-09-19	2005-09-19	ENSG00000101473	ENSG00000101473	3.1.2.27	"""Acyl CoA thioesterases"""	15919	protein-coding gene	gene with protein product	"""choloyl-CoA hydrolase"""	608123	"""peroxisomal acyl-CoA thioesterase"", ""peroxisomal acyl-CoA thioesterase 1"""	PTE1		10092594, 9153233, 16103133, 16940157	Standard	NM_005469		Approved	hACTE-III, hTE, PTE-2	uc002xqa.2	O14734	OTTHUMG00000033045	ENST00000217455.4:c.676G>A	20.37:g.44472331C>T	ENSP00000217455:p.Val226Met	Somatic		Capture	Illumina HiSeq	Phase_I	43905738	NM_005469	O15261|Q17RX4	Missense_Mutation	SNP	ENST00000217455.4	37	CCDS13378.1	.	.	.	.	.	.	.	.	.	.	C	31	5.103083	0.94245	.	.	ENSG00000101473	ENST00000217455	.	.	.	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.76485	0.3994	L	0.58510	1.815	0.80722	D	1	D;D	0.89917	0.995;1.0	P;D	0.77004	0.883;0.989	T	0.75587	-0.3266	9	0.44086	T	0.13	.	18.5723	0.91140	0.0:1.0:0.0:0.0	.	106;226	E9PRD4;O14734	.;ACOT8_HUMAN	M	226	.	ENSP00000217455:V226M	V	-	1	0	ACOT8	43905738	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	7.320000	0.79064	2.620000	0.88729	0.655000	0.94253	GTG		0.602	ACOT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080338.2	NM_183386	
CTSA	5476	broad.mit.edu	37	20	44522702	44522702	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:44522702C>T	ENST00000372459.2	+	7	961	c.768C>T	c.(766-768)tgC>tgT	p.C256C	CTSA_ENST00000191018.5_Silent_p.C256C|NEURL2_ENST00000372518.4_5'Flank|RP3-337O18.9_ENST00000607703.1_RNA|CTSA_ENST00000354880.5_Silent_p.C257C|CTSA_ENST00000372484.3_Silent_p.C274C			P10619	PPGB_HUMAN	cathepsin A	256					glycosphingolipid metabolic process (GO:0006687)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|enzyme activator activity (GO:0008047)|serine-type carboxypeptidase activity (GO:0004185)	p.C274C(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				ACCTGGAATGCGTGACCAATG	0.498																																					p.C274C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C822T	20						.						158.0	127.0	137.0					20																	44522702		2203	4300	6503	43956109	SO:0001819	synonymous_variant	5476	exon8			M22960	CCDS13385.2, CCDS46609.1, CCDS54467.1	20q13.12	2012-02-10	2006-12-05	2006-12-05	ENSG00000064601	ENSG00000064601	3.4.16.5	"""Cathepsins"""	9251	protein-coding gene	gene with protein product	"""carboxypeptidase C"", ""lysosomal protective protein"", ""carboxypeptidase-L"", ""carboxypeptidase Y-like kininase"", ""deamidase"", ""lysosomal carboxypeptidase A"", ""urinary kininase"""	613111	"""protective protein for beta-galactosidase (galactosialidosis)"""	GSL, PPGB		2071143	Standard	NM_000308		Approved		uc002xqh.3	P10619	OTTHUMG00000033078	ENST00000372459.2:c.768C>T	20.37:g.44522702C>T		Somatic		Capture	Illumina HiSeq	Phase_I	43956109	NM_000308	B2R798|Q561W6|Q5JZH1|Q96KJ2|Q9BR08|Q9BW68	Silent	SNP	ENST00000372459.2	37	CCDS46609.1																																																																																				0.498	CTSA-012	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471297.2	NM_000308	
SLC12A5	57468	broad.mit.edu	37	20	44664167	44664167	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:44664167C>T	ENST00000454036.2	+	3	390	c.341C>T	c.(340-342)cCg>cTg	p.P114L	SLC12A5_ENST00000608944.1_Missense_Mutation_p.P40L|SLC12A5_ENST00000372315.1_Missense_Mutation_p.P91L|SLC12A5_ENST00000243964.3_Missense_Mutation_p.P91L	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	114					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.P91L(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)	AAAAAGAAGCCGGTGCAGGTG	0.567																																					p.P91L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C272T	20						.						50.0	59.0	56.0					20																	44664167		2203	4300	6503	44097574	SO:0001583	missense	57468	exon3			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.341C>T	20.37:g.44664167C>T	ENSP00000387694:p.Pro114Leu	Somatic		Capture	Illumina HiSeq	Phase_I	44097574	NM_020708	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Missense_Mutation	SNP	ENST00000454036.2	37	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	C	16.37	3.105107	0.56291	.	.	ENSG00000124140	ENST00000454036;ENST00000372315;ENST00000539566;ENST00000243964	D;D;D;D	0.95342	-1.95;-3.26;-3.68;-1.93	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	D	0.91389	0.7283	L	0.46157	1.445	0.80722	D	1	P;P;B	0.37688	0.602;0.605;0.054	B;B;B	0.32393	0.069;0.145;0.006	D	0.92168	0.5741	10	0.59425	D	0.04	.	16.6093	0.84858	0.0:1.0:0.0:0.0	.	114;91;91	Q9H2X9;Q9H2X9-2;A8K143	S12A5_HUMAN;.;.	L	114;91;91;91	ENSP00000387694:P114L;ENSP00000361389:P91L;ENSP00000446091:P91L;ENSP00000243964:P91L	ENSP00000243964:P91L	P	+	2	0	SLC12A5	44097574	1.000000	0.71417	0.995000	0.50966	0.587000	0.36485	4.533000	0.60615	2.494000	0.84150	0.563000	0.77884	CCG		0.567	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		
SLC12A5	57468	broad.mit.edu	37	20	44673678	44673678	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:44673678G>A	ENST00000454036.2	+	12	1586	c.1537G>A	c.(1537-1539)Gga>Aga	p.G513R	SLC12A5_ENST00000243964.3_Missense_Mutation_p.G490R	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	513					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.G490R(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)	AATTGTCATCGGATCCTTCTT	0.607																																					p.G490R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1468A	20						.						161.0	150.0	154.0					20																	44673678		2203	4300	6503	44107085	SO:0001583	missense	57468	exon12			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.1537G>A	20.37:g.44673678G>A	ENSP00000387694:p.Gly513Arg	Somatic		Capture	Illumina HiSeq	Phase_I	44107085	NM_020708	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Missense_Mutation	SNP	ENST00000454036.2	37	CCDS46610.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.495330	0.85069	.	.	ENSG00000124140	ENST00000454036;ENST00000243964	D;D	0.98914	-5.23;-5.23	4.32	4.32	0.51571	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.99498	0.9821	H	0.98612	4.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.995	D	0.97825	1.0259	10	0.87932	D	0	.	15.5477	0.76118	0.0:0.0:1.0:0.0	.	513;490	Q9H2X9;Q9H2X9-2	S12A5_HUMAN;.	R	513;490	ENSP00000387694:G513R;ENSP00000243964:G490R	ENSP00000243964:G490R	G	+	1	0	SLC12A5	44107085	1.000000	0.71417	0.992000	0.48379	0.780000	0.44128	9.263000	0.95617	2.225000	0.72522	0.313000	0.20887	GGA		0.607	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		
ELMO2	63916	broad.mit.edu	37	20	45002162	45002162	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:45002162C>T	ENST00000290246.6	-	16	1486	c.1292G>A	c.(1291-1293)cGc>cAc	p.R431H	ELMO2_ENST00000352077.2_Missense_Mutation_p.R429H|ELMO2_ENST00000454865.2_Missense_Mutation_p.R163H|ELMO2_ENST00000445496.2_Missense_Mutation_p.R248H|ELMO2_ENST00000372176.1_Missense_Mutation_p.R343H|ELMO2_ENST00000488853.1_5'Flank|ELMO2_ENST00000439931.2_Missense_Mutation_p.R443H|ELMO2_ENST00000396391.1_Missense_Mutation_p.R431H	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	431	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)	p.R431H(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				GTAGTCATTGCGTCCTTCATT	0.498																																					p.R431H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1292A	20						.						115.0	101.0	106.0					20																	45002162		2203	4300	6503	44435569	SO:0001583	missense	63916	exon15			AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"""Engulfment and cell motility proteins"""	17233	protein-coding gene	gene with protein product		606421	"""engulfment and cell motility 2 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.1292G>A	20.37:g.45002162C>T	ENSP00000290246:p.Arg431His	Somatic		Capture	Illumina HiSeq	Phase_I	44435569	NM_182764	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Missense_Mutation	SNP	ENST00000290246.6	37	CCDS13398.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.235861	0.79800	.	.	ENSG00000062598	ENST00000290246;ENST00000372176;ENST00000396391;ENST00000439931;ENST00000445496;ENST00000454865;ENST00000352077;ENST00000425546	T;T;T;T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57	5.1	5.1	0.69264	Engulfment/cell motility, ELMO (2);	0.050698	0.85682	D	0.000000	T	0.28366	0.0701	N	0.08118	0	0.58432	D	0.999995	P;D;P;P;P	0.54601	0.939;0.967;0.892;0.892;0.892	P;P;B;B;B	0.51701	0.677;0.627;0.212;0.105;0.212	T	0.27773	-1.0064	10	0.72032	D	0.01	-14.2501	17.6874	0.88259	0.0:1.0:0.0:0.0	.	443;163;431;248;431	B4DRL5;B4DZ20;E9PBG2;B7Z1S8;Q96JJ3	.;.;.;.;ELMO2_HUMAN	H	431;343;431;443;248;163;429;219	ENSP00000290246:R431H;ENSP00000361249:R343H;ENSP00000379673:R431H;ENSP00000396519:R443H;ENSP00000409920:R248H;ENSP00000415641:R163H;ENSP00000326172:R429H;ENSP00000388962:R219H	ENSP00000290246:R431H	R	-	2	0	ELMO2	44435569	1.000000	0.71417	0.996000	0.52242	0.941000	0.58515	5.878000	0.69682	2.644000	0.89710	0.561000	0.74099	CGC		0.498	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086	
SLC2A10	81031	broad.mit.edu	37	20	45354097	45354097	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:45354097C>T	ENST00000359271.2	+	2	672	c.422C>T	c.(421-423)gCa>gTa	p.A141V		NM_030777.3	NP_110404.1	O95528	GTR10_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 10	141					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sugar:proton symporter activity (GO:0005351)	p.A141V(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	34		Myeloproliferative disorder(115;0.0122)				CTCTATGAGGCAGGCATCACC	0.617																																					p.A141V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C422T	20						.						104.0	94.0	97.0					20																	45354097		2203	4300	6503	44787504	SO:0001583	missense	81031	exon2			AL137188	CCDS13402.1	20q13.12	2013-05-22			ENSG00000197496	ENSG00000197496		"""Solute carriers"""	13444	protein-coding gene	gene with protein product		606145				11247674	Standard	NM_030777		Approved	GLUT10	uc002xsl.3	O95528	OTTHUMG00000032657	ENST00000359271.2:c.422C>T	20.37:g.45354097C>T	ENSP00000352216:p.Ala141Val	Somatic		Capture	Illumina HiSeq	Phase_I	44787504	NM_030777	A8K4J6|Q3MIX5|Q9H4I6	Missense_Mutation	SNP	ENST00000359271.2	37	CCDS13402.1	.	.	.	.	.	.	.	.	.	.	C	0.089	-1.170606	0.01660	.	.	ENSG00000197496	ENST00000359271	T	0.72167	-0.63	5.31	1.81	0.25067	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.633878	0.16617	N	0.206643	T	0.41442	0.1159	N	0.01267	-0.92	0.09310	N	1	B	0.15719	0.014	B	0.20577	0.03	T	0.41770	-0.9490	10	0.48119	T	0.1	5.0995	10.7065	0.45958	0.0:0.6941:0.0:0.3059	.	141	O95528	GTR10_HUMAN	V	141	ENSP00000352216:A141V	ENSP00000352216:A141V	A	+	2	0	SLC2A10	44787504	0.153000	0.22777	0.591000	0.28745	0.193000	0.23685	0.777000	0.26718	0.611000	0.30052	0.407000	0.27541	GCA		0.617	SLC2A10-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079578.2		
ZMYND8	23613	broad.mit.edu	37	20	45874843	45874843	+	Silent	SNP	G	G	A	rs141781562	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:45874843G>A	ENST00000311275.7	-	14	2386	c.2133C>T	c.(2131-2133)agC>agT	p.S711S	ZMYND8_ENST00000468376.2_5'UTR|ZMYND8_ENST00000446994.2_Silent_p.S648S|ZMYND8_ENST00000458360.2_Silent_p.S706S|ZMYND8_ENST00000540497.1_Silent_p.S659S|ZMYND8_ENST00000536340.1_Silent_p.S738S|ZMYND8_ENST00000372023.3_Silent_p.S706S|ZMYND8_ENST00000352431.2_Silent_p.S731S|ZMYND8_ENST00000396281.4_Silent_p.S711S|ZMYND8_ENST00000461685.1_Silent_p.S731S|ZMYND8_ENST00000262975.4_Silent_p.S711S|ZMYND8_ENST00000360911.3_Silent_p.S706S|ZMYND8_ENST00000355972.4_Silent_p.S711S|ZMYND8_ENST00000471951.2_Silent_p.S731S	NM_001281772.1|NM_001281778.1|NM_001281783.1	NP_001268701.1|NP_001268707.1|NP_001268712.1	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8	711					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|zinc ion binding (GO:0008270)	p.S731S(1)		NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			TGACAAGTTCGCTCTCTGAAT	0.463													G|||	5	0.000998403	0.003	0.0014	5008	,	,		21464	0.0		0.0	False		,,,				2504	0.0				p.S731S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2193T	20						.						147.0	143.0	144.0					20																	45874843		2203	4300	6503	45308250	SO:0001819	synonymous_variant	23613	exon14			U48251	CCDS13404.1, CCDS13405.1, CCDS46613.1, CCDS63300.1, CCDS63301.1, CCDS63304.1, CCDS63306.1, CCDS74738.1	20q13.12	2013-01-28	2007-01-29	2007-01-29	ENSG00000101040	ENSG00000101040		"""Zinc fingers, MYND-type"", ""Zinc fingers, PHD-type"""	9397	protein-coding gene	gene with protein product		615713	"""protein kinase C binding protein 1"""	PRKCBP1			Standard	NM_001281769		Approved	RACK7	uc002xtb.1	Q9ULU4	OTTHUMG00000032667	ENST00000311275.7:c.2133C>T	20.37:g.45874843G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45308250	NM_012408	B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Silent	SNP	ENST00000311275.7	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	9.010	0.982366	0.18889	.	.	ENSG00000101040	ENST00000467200	.	.	.	5.91	-10.5	0.00291	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.9477	17.8955	0.88886	0.725:0.0:0.275:0.0	.	.	.	.	X	639	.	.	R	-	1	2	ZMYND8	45308250	0.044000	0.20184	0.459000	0.27081	0.984000	0.73092	-0.555000	0.05999	-2.002000	0.00963	-1.021000	0.02439	CGA		0.463	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047	
NCOA3	8202	broad.mit.edu	37	20	46279984	46279984	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:46279984G>A	ENST00000371998.3	+	20	4101	c.3910G>A	c.(3910-3912)Gct>Act	p.A1304T	NCOA3_ENST00000371997.3_Missense_Mutation_p.A1295T|NCOA3_ENST00000341724.6_Missense_Mutation_p.A1230T|NCOA3_ENST00000372004.3_Missense_Mutation_p.A1300T			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1304	Acetyltransferase.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|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)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.A1304T(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						AATGCCACAAGCTCCTCCGCA	0.473																																					p.A1303T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3907A	20						.						105.0	97.0	100.0					20																	46279984		2203	4300	6503	45713391	SO:0001583	missense	8202	exon20			AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3910G>A	20.37:g.46279984G>A	ENSP00000361066:p.Ala1304Thr	Somatic		Capture	Illumina HiSeq	Phase_I	45713391	NM_001174087	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	G	16.32	3.090770	0.55968	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.30182	1.54;4.53;4.54;1.54	6.17	5.22	0.72569	Domain of unknown function DUF1518 (1);	0.138010	0.50627	D	0.000120	T	0.35885	0.0947	L	0.52759	1.655	0.36808	D	0.885755	B;B;B;B;B;B	0.25521	0.065;0.04;0.128;0.128;0.052;0.065	B;B;B;B;B;B	0.34093	0.084;0.016;0.175;0.112;0.05;0.084	T	0.36065	-0.9763	10	0.48119	T	0.1	-3.9627	17.0474	0.86508	0.0:0.0:0.8718:0.1282	.	1304;1295;1307;1299;1300;1304	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	T	1300;1230;1300;1304;1295	ENSP00000342123:A1230T;ENSP00000361073:A1300T;ENSP00000361066:A1304T;ENSP00000361065:A1295T	ENSP00000345671:A1300T	A	+	1	0	NCOA3	45713391	1.000000	0.71417	0.045000	0.18777	0.657000	0.38888	4.086000	0.57664	1.602000	0.50124	0.655000	0.94253	GCT		0.473	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
SULF2	55959	broad.mit.edu	37	20	46307432	46307432	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:46307432C>T	ENST00000359930.4	-	8	2032	c.1181G>A	c.(1180-1182)cGg>cAg	p.R394Q	SULF2_ENST00000484875.1_Missense_Mutation_p.R394Q|CTD-2653D5.1_ENST00000526566.2_RNA|SULF2_ENST00000467815.1_Missense_Mutation_p.R394Q|SULF2_ENST00000361612.4_Missense_Mutation_p.R394Q	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	394					bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)	p.R394Q(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						ATTCACCGGCCGCTCCGTGTC	0.607																																					p.R394Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1181A	20						.						133.0	129.0	130.0					20																	46307432		2203	4300	6503	45740839	SO:0001583	missense	55959	exon8			AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.1181G>A	20.37:g.46307432C>T	ENSP00000353007:p.Arg394Gln	Somatic		Capture	Illumina HiSeq	Phase_I	45740839	NM_198596	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	.	.	.	.	.	.	.	.	.	.	c	12.42	1.933775	0.34096	.	.	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000467815	D;D;D;D	0.96265	-3.96;-3.96;-3.96;-3.96	5.37	4.43	0.53597	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.104681	0.64402	D	0.000014	D	0.92328	0.7566	N	0.25890	0.77	0.40243	D	0.977983	B;B	0.20164	0.042;0.023	B;B	0.17098	0.017;0.017	D	0.89053	0.3457	10	0.36615	T	0.2	-23.9227	14.2854	0.66243	0.0:0.9281:0.0:0.0719	.	394;394	Q8IWU5-2;Q8IWU5	.;SULF2_HUMAN	Q	394	ENSP00000353007:R394Q;ENSP00000418290:R394Q;ENSP00000354662:R394Q;ENSP00000418442:R394Q	ENSP00000353007:R394Q	R	-	2	0	SULF2	45740839	0.939000	0.31865	0.999000	0.59377	0.340000	0.28889	1.282000	0.33226	1.275000	0.44379	-0.461000	0.05368	CGG		0.607	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837	
PREX1	57580	broad.mit.edu	37	20	47364417	47364417	+	Splice_Site	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:47364417C>T	ENST00000371941.3	-	2	242	c.220G>A	c.(220-222)Gca>Aca	p.A74T	PREX1_ENST00000396220.1_Splice_Site_p.A74T	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	74	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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.A74S(4)|p.A74T(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)			TGCAGGAATGCCTGGAGGAGA	0.592																																					p.A74T												.	.	6	Substitution - Missense(6)	lung(4)|large_intestine(2)	c.G220A	20						.						84.0	76.0	79.0					20																	47364417		2203	4300	6503	46797824	SO:0001630	splice_region_variant	57580	exon2			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.220-1G>A	20.37:g.47364417C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46797824	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.819170	0.90873	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.67523	-0.27;-0.27	4.54	4.54	0.55810	Dbl homology (DH) domain (5);	0.000000	0.48286	U	0.000186	T	0.70159	0.3192	N	0.16602	0.42	0.58432	D	0.999999	D	0.76494	0.999	D	0.74348	0.983	T	0.76132	-0.3071	10	0.72032	D	0.01	.	17.1397	0.86749	0.0:1.0:0.0:0.0	.	74	Q8TCU6	PREX1_HUMAN	T	74	ENSP00000361009:A74T;ENSP00000379522:A74T	ENSP00000361009:A74T	A	-	1	0	PREX1	46797824	1.000000	0.71417	0.979000	0.43373	0.884000	0.51177	5.989000	0.70587	2.373000	0.80994	0.442000	0.29010	GCA		0.592	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	Missense_Mutation
CSE1L	1434	broad.mit.edu	37	20	47688880	47688880	+	Missense_Mutation	SNP	G	G	A	rs149344844		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:47688880G>A	ENST00000262982.2	+	9	949	c.826G>A	c.(826-828)Gca>Aca	p.A276T	CSE1L_ENST00000542325.1_Missense_Mutation_p.A59T|CSE1L_ENST00000396192.3_Intron	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	276					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)	p.A276T(1)		breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			TGATAATGCCGCACTCTATGC	0.403																																					p.A276T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G826A	20						.	G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	138.0	130.0	133.0		826	5.4	1.0	20	dbSNP_134	133	0,8600		0,0,4300	no	missense	CSE1L	NM_001316.2	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	276/972	47688880	1,13005	2203	4300	6503	47122287	SO:0001583	missense	1434	exon9			U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"""Exportins"""	2431	protein-coding gene	gene with protein product	"""cellular apoptosis susceptibility"""	601342	"""chromosome segregation 1 (yeast homolog)-like"""			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.826G>A	20.37:g.47688880G>A	ENSP00000262982:p.Ala276Thr	Somatic		Capture	Illumina HiSeq	Phase_I	47122287	NM_001316	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Missense_Mutation	SNP	ENST00000262982.2	37	CCDS13412.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.553873	0.86231	2.27E-4	0.0	ENSG00000124207	ENST00000417408;ENST00000262982;ENST00000542325	T;T	0.66460	-0.21;-0.21	5.39	5.39	0.77823	Armadillo-like helical (1);Armadillo-type fold (1);Exportin/Importin, Cse1-like (1);	0.000000	0.85682	D	0.000000	T	0.50103	0.1596	N	0.16368	0.405	0.80722	D	1	P;P	0.40211	0.707;0.707	B;B	0.34722	0.188;0.188	T	0.49082	-0.8976	10	0.18276	T	0.48	-15.8762	19.5067	0.95121	0.0:0.0:1.0:0.0	.	59;276	B4DUC5;P55060	.;XPO2_HUMAN	T	42;276;59	ENSP00000262982:A276T;ENSP00000446477:A59T	ENSP00000262982:A276T	A	+	1	0	CSE1L	47122287	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.813000	0.99286	2.669000	0.90835	0.655000	0.94253	GCA		0.403	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316	
PTGIS	5740	broad.mit.edu	37	20	48156157	48156157	+	Missense_Mutation	SNP	C	C	T	rs145802460	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:48156157C>T	ENST00000244043.4	-	5	652	c.623G>A	c.(622-624)cGc>cAc	p.R208H	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	208					apoptotic signaling pathway (GO:0097190)|arachidonic acid metabolic process (GO:0019369)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|positive regulation of angiogenesis (GO:0045766)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	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)|prostaglandin-I synthase activity (GO:0008116)	p.R208H(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Epoprostenol(DB01240)|Phenylbutazone(DB00812)	GTCGAGCTGGCGAAAGGTGTG	0.642																																					p.R208H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G623A	20						.	C	HIS/ARG	0,4406		0,0,2203	49.0	48.0	48.0		623	4.8	1.0	20	dbSNP_134	48	7,8593	5.0+/-18.6	0,7,4293	yes	missense	PTGIS	NM_000961.3	29	0,7,6496	TT,TC,CC		0.0814,0.0,0.0538	probably-damaging	208/501	48156157	7,12999	2203	4300	6503	47589564	SO:0001583	missense	5740	exon5				CCDS13419.1	20q13	2013-11-18			ENSG00000124212	ENSG00000124212	5.3.99.4	"""Cytochrome P450s"""	9603	protein-coding gene	gene with protein product	"""cytochrome P450, family 8, subfamily A, polypeptide 1"""	601699				8812456	Standard	NM_000961		Approved	PGIS, CYP8A1	uc002xut.3	Q16647	OTTHUMG00000033077	ENST00000244043.4:c.623G>A	20.37:g.48156157C>T	ENSP00000244043:p.Arg208His	Somatic		Capture	Illumina HiSeq	Phase_I	47589564	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Missense_Mutation	SNP	ENST00000244043.4	37	CCDS13419.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.252320	0.80135	0.0	8.14E-4	ENSG00000124212	ENST00000244043	T	0.66815	-0.23	4.85	4.85	0.62838	.	0.216019	0.37095	N	0.002243	T	0.77624	0.4158	M	0.75615	2.305	0.44316	D	0.997196	D	0.89917	1.0	D	0.87578	0.998	T	0.73720	-0.3894	10	0.14252	T	0.57	-13.5886	11.4291	0.50029	0.0:0.9107:0.0:0.0893	.	208	Q16647	PTGIS_HUMAN	H	208	ENSP00000244043:R208H	ENSP00000244043:R208H	R	-	2	0	PTGIS	47589564	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.648000	0.37271	2.416000	0.81992	0.561000	0.74099	CGC		0.642	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2		
SLC23A2	9962	broad.mit.edu	37	20	4893594	4893594	+	Missense_Mutation	SNP	C	C	T	rs142322986	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:4893594C>T	ENST00000379333.1	-	4	531	c.139G>A	c.(139-141)Ggt>Agt	p.G47S	SLC23A2_ENST00000468355.1_5'UTR|SLC23A2_ENST00000424750.2_Missense_Mutation_p.G47S|SLC23A2_ENST00000338244.1_Missense_Mutation_p.G47S	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	47					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)	p.G47S(1)		endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						TCCTGCTCACCGCTGGAGGTG	0.547													C|||	6	0.00119808	0.0045	0.0	5008	,	,		14229	0.0		0.0	False		,,,				2504	0.0				p.G47S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G139A	20						.	C	SER/GLY,SER/GLY	16,4390	24.3+/-50.5	0,16,2187	209.0	169.0	183.0		139,139	4.6	0.1	20	dbSNP_134	183	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	SLC23A2	NM_005116.5,NM_203327.1	56,56	0,17,6486	TT,TC,CC		0.0116,0.3631,0.1307	benign,benign	47/651,47/651	4893594	17,12989	2203	4300	6503	4841594	SO:0001583	missense	9962	exon4			AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"""Solute carriers"""	10973	protein-coding gene	gene with protein product		603791	"""solute carrier family 23 (nucleobase transporters), member 1"""	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.139G>A	20.37:g.4893594C>T	ENSP00000368637:p.Gly47Ser	Somatic		Capture	Illumina HiSeq	Phase_I	4841594	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Missense_Mutation	SNP	ENST00000379333.1	37	CCDS13085.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	16.15	3.041377	0.55003	0.003631	1.16E-4	ENSG00000089057	ENST00000379333;ENST00000338244;ENST00000424750	T;T;T	0.52057	0.68;0.68;0.68	5.56	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.30135	0.0755	N	0.24115	0.695	0.27026	N	0.964356	B;B;B	0.26400	0.148;0.148;0.148	B;B;B	0.16722	0.016;0.016;0.01	T	0.12967	-1.0527	10	0.13853	T	0.58	-16.0777	11.955	0.52976	0.0:0.9161:0.0:0.0839	.	47;47;47	B4DJZ1;A0MSJ5;Q9UGH3	.;.;S23A2_HUMAN	S	47	ENSP00000368637:G47S;ENSP00000344322:G47S;ENSP00000406601:G47S	ENSP00000344322:G47S	G	-	1	0	SLC23A2	4841594	0.958000	0.32768	0.109000	0.21407	0.686000	0.39977	3.950000	0.56676	1.338000	0.45544	0.655000	0.94253	GGT		0.547	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1		
TMEM189-UBE2V1	387522	broad.mit.edu	37	20	48744625	48744625	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:48744625A>G	ENST00000341698.2	-	5	577	c.578T>C	c.(577-579)tTt>tCt	p.F193S	TMEM189_ENST00000557021.1_Missense_Mutation_p.F193S|TMEM189_ENST00000371656.2_Missense_Mutation_p.F118S|TMEM189_ENST00000371650.5_Missense_Mutation_p.F190S|TMEM189_ENST00000371652.4_Missense_Mutation_p.F193S	NM_001257399.1	NP_001244328.1			TMEM189-UBE2V1 readthrough									p.F193S(2)		breast(1)|endometrium(4)|large_intestine(6)|lung(6)	17			BRCA - Breast invasive adenocarcinoma(9;8.29e-07)			TGGCAGCCCAAAGTACGTGTG	0.582																																					p.F193S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T578C	20						.						217.0	144.0	169.0					20																	48744625		2203	4300	6503	48178032	SO:0001583	missense	387522	exon5			U39361	CCDS13424.1	20q13.13	2011-05-31			ENSG00000124208	ENSG00000124208			33521	other	readthrough						11076860	Standard	NM_199203		Approved	Kua-UEV, CROC-1B	uc002xvf.3		OTTHUMG00000033085	ENST00000341698.2:c.578T>C	20.37:g.48744625A>G	ENSP00000344166:p.Phe193Ser	Somatic		Capture	Illumina HiSeq	Phase_I	48178032	NM_199129		Missense_Mutation	SNP	ENST00000341698.2	37	CCDS13424.1	.	.	.	.	.	.	.	.	.	.	A	18.25	3.581900	0.65992	.	.	ENSG00000124208;ENSG00000240849;ENSG00000240849;ENSG00000240849;ENSG00000240849	ENST00000341698;ENST00000557021;ENST00000371650;ENST00000371656;ENST00000371652	T;T;T;T	0.50001	0.76;0.76;1.0;1.01	4.94	4.94	0.65067	Kua-ubiquitin conjugating enzyme hybrid, localisation (1);	0.198566	0.23960	U	0.042873	T	0.57829	0.2080	L	0.49455	1.56	0.36687	D	0.879391	B;B;B;B	0.30542	0.032;0.284;0.284;0.13	B;P;P;B	0.50136	0.09;0.632;0.565;0.125	T	0.59847	-0.7377	10	0.19590	T	0.45	-1.9332	14.5871	0.68335	1.0:0.0:0.0:0.0	.	118;190;193;193	Q5TGE2;Q5TGE1;A5PLL7;G3V2F7	.;.;TM189_HUMAN;.	S	193;193;190;118;193	ENSP00000344166:F193S;ENSP00000450635:F193S;ENSP00000360713:F190S;ENSP00000360715:F193S	ENSP00000360713:F190S	F	-	2	0	TMEM189-UBE2V1;TMEM189	48178032	1.000000	0.71417	0.995000	0.50966	0.936000	0.57629	8.905000	0.92613	1.841000	0.53522	0.379000	0.24179	TTT		0.582	TMEM189-UBE2V1-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000080532.5		
BCAS4	55653	broad.mit.edu	37	20	49458351	49458351	+	Missense_Mutation	SNP	G	G	A	rs375780908		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:49458351G>A	ENST00000358791.5	+	4	503	c.403G>A	c.(403-405)Gtg>Atg	p.V135M	BCAS4_ENST00000371608.2_Missense_Mutation_p.V135M|BCAS4_ENST00000609336.1_Missense_Mutation_p.V105M|BCAS4_ENST00000262591.5_Intron	NM_017843.3	NP_060313.3	Q8TDM0	BCAS4_HUMAN	breast carcinoma amplified sequence 4	135						cytoplasm (GO:0005737)		p.V135M(2)		large_intestine(2)|lung(2)|pancreas(1)|upper_aerodigestive_tract(1)	6						GGAAGCAGACGTGCTTCAGGC	0.637																																					p.V135M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G403A	20						.	G	MET/VAL,MET/VAL,	0,4406		0,0,2203	64.0	51.0	55.0		403,403,	4.5	0.9	20		55	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,intron	BCAS4	NM_017843.3,NM_198799.2,NM_001010974.1	21,21,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,	135/212,135/204,	49458351	2,13004	2203	4300	6503	48891758	SO:0001583	missense	55653	exon4			AK000502	CCDS13432.2, CCDS33487.1	20q13	2008-07-03			ENSG00000124243	ENSG00000124243			14367	protein-coding gene	gene with protein product		607471				12378525	Standard	NM_001010974		Approved	FLJ20495, CNOL	uc002xvq.3	Q8TDM0	OTTHUMG00000032735	ENST00000358791.5:c.403G>A	20.37:g.49458351G>A	ENSP00000351642:p.Val135Met	Somatic		Capture	Illumina HiSeq	Phase_I	48891758	NM_198799	Q5TD52|Q5TD53|Q5TD54|Q5U5K7|Q5XKE8|Q8IXI7|Q8NEZ6|Q8TDL9|Q9NX13|Q9Y511	Missense_Mutation	SNP	ENST00000358791.5	37	CCDS33487.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.596311	0.46318	0.0	2.33E-4	ENSG00000124243	ENST00000358791;ENST00000355583;ENST00000371608	T;T	0.64085	1.04;-0.08	4.48	4.48	0.54585	.	0.147912	0.44097	D	0.000482	T	0.78027	0.4219	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.923;0.999	T	0.81191	-0.1045	10	0.87932	D	0	-6.0563	12.6814	0.56924	0.0:0.0:1.0:0.0	.	135;135	Q8TDM0-3;Q8TDM0	.;BCAS4_HUMAN	M	135	ENSP00000351642:V135M;ENSP00000360669:V135M	ENSP00000347789:V135M	V	+	1	0	BCAS4	48891758	0.971000	0.33674	0.864000	0.33941	0.149000	0.21700	3.251000	0.51453	2.048000	0.60808	0.561000	0.74099	GTG		0.637	BCAS4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079700.1	NM_017843	
NFATC2	4773	broad.mit.edu	37	20	50092117	50092117	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:50092117G>A	ENST00000396009.3	-	4	1632	c.1413C>T	c.(1411-1413)caC>caT	p.H471H	NFATC2_ENST00000371564.3_Silent_p.H471H|NFATC2_ENST00000609507.1_Silent_p.H252H|NFATC2_ENST00000609943.1_Silent_p.H451H|NFATC2_ENST00000610033.1_Silent_p.H252H|NFATC2_ENST00000414705.1_Silent_p.H451H	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	471	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H471H(1)	EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					GGTAGAAGGCGTGCGGCTTAA	0.527																																					p.H471H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1413T	20						.						181.0	166.0	171.0					20																	50092117		2203	4300	6503	49525524	SO:0001819	synonymous_variant	4773	exon4			U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"""Nuclear factor of activated T-cells"""	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.1413C>T	20.37:g.50092117G>A		Somatic		Capture	Illumina HiSeq	Phase_I	49525524	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Silent	SNP	ENST00000396009.3	37	CCDS13437.1																																																																																				0.527	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340	
CDS2	8760	broad.mit.edu	37	20	5157302	5157302	+	Silent	SNP	C	C	T	rs536071538	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:5157302C>T	ENST00000460006.1	+	4	607	c.300C>T	c.(298-300)tgC>tgT	p.C100C	CDS2_ENST00000535100.1_5'Flank|CDS2_ENST00000379070.3_3'UTR|CDS2_ENST00000379062.4_Intron	NM_003818.3	NP_003809.1	O95674	CDS2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	100					CDP-diacylglycerol biosynthetic process (GO:0016024)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	phosphatidate cytidylyltransferase activity (GO:0004605)	p.C100C(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|prostate(1)|stomach(1)	14						AGGTGATGTGCGTTCAGATTA	0.448													C|||	2	0.000399361	0.0	0.0	5008	,	,		18679	0.002		0.0	False		,,,				2504	0.0				p.C100C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C300T	20						.						223.0	202.0	209.0					20																	5157302		2203	4300	6503	5105302	SO:0001819	synonymous_variant	8760	exon4			AF069532	CCDS13088.1	20p13	2006-03-28			ENSG00000101290	ENSG00000101290	2.7.7.41		1801	protein-coding gene	gene with protein product		603549				9806839, 9889000	Standard	NM_003818		Approved		uc002wls.3	O95674	OTTHUMG00000031801	ENST00000460006.1:c.300C>T	20.37:g.5157302C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5105302	NM_003818	B2RDC6|D3DW04|Q5TDY2|Q5TDY3|Q5TDY4|Q5TDY5|Q9BYK5|Q9NTT2	Silent	SNP	ENST00000460006.1	37	CCDS13088.1																																																																																				0.448	CDS2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077858.2		
ZFP64	55734	broad.mit.edu	37	20	50768732	50768732	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:50768732C>T	ENST00000216923.4	-	6	2348	c.1999G>A	c.(1999-2001)Gca>Aca	p.A667T	ZFP64_ENST00000371518.2_Intron|ZFP64_ENST00000346617.4_Missense_Mutation_p.A613T|ZFP64_ENST00000361387.2_Intron|ZFP64_ENST00000371515.4_Missense_Mutation_p.A665T|ZFP64_ENST00000477786.1_Intron	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	667					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.A667T(2)		breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						GGATGGGCTGCCCCTTGAATG	0.512																																					p.A667T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1999A	20						.						80.0	72.0	75.0					20																	50768732		2203	4300	6503	50202139	SO:0001583	missense	55734	exon6			AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.1999G>A	20.37:g.50768732C>T	ENSP00000216923:p.Ala667Thr	Somatic		Capture	Illumina HiSeq	Phase_I	50202139	NM_018197	Q9NTS7|Q9NVH4	Missense_Mutation	SNP	ENST00000216923.4	37	CCDS13440.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.287615	0.23478	.	.	ENSG00000020256	ENST00000216923;ENST00000346617;ENST00000371515;ENST00000546083	T;T;T	0.07327	3.2;3.25;3.21	5.54	5.54	0.83059	.	0.212553	0.32503	N	0.006009	T	0.07863	0.0197	N	0.14661	0.345	0.09310	N	1	B;B;B	0.19817	0.039;0.023;0.023	B;B;B	0.21360	0.034;0.015;0.015	T	0.33574	-0.9863	10	0.72032	D	0.01	-6.0945	19.4986	0.95083	0.0:1.0:0.0:0.0	.	613;665;667	Q9NPA5-2;Q5JWM1;Q9NPA5	.;.;ZF64A_HUMAN	T	667;613;665;509	ENSP00000216923:A667T;ENSP00000344615:A613T;ENSP00000360570:A665T	ENSP00000216923:A667T	A	-	1	0	ZFP64	50202139	0.032000	0.19561	0.008000	0.14137	0.077000	0.17291	2.853000	0.48317	2.598000	0.87819	0.650000	0.86243	GCA		0.512	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197	
AURKA	6790	broad.mit.edu	37	20	54948524	54948524	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:54948524C>T	ENST00000347343.2	-	7	1061	c.794G>A	c.(793-795)gGa>gAa	p.G265E	AURKA_ENST00000395907.1_Missense_Mutation_p.G265E|AURKA_ENST00000395915.3_Missense_Mutation_p.G265E|AURKA_ENST00000395909.4_Missense_Mutation_p.G265E|AURKA_ENST00000395913.3_Missense_Mutation_p.G265E|AURKA_ENST00000371356.2_Missense_Mutation_p.G265E|AURKA_ENST00000395911.1_Missense_Mutation_p.G265E|AURKA_ENST00000312783.6_Missense_Mutation_p.G265E|AURKA_ENST00000395914.1_Missense_Mutation_p.G265E	NM_003600.2	NP_003591.2	O14965	AURKA_HUMAN	aurora kinase A	265	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|anterior/posterior axis specification (GO:0009948)|centrosome localization (GO:0051642)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|negative regulation of spindle checkpoint (GO:0090233)|neuron projection extension (GO:1990138)|positive regulation of mitosis (GO:0045840)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein autophosphorylation (GO:0046777)|protein localization to centrosome (GO:0071539)|protein phosphorylation (GO:0006468)|regulation of centrosome cycle (GO:0046605)|regulation of protein stability (GO:0031647)|spindle assembly involved in female meiosis I (GO:0007057)|spindle stabilization (GO:0043146)	axon hillock (GO:0043203)|centrosome (GO:0005813)|cytosol (GO:0005829)|germinal vesicle (GO:0042585)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.G265E(1)		breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|lung(9)|ovary(2)|prostate(1)|skin(2)	22			Colorectal(105;0.202)			TCCAGCTGATCCAAGAAGTAA	0.383																																					p.G265E	Melanoma(34;439 1292 51416 52695)|GBM(144;1525 2517 48902 51835)|Esophageal Squamous(191;569 2880 14195 30540)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G794A	20						.						117.0	106.0	110.0					20																	54948524		2203	4300	6503	54381931	SO:0001583	missense	6790	exon8			BC001280	CCDS13451.1	20q13	2012-07-23	2003-07-21	2003-07-23	ENSG00000087586	ENSG00000087586		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	11393	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 47"", ""Aurora-A kinase"""	603072	"""serine/threonine kinase 15"", "" serine/threonine kinase 6"""	STK15, STK6		9174055, 9771714	Standard	NM_003600		Approved	BTAK, AurA, STK7, ARK1, PPP1R47, AIK	uc002xxi.1	O14965	OTTHUMG00000032796	ENST00000347343.2:c.794G>A	20.37:g.54948524C>T	ENSP00000216911:p.Gly265Glu	Somatic		Capture	Illumina HiSeq	Phase_I	54381931	NM_198436	E1P5F9|O60445|O75873|Q9BQD6|Q9UPG5	Missense_Mutation	SNP	ENST00000347343.2	37	CCDS13451.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.019705	0.93462	.	.	ENSG00000087586	ENST00000395909;ENST00000395914;ENST00000347343;ENST00000395915;ENST00000312783;ENST00000371356;ENST00000395913;ENST00000395911;ENST00000395907;ENST00000441357	T;T;T;T;T;T;T;T;T;T	0.08282	3.11;3.11;3.11;3.11;3.11;3.11;3.11;3.11;3.11;3.11	5.17	5.17	0.71159	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	0.64402	D	0.000001	T	0.23410	0.0566	L	0.41710	1.295	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.998;0.999;1.0;1.0	T	0.00581	-1.1660	10	0.87932	D	0	-43.4314	19.0336	0.92969	0.0:1.0:0.0:0.0	.	265;197;265;265;265	Q5QPD4;B4DX16;A3KFJ0;B2R6Z3;O14965	.;.;.;.;AURKA_HUMAN	E	265	ENSP00000379245:G265E;ENSP00000379250:G265E;ENSP00000216911:G265E;ENSP00000379251:G265E;ENSP00000321591:G265E;ENSP00000360407:G265E;ENSP00000379249:G265E;ENSP00000379247:G265E;ENSP00000379243:G265E;ENSP00000393452:G265E	ENSP00000321591:G265E	G	-	2	0	AURKA	54381931	1.000000	0.71417	0.303000	0.25071	0.970000	0.65996	7.676000	0.84012	2.572000	0.86782	0.591000	0.81541	GGA		0.383	AURKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079804.3	NM_003600	
FAM209A	200232	broad.mit.edu	37	20	55100044	55100044	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:55100044G>A	ENST00000371328.3	+	1	503	c.180G>A	c.(178-180)tgG>tgA	p.W60*	FAM209A_ENST00000481560.1_3'UTR|GCNT7_ENST00000243913.4_Intron	NM_001012971.3	NP_001012989.2	Q5JX71	F209A_HUMAN	family with sequence similarity 209, member A	60						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.W60*(1)									GGAGCAAATGGCTCTGGCTTC	0.473																																					p.W60X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G180A	20						.						145.0	132.0	136.0					20																	55100044		2203	4300	6503	54533451	SO:0001587	stop_gained	388799	exon1			AL109806	CCDS33493.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000124103	ENSG00000124103			16100	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 106"""	C20orf106			Standard	NM_001012971		Approved	dJ1153D9.3		Q5JX71	OTTHUMG00000032799	ENST00000371328.3:c.180G>A	20.37:g.55100044G>A	ENSP00000360379:p.Trp60*	Somatic		Capture	Illumina HiSeq	Phase_I	54533451	NM_001012971	Q05C43	Nonsense_Mutation	SNP	ENST00000371328.3	37	CCDS33493.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.861253	0.91433	.	.	ENSG00000124103	ENST00000371328	.	.	.	5.32	5.32	0.75619	.	0.000000	0.47455	D	0.000230	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.8665	14.4909	0.67649	0.0:0.0:1.0:0.0	.	.	.	.	X	60	.	ENSP00000360379:W60X	W	+	3	0	C20orf106	54533451	1.000000	0.71417	1.000000	0.80357	0.059000	0.15707	2.711000	0.47177	2.475000	0.83589	0.467000	0.42956	TGG		0.473	FAM209A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079815.2		
RBM38	55544	broad.mit.edu	37	20	55967808	55967808	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:55967808C>T	ENST00000356208.5	+	2	511	c.336C>T	c.(334-336)ggC>ggT	p.G112G	RBM38_ENST00000440234.2_Silent_p.G112G|RBM38_ENST00000371219.2_Silent_p.G31G|RP4-800J21.3_ENST00000417346.1_RNA	NM_017495.5	NP_059965.2	Q9H0Z9	RBM38_HUMAN	RNA binding motif protein 38	112					3'-UTR-mediated mRNA stabilization (GO:0070935)|cell cycle (GO:0007049)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|regulation of myotube differentiation (GO:0010830)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G112G(1)		large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	Lung NSC(12;0.00242)|all_lung(29;0.00767)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.55e-12)|Epithelial(14;9.49e-09)|all cancers(14;5.01e-08)			CATATCTGGGCGCCAAGCCGC	0.607																																					p.A112V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C335T	20						.						49.0	59.0	56.0					20																	55967808		1969	4178	6147	55401214	SO:0001819	synonymous_variant	55544	exon2			X75314	CCDS46617.1, CCDS46618.1	20q13.31	2013-02-12	2006-07-11	2006-07-11	ENSG00000132819	ENSG00000132819		"""RNA binding motif (RRM) containing"""	15818	protein-coding gene	gene with protein product		612428	"""RNA-binding region (RNP1, RRM) containing 1"""	RNPC1			Standard	NM_017495		Approved	HSRNASEB, SEB4D, seb4B, dJ800J21.2	uc010zzj.2	Q9H0Z9	OTTHUMG00000032820	ENST00000356208.5:c.336C>T	20.37:g.55967808C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55401214	NM_017495	A6NDK1|A6NMU6|Q15350|Q15351|Q9BYK3|Q9BYK4	Silent	SNP	ENST00000356208.5	37	CCDS46617.1																																																																																				0.607	RBM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079843.4	NM_183425	
PCK1	5105	broad.mit.edu	37	20	56139620	56139620	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:56139620G>A	ENST00000319441.4	+	8	1433	c.1269G>A	c.(1267-1269)ccG>ccA	p.P423P	PCK1_ENST00000543666.1_Silent_p.P106P|PCK1_ENST00000535860.1_3'UTR	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	423					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)	p.P423P(1)		endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			GGGAGTCTCCGGAAGGTGTTC	0.562																																					p.P423P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1269A	20						.						119.0	117.0	118.0					20																	56139620		2203	4300	6503	55573026	SO:0001819	synonymous_variant	5105	exon8				CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.1269G>A	20.37:g.56139620G>A		Somatic		Capture	Illumina HiSeq	Phase_I	55573026	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	37	CCDS13460.1																																																																																				0.562	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
NPEPL1	79716	broad.mit.edu	37	20	57269510	57269510	+	Silent	SNP	C	C	T	rs376159484		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:57269510C>T	ENST00000356091.6	+	3	657	c.369C>T	c.(367-369)tcC>tcT	p.S123S	STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525817.1_Silent_p.S75S|NPEPL1_ENST00000525967.1_Silent_p.S95S	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	123						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)	p.S123S(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)			TCTTTGCTTCCGCCTGTGCCC	0.657																																					p.R124C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C370T	20						.	C	,,	2,4084		0,2,2041	66.0	74.0	72.0		285,225,369	-9.1	0.1	20		72	1,8377		0,1,4188	no	coding-synonymous,coding-synonymous,coding-synonymous	NPEPL1	NM_001204872.1,NM_001204873.1,NM_024663.3	,,	0,3,6229	TT,TC,CC		0.0119,0.0489,0.0241	,,	95/496,75/476,123/524	57269510	3,12461	2043	4189	6232	56702917	SO:0001819	synonymous_variant	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.369C>T	20.37:g.57269510C>T		Somatic		Capture	Illumina HiSeq	Phase_I	56702917	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Silent	SNP	ENST00000356091.6	37	CCDS46621.1																																																																																				0.657	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
GNAS	2778	broad.mit.edu	37	20	57428368	57428368	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:57428368C>T	ENST00000371100.4	+	1	600	c.48C>T	c.(46-48)cgC>cgT	p.R16R	GNAS_ENST00000464624.2_3'UTR|GNAS-AS1_ENST00000598163.1_RNA|GNAS_ENST00000306120.3_5'Flank|GNAS-AS1_ENST00000424094.2_RNA|GNAS_ENST00000371098.2_Intron|GNAS_ENST00000371099.2_Silent_p.R16R|GNAS_ENST00000371075.3_Intron|GNAS_ENST00000371102.4_Silent_p.R16R|GNAS_ENST00000313949.7_Intron	NM_001077490.1|NM_080425.2	NP_001070958.1|NP_536350.2	P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R16R(1)		adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			CAGGACAACGCGATATCCCCC	0.607			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)																											p.R16R	Colon(117;935 1597 6045 8307 46442)		Dom	yes		20	20q13.2	2778	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	yes	E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C48T	20						.						19.0	22.0	21.0					20																	57428368		692	1590	2282	56861763	SO:0001819	synonymous_variant	2778	exon1			M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"""secretogranin VI"""	139320	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371100.4:c.48C>T	20.37:g.57428368C>T		Somatic		Capture	Illumina HiSeq	Phase_I	56861763	NM_080425	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Silent	SNP	ENST00000371100.4	37	CCDS46622.1																																																																																				0.607	GNAS-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080417.3	NM_000516	
ZNF831	128611	broad.mit.edu	37	20	57829432	57829432	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:57829432G>A	ENST00000371030.2	+	5	4668	c.4668G>A	c.(4666-4668)tcG>tcA	p.S1556S		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1556							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.S1556S(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					TTTCAGATTCGGTTCCACTGG	0.478																																					p.S1556S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4668A	20						.						44.0	45.0	45.0					20																	57829432		1924	4149	6073	57262827	SO:0001819	synonymous_variant	128611	exon5			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.4668G>A	20.37:g.57829432G>A		Somatic		Capture	Illumina HiSeq	Phase_I	57262827	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	37	CCDS42894.1																																																																																				0.478	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
SYCP2	10388	broad.mit.edu	37	20	58467202	58467202	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:58467202G>A	ENST00000357552.3	-	24	2432	c.2207C>T	c.(2206-2208)tCg>tTg	p.S736L	SYCP2_ENST00000371001.2_Missense_Mutation_p.S736L			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	736					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)	p.S736L(1)		NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			ATATATCAGCGATTCTTCAAT	0.343																																					p.S736L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2207T	20						.						113.0	114.0	113.0					20																	58467202		2202	4300	6502	57900597	SO:0001583	missense	10388	exon23			Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.2207C>T	20.37:g.58467202G>A	ENSP00000350162:p.Ser736Leu	Somatic		Capture	Illumina HiSeq	Phase_I	57900597	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	37	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.122046	0.77436	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.36157	1.43;1.43;1.27	5.18	5.18	0.71444	.	0.190685	0.38548	N	0.001648	T	0.58192	0.2105	M	0.68952	2.095	0.38064	D	0.936165	D	0.89917	1.0	D	0.87578	0.998	T	0.64084	-0.6490	10	0.72032	D	0.01	-12.4706	14.5391	0.67980	0.0:0.0:1.0:0.0	.	736	Q9BX26	SYCP2_HUMAN	L	736	ENSP00000360040:S736L;ENSP00000350162:S736L;ENSP00000402456:S736L	ENSP00000350162:S736L	S	-	2	0	SYCP2	57900597	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	5.048000	0.64238	2.578000	0.87016	0.491000	0.48974	TCG		0.343	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	
LRRN4	164312	broad.mit.edu	37	20	6021805	6021805	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:6021805C>T	ENST00000378858.4	-	5	2310	c.2086G>A	c.(2086-2088)Gcc>Acc	p.A696T		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	696					long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)		p.A696T(1)		breast(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	27						ACGGTGCTGGCGAGCAACAGG	0.697																																					p.A696T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2086A	20						.						12.0	12.0	12.0					20																	6021805		2194	4283	6477	5969805	SO:0001583	missense	164312	exon5			AL118505	CCDS13097.1	20p12.3	2013-02-11	2008-05-20	2008-05-20	ENSG00000125872	ENSG00000125872		"""Fibronectin type III domain containing"""	16208	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 75"""	C20orf75		15870286	Standard	NM_152611		Approved	dJ1056H1.1, NLRR4	uc002wmo.3	Q8WUT4	OTTHUMG00000031825	ENST00000378858.4:c.2086G>A	20.37:g.6021805C>T	ENSP00000368135:p.Ala696Thr	Somatic		Capture	Illumina HiSeq	Phase_I	5969805	NM_152611	A8K258|Q5JWV6|Q9H419	Missense_Mutation	SNP	ENST00000378858.4	37	CCDS13097.1	.	.	.	.	.	.	.	.	.	.	C	10.90	1.481446	0.26598	.	.	ENSG00000125872	ENST00000378858	T	0.59224	0.28	5.54	-4.16	0.03869	.	1.250140	0.05551	N	0.567519	T	0.33556	0.0867	N	0.08118	0	0.09310	N	1	B	0.29671	0.254	B	0.14578	0.011	T	0.28364	-1.0046	10	0.62326	D	0.03	-3.7644	10.8184	0.46591	0.0:0.2232:0.5465:0.2302	.	696	Q8WUT4	LRRN4_HUMAN	T	696	ENSP00000368135:A696T	ENSP00000368135:A696T	A	-	1	0	LRRN4	5969805	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.449000	0.02392	-0.544000	0.06232	0.655000	0.94253	GCC		0.697	LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611	
SYCP2	10388	broad.mit.edu	37	20	58467742	58467742	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:58467742A>G	ENST00000357552.3	-	23	2033	c.1808T>C	c.(1807-1809)tTa>tCa	p.L603S	SYCP2_ENST00000371001.2_Missense_Mutation_p.L603S			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	603					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)	p.L603S(1)		NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			GATGTTGTCTAAAACACCAGG	0.323																																					p.L603S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1808C	20						.						92.0	86.0	88.0					20																	58467742		2202	4297	6499	57901137	SO:0001583	missense	10388	exon22			Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.1808T>C	20.37:g.58467742A>G	ENSP00000350162:p.Leu603Ser	Somatic		Capture	Illumina HiSeq	Phase_I	57901137	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	37	CCDS13482.1	.	.	.	.	.	.	.	.	.	.	A	6.522	0.464504	0.12402	.	.	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834	T;T;T	0.23950	2.09;2.09;1.88	5.47	1.9	0.25705	.	0.816091	0.10823	N	0.630198	T	0.26919	0.0659	M	0.66939	2.045	0.09310	N	1	B	0.20550	0.046	B	0.20184	0.028	T	0.25882	-1.0119	10	0.49607	T	0.09	-0.55	7.3898	0.26903	0.7401:0.0:0.2599:0.0	.	603	Q9BX26	SYCP2_HUMAN	S	603	ENSP00000360040:L603S;ENSP00000350162:L603S;ENSP00000402456:L603S	ENSP00000350162:L603S	L	-	2	0	SYCP2	57901137	0.379000	0.25123	0.001000	0.08648	0.493000	0.33554	0.502000	0.22594	0.105000	0.17753	0.477000	0.44152	TTA		0.323	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	
CDH4	1002	broad.mit.edu	37	20	60485619	60485619	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:60485619C>T	ENST00000360469.5	+	9	1418	c.1330C>T	c.(1330-1332)Cgc>Tgc	p.R444C	CDH4_ENST00000543233.1_Missense_Mutation_p.R370C	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	444	Cadherin 3. {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.R444C(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)			CTTCAGCGTCCGCACAGACCC	0.597																																					p.R444C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1330T	20						.						114.0	84.0	94.0					20																	60485619		2203	4300	6503	59919014	SO:0001583	missense	1002	exon9			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.1330C>T	20.37:g.60485619C>T	ENSP00000353656:p.Arg444Cys	Somatic		Capture	Illumina HiSeq	Phase_I	59919014	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	c	13.59	2.283023	0.40394	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.52295	0.67;0.67	4.66	3.64	0.41730	Cadherin (4);Cadherin-like (1);	0.112995	0.56097	D	0.000022	T	0.62804	0.2458	M	0.67397	2.05	0.58432	D	0.999999	D	0.89917	1.0	D	0.74674	0.984	T	0.63435	-0.6638	9	.	.	.	.	11.5273	0.50586	0.3246:0.6754:0.0:0.0	.	444	P55283	CADH4_HUMAN	C	444;352;370	ENSP00000353656:R444C;ENSP00000443301:R370C	.	R	+	1	0	CDH4	59919014	1.000000	0.71417	1.000000	0.80357	0.133000	0.20885	2.362000	0.44169	2.145000	0.66743	0.556000	0.70494	CGC		0.597	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794	
MTG2	26164	broad.mit.edu	37	20	60768527	60768527	+	Silent	SNP	C	C	T	rs535050204		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:60768527C>T	ENST00000370823.3	+	2	69	c.51C>T	c.(49-51)ggC>ggT	p.G17G	MTG2_ENST00000536470.1_Intron|MTG2_ENST00000436421.2_Silent_p.G17G	NM_015666.3	NP_056481.1	Q9H4K7	MTG2_HUMAN	mitochondrial ribosome-associated GTPase 2	17	Localized in the mitochondria.				GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)	p.G17G(1)									TGTTTCAGGGCGTGGGGCATT	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		19752	0.001		0.0	False		,,,				2504	0.0				p.G17G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C51T	20						.						100.0	102.0	101.0					20																	60768527		2203	4300	6503	60201922	SO:0001819	synonymous_variant	26164	exon2			AK001603	CCDS13492.1	20q13.33	2013-05-24	2013-05-24	2013-05-24	ENSG00000101181	ENSG00000101181			16239	protein-coding gene	gene with protein product		610919	"""GTP-binding protein 5 (putative)"", ""GTP binding protein 5 (putative)"""	GTPBP5		17054726, 23396448	Standard	NM_015666		Approved	FLJ10741, dJ1005F21.2, ObgH1		Q9H4K7	OTTHUMG00000032897	ENST00000370823.3:c.51C>T	20.37:g.60768527C>T		Somatic		Capture	Illumina HiSeq	Phase_I	60201922	NM_015666	A6NDR3|B4DR85|Q96I17|Q9NVG9|Q9UFR4	Silent	SNP	ENST00000370823.3	37	CCDS13492.1																																																																																				0.582	MTG2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079989.1	NM_015666	
SLC17A9	63910	broad.mit.edu	37	20	61598764	61598764	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:61598764C>A	ENST00000370351.4	+	13	1354	c.1223C>A	c.(1222-1224)gCc>gAc	p.A408D	SLC17A9_ENST00000370349.3_Missense_Mutation_p.A402D|SLC17A9_ENST00000488738.1_3'UTR	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	408					exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.A408D(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						AACCTTGTGGCCATCATCAGC	0.612																																					p.A408D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1223A	20						.						173.0	190.0	184.0					20																	61598764		2088	4214	6302	61069209	SO:0001583	missense	63910	exon13			AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"""Solute carriers"""	16192	protein-coding gene	gene with protein product		612107	"""chromosome 20 open reading frame 59"", ""solute carrier family 17, member 9"""	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.1223C>A	20.37:g.61598764C>A	ENSP00000359376:p.Ala408Asp	Somatic		Capture	Illumina HiSeq	Phase_I	61069209	NM_022082	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Missense_Mutation	SNP	ENST00000370351.4	37	CCDS42901.1	.	.	.	.	.	.	.	.	.	.	C	19.04	3.750203	0.69533	.	.	ENSG00000101194	ENST00000370351;ENST00000370349	T;T	0.64260	-0.09;-0.09	4.6	4.6	0.57074	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.229750	0.45867	D	0.000334	T	0.77738	0.4175	M	0.81942	2.565	0.54753	D	0.999984	D;D	0.71674	0.997;0.998	D;D	0.74674	0.964;0.984	T	0.80699	-0.1266	10	0.87932	D	0	.	11.3304	0.49473	0.0:0.9155:0.0:0.0845	.	408;402	Q9BYT1;Q9BYT1-2	S17A9_HUMAN;.	D	408;402	ENSP00000359376:A408D;ENSP00000359374:A402D	ENSP00000359374:A402D	A	+	2	0	SLC17A9	61069209	0.997000	0.39634	0.923000	0.36655	0.645000	0.38454	3.710000	0.54860	2.262000	0.75019	0.561000	0.74099	GCC		0.612	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082	
GMEB2	26205	broad.mit.edu	37	20	62221454	62221454	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:62221454G>A	ENST00000266068.1	-	9	2059	c.1581C>T	c.(1579-1581)caC>caT	p.H527H	GMEB2_ENST00000370069.1_Silent_p.H476H|GMEB2_ENST00000370077.1_Silent_p.H527H			Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2	527					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)	p.H527H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			ACTTCCGCTCGTGGTCCTCTG	0.711																																					p.H527H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1581T	20						.						19.0	19.0	19.0					20																	62221454		2188	4263	6451	61691898	SO:0001819	synonymous_variant	26205	exon10			AF173867	CCDS13528.1	20q13.33	2008-07-02			ENSG00000101216	ENSG00000101216			4371	protein-coding gene	gene with protein product		607451				10523663, 11743720	Standard	NM_012384		Approved	P79PIF, KIAA1269, PIF79	uc002yfq.1	Q9UKD1	OTTHUMG00000032988	ENST00000266068.1:c.1581C>T	20.37:g.62221454G>A		Somatic		Capture	Illumina HiSeq	Phase_I	61691898	NM_012384	E1P5J3|Q5TDS0|Q9H431|Q9H4X7|Q9H4X8|Q9UF78|Q9ULF1	Silent	SNP	ENST00000266068.1	37	CCDS13528.1																																																																																				0.711	GMEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080166.1	NM_012384	
GMEB2	26205	broad.mit.edu	37	20	62223462	62223462	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:62223462C>T	ENST00000266068.1	-	8	1343	c.865G>A	c.(865-867)Ggc>Agc	p.G289S	GMEB2_ENST00000370069.1_Missense_Mutation_p.G238S|GMEB2_ENST00000370077.1_Missense_Mutation_p.G289S			Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2	289					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)	p.G289S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			TCCAGCATGCCGAAGTTCTGC	0.597																																					p.G289S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G865A	20						.						111.0	81.0	91.0					20																	62223462		2203	4300	6503	61693906	SO:0001583	missense	26205	exon9			AF173867	CCDS13528.1	20q13.33	2008-07-02			ENSG00000101216	ENSG00000101216			4371	protein-coding gene	gene with protein product		607451				10523663, 11743720	Standard	NM_012384		Approved	P79PIF, KIAA1269, PIF79	uc002yfq.1	Q9UKD1	OTTHUMG00000032988	ENST00000266068.1:c.865G>A	20.37:g.62223462C>T	ENSP00000266068:p.Gly289Ser	Somatic		Capture	Illumina HiSeq	Phase_I	61693906	NM_012384	E1P5J3|Q5TDS0|Q9H431|Q9H4X7|Q9H4X8|Q9UF78|Q9ULF1	Missense_Mutation	SNP	ENST00000266068.1	37	CCDS13528.1	.	.	.	.	.	.	.	.	.	.	C	36	5.625680	0.96671	.	.	ENSG00000101216	ENST00000370069;ENST00000370077;ENST00000266068	T;T;T	0.72167	-0.63;-0.07;-0.07	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.81564	0.4849	M	0.63843	1.955	0.80722	D	1	D	0.76494	0.999	P	0.62382	0.901	T	0.83314	-0.0021	10	0.72032	D	0.01	-11.0698	18.6267	0.91342	0.0:1.0:0.0:0.0	.	289	Q9UKD1	GMEB2_HUMAN	S	238;289;289	ENSP00000359086:G238S;ENSP00000359094:G289S;ENSP00000266068:G289S	ENSP00000266068:G289S	G	-	1	0	GMEB2	61693906	1.000000	0.71417	0.971000	0.41717	0.947000	0.59692	5.597000	0.67577	2.479000	0.83701	0.655000	0.94253	GGC		0.597	GMEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080166.1	NM_012384	
ZBTB46	140685	broad.mit.edu	37	20	62421759	62421759	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:62421759C>T	ENST00000245663.4	-	2	502	c.352G>A	c.(352-354)Gtg>Atg	p.V118M	ZBTB46_ENST00000395104.1_Missense_Mutation_p.V118M|ZBTB46_ENST00000302995.2_Missense_Mutation_p.V118M|ZBTB46_ENST00000480766.1_5'Flank	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	118					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.V118M(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					CAGGCTTGCACGATGTCCGTC	0.602																																					p.V118M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G352A	20						.						40.0	33.0	36.0					20																	62421759		2203	4300	6503	61892203	SO:0001583	missense	140685	exon2			AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16094	protein-coding gene	gene with protein product	"""BTB-ZF protein expressed in effector lymphocytes"""	614639	"""BTB (POZ) domain containing 4"""	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.352G>A	20.37:g.62421759C>T	ENSP00000245663:p.Val118Met	Somatic		Capture	Illumina HiSeq	Phase_I	61892203	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Missense_Mutation	SNP	ENST00000245663.4	37	CCDS13538.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.731185	0.89390	.	.	ENSG00000130584	ENST00000245663;ENST00000302995;ENST00000395104	T;T;T	0.72615	-0.67;-0.67;-0.67	5.65	5.65	0.86999	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.85084	0.5616	M	0.77103	2.36	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.86317	0.1690	10	0.87932	D	0	.	18.7103	0.91653	0.0:1.0:0.0:0.0	.	118	Q86UZ6	ZBT46_HUMAN	M	118	ENSP00000245663:V118M;ENSP00000303102:V118M;ENSP00000378536:V118M	ENSP00000245663:V118M	V	-	1	0	ZBTB46	61892203	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	7.680000	0.84062	2.679000	0.91253	0.655000	0.94253	GTG		0.602	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
SLC52A3	113278	broad.mit.edu	37	20	745893	745893	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:745893C>T	ENST00000217254.7	-	2	767	c.526G>A	c.(526-528)Gta>Ata	p.V176I	SLC52A3_ENST00000473664.1_5'UTR|SLC52A3_ENST00000381944.3_Missense_Mutation_p.V176I	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	176					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.V176I(1)									GGGCTTGGTACGCTGTCTGAT	0.587																																					p.V176I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G526A	20						.						84.0	78.0	80.0					20																	745893		2203	4300	6503	693893	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.526G>A	20.37:g.745893C>T	ENSP00000217254:p.Val176Ile	Somatic		Capture	Illumina HiSeq	Phase_I	693893	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Missense_Mutation	SNP	ENST00000217254.7	37	CCDS13007.1	.	.	.	.	.	.	.	.	.	.	C	7.318	0.616387	0.14129	.	.	ENSG00000101276	ENST00000217254;ENST00000381944	T;T	0.72282	-0.64;-0.64	4.38	-0.963	0.10330	.	0.994052	0.08153	N	0.989814	T	0.43166	0.1235	N	0.08118	0	0.09310	N	1	B;B	0.22080	0.064;0.011	B;B	0.15484	0.013;0.006	T	0.20306	-1.0279	10	0.25751	T	0.34	-6.4817	3.059	0.06194	0.1273:0.0789:0.2607:0.5331	.	176;176	Q9NQ40-2;Q9NQ40	.;RFT2_HUMAN	I	176	ENSP00000217254:V176I;ENSP00000371370:V176I	ENSP00000217254:V176I	V	-	1	0	C20orf54	693893	1.000000	0.71417	0.007000	0.13788	0.002000	0.02628	1.227000	0.32576	0.015000	0.14971	-1.640000	0.00773	GTA		0.587	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
BMP2	650	broad.mit.edu	37	20	6759223	6759223	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:6759223C>T	ENST00000378827.4	+	3	1897	c.678C>T	c.(676-678)ttC>ttT	p.F226F		NM_001200.2	NP_001191.1	P12643	BMP2_HUMAN	bone morphogenetic protein 2	226					activation of MAPK activity (GO:0000187)|atrioventricular valve morphogenesis (GO:0003181)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|bone mineralization (GO:0030282)|bone mineralization involved in bone maturation (GO:0035630)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiocyte differentiation (GO:0035051)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation (GO:0002062)|corticotropin hormone secreting cell differentiation (GO:0060128)|embryo development (GO:0009790)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchyme development (GO:0060485)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of calcium-independent cell-cell adhesion (GO:0051042)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell differentiation (GO:2000726)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|organ morphogenesis (GO:0009887)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|pericardium development (GO:0060039)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of odontogenesis (GO:0042482)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of Wnt signaling pathway by BMP signaling pathway (GO:0060804)|protein destabilization (GO:0031648)|protein phosphorylation (GO:0006468)|proteoglycan metabolic process (GO:0006029)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP receptor binding (GO:0070700)|phosphatase activator activity (GO:0019211)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)|retinol dehydrogenase activity (GO:0004745)|SMAD binding (GO:0046332)	p.F226F(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	13						ACCATGGATTCGTGGTGGAAG	0.522																																					p.F226F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C678T	20						.						54.0	46.0	49.0					20																	6759223		2203	4300	6503	6707223	SO:0001819	synonymous_variant	650	exon3				CCDS13099.1	20p12	2014-01-30			ENSG00000125845	ENSG00000125845		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1069	protein-coding gene	gene with protein product		112261		BMP2A		2376592	Standard	NM_001200		Approved		uc002wmu.1	P12643	OTTHUMG00000031833	ENST00000378827.4:c.678C>T	20.37:g.6759223C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6707223	NM_001200		Silent	SNP	ENST00000378827.4	37	CCDS13099.1																																																																																				0.522	BMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077918.3		
PLCB1	23236	broad.mit.edu	37	20	8755222	8755222	+	Silent	SNP	G	G	T	rs45464693	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:8755222G>T	ENST00000338037.6	+	27	2994	c.2967G>T	c.(2965-2967)acG>acT	p.T989T	PLCB1_ENST00000378641.3_Silent_p.T989T|PLCB1_ENST00000378637.2_Silent_p.T989T|PLCB1_ENST00000494924.1_3'UTR	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	989					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)	p.T989T(1)		NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						GTTCATCAACGATTGAGCAAG	0.468																																					p.T989T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2967T	20						.						124.0	124.0	124.0					20																	8755222		2203	4300	6503	8703222	SO:0001819	synonymous_variant	23236	exon27			AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.2967G>T	20.37:g.8755222G>T		Somatic		Capture	Illumina HiSeq	Phase_I	8703222	NM_182734	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Silent	SNP	ENST00000338037.6	37	CCDS13102.1																																																																																				0.468	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		
TPD52L2	7165	broad.mit.edu	37	20	62505152	62505152	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr20:62505152C>T	ENST00000346249.4	+	3	373	c.297C>T	c.(295-297)gaC>gaT	p.D99D	TPD52L2_ENST00000358548.4_Silent_p.D99D|TPD52L2_ENST00000352482.4_Silent_p.D99D|TPD52L2_ENST00000369927.4_Silent_p.D76D|TPD52L2_ENST00000348257.5_Silent_p.D99D|TPD52L2_ENST00000351424.4_Silent_p.D99D|TPD52L2_ENST00000217121.5_Silent_p.D99D	NM_001243891.1|NM_003288.3	NP_001230820.1|NP_003279.2	O43399	TPD54_HUMAN	tumor protein D52-like 2	99					regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.D99D(1)		endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(38;1.3e-12)|all_epithelial(29;2.23e-14)|Lung NSC(23;5.92e-10)|all_lung(23;2.08e-09)					GCTGGCATGACGTGCAGGTCT	0.662																																					p.D99D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C297T	20						.						35.0	34.0	35.0					20																	62505152		2201	4297	6498	61975596	SO:0001819	synonymous_variant	7165	exon3			AF004430	CCDS13540.1, CCDS13541.1, CCDS13542.1, CCDS13543.1, CCDS13544.1, CCDS13545.1, CCDS58785.1, CCDS74752.1, CCDS74753.1	20q13.2-q13.3	2007-12-19			ENSG00000101150	ENSG00000101150			12007	protein-coding gene	gene with protein product		603747				9484778	Standard	NM_199360		Approved	D54, hD54	uc002ygy.3	O43399	OTTHUMG00000033009	ENST00000346249.4:c.297C>T	20.37:g.62505152C>T		Somatic		Capture	Illumina HiSeq	Phase_I	61975596	NM_199363	B4DPJ6|E1P5G7|O43398|Q5JWU5|Q5JWU6|Q5JWU8|Q5U0E0|Q9H3Z6	Missense_Mutation	SNP	ENST00000346249.4	37	CCDS13540.1																																																																																				0.662	TPD52L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080248.1		
POTED	317754	broad.mit.edu	37	21	14982983	14982983	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:14982983G>A	ENST00000299443.5	+	1	486	c.434G>A	c.(433-435)aGa>aAa	p.R145K		NM_174981.3|NM_207355.2	NP_778146.2|NP_997238.2	Q86YR6	POTED_HUMAN	POTE ankyrin domain family, member D	145						plasma membrane (GO:0005886)		p.R145K(1)		central_nervous_system(1)|large_intestine(10)|liver(2)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	33						AAGCTCCACAGAGCTGCCTGG	0.572																																					p.R145K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G434A	21						.						23.0	32.0	30.0					21																	14982983		732	3078	3810	13904854	SO:0001583	missense	317754	exon1			AY172978	CCDS13562.1	21q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000166351	ENSG00000166351		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	23822	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 1"""	607549	"""ankyrin repeat domain 21"", ""ANKRD26-like family B, member 3"""	ANKRD21, A26B3		12475935, 15276201, 16364570	Standard	NM_174981		Approved	POTE, POTE-21, POTE21, CT104.1	uc002yjb.1	Q86YR6	OTTHUMG00000074197	ENST00000299443.5:c.434G>A	21.37:g.14982983G>A	ENSP00000299443:p.Arg145Lys	Somatic		Capture	Illumina HiSeq	Phase_I	13904854	NM_174981	C9JCF7	Missense_Mutation	SNP	ENST00000299443.5	37	CCDS13562.1	.	.	.	.	.	.	.	.	.	.	G	6.369	0.436197	0.12104	.	.	ENSG00000166351	ENST00000299443	T	0.52526	0.66	1.29	-1.73	0.08081	Ankyrin repeat-containing domain (3);	.	.	.	.	T	0.35480	0.0933	L	0.53249	1.67	0.09310	N	1	B	0.26041	0.14	B	0.26202	0.067	T	0.27739	-1.0065	9	0.25106	T	0.35	.	4.2927	0.10886	0.5449:0.0:0.4551:0.0	.	145	Q86YR6	POTED_HUMAN	K	145	ENSP00000299443:R145K	ENSP00000299443:R145K	R	+	2	0	POTED	13904854	0.306000	0.24490	0.185000	0.23176	0.087000	0.18053	-0.620000	0.05565	-0.465000	0.06953	0.184000	0.17185	AGA		0.572	POTED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157660.1	NM_174981	
TMPRSS15	5651	broad.mit.edu	37	21	19775798	19775798	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:19775798G>A	ENST00000284885.3	-	1	175	c.142C>T	c.(142-144)Cga>Tga	p.R48*		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	48						brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.R48*(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						GACTTACCTCGTTGGGATTCC	0.428																																					p.R48X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C142T	21						.						132.0	119.0	124.0					21																	19775798		2203	4300	6503	18697669	SO:0001587	stop_gained	5651	exon1				CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.142C>T	21.37:g.19775798G>A	ENSP00000284885:p.Arg48*	Somatic		Capture	Illumina HiSeq	Phase_I	18697669	NM_002772	Q2NKL7	Nonsense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.551515	0.86127	.	.	ENSG00000154646	ENST00000284885	.	.	.	5.16	-3.41	0.04839	.	1.718880	0.02789	N	0.121817	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.1053	0.20069	0.0:0.3333:0.33:0.3366	.	.	.	.	X	48	.	.	R	-	1	2	TMPRSS15	18697669	0.000000	0.05858	0.000000	0.03702	0.160000	0.22226	-0.442000	0.06871	-0.802000	0.04421	-0.309000	0.09137	CGA		0.428	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
ADAMTS5	11096	broad.mit.edu	37	21	28337872	28337872	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:28337872G>A	ENST00000284987.5	-	1	960	c.839C>T	c.(838-840)gCg>gTg	p.A280V		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	280	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.A280V(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						ATACAACCGCGCCATGGACGC	0.682																																					p.A280V	Esophageal Squamous(53;683 1080 10100 14424 45938)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C839T	21						.						22.0	21.0	22.0					21																	28337872		2203	4300	6503	27259743	SO:0001583	missense	11096	exon1			AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.839C>T	21.37:g.28337872G>A	ENSP00000284987:p.Ala280Val	Somatic		Capture	Illumina HiSeq	Phase_I	27259743	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	G	12.88	2.069752	0.36470	.	.	ENSG00000154736	ENST00000284987	T	0.61742	0.08	4.74	3.86	0.44501	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.404891	0.24231	N	0.040345	T	0.22126	0.0533	N	0.03115	-0.41	0.41997	D	0.990871	B	0.33266	0.404	B	0.15484	0.013	T	0.31166	-0.9953	10	0.02654	T	1	.	7.5397	0.27731	0.1561:0.1387:0.7052:0.0	.	280	Q9UNA0	ATS5_HUMAN	V	280	ENSP00000284987:A280V	ENSP00000284987:A280V	A	-	2	0	ADAMTS5	27259743	0.995000	0.38212	0.980000	0.43619	0.975000	0.68041	2.209000	0.42806	1.216000	0.43427	0.561000	0.74099	GCG		0.682	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
LTN1	26046	broad.mit.edu	37	21	30318545	30318545	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:30318545C>T	ENST00000361371.5	-	20	3631	c.3552G>A	c.(3550-3552)gaG>gaA	p.E1184E	LTN1_ENST00000389194.2_Silent_p.E1230E			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	1184					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.E1184E(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						CATGTAATAGCTCTCCATCAT	0.284																																					p.E1230E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3690A	21						.						70.0	75.0	73.0					21																	30318545		2201	4293	6494	29240416	SO:0001819	synonymous_variant	26046	exon20			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.3552G>A	21.37:g.30318545C>T		Somatic		Capture	Illumina HiSeq	Phase_I	29240416	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Silent	SNP	ENST00000361371.5	37																																																																																					0.284	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
KRTAP27-1	643812	broad.mit.edu	37	21	31709773	31709773	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:31709773C>T	ENST00000382835.2	-	1	239	c.214G>A	c.(214-216)Gac>Aac	p.D72N		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	72						intermediate filament (GO:0005882)		p.D72N(1)		endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						CAGCTATCGTCTGTGAATAAG	0.473																																					p.D72N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G214A	21						.						163.0	155.0	158.0					21																	31709773		2203	4300	6503	30631644	SO:0001583	missense	643812	exon1			AB096937	CCDS33532.1	21q22.11	2007-11-23			ENSG00000206107	ENSG00000206107		"""Keratin associated proteins"""	33864	protein-coding gene	gene with protein product							Standard	NM_001077711		Approved		uc002ynx.1	Q3LI81	OTTHUMG00000059577	ENST00000382835.2:c.214G>A	21.37:g.31709773C>T	ENSP00000372286:p.Asp72Asn	Somatic		Capture	Illumina HiSeq	Phase_I	30631644	NM_001077711		Missense_Mutation	SNP	ENST00000382835.2	37	CCDS33532.1	.	.	.	.	.	.	.	.	.	.	C	11.41	1.631013	0.28978	.	.	ENSG00000206107	ENST00000382835	T	0.30981	1.51	4.34	3.45	0.39498	.	1.649240	0.03647	N	0.240401	T	0.18045	0.0433	N	0.08118	0	0.09310	N	1	B	0.26195	0.144	B	0.25291	0.059	T	0.19877	-1.0292	10	0.17832	T	0.49	-0.9765	8.2138	0.31499	0.0:0.8915:0.0:0.1085	.	72	Q3LI81	KR271_HUMAN	N	72	ENSP00000372286:D72N	ENSP00000372286:D72N	D	-	1	0	KRTAP27-1	30631644	0.000000	0.05858	0.004000	0.12327	0.016000	0.09150	0.496000	0.22499	1.410000	0.46936	0.591000	0.81541	GAC		0.473	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711	
KRTAP13-1	140258	broad.mit.edu	37	21	31768507	31768507	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:31768507G>A	ENST00000355459.2	+	1	116	c.103G>A	c.(103-105)Gtc>Atc	p.V35I		NM_181599.2	NP_853630.2	Q8IUC0	KR131_HUMAN	keratin associated protein 13-1	35						intermediate filament (GO:0005882)		p.V35I(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CAGCAACCAGGTCTACAGCAC	0.607																																					p.V35I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G103A	21						.						115.0	110.0	112.0					21																	31768507		2203	4300	6503	30690378	SO:0001583	missense	140258	exon1			AJ457066	CCDS13590.2	21q22.11	2013-06-20			ENSG00000198390	ENSG00000198390		"""Keratin associated proteins"""	18924	protein-coding gene	gene with protein product		608718				12359730	Standard	NM_181599		Approved	KAP13.1	uc002yoa.3	Q8IUC0	OTTHUMG00000057800	ENST00000355459.2:c.103G>A	21.37:g.31768507G>A	ENSP00000347635:p.Val35Ile	Somatic		Capture	Illumina HiSeq	Phase_I	30690378	NM_181599	Q14D20|Q3LI79	Missense_Mutation	SNP	ENST00000355459.2	37	CCDS13590.2	.	.	.	.	.	.	.	.	.	.	G	9.866	1.197613	0.22037	.	.	ENSG00000198390	ENST00000355459	T	0.03272	3.99	4.45	-3.89	0.04193	.	1.257560	0.06150	N	0.674021	T	0.13543	0.0328	M	0.85710	2.77	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.27806	-1.0063	10	0.32370	T	0.25	.	1.4287	0.02328	0.1506:0.2185:0.2885:0.3424	.	35	Q8IUC0	KR131_HUMAN	I	35	ENSP00000347635:V35I	ENSP00000347635:V35I	V	+	1	0	KRTAP13-1	30690378	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-1.038000	0.03553	-0.820000	0.04318	-0.133000	0.14855	GTC		0.607	KRTAP13-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128252.3		
TIAM1	7074	broad.mit.edu	37	21	32525054	32525054	+	Missense_Mutation	SNP	G	G	A	rs148623159		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:32525054G>A	ENST00000286827.3	-	20	3737	c.3266C>T	c.(3265-3267)aCg>aTg	p.T1089M	TIAM1_ENST00000541036.1_Missense_Mutation_p.T1029M	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1089	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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.T1089M(6)		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						TACCATTTCCGTTAAATTTCC	0.333																																					p.T1089M												.	.	6	Substitution - Missense(6)	lung(4)|large_intestine(2)	c.C3266T	21						.	G	MET/THR	0,4406		0,0,2203	59.0	61.0	60.0		3266	4.7	1.0	21	dbSNP_134	60	1,8599	1.2+/-3.3	0,1,4299	no	missense	TIAM1	NM_003253.2	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	1089/1592	32525054	1,13005	2203	4300	6503	31446925	SO:0001583	missense	7074	exon20				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.3266C>T	21.37:g.32525054G>A	ENSP00000286827:p.Thr1089Met	Somatic		Capture	Illumina HiSeq	Phase_I	31446925	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.544610	0.45280	0.0	1.16E-4	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.63417	-0.04;-0.04	5.63	4.74	0.60224	Dbl homology (DH) domain (5);	0.060669	0.64402	D	0.000002	T	0.54062	0.1835	L	0.41492	1.28	0.47153	D	0.999337	B;B;B	0.14805	0.009;0.011;0.011	B;B;B	0.12837	0.005;0.008;0.008	T	0.54801	-0.8239	10	0.66056	D	0.02	.	14.0158	0.64523	0.0718:0.0:0.9282:0.0	.	1029;1029;1089	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	M	1089;930;1029	ENSP00000286827:T1089M;ENSP00000441570:T1029M	ENSP00000286827:T1089M	T	-	2	0	TIAM1	31446925	1.000000	0.71417	0.959000	0.39883	0.984000	0.73092	3.683000	0.54663	2.673000	0.90976	0.650000	0.86243	ACG		0.333	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
SCAF4	57466	broad.mit.edu	37	21	33044576	33044576	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:33044576C>T	ENST00000286835.7	-	20	2962	c.2580G>A	c.(2578-2580)caG>caA	p.Q860Q	SCAF4_ENST00000434667.3_Silent_p.Q845Q|SCAF4_ENST00000399804.1_Silent_p.Q838Q	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	860						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.Q860Q(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						CTGGAGGGCGCTGGAGTGGGA	0.617																																					p.Q845Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2535A	21						.						51.0	54.0	53.0					21																	33044576		2203	4300	6503	31966447	SO:0001819	synonymous_variant	57466	exon19			AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"""RNA binding motif (RRM) containing"""	19304	protein-coding gene	gene with protein product			"""splicing factor, arginine/serine-rich 15"""	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.2580G>A	21.37:g.33044576C>T		Somatic		Capture	Illumina HiSeq	Phase_I	31966447	NM_001145444	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Silent	SNP	ENST00000286835.7	37	CCDS33537.1																																																																																				0.617	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889	
SYNJ1	8867	broad.mit.edu	37	21	34072303	34072303	+	Silent	SNP	G	G	A	rs551070196		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:34072303G>A	ENST00000322229.7	-	3	323	c.324C>T	c.(322-324)atC>atT	p.I108I	SYNJ1_ENST00000433931.2_Silent_p.I147I|SYNJ1_ENST00000357345.3_Silent_p.I108I|SYNJ1_ENST00000382499.2_Silent_p.I147I|SYNJ1_ENST00000382491.3_Silent_p.I108I			O43426	SYNJ1_HUMAN	synaptojanin 1	108					cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)	p.I108I(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						CTGAAGAATCGATTCGCAGTG	0.378													G|||	1	0.000199681	0.0	0.0	5008	,	,		17176	0.001		0.0	False		,,,				2504	0.0				p.I147I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C441T	21						.						66.0	65.0	65.0					21																	34072303		2203	4300	6503	32994174	SO:0001819	synonymous_variant	8867	exon4			AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.324C>T	21.37:g.34072303G>A		Somatic		Capture	Illumina HiSeq	Phase_I	32994174	NM_003895	O43425|O94984|Q4KMR1	Silent	SNP	ENST00000322229.7	37	CCDS54484.1																																																																																				0.378	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
SON	6651	broad.mit.edu	37	21	34924902	34924902	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:34924902G>A	ENST00000356577.4	+	3	3840	c.3365G>A	c.(3364-3366)cGt>cAt	p.R1122H	SON_ENST00000290239.6_Missense_Mutation_p.R1122H|SON_ENST00000381692.2_Intron|SON_ENST00000300278.4_Missense_Mutation_p.R1122H|SON_ENST00000381679.4_Missense_Mutation_p.R1122H	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1122	14 X 6 AA repeats of [ED]-R-S-M-M-S.				cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R1122H(2)		breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						ACTGCTGATCGTTCAATGATG	0.473																																					p.R1122H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3365A	21						.						204.0	163.0	177.0					21																	34924902		2203	4300	6503	33846772	SO:0001583	missense	6651	exon3			AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.3365G>A	21.37:g.34924902G>A	ENSP00000348984:p.Arg1122His	Somatic		Capture	Illumina HiSeq	Phase_I	33846772	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.39|16.39	3.109550|3.109550	0.56398|0.56398	.|.	.|.	ENSG00000159140|ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679|ENST00000436227	T;T;T;T|.	0.21543|.	2.17;2.15;2.13;2.0|.	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	0.000000|.	0.51477|.	D|.	0.000095|.	T|T	0.66645|0.66645	0.2810|0.2810	L|L	0.54323|0.54323	1.7|1.7	0.34891|0.34891	D|D	0.745551|0.745551	D;D;D;D;D|.	0.89917|.	1.0;1.0;0.973;1.0;1.0|.	D;D;P;D;D|.	0.87578|.	0.998;0.996;0.632;0.998;0.998|.	T|T	0.71185|0.71185	-0.4667|-0.4667	10|5	0.66056|.	D|.	0.02|.	.|.	17.5338|17.5338	0.87822|0.87822	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1122;1122;803;1122;1122|.	P18583-10;P18583;P18583-2;P18583-3;P18583-6|.	.;SON_HUMAN;.;.;.|.	H|I	1122|117	ENSP00000348984:R1122H;ENSP00000290239:R1122H;ENSP00000300278:R1122H;ENSP00000371095:R1122H|.	ENSP00000290239:R1122H|.	R|V	+|+	2|1	0|0	SON|SON	33846772|33846772	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.820000|3.820000	0.55693|0.55693	2.733000|2.733000	0.93635|0.93635	0.655000|0.655000	0.94253|0.94253	CGT|GTT		0.473	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
TTC3	7267	broad.mit.edu	37	21	38525455	38525455	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:38525455T>C	ENST00000399017.2	+	27	5365	c.2618T>C	c.(2617-2619)gTt>gCt	p.V873A	TTC3_ENST00000354749.2_Missense_Mutation_p.V873A|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000540756.1_Missense_Mutation_p.V563A|TTC3_ENST00000355666.1_Missense_Mutation_p.V873A	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	873					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.V873A(1)		breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GTGGACTATGTTATTCGCCAC	0.368																																					p.V873A	Ovarian(38;194 1649 35661)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2618C	21						.						92.0	100.0	97.0					21																	38525455		2203	4299	6502	37447325	SO:0001583	missense	7267	exon27			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.2618T>C	21.37:g.38525455T>C	ENSP00000381981:p.Val873Ala	Somatic		Capture	Illumina HiSeq	Phase_I	37447325	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	T	15.19	2.760527	0.49468	.	.	ENSG00000182670	ENST00000418766;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	T;T;T;T;T;T	0.46451	2.66;2.66;2.99;0.87;2.99;2.99	5.31	4.16	0.48862	.	0.236635	0.29253	N	0.012692	T	0.57784	0.2077	L	0.57536	1.79	0.30515	N	0.769071	P;D	0.69078	0.869;0.997	B;D	0.72625	0.352;0.978	T	0.61332	-0.7084	10	0.87932	D	0	-11.5893	11.063	0.47959	0.0:0.0742:0.0:0.9258	.	563;873	B4DSZ9;P53804	.;TTC3_HUMAN	A	873;855;873;563;873;873	ENSP00000403943:V873A;ENSP00000391891:V855A;ENSP00000347889:V873A;ENSP00000442875:V563A;ENSP00000381981:V873A;ENSP00000346791:V873A	ENSP00000346791:V873A	V	+	2	0	TTC3	37447325	1.000000	0.71417	0.974000	0.42286	0.958000	0.62258	3.755000	0.55197	0.963000	0.38082	0.528000	0.53228	GTT		0.368	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
ERG	2078	broad.mit.edu	37	21	39775601	39775601	+	Missense_Mutation	SNP	C	C	T	rs146705250		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:39775601C>T	ENST00000417133.2	-	6	625	c.440G>A	c.(439-441)cGg>cAg	p.R147Q	ERG_ENST00000453032.2_Missense_Mutation_p.R48Q|ERG_ENST00000398919.2_Missense_Mutation_p.R147Q|ERG_ENST00000442448.1_Missense_Mutation_p.R147Q|ERG_ENST00000398897.1_Missense_Mutation_p.R48Q|ERG_ENST00000288319.7_Missense_Mutation_p.R140Q|ERG_ENST00000398911.1_Missense_Mutation_p.R147Q|ERG_ENST00000398905.1_Missense_Mutation_p.R140Q|ERG_ENST00000398910.1_Missense_Mutation_p.R147Q|ERG_ENST00000429727.2_Intron|ERG_ENST00000398907.1_Missense_Mutation_p.R140Q	NM_001136154.1|NM_001243432.1	NP_001129626.1|NP_001230361.1	Q12809	KCNH2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog	0					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)	p.R147Q(1)	EWSR1/ERG(178)|NDRG1/ERG(5)|TMPRSS2/ERG(3582)|FUS/ERG(167)|SLC45A3/ERG(50)	lung(2)|ovary(1)|skin(1)	4		Prostate(19;3.6e-06)			Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	CAGCCACTGCCGCACATGGTC	0.502			T	"""EWSR1, TMPRSS2, ELF4, FUS, HERPUD1, NDRG1"""	"""Ewing sarcoma, prostate, AML"""																																p.R147Q	Esophageal Squamous(130;336 1700 3010 3083 40589)		Dom	yes		21	21q22.3	2078	v-ets erythroblastosis virus E26 oncogene like (avian)		"""M, E, L"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G440A	21						.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	84.0	75.0	78.0		440,143,440,419	4.8	1.0	21	dbSNP_134	78	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	ERG	NM_001136154.1,NM_001136155.1,NM_004449.4,NM_182918.3	43,43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	147/487,48/388,147/463,140/480	39775601	1,13005	2203	4300	6503	38697471	SO:0001583	missense	2078	exon6				CCDS13657.1, CCDS13658.1, CCDS46648.1, CCDS46649.1, CCDS58789.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157554	ENSG00000157554			3446	protein-coding gene	gene with protein product	"""v-ets avian erythroblastosis virus E26 oncogene related"", ""transcriptional regulator ERG (transforming protein ERG)"", ""v-ets erythroblastosis virus E26 oncogene like"", ""TMPRSS2-ERG prostate cancer specific"""	165080	"""v-ets avian erythroblastosis virus E26 oncogene related"""			3274086	Standard	NM_001136154		Approved	erg-3, p55	uc002yxa.3	P11308	OTTHUMG00000090767	ENST00000417133.2:c.440G>A	21.37:g.39775601C>T	ENSP00000414150:p.Arg147Gln	Somatic		Capture	Illumina HiSeq	Phase_I	38697471	NM_001136154	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000417133.2	37	CCDS46648.1	.	.	.	.	.	.	.	.	.	.	C	31	5.071399	0.93950	0.0	1.16E-4	ENSG00000157554	ENST00000398905;ENST00000398907;ENST00000288319;ENST00000398897;ENST00000398911;ENST00000417133;ENST00000398910;ENST00000442448;ENST00000453032;ENST00000398919	T;T;T;T;T;T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57	4.79	4.79	0.61399	Sterile alpha motif/pointed domain (2);Pointed domain (3);	0.000000	0.85682	D	0.000000	T	0.31544	0.0800	N	0.20807	0.61	0.80722	D	1	P;P;P;P;P	0.52463	0.839;0.952;0.95;0.953;0.789	B;P;P;P;B	0.50860	0.326;0.652;0.632;0.486;0.227	T	0.05869	-1.0859	10	0.36615	T	0.2	.	18.2309	0.89934	0.0:1.0:0.0:0.0	.	147;140;147;147;140	P11308;B5MDW0;P11308-6;P11308-1;P11308-4	ERG_HUMAN;.;.;.;.	Q	140;140;140;48;147;147;147;147;48;147	ENSP00000381877:R140Q;ENSP00000381879:R140Q;ENSP00000288319:R140Q;ENSP00000381871:R48Q;ENSP00000381882:R147Q;ENSP00000414150:R147Q;ENSP00000381881:R147Q;ENSP00000394694:R147Q;ENSP00000396268:R48Q;ENSP00000381891:R147Q	ENSP00000288319:R140Q	R	-	2	0	ERG	38697471	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.740000	0.84986	2.358000	0.79984	0.655000	0.94253	CGG		0.502	ERG-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207532.2	NM_182918	
UBASH3A	53347	broad.mit.edu	37	21	43838596	43838596	+	Silent	SNP	G	G	A	rs144754371	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:43838596G>A	ENST00000319294.6	+	7	955	c.924G>A	c.(922-924)acG>acA	p.T308T	RNU6-1149P_ENST00000516810.1_RNA|UBASH3A_ENST00000291535.6_Silent_p.T270T|UBASH3A_ENST00000398367.1_Silent_p.T270T	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	308	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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.T308T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						TGGACCCCACGCAGCAGGACG	0.582																																					p.T270T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G810A	21						.	G	,	2,4404	4.2+/-10.8	0,2,2201	81.0	81.0	81.0		810,924	-10.3	0.0	21	dbSNP_134	81	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous	UBASH3A	NM_001001895.2,NM_018961.3	,	0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308	,	270/624,308/662	43838596	4,13002	2203	4300	6503	42711665	SO:0001819	synonymous_variant	53347	exon6			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.924G>A	21.37:g.43838596G>A		Somatic		Capture	Illumina HiSeq	Phase_I	42711665	NM_001001895	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Silent	SNP	ENST00000319294.6	37	CCDS13687.1																																																																																				0.582	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
PDE9A	5152	broad.mit.edu	37	21	44189193	44189193	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:44189193A>C	ENST00000291539.6	+	17	1578	c.1518A>C	c.(1516-1518)aaA>aaC	p.K506N	PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000328862.6_Missense_Mutation_p.K480N|PDE9A_ENST00000539837.1_Missense_Mutation_p.K378N|PDE9A_ENST00000398227.3_Missense_Mutation_p.K346N|PDE9A_ENST00000335512.4_Missense_Mutation_p.K446N|PDE9A_ENST00000349112.3_Missense_Mutation_p.K378N|PDE9A_ENST00000398232.3_Missense_Mutation_p.K439N|PDE9A_ENST00000398225.3_Missense_Mutation_p.K465N|PDE9A_ENST00000398229.3_Missense_Mutation_p.K372N|PDE9A_ENST00000335440.6_Missense_Mutation_p.K404N|PDE9A_ENST00000398234.3_Missense_Mutation_p.K405N|PDE9A_ENST00000398224.3_Missense_Mutation_p.K379N|PDE9A_ENST00000398236.3_Missense_Mutation_p.K420N|PDE9A_ENST00000380328.2_Missense_Mutation_p.K453N	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	506	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)	p.K506N(1)		breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	ACCGAGACAAAGTGACCAAGG	0.507																																					p.K420N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1260C	21						.						208.0	165.0	180.0					21																	44189193		2203	4300	6503	43062262	SO:0001583	missense	5152	exon15			AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.1518A>C	21.37:g.44189193A>C	ENSP00000291539:p.Lys506Asn	Somatic		Capture	Illumina HiSeq	Phase_I	43062262	NM_001001574	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Missense_Mutation	SNP	ENST00000291539.6	37	CCDS13690.1	.	.	.	.	.	.	.	.	.	.	A	17.38	3.374415	0.61735	.	.	ENSG00000160191	ENST00000335512;ENST00000539837;ENST00000291539;ENST00000380328;ENST00000398232;ENST00000398234;ENST00000398236;ENST00000328862;ENST00000335440;ENST00000398225;ENST00000398229;ENST00000398227;ENST00000349112;ENST00000398224	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21;-1.21	4.75	3.61	0.41365	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.85682	D	0.000000	D	0.85031	0.5604	M	0.74467	2.265	0.44424	D	0.997346	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;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.995;0.997;0.995;0.995;0.999;0.999;0.997;0.994;0.994;0.99;0.99;0.999;0.997;0.99;0.997	T	0.81938	-0.0704	10	0.29301	T	0.29	.	9.8758	0.41202	0.9187:0.0:0.0813:0.0	.	439;420;405;480;465;398;446;289;346;372;378;404;453;379;506	O76083-13;O76083-8;O76083-6;O76083-15;O76083-14;O76083-16;O76083-2;O76083-10;O76083-9;O76083-11;O76083-4;O76083-12;O76083-5;O76083-3;O76083	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PDE9A_HUMAN	N	446;378;506;453;439;405;420;480;404;465;372;346;378;379	ENSP00000335242:K446N;ENSP00000441899:K378N;ENSP00000291539:K506N;ENSP00000369685:K453N;ENSP00000381287:K439N;ENSP00000381289:K405N;ENSP00000381291:K420N;ENSP00000328699:K480N;ENSP00000335365:K404N;ENSP00000381281:K465N;ENSP00000381285:K372N;ENSP00000381283:K346N;ENSP00000344730:K378N;ENSP00000381280:K379N	ENSP00000291539:K506N	K	+	3	2	PDE9A	43062262	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	2.175000	0.42491	0.688000	0.31529	0.260000	0.18958	AAA		0.507	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		
TRAPPC10	7109	broad.mit.edu	37	21	45499489	45499489	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:45499489C>A	ENST00000291574.4	+	12	1689	c.1514C>A	c.(1513-1515)gCa>gAa	p.A505E		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	505					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)	p.A505E(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						CTTCAAGGAGCACTGAAAAAC	0.453																																					p.A505E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1514A	21						.						81.0	76.0	78.0					21																	45499489		2203	4300	6503	44323917	SO:0001583	missense	7109	exon12			U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.1514C>A	21.37:g.45499489C>A	ENSP00000291574:p.Ala505Glu	Somatic		Capture	Illumina HiSeq	Phase_I	44323917	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	37	CCDS13704.1	.	.	.	.	.	.	.	.	.	.	C	35	5.417818	0.96092	.	.	ENSG00000160218	ENST00000291574	D	0.82893	-1.66	5.38	5.38	0.77491	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.87450	0.6180	L	0.48642	1.525	0.80722	D	1	D	0.65815	0.995	P	0.59703	0.862	D	0.88468	0.3060	10	0.72032	D	0.01	.	18.7206	0.91691	0.0:1.0:0.0:0.0	.	505	P48553	TPC10_HUMAN	E	505	ENSP00000291574:A505E	ENSP00000291574:A505E	A	+	2	0	TRAPPC10	44323917	1.000000	0.71417	0.926000	0.36857	0.985000	0.73830	6.999000	0.76283	2.503000	0.84419	0.591000	0.81541	GCA		0.453	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
ITGB2	3689	broad.mit.edu	37	21	46330685	46330685	+	Missense_Mutation	SNP	G	G	A	rs61737078	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:46330685G>A	ENST00000397850.2	-	3	465	c.13C>T	c.(13-15)Cgc>Tgc	p.R5C	ITGB2_ENST00000397852.1_Missense_Mutation_p.R5C|ITGB2_ENST00000355153.4_Missense_Mutation_p.R5C|ITGB2_ENST00000397857.1_Missense_Mutation_p.R5C|ITGB2_ENST00000397854.3_Missense_Mutation_p.R5C|ITGB2_ENST00000397846.3_Missense_Mutation_p.R5C|ITGB2_ENST00000523126.1_5'Flank|ITGB2_ENST00000302347.5_Missense_Mutation_p.R5C			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	5					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|receptor clustering (GO:0043113)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|glycoprotein binding (GO:0001948)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)	p.R5C(1)		breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(4)|skin(3)	35				Colorectal(79;0.0669)	Simvastatin(DB00641)	AGTGGGGGGCGCAGGCCCAGC	0.667													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19064	0.0		0.0	False		,,,				2504	0.0				p.R5C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C13T	21						.	G	CYS/ARG,CYS/ARG	17,4387	22.3+/-47.3	0,17,2185	37.0	41.0	40.0		13,13	-3.3	0.0	21	dbSNP_129	40	0,8600		0,0,4300	yes	missense,missense	ITGB2	NM_001127491.1,NM_000211.3	180,180	0,17,6485	AA,AG,GG		0.0,0.386,0.1307	benign,benign	5/770,5/770	46330685	17,12987	2202	4300	6502	45155113	SO:0001583	missense	3689	exon2			AK222505	CCDS13716.1	21q22.3	2014-09-17	2006-03-02		ENSG00000160255	ENSG00000160255		"""CD molecules"", ""Complement system"", ""Integrins"""	6155	protein-coding gene	gene with protein product		600065	"""integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit)"""	CD18, MFI7			Standard	NM_000211		Approved	LFA-1, MAC-1	uc002zgf.3	P05107	OTTHUMG00000090257	ENST00000397850.2:c.13C>T	21.37:g.46330685G>A	ENSP00000380948:p.Arg5Cys	Somatic		Capture	Illumina HiSeq	Phase_I	45155113	NM_001127491	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Missense_Mutation	SNP	ENST00000397850.2	37	CCDS13716.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	4.575	0.106908	0.08780	0.00386	0.0	ENSG00000160255	ENST00000397852;ENST00000397857;ENST00000397854;ENST00000355153;ENST00000397850;ENST00000302347;ENST00000545414;ENST00000523663;ENST00000522931;ENST00000517563;ENST00000517819;ENST00000397846;ENST00000521995	D;D;D;D;D;D;D;D;D;D;D;D	0.92495	-2.74;-2.74;-2.51;-2.74;-2.74;-2.74;-2.73;-3.05;-1.91;-2.42;-2.52;-2.11	3.78	-3.26	0.05064	.	.	.	.	.	T	0.72317	0.3445	N	0.08118	0	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.01281	0.0;0.0	T	0.62770	-0.6784	9	0.38643	T	0.18	.	3.2651	0.06863	0.299:0.0:0.2441:0.4569	.	5;5	A8MYE6;P05107	.;ITB2_HUMAN	C	5	ENSP00000380950:R5C;ENSP00000380955:R5C;ENSP00000380952:R5C;ENSP00000347279:R5C;ENSP00000380948:R5C;ENSP00000303242:R5C;ENSP00000428503:R5C;ENSP00000428979:R5C;ENSP00000428413:R5C;ENSP00000428870:R5C;ENSP00000380944:R5C;ENSP00000429683:R5C	ENSP00000303242:R5C	R	-	1	0	ITGB2	45155113	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-1.632000	0.02024	-0.483000	0.06772	-1.119000	0.02030	CGC		0.667	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
PCNT	5116	broad.mit.edu	37	21	47769672	47769672	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:47769672G>A	ENST00000359568.5	+	8	1389	c.1282G>A	c.(1282-1284)Ggc>Agc	p.G428S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	428	Glu-rich.				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.G428S(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)					GTCCGAGCACGGCCGGTGTTT	0.468																																					p.G428S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1282A	21						.						99.0	99.0	99.0					21																	47769672		2203	4300	6503	46594100	SO:0001583	missense	5116	exon8			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.1282G>A	21.37:g.47769672G>A	ENSP00000352572:p.Gly428Ser	Somatic		Capture	Illumina HiSeq	Phase_I	46594100	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	G	5.408	0.260467	0.10239	.	.	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.19669	2.13	3.87	-0.138	0.13464	.	0.605571	0.13051	N	0.417680	T	0.06690	0.0171	N	0.08118	0	0.09310	N	1	B;B	0.21905	0.062;0.037	B;B	0.11329	0.006;0.005	T	0.35276	-0.9795	10	0.09590	T	0.72	.	1.1855	0.01854	0.2987:0.0913:0.3133:0.2968	.	310;428	O95613-2;O95613	.;PCNT_HUMAN	S	428;415	ENSP00000352572:G428S	ENSP00000338675:G415S	G	+	1	0	PCNT	46594100	0.000000	0.05858	0.015000	0.15790	0.005000	0.04900	-0.556000	0.05992	-0.006000	0.14370	-0.442000	0.05670	GGC		0.468	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
DIP2A	23181	broad.mit.edu	37	21	47977645	47977645	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:47977645C>T	ENST00000417564.2	+	31	3798	c.3777C>T	c.(3775-3777)ggC>ggT	p.G1259G	DIP2A_ENST00000318711.7_Silent_p.G1260G|DIP2A_ENST00000400274.1_Silent_p.G1255G			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1259					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.G1259G(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)		AGGGCCTAGGCGCACAGACGG	0.577																																					p.G1259G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3777T	21						.						34.0	40.0	38.0					21																	47977645		2076	4241	6317	46802073	SO:0001819	synonymous_variant	23181	exon31			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.3777C>T	21.37:g.47977645C>T		Somatic		Capture	Illumina HiSeq	Phase_I	46802073	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	37	CCDS46655.1																																																																																				0.577	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
LIPI	149998	broad.mit.edu	37	21	15561404	15561404	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:15561404delT	ENST00000536861.1	-	2	382	c.383delA	c.(382-384)aacfs	p.N128fs	LIPI_ENST00000344577.2_Frame_Shift_Del_p.N149fs			Q6XZB0	LIPI_HUMAN	lipase, member I	128					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)	p.N149fs*7(1)		endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		TTTTCTGGTGTTTTTAACTGC	0.323																																					p.N149fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.446delA	21						.						39.0	43.0	42.0					21																	15561404		2203	4300	6503	14483275	SO:0001589	frameshift_variant	149998	exon2			BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"""membrane-associated phospholipase A1 beta"", ""cancer/testis antigen 17"""	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.383delA	21.37:g.15561404delT	ENSP00000440381:p.Asn128fs	Somatic		Capture	Illumina HiSeq	Phase_I	14483275	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Frame_Shift_Del	DEL	ENST00000536861.1	37																																																																																					0.323	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996	
TTC3	7267	broad.mit.edu	37	21	38524243	38524243	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:38524243delA	ENST00000399017.2	+	26	5074	c.2327delA	c.(2326-2328)caafs	p.Q776fs	TTC3_ENST00000354749.2_Frame_Shift_Del_p.Q776fs|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000540756.1_Frame_Shift_Del_p.Q466fs|TTC3_ENST00000355666.1_Frame_Shift_Del_p.Q776fs	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	776					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E779fs*5(2)		breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				AGAAAGATCCAAAAAAAAGAA	0.343																																					p.Q776fs	Ovarian(38;194 1649 35661)											.	.	2	Deletion - Frameshift(2)	ovary(1)|large_intestine(1)	c.2327delA	21						.						82.0	80.0	81.0					21																	38524243		2203	4300	6503	37446113	SO:0001589	frameshift_variant	7267	exon26			D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.2327delA	21.37:g.38524243delA	ENSP00000381981:p.Gln776fs	Somatic		Capture	Illumina HiSeq	Phase_I	37446113	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Frame_Shift_Del	DEL	ENST00000399017.2	37	CCDS13651.1																																																																																				0.343	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
MX1	4599	broad.mit.edu	37	21	42817475	42817475	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:42817475delA	ENST00000398600.2	+	14	2134	c.1109delA	c.(1108-1110)gaafs	p.E370fs	MX1_ENST00000398598.3_Frame_Shift_Del_p.E370fs|MX1_ENST00000288383.6_Frame_Shift_Del_p.E347fs|AP001610.5_ENST00000411427.1_RNA|MX1_ENST00000455164.2_Frame_Shift_Del_p.E370fs	NM_001144925.1	NP_001138397.1	P20591	MX1_HUMAN	MX dynamin-like GTPase 1	370	Middle domain.|Stalk.				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.M372fs*4(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)				GACGAAAATGAAAAAATGTTC	0.448																																					p.E370fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1109delA	21						.						97.0	87.0	91.0					21																	42817475		2203	4300	6503	41739345	SO:0001589	frameshift_variant	4599	exon14				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.1109delA	21.37:g.42817475delA	ENSP00000381601:p.Glu370fs	Somatic		Capture	Illumina HiSeq	Phase_I	41739345	NM_001144925	B2RDA5|B3KU10|C9IYV7|C9J8D6|C9JN19|C9JN88|C9JUL1|C9JZS6|D3DSI8|Q86YP5|Q96CI3	Frame_Shift_Del	DEL	ENST00000398600.2	37	CCDS13673.1																																																																																				0.448	MX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195161.2		
PCNT	5116	broad.mit.edu	37	21	47836237	47836237	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:47836237delG	ENST00000359568.5	+	30	6512	c.6405delG	c.(6403-6405)acgfs	p.T2135fs	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2135					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.G2137fs*2(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)					ATACAGCCACGGGGGGTGTAA	0.488																																					p.T2135fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.6405delG	21						.						81.0	84.0	83.0					21																	47836237		2203	4300	6503	46660665	SO:0001589	frameshift_variant	5116	exon30			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.6405delG	21.37:g.47836237delG	ENSP00000352572:p.Thr2135fs	Somatic		Capture	Illumina HiSeq	Phase_I	46660665	NM_006031	O43152|Q7Z7C9	Frame_Shift_Del	DEL	ENST00000359568.5	37	CCDS33592.1																																																																																				0.488	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
S100B	6285	broad.mit.edu	37	21	48022289	48022289	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr21:48022289C>T	ENST00000291700.4	-	2	236	c.40G>A	c.(40-42)Gtt>Att	p.V14I	S100B_ENST00000367071.4_Missense_Mutation_p.V14I|S100B_ENST00000397648.1_Missense_Mutation_p.V14I	NM_006272.2	NP_006263.1	P04271	S100B_HUMAN	S100 calcium binding protein B	14	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				astrocyte differentiation (GO:0048708)|axonogenesis (GO:0007409)|cell proliferation (GO:0008283)|cellular response to hypoxia (GO:0071456)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of cell shape (GO:0008360)|regulation of neuronal synaptic plasticity (GO:0048168)|response to glucocorticoid (GO:0051384)|response to methylmercury (GO:0051597)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RAGE receptor binding (GO:0050786)|S100 protein binding (GO:0044548)|tau protein binding (GO:0048156)|zinc ion binding (GO:0008270)	p.V14I(1)		endometrium(1)|large_intestine(2)|lung(1)|skin(1)	5	Breast(49;0.247)	Lung NSC(3;0.245)		OV - Ovarian serous cystadenocarcinoma(3;1.84e-06)|Epithelial(3;4.45e-06)|all cancers(3;2.07e-05)|Colorectal(79;0.241)	Olopatadine(DB00768)	TGGTGGAAAACGTCGATGAGG	0.468																																					p.V14I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G40A	21						.						130.0	112.0	118.0					21																	48022289		2203	4300	6503	46846717	SO:0001583	missense	6285	exon2			M59488	CCDS13736.1	21q22.3	2013-01-10	2006-09-11		ENSG00000160307	ENSG00000160307		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	10500	protein-coding gene	gene with protein product		176990	"""S100 calcium binding protein, beta (neural)"""			2394738, 1998503	Standard	NM_006272		Approved	S100beta	uc002zju.1	P04271	OTTHUMG00000090715	ENST00000291700.4:c.40G>A	21.37:g.48022289C>T	ENSP00000291700:p.Val14Ile	Somatic		Capture	Illumina HiSeq	Phase_I	46846717	NM_006272	D3DSN6	Missense_Mutation	SNP	ENST00000291700.4	37	CCDS13736.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.300166	0.40694	.	.	ENSG00000160307	ENST00000291700;ENST00000367071;ENST00000397648	T;T;T	0.12984	2.63;2.63;2.63	5.48	4.38	0.52667	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	0.338329	0.30979	N	0.008484	T	0.08802	0.0218	.	.	.	0.09310	N	1	P;P	0.49635	0.926;0.602	B;B	0.38616	0.277;0.253	T	0.32561	-0.9902	9	0.23302	T	0.38	-10.7525	12.1131	0.53850	0.0:0.8847:0.0:0.1153	.	14;14	A8MRB1;P04271	.;S100B_HUMAN	I	14	ENSP00000291700:V14I;ENSP00000356038:V14I;ENSP00000380769:V14I	ENSP00000291700:V14I	V	-	1	0	S100B	46846717	0.006000	0.16342	0.705000	0.30386	0.324000	0.28378	0.586000	0.23894	2.744000	0.94065	0.655000	0.94253	GTT		0.468	S100B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207427.1	NM_006272	
CECR5	27440	broad.mit.edu	37	22	17619090	17619090	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:17619090C>T	ENST00000336737.4	-	8	1118	c.1093G>A	c.(1093-1095)Gtc>Atc	p.V365I	CECR5_ENST00000399852.3_Missense_Mutation_p.V165I|CECR5_ENST00000155674.5_Missense_Mutation_p.V335I	NM_033070.2	NP_149061.1	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5	365						mitochondrion (GO:0005739)		p.V365I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(10)|pancreas(1)|prostate(1)	21		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)				GGATTGTAGACGCCTGTACAC	0.622																																					p.V365I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1093A	22						.						96.0	85.0	88.0					22																	17619090		2203	4300	6503	15999090	SO:0001583	missense	27440	exon8			AF273270	CCDS13741.1, CCDS33595.1	22q11.2	2008-06-12			ENSG00000069998	ENSG00000069998			1843	protein-coding gene	gene with protein product						11381032	Standard	NM_017829		Approved		uc002zmf.3	Q9BXW7	OTTHUMG00000150071	ENST00000336737.4:c.1093G>A	22.37:g.17619090C>T	ENSP00000337358:p.Val365Ile	Somatic		Capture	Illumina HiSeq	Phase_I	15999090	NM_033070	B2RCK5|Q9BXW8|Q9NWA8|Q9NX41	Missense_Mutation	SNP	ENST00000336737.4	37	CCDS33595.1	.	.	.	.	.	.	.	.	.	.	C	13.60	2.285353	0.40394	.	.	ENSG00000069998	ENST00000155674;ENST00000336737;ENST00000399852	T;T;T	0.31769	1.48;1.48;1.87	4.47	2.38	0.29361	HAD-like domain (2);	0.060657	0.64402	N	0.000002	T	0.39332	0.1074	L	0.54323	1.7	0.34206	D	0.673781	P;P;P;D	0.69078	0.916;0.935;0.936;0.997	B;P;P;P	0.55545	0.413;0.556;0.465;0.778	T	0.53373	-0.8448	10	0.51188	T	0.08	-20.9089	9.8537	0.41073	0.0:0.8318:0.0:0.1682	.	335;165;365;229	Q9BXW7-2;A8MYZ9;Q9BXW7;B3KVW8	.;.;CECR5_HUMAN;.	I	335;365;165	ENSP00000155674:V335I;ENSP00000337358:V365I;ENSP00000382745:V165I	ENSP00000155674:V335I	V	-	1	0	CECR5	15999090	1.000000	0.71417	0.179000	0.23059	0.050000	0.14768	4.411000	0.59781	0.511000	0.28236	-0.215000	0.12644	GTC		0.622	CECR5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316100.1	NM_017829	
SLC25A18	83733	broad.mit.edu	37	22	18070834	18070834	+	Missense_Mutation	SNP	C	C	T	rs374782328		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:18070834C>T	ENST00000327451.6	+	9	1257	c.719C>T	c.(718-720)aCg>aTg	p.T240M	SLC25A18_ENST00000399813.1_Missense_Mutation_p.T240M|AC004019.13_ENST00000443935.1_RNA	NM_031481.1	NP_113669.1	Q9H1K4	GHC2_HUMAN	solute carrier family 25 (glutamate carrier), member 18	240						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	symporter activity (GO:0015293)	p.T240M(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)	18				Lung(27;0.124)		GTCGCAGTGACGCCTCTAGAT	0.507													C|||	1	0.000199681	0.0	0.0	5008	,	,		20958	0.0		0.0	False		,,,				2504	0.001				p.T240M	Colon(118;1560 1625 18964 29606 50093)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C719T	22						.	C	MET/THR	0,4406		0,0,2203	137.0	106.0	117.0		719	3.8	0.2	22		117	1,8599	1.2+/-3.3	0,1,4299	no	missense	SLC25A18	NM_031481.1	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	240/316	18070834	1,13005	2203	4300	6503	16450834	SO:0001583	missense	83733	exon9			AY008285	CCDS13744.1	22q11.2	2013-05-22	2012-03-29		ENSG00000182902	ENSG00000182902		"""Solute carriers"""	10988	protein-coding gene	gene with protein product		609303	"""solute carrier family 25 (mitochondrial carrier), member 18"""			11381032, 11897791	Standard	NM_031481		Approved		uc002zmp.1	Q9H1K4	OTTHUMG00000150089	ENST00000327451.6:c.719C>T	22.37:g.18070834C>T	ENSP00000329033:p.Thr240Met	Somatic		Capture	Illumina HiSeq	Phase_I	16450834	NM_031481		Missense_Mutation	SNP	ENST00000327451.6	37	CCDS13744.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.143218	0.57044	0.0	1.16E-4	ENSG00000182902	ENST00000327451;ENST00000399813	T;T	0.79141	-1.24;-1.24	4.83	3.81	0.43845	Mitochondrial carrier domain (2);	0.163193	0.53938	D	0.000057	D	0.87565	0.6209	M	0.83852	2.665	0.50467	D	0.999873	D	0.89917	1.0	D	0.76575	0.988	D	0.88860	0.3325	10	0.87932	D	0	.	12.346	0.55122	0.0:0.9152:0.0:0.0848	.	240	Q9H1K4	GHC2_HUMAN	M	240	ENSP00000329033:T240M;ENSP00000382710:T240M	ENSP00000329033:T240M	T	+	2	0	SLC25A18	16450834	0.997000	0.39634	0.176000	0.23000	0.636000	0.38137	3.550000	0.53691	1.159000	0.42565	0.555000	0.69702	ACG		0.507	SLC25A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316214.3	NM_031481	
MICAL3	57553	broad.mit.edu	37	22	18347516	18347516	+	Intron	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:18347516G>A	ENST00000441493.2	-	19	2958				MICAL3_ENST00000414725.2_Intron|MICAL3_ENST00000585038.1_Silent_p.C1042C|MICAL3_ENST00000207726.7_Intron|MICAL3_ENST00000383094.3_Intron|MICAL3_ENST00000444520.1_Intron|MICAL3_ENST00000429452.1_Silent_p.C1042C|MICAL3_ENST00000400561.2_Intron	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3						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.C1042C(1)		large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_epithelial(15;0.198)		Lung(27;0.0427)		CAAGCAGCTGGCACATGAAAA	0.562																																					p.C1042C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3126T	22						.						41.0	43.0	42.0					22																	18347516		1568	3582	5150	16727516	SO:0001627	intron_variant	57553	exon23			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.2605+148C>T	22.37:g.18347516G>A		Somatic		Capture	Illumina HiSeq	Phase_I	16727516	NM_001136004	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	37	CCDS46659.1																																																																																				0.562	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
DGCR2	9993	broad.mit.edu	37	22	19052389	19052389	+	Missense_Mutation	SNP	G	G	A	rs138741169		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:19052389G>A	ENST00000263196.7	-	4	767	c.520C>T	c.(520-522)Cgg>Tgg	p.R174W	DGCR2_ENST00000473832.1_5'UTR|DGCR2_ENST00000537045.1_Missense_Mutation_p.R133W|DGCR2_ENST00000545799.1_Missense_Mutation_p.R171W	NM_001184781.1|NM_005137.2	NP_001171710.1|NP_005128.1	P98153	IDD_HUMAN	DiGeorge syndrome critical region gene 2	174	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell adhesion (GO:0007155)|cognition (GO:0050890)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.R174W(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)	18	Colorectal(54;0.0993)					CCAAAGCTCCGCTCGGGCTGG	0.622													G|||	1	0.000199681	0.0	0.0	5008	,	,		20083	0.001		0.0	False		,,,				2504	0.0				p.R130W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C388T	22						.	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	56.0	51.0	53.0		397,388,511,520	3.8	1.0	22	dbSNP_134	53	0,8600		0,0,4300	no	missense,missense,missense,missense	DGCR2	NM_001173533.1,NM_001173534.1,NM_001184781.1,NM_005137.2	101,101,101,101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	133/510,130/507,171/548,174/551	19052389	1,13005	2203	4300	6503	17432389	SO:0001583	missense	9993	exon3			D79985	CCDS33598.1, CCDS54496.1	22q11.21	2008-06-12			ENSG00000070413	ENSG00000070413			2845	protein-coding gene	gene with protein product	"""integral membrane protein DGCR2"""	600594				7655455, 8630060	Standard	NM_005137		Approved	KIAA0163, LAN, IDD, DGS-C, SEZ-12	uc002zoq.1	P98153	OTTHUMG00000150141	ENST00000263196.7:c.520C>T	22.37:g.19052389G>A	ENSP00000263196:p.Arg174Trp	Somatic		Capture	Illumina HiSeq	Phase_I	17432389	NM_001173534	A6NIB5|A8K6K5|B5TY34|B7Z935	Missense_Mutation	SNP	ENST00000263196.7	37	CCDS33598.1	.	.	.	.	.	.	.	.	.	.	G	19.10	3.762172	0.69763	2.27E-4	0.0	ENSG00000070413	ENST00000537045;ENST00000263196;ENST00000545799;ENST00000447928	T;D;D	0.97161	0.84;-4.27;-4.12	4.96	3.85	0.44370	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.330523	0.35555	N	0.003135	D	0.95674	0.8593	L	0.49350	1.555	0.36674	D	0.878674	D;D	0.65815	0.995;0.986	P;B	0.48795	0.59;0.386	D	0.96079	0.9052	10	0.45353	T	0.12	.	12.0328	0.53408	0.0:0.0:0.7024:0.2976	.	130;174	B7Z3T5;P98153	.;IDD_HUMAN	W	133;174;171;174	ENSP00000440062:R133W;ENSP00000263196:R174W;ENSP00000445069:R171W	ENSP00000263196:R174W	R	-	1	2	DGCR2	17432389	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	2.318000	0.43779	2.297000	0.77311	0.467000	0.42956	CGG		0.622	DGCR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316504.1	NM_005137	
C22orf29	79680	broad.mit.edu	37	22	19839750	19839750	+	Missense_Mutation	SNP	C	C	T	rs9618711		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:19839750C>T	ENST00000405640.1	-	2	703	c.35G>A	c.(34-36)cGc>cAc	p.R12H	GNB1L_ENST00000403325.1_Intron|GNB1L_ENST00000329517.6_Intron|C22orf29_ENST00000328554.4_Missense_Mutation_p.R12H|C22orf29_ENST00000407472.1_Missense_Mutation_p.R12H|C22orf29_ENST00000484072.1_Intron|GNB1L_ENST00000405009.1_Intron|GNB1L_ENST00000460402.1_Intron			Q7L3V2	BOP_HUMAN	chromosome 22 open reading frame 29	12					mitochondrial outer membrane permeabilization (GO:0097345)|regulation of mitochondrial membrane potential (GO:0051881)	mitochondrion (GO:0005739)		p.R12H(1)		NS(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	7	Colorectal(54;0.0993)					GATGGGAATGCGAGGGCCCTG	0.637																																					p.R12H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G35A	22						.	C	HIS/ARG,	0,4406		0,0,2203	56.0	56.0	56.0		35,	-2.1	0.0	22	dbSNP_119	56	1,8589		0,1,4294	no	missense,intron	GNB1L,C22orf29	NM_024627.5,NM_053004.2	29,	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,	12/365,	19839750	1,12995	2203	4295	6498	18219750	SO:0001583	missense	79680	exon3			BX640998	CCDS13769.1	22q11.21	2006-07-05			ENSG00000215012	ENSG00000215012			26112	protein-coding gene	gene with protein product						12477932	Standard	NM_024627		Approved	FLJ21125	uc002zqh.3	Q7L3V2	OTTHUMG00000030314	ENST00000405640.1:c.35G>A	22.37:g.19839750C>T	ENSP00000384924:p.Arg12His	Somatic		Capture	Illumina HiSeq	Phase_I	18219750	NM_024627	A8K5E7|D3DX21|Q6MZM8|Q6N000|Q9H7A0	Missense_Mutation	SNP	ENST00000405640.1	37	CCDS13769.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.920401	0.33908	0.0	1.16E-4	ENSG00000215012	ENST00000407472;ENST00000328554;ENST00000405640;ENST00000416337	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	3.69	-2.1	0.07210	.	.	.	.	.	T	0.12220	0.0297	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.23226	-1.0194	9	0.33940	T	0.23	-0.2253	3.3818	0.07257	0.1819:0.3924:0.0:0.4257	rs9618711	12	Q7L3V2	CV029_HUMAN	H	12	ENSP00000386111:R12H;ENSP00000330596:R12H;ENSP00000384924:R12H;ENSP00000392994:R12H	ENSP00000330596:R12H	R	-	2	0	C22orf29	18219750	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.577000	0.05847	-0.296000	0.08947	-0.136000	0.14681	CGC		0.637	C22orf29-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317290.2	NM_024627	
RIMBP3	85376	broad.mit.edu	37	22	20460135	20460135	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:20460135G>A	ENST00000426804.1	-	1	1651	c.1167C>T	c.(1165-1167)cgC>cgT	p.R389R		NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	389								p.R389R(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			TATAACAGCGGCGCGCCAGCA	0.652																																					p.R389R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1167T	22						.						16.0	15.0	15.0					22																	20460135		1104	1665	2769	18840135	SO:0001819	synonymous_variant	85376	exon1			AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.1167C>T	22.37:g.20460135G>A		Somatic		Capture	Illumina HiSeq	Phase_I	18840135	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	Silent	SNP	ENST00000426804.1	37	CCDS46665.1																																																																																				0.652	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672	
KLHL22	84861	broad.mit.edu	37	22	20800820	20800820	+	Silent	SNP	G	G	A	rs368031253		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:20800820G>A	ENST00000328879.4	-	6	1605	c.1449C>T	c.(1447-1449)cgC>cgT	p.R483R	KLHL22_ENST00000440659.2_Silent_p.R340R	NM_032775.3	NP_116164.2	Q53GT1	KLH22_HUMAN	kelch-like family member 22	483					cell division (GO:0051301)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein monoubiquitination (GO:0006513)	centrosome (GO:0005813)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|polar microtubule (GO:0005827)		p.R483R(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|skin(2)|upper_aerodigestive_tract(1)	20	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			CGTGCCAGGCGCGCCGCACAG	0.617																																					p.R483R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1449T	22						.	G		1,4405	2.1+/-5.4	0,1,2202	161.0	124.0	136.0		1449	-9.1	0.9	22		136	0,8600		0,0,4300	no	coding-synonymous	KLHL22	NM_032775.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		483/635	20800820	1,13005	2203	4300	6503	19130820	SO:0001819	synonymous_variant	84861	exon6				CCDS13780.1	22q11.21	2013-01-30	2013-01-30		ENSG00000099910	ENSG00000099910		"""Kelch-like"", ""BTB/POZ domain containing"""	25888	protein-coding gene	gene with protein product			"""kelch-like 22 (Drosophila)"""			12477932	Standard	NM_032775		Approved	FLJ14360, KELCHL	uc002zsl.2	Q53GT1	OTTHUMG00000150778	ENST00000328879.4:c.1449C>T	22.37:g.20800820G>A		Somatic		Capture	Illumina HiSeq	Phase_I	19130820	NM_032775	A8K3Q4|A8MTV3|B7Z2G1|D3DX30|Q96B68|Q96KC6	Silent	SNP	ENST00000328879.4	37	CCDS13780.1																																																																																				0.617	KLHL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320045.2	NM_032775	
LZTR1	8216	broad.mit.edu	37	22	21341837	21341837	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:21341837C>T	ENST00000215739.8	+	4	724	c.365C>T	c.(364-366)tCg>tTg	p.S122L	LZTR1_ENST00000389355.3_Missense_Mutation_p.S103L|LZTR1_ENST00000479606.1_3'UTR	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	122			S -> L (in SWNTS2). {ECO:0000269|PubMed:24362817}.		anatomical structure morphogenesis (GO:0009653)|regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S122L(1)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)	42	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			TACCACCACTCGGCCGTCGTC	0.657																																					p.S122L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C365T	22						.						73.0	65.0	68.0					22																	21341837		2203	4300	6503	19671837	SO:0001583	missense	8216	exon4			D38496	CCDS33606.1	22q11.21	2013-01-09	2004-12-10		ENSG00000099949	ENSG00000099949		"""BTB/POZ domain containing"""	6742	protein-coding gene	gene with protein product		600574	"""leucine-zipper-like transcriptional regulator 1"""			7633402, 16356934	Standard	NM_006767		Approved	LZTR-1, BTBD29	uc002zto.3	Q8N653	OTTHUMG00000150878	ENST00000215739.8:c.365C>T	22.37:g.21341837C>T	ENSP00000215739:p.Ser122Leu	Somatic		Capture	Illumina HiSeq	Phase_I	19671837	NM_006767	Q14776|Q20WK0	Missense_Mutation	SNP	ENST00000215739.8	37	CCDS33606.1	.	.	.	.	.	.	.	.	.	.	C	35	5.521966	0.96416	.	.	ENSG00000099949	ENST00000539817;ENST00000215739;ENST00000389355	T;T	0.68903	0.66;-0.36	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.84951	0.5586	M	0.90198	3.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.91635	0.999;0.998;0.986	D	0.87374	0.2352	10	0.66056	D	0.02	-16.3399	16.4657	0.84078	0.0:1.0:0.0:0.0	.	103;122;81	B7Z3T9;Q8N653;F5GXU8	.;LZTR1_HUMAN;.	L	81;122;103	ENSP00000215739:S122L;ENSP00000374006:S103L	ENSP00000215739:S122L	S	+	2	0	LZTR1	19671837	1.000000	0.71417	0.977000	0.42913	0.983000	0.72400	7.351000	0.79395	2.746000	0.94184	0.655000	0.94253	TCG		0.657	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767	
MMP11	4320	broad.mit.edu	37	22	24122685	24122685	+	Missense_Mutation	SNP	G	G	A	rs143231653		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:24122685G>A	ENST00000215743.3	+	3	530	c.478G>A	c.(478-480)Gcc>Acc	p.A160T	MMP11_ENST00000477567.1_3'UTR	NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	160					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.A160T(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)	GATCGACTTCGCCAGGTGAAT	0.642																																					p.A160T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G478A	22						.	G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	80.0	70.0	73.0		478	0.5	1.0	22	dbSNP_134	73	0,8600		0,0,4300	no	missense	MMP11	NM_005940.3	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	160/489	24122685	1,13005	2203	4300	6503	22452685	SO:0001583	missense	4320	exon3				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.478G>A	22.37:g.24122685G>A	ENSP00000215743:p.Ala160Thr	Somatic		Capture	Illumina HiSeq	Phase_I	22452685	NM_005940	Q5FX24|Q6PEZ6|Q9UC26	Missense_Mutation	SNP	ENST00000215743.3	37	CCDS13816.1	.	.	.	.	.	.	.	.	.	.	G	10.31	1.314165	0.23908	2.27E-4	0.0	ENSG00000099953	ENST00000215743	T	0.22336	1.96	5.08	0.5	0.16919	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.264701	0.44097	N	0.000482	T	0.11410	0.0278	N	0.25144	0.715	0.26385	N	0.976663	B	0.24533	0.105	B	0.10450	0.005	T	0.23297	-1.0192	10	0.28530	T	0.3	.	8.8913	0.35434	0.695:0.0:0.305:0.0	.	160	P24347	MMP11_HUMAN	T	160	ENSP00000215743:A160T	ENSP00000215743:A160T	A	+	1	0	MMP11	22452685	0.956000	0.32656	0.964000	0.40570	0.504000	0.33889	1.783000	0.38664	-0.068000	0.12953	-0.312000	0.09012	GCC		0.642	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940	
SLC2A11	66035	broad.mit.edu	37	22	24224966	24224966	+	Silent	SNP	C	C	T	rs371467287		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:24224966C>T	ENST00000345044.6	+	8	1162	c.894C>T	c.(892-894)tcC>tcT	p.S298S	SLC2A11_ENST00000316185.8_Silent_p.S301S|RN7SL268P_ENST00000491172.2_RNA|SLC2A11_ENST00000398356.2_Silent_p.S305S|AP000350.10_ENST00000433835.3_Intron|SLC2A11_ENST00000467660.1_3'UTR			Q9BYW1	GTR11_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 11	298					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)	p.S305S(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	12						ACGCCTCCTCCGTGTTCCGGA	0.652																																					p.S298S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C894T	22						.	T	,,	0,4406		0,0,2203	76.0	52.0	60.0		894,903,915	-8.2	0.0	22		60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC2A11	NM_001024938.2,NM_001024939.2,NM_030807.3	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	298/497,301/500,305/504	24224966	1,13005	2203	4300	6503	22554966	SO:0001819	synonymous_variant	66035	exon8			AJ271290	CCDS13818.1, CCDS33616.1, CCDS46673.1, CCDS74828.1	22q11.23	2013-05-22			ENSG00000133460	ENSG00000133460		"""Solute carriers"""	14239	protein-coding gene	gene with protein product		610367					Standard	NM_001024938		Approved	GLUT11, GLUT10	uc002zyp.4	Q9BYW1	OTTHUMG00000166469	ENST00000345044.6:c.894C>T	22.37:g.24224966C>T		Somatic		Capture	Illumina HiSeq	Phase_I	22554966	NM_001024938	E9PH55|Q542Y4|Q6ICJ5|Q8WXF9|Q8WYM4	Silent	SNP	ENST00000345044.6	37	CCDS46673.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	11.41|11.41	1.630528|1.630528	0.28978|0.28978	0.0|0.0	1.16E-4|1.16E-4	ENSG00000251357|ENSG00000251357	ENST00000502845|ENST00000421180	.|.	.|.	.|.	4.12|4.12	-8.23|-8.23	0.01033|0.01033	.|.	.|.	.|.	.|.	.|.	T|T	0.15739|0.15739	0.0379|0.0379	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999999|0.999999	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.19451|0.19451	-1.0305|-1.0305	4|4	.|.	.|.	.|.	.|.	2.368|2.368	0.04324|0.04324	0.0987:0.2423:0.2933:0.3658|0.0987:0.2423:0.2933:0.3658	.|.	.|.	.|.	.|.	L|C	70|162	.|.	.|.	P|R	+|+	2|1	0|0	AP000350.10|AP000350.10	22554966|22554966	0.000000|0.000000	0.05858|0.05858	0.011000|0.011000	0.14972|0.14972	0.001000|0.001000	0.01503|0.01503	-4.557000|-4.557000	0.00216|0.00216	-1.857000|-1.857000	0.01159|0.01159	-1.830000|-1.830000	0.00593|0.00593	CCG|CGT		0.652	SLC2A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319889.3	NM_030807	
SPECC1L	23384	broad.mit.edu	37	22	24726395	24726395	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:24726395C>T	ENST00000314328.9	+	8	2677	c.2392C>T	c.(2392-2394)Cgc>Tgc	p.R798C	SPECC1L_ENST00000541492.1_Missense_Mutation_p.R798C|SPECC1L_ENST00000437398.1_Missense_Mutation_p.R798C|SPECC1L-ADORA2A_ENST00000358654.2_Missense_Mutation_p.R798C	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	798					actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)		p.R798C(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						AATAAAGTCACGCAAGTAAGT	0.383																																					p.R798C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2392T	22						.						74.0	77.0	76.0					22																	24726395		2203	4300	6503	23056395	SO:0001583	missense	23384	exon7			AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"""cytokinesis and spindle organization A"", ""cytospin A"""	614140	"""SPECC1-like"""			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.2392C>T	22.37:g.24726395C>T	ENSP00000325785:p.Arg798Cys	Somatic		Capture	Illumina HiSeq	Phase_I	23056395	NM_001145468	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	37	CCDS33619.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.580927	0.86748	.	.	ENSG00000100014	ENST00000398280;ENST00000437398;ENST00000314328;ENST00000541492	T;T;T	0.43294	0.95;0.95;0.95	5.94	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.60612	0.2282	L	0.56769	1.78	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.949;0.99	T	0.56745	-0.7928	9	.	.	.	-17.1293	17.0133	0.86412	0.1356:0.8644:0.0:0.0	.	798;798	F5H1H6;Q69YQ0	.;CYTSA_HUMAN	C	826;798;798;798	ENSP00000393363:R798C;ENSP00000325785:R798C;ENSP00000439633:R798C	.	R	+	1	0	SPECC1L	23056395	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.531000	0.60602	2.816000	0.96949	0.561000	0.74099	CGC		0.383	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330	
SPECC1L	23384	broad.mit.edu	37	22	24808659	24808659	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:24808659G>A	ENST00000314328.9	+	16	3533	c.3248G>A	c.(3247-3249)gGc>gAc	p.G1083D	SPECC1L_ENST00000541492.1_Missense_Mutation_p.G1044D|SPECC1L_ENST00000437398.1_Missense_Mutation_p.G1083D|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	1083	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)		p.G1083D(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						GAAAGTGTCGGCATCAAATCC	0.507																																					p.G1083D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3248A	22						.						98.0	80.0	86.0					22																	24808659		2203	4300	6503	23138659	SO:0001583	missense	23384	exon15			AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"""cytokinesis and spindle organization A"", ""cytospin A"""	614140	"""SPECC1-like"""			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.3248G>A	22.37:g.24808659G>A	ENSP00000325785:p.Gly1083Asp	Somatic		Capture	Illumina HiSeq	Phase_I	23138659	NM_001145468	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	37	CCDS33619.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.982741	0.93044	.	.	ENSG00000100014	ENST00000437398;ENST00000314328;ENST00000541492	D;D;T	0.96491	-4.03;-4.03;-0.44	5.67	5.67	0.87782	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.98036	0.9353	M	0.78223	2.4	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.97994	1.0356	10	0.48119	T	0.1	-29.26	18.7488	0.91806	0.0:0.0:1.0:0.0	.	1044;1083	F5H1H6;Q69YQ0	.;CYTSA_HUMAN	D	1083;1083;1044	ENSP00000393363:G1083D;ENSP00000325785:G1083D;ENSP00000439633:G1044D	ENSP00000325785:G1083D	G	+	2	0	SPECC1L	23138659	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.523000	0.98034	2.686000	0.91538	0.561000	0.74099	GGC		0.507	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330	
ADORA2A	135	broad.mit.edu	37	22	24836712	24836712	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:24836712C>T	ENST00000337539.7	+	3	953	c.494C>T	c.(493-495)gCc>gTc	p.A165V	ADORA2A-AS1_ENST00000543438.1_RNA|ADORA2A_ENST00000496497.1_3'UTR|ADORA2A-AS1_ENST00000326341.4_RNA|ADORA2A-AS1_ENST00000427813.2_RNA|SPECC1L-ADORA2A_ENST00000358654.2_3'UTR	NM_000675.4|NM_001278497.1|NM_001278498.1|NM_001278499.1|NM_001278500.1	NP_000666.2|NP_001265426.1|NP_001265427.1|NP_001265428.1|NP_001265429.1	P29274	AA2AR_HUMAN	adenosine A2a receptor	165					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|apoptotic process (GO:0006915)|blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cAMP biosynthetic process (GO:0006171)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|central nervous system development (GO:0007417)|inflammatory response (GO:0006954)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phagocytosis (GO:0006909)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|sensory perception (GO:0007600)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|G-protein coupled adenosine receptor activity (GO:0001609)|identical protein binding (GO:0042802)	p.A165V(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(7)|skin(1)	21	Colorectal(2;0.196)				Adenosine(DB00640)|Caffeine(DB00201)|Defibrotide(DB04932)|Dyphylline(DB00651)|Enprofylline(DB00824)|Mefloquine(DB00358)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Regadenoson(DB06213)|Theobromine(DB01412)|Theophylline(DB00277)	GGCCAAGTGGCCTGTCTCTTT	0.567																																					p.A165V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C494T	22						.						209.0	197.0	201.0					22																	24836712		2203	4300	6503	23166712	SO:0001583	missense	135	exon3			X68486	CCDS13826.1	22q11.23	2012-08-08			ENSG00000128271	ENSG00000128271		"""GPCR / Class A : Adenosine receptors"""	263	protein-coding gene	gene with protein product		102776		ADORA2		1662665, 2541503	Standard	NM_001278497		Approved	RDC8	uc002zzy.4	P29274	OTTHUMG00000150761	ENST00000337539.7:c.494C>T	22.37:g.24836712C>T	ENSP00000336630:p.Ala165Val	Somatic		Capture	Illumina HiSeq	Phase_I	23166712	NM_000675	B2R7E0	Missense_Mutation	SNP	ENST00000337539.7	37	CCDS13826.1	.	.	.	.	.	.	.	.	.	.	C	11.83	1.754602	0.31046	.	.	ENSG00000128271	ENST00000444262;ENST00000541988;ENST00000337539;ENST00000417596	T;T	0.41065	1.01;1.01	4.68	3.58	0.41010	GPCR, rhodopsin-like superfamily (1);	0.425221	0.23770	N	0.044738	T	0.21841	0.0526	N	0.10707	0.03	0.27678	N	0.946548	B	0.18968	0.032	B	0.14578	0.011	T	0.10019	-1.0648	10	0.29301	T	0.29	-28.2742	11.2106	0.48795	0.3134:0.6866:0.0:0.0	.	165	P29274	AA2AR_HUMAN	V	165	ENSP00000414802:A165V;ENSP00000336630:A165V	ENSP00000336630:A165V	A	+	2	0	ADORA2A	23166712	0.746000	0.28272	1.000000	0.80357	0.791000	0.44710	0.894000	0.28350	2.303000	0.77524	0.462000	0.41574	GCC		0.567	ADORA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319971.2	NM_000675	
SGSM1	129049	broad.mit.edu	37	22	25282668	25282668	+	Silent	SNP	C	C	T	rs34478910		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:25282668C>T	ENST00000400359.4	+	17	1915	c.1908C>T	c.(1906-1908)ttC>ttT	p.F636F	SGSM1_ENST00000400358.4_Silent_p.F581F	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	636	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)	p.F581F(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						ACTACCAGTTCGGGATGACGG	0.592																																					p.F581F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1743T	22						.						24.0	23.0	24.0					22																	25282668		1959	4152	6111	23612668	SO:0001819	synonymous_variant	129049	exon16			AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.1908C>T	22.37:g.25282668C>T		Somatic		Capture	Illumina HiSeq	Phase_I	23612668	NM_001098497	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	37	CCDS46674.1																																																																																				0.592	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
TMEM211	255349	broad.mit.edu	37	22	25331335	25331335	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:25331335C>T	ENST00000423535.1	-	3	567	c.568G>A	c.(568-570)Gag>Aag	p.E190K	TMEM211_ENST00000407886.1_Missense_Mutation_p.E119K|TMEM211_ENST00000382744.1_Missense_Mutation_p.E119K			Q6ICI0	TM211_HUMAN	transmembrane protein 211	190						integral component of membrane (GO:0016021)		p.E119K(1)		endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						ATGATTCTCTCGGTGGCACTG	0.493																																					p.E119K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G355A	22						.						100.0	96.0	98.0					22																	25331335		2203	4300	6503	23661335	SO:0001583	missense	255349	exon3				CCDS33624.1	22q11.23	2009-01-12			ENSG00000206069	ENSG00000206069			33725	protein-coding gene	gene with protein product							Standard	NM_001001663		Approved	bA9F11.1	uc003abk.1	Q6ICI0	OTTHUMG00000150790	ENST00000423535.1:c.568G>A	22.37:g.25331335C>T	ENSP00000387813:p.Glu190Lys	Somatic		Capture	Illumina HiSeq	Phase_I	23661335	NM_001001663		Missense_Mutation	SNP	ENST00000423535.1	37		.	.	.	.	.	.	.	.	.	.	C	6.691	0.496040	0.12762	.	.	ENSG00000206069	ENST00000407886;ENST00000423535;ENST00000382744	T;T;T	0.78595	-1.19;-0.73;-1.19	4.26	1.91	0.25777	.	0.848961	0.10395	N	0.679906	T	0.65821	0.2728	L	0.54323	1.7	0.09310	N	1	P	0.43662	0.814	B	0.30943	0.122	T	0.57294	-0.7836	10	0.62326	D	0.03	-26.1723	6.0296	0.19673	0.0:0.6197:0.2701:0.1102	.	190	Q6ICI0	TM211_HUMAN	K	119;190;119	ENSP00000385494:E119K;ENSP00000387813:E190K;ENSP00000372192:E119K	ENSP00000372192:E119K	E	-	1	0	TMEM211	23661335	0.000000	0.05858	0.002000	0.10522	0.024000	0.10985	0.157000	0.16402	0.431000	0.26258	-0.463000	0.05309	GAG		0.493	TMEM211-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001663	
TFIP11	24144	broad.mit.edu	37	22	26906062	26906062	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:26906062C>T	ENST00000407690.1	-	4	460	c.177G>A	c.(175-177)tcG>tcA	p.S59S	TFIP11_ENST00000405938.1_Silent_p.S59S|CTA-445C9.14_ENST00000566814.1_RNA|CTA-445C9.14_ENST00000565764.1_RNA|TFIP11_ENST00000407431.1_Silent_p.S59S|TFIP11_ENST00000407148.1_Silent_p.S59S	NM_012143.2	NP_036275.1	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	59					biomineral tissue development (GO:0031214)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|spliceosomal complex disassembly (GO:0000390)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	DNA binding (GO:0003677)	p.S59S(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25						TCTCATCATCCGAGTCTCGCT	0.582																																					p.S59S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G177A	22						.						165.0	139.0	148.0					22																	26906062		2203	4300	6503	25236062	SO:0001819	synonymous_variant	24144	exon4			AL050258	CCDS13838.1	22q12.1	2013-01-28			ENSG00000100109	ENSG00000100109		"""G patch domain containing"""	17165	protein-coding gene	gene with protein product		612747				10806191, 11230166	Standard	NM_012143		Approved	TIP39, DKFZP434B194, Spp382	uc003acs.2	Q9UBB9	OTTHUMG00000150883	ENST00000407690.1:c.177G>A	22.37:g.26906062C>T		Somatic		Capture	Illumina HiSeq	Phase_I	25236062	NM_012143	O95908|Q20WL0|Q5H8V8|Q9UGV7|Q9Y2Q8	Silent	SNP	ENST00000407690.1	37	CCDS13838.1																																																																																				0.582	TFIP11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320750.1	NM_001008697	
TBC1D10A	83874	broad.mit.edu	37	22	30695501	30695501	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:30695501G>A	ENST00000215790.7	-	3	513	c.349C>T	c.(349-351)Cgg>Tgg	p.R117W	TBC1D10A_ENST00000403477.3_Missense_Mutation_p.R124W|TBC1D10A_ENST00000403362.1_Missense_Mutation_p.R29W|RP1-130H16.18_ENST00000447976.1_5'Flank|TBC1D10A_ENST00000490449.1_5'Flank	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	117	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				activation of cysteine-type endopeptidase activity (GO:0097202)|positive regulation of proteolysis (GO:0045862)|retrograde transport, endosome to Golgi (GO:0042147)	extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rab GTPase activator activity (GO:0005097)	p.R117W(2)		cervix(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						GCACGGCCCCGCAGAGAAGGC	0.582																																					p.R117W												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C349T	22						.						155.0	118.0	130.0					22																	30695501		2203	4300	6503	29025501	SO:0001583	missense	83874	exon3			AF331038	CCDS13874.1, CCDS56227.1	22q12.2	2013-07-09	2005-03-10	2005-03-10	ENSG00000099992	ENSG00000099992			23609	protein-coding gene	gene with protein product	"""EBP50-PDZ interactor of 64 kD"""	610020	"""TBC1 domain family, member 10"""	TBC1D10		11285285, 20404108	Standard	NM_001204240		Approved	EPI64, AC004997.C22.2	uc010gvu.3	Q9BXI6	OTTHUMG00000150924	ENST00000215790.7:c.349C>T	22.37:g.30695501G>A	ENSP00000215790:p.Arg117Trp	Somatic		Capture	Illumina HiSeq	Phase_I	29025501	NM_031937	B3KXT8|O76053|Q20WK7|Q543A2	Missense_Mutation	SNP	ENST00000215790.7	37	CCDS13874.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.062487	0.76187	.	.	ENSG00000099992	ENST00000215790;ENST00000403477;ENST00000403362;ENST00000393906	T;T;T;T	0.34667	1.35;1.35;1.35;1.35	5.06	1.59	0.23543	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.74696	0.3750	H	0.99435	4.565	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	0.83019	-0.0168	9	.	.	.	.	13.0035	0.58690	0.0:0.0:0.5783:0.4217	.	117;124;117	Q20WK7;B3KXT8;Q9BXI6	.;.;TB10A_HUMAN	W	117;124;29;29	ENSP00000215790:R117W;ENSP00000384996:R124W;ENSP00000385050:R29W;ENSP00000377484:R29W	.	R	-	1	2	TBC1D10A	29025501	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	1.703000	0.37846	0.196000	0.20367	0.561000	0.74099	CGG		0.582	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320550.1	NM_031937	
MTFP1	51537	broad.mit.edu	37	22	30823344	30823344	+	Missense_Mutation	SNP	G	G	A	rs112718421		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:30823344G>A	ENST00000266263.5	+	3	732	c.382G>A	c.(382-384)Gcg>Acg	p.A128T	MTFP1_ENST00000355143.4_Intron|MTFP1_ENST00000407550.3_Missense_Mutation_p.A105T|RP4-539M6.19_ENST00000439838.1_Missense_Mutation_p.A300T	NM_016498.4	NP_057582.2	Q9UDX5	MTFP1_HUMAN	mitochondrial fission process 1	128					apoptotic process (GO:0006915)|mitochondrial fission (GO:0000266)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.A128T(1)		endometrium(1)|large_intestine(1)|lung(2)	4						GACCACCACCGCGCTTGGGCT	0.597																																					p.A128T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G382A	22						.	G	,THR/ALA	0,4406		0,0,2203	144.0	122.0	129.0		,382	1.2	0.0	22	dbSNP_132	129	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	MTFP1	NM_001003704.2,NM_016498.4	,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	,128/167	30823344	1,13005	2203	4300	6503	29153344	SO:0001583	missense	51537	exon3			AF151076	CCDS33634.1, CCDS33635.1	22q	2010-09-02			ENSG00000242114	ENSG00000242114			26945	protein-coding gene	gene with protein product		610235				15155745, 15985469	Standard	NM_016498		Approved	MTP18, HSPC242		Q9UDX5	OTTHUMG00000151057	ENST00000266263.5:c.382G>A	22.37:g.30823344G>A	ENSP00000266263:p.Ala128Thr	Somatic		Capture	Illumina HiSeq	Phase_I	29153344	NM_016498	A6NFQ5|Q9H3K1|Q9P0N6	Missense_Mutation	SNP	ENST00000266263.5	37	CCDS33635.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.709710	0.30322	0.0	1.16E-4	ENSG00000249590;ENSG00000242114;ENSG00000242114	ENST00000439838;ENST00000266263;ENST00000407550	T	0.69926	-0.44	5.01	1.24	0.21308	.	0.210231	0.49916	N	0.000138	T	0.57169	0.2035	L	0.52905	1.665	0.80722	D	1	B	0.22800	0.075	B	0.29524	0.103	T	0.42515	-0.9447	10	0.21540	T	0.41	-0.1323	8.5816	0.33632	0.2928:0.0:0.7072:0.0	.	128	Q9UDX5	MTFP1_HUMAN	T	300;128;105	ENSP00000415178:A300T	ENSP00000266263:A128T	A	+	1	0	MTFP1;RP4-539M6.19	29153344	0.999000	0.42202	0.001000	0.08648	0.110000	0.19582	3.862000	0.56009	0.137000	0.18759	0.655000	0.94253	GCG		0.597	MTFP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321126.3	NM_016498	
SEC14L3	266629	broad.mit.edu	37	22	30857436	30857436	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:30857436G>A	ENST00000215812.4	-	11	1032	c.942C>T	c.(940-942)atC>atT	p.I314I	SEC14L3_ENST00000415957.2_Silent_p.I255I|SEC14L3_ENST00000540910.1_Silent_p.I237I|SEC14L3_ENST00000403066.1_Silent_p.I255I|SEC14L3_ENST00000539629.1_Silent_p.I255I|SEC14L3_ENST00000401751.1_Silent_p.I255I|SEC14L3_ENST00000402286.1_Silent_p.I237I	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	314	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)	p.I314I(1)		NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	CTCCGAAGCCGATGTCCGCAC	0.607																																					p.I314I	Esophageal Squamous(108;290 1516 3584 23771 37333)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C942T	22						.						58.0	53.0	55.0					22																	30857436		2203	4300	6503	29187436	SO:0001819	synonymous_variant	266629	exon11			AY158086	CCDS13877.1, CCDS58800.1, CCDS58801.1	22q12.2	2013-09-23			ENSG00000100012	ENSG00000100012			18655	protein-coding gene	gene with protein product		612824					Standard	NM_174975		Approved	TAP2	uc003ahy.3	Q9UDX4	OTTHUMG00000151259	ENST00000215812.4:c.942C>T	22.37:g.30857436G>A		Somatic		Capture	Illumina HiSeq	Phase_I	29187436	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Silent	SNP	ENST00000215812.4	37	CCDS13877.1																																																																																				0.607	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975	
PES1	23481	broad.mit.edu	37	22	30977518	30977518	+	Silent	SNP	C	C	T	rs147244950		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:30977518C>T	ENST00000405677.1	-	9	1270	c.327G>A	c.(325-327)ccG>ccA	p.P109P	PES1_ENST00000335214.6_Silent_p.P248P|PES1_ENST00000354694.7_Silent_p.P248P|PES1_ENST00000402284.3_Silent_p.P231P|PES1_ENST00000402281.1_Silent_p.P109P	NM_001282328.1	NP_001269257.1			pescadillo ribosomal biogenesis factor 1									p.P248P(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	29						GTCCTACCTTCGGGGGATAGT	0.617																																					p.P248P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G744A	22						.	C		0,4406		0,0,2203	55.0	47.0	50.0		744	0.4	1.0	22	dbSNP_134	50	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PES1	NM_014303.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		248/589	30977518	1,13005	2203	4300	6503	29307518	SO:0001819	synonymous_variant	23481	exon7			U78310	CCDS13880.1, CCDS58802.1, CCDS74842.1	22q12.1	2012-02-23	2012-02-23		ENSG00000100029	ENSG00000100029			8848	protein-coding gene	gene with protein product		605819	"""pescadillo (zebrafish) homolog 1, containing BRCT domain"", ""pescadillo homolog 1, containing BRCT domain (zebrafish)"""			8985183, 10591208, 17353269	Standard	NM_014303		Approved	PES	uc003aij.2	O00541	OTTHUMG00000151077	ENST00000405677.1:c.327G>A	22.37:g.30977518C>T		Somatic		Capture	Illumina HiSeq	Phase_I	29307518	NM_014303		Silent	SNP	ENST00000405677.1	37																																																																																					0.617	PES1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000321189.2	NM_014303	
TCN2	6948	broad.mit.edu	37	22	31019011	31019011	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:31019011C>T	ENST00000215838.3	+	8	1657	c.1163C>T	c.(1162-1164)gCg>gTg	p.A388V	TCN2_ENST00000407817.3_Missense_Mutation_p.A361V|TCN2_ENST00000405742.3_Missense_Mutation_p.A384V			P20062	TCO2_HUMAN	transcobalamin II	388					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)	p.A388V(2)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|prostate(2)|urinary_tract(1)	22					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATGGGGAAAGCGGCCGGAGAA	0.562																																					p.A361V												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.C1082T	22						.						93.0	88.0	89.0					22																	31019011		2203	4300	6503	29349011	SO:0001583	missense	6948	exon8				CCDS13881.1, CCDS54519.1	22q12.2	2014-09-17	2010-05-11		ENSG00000185339	ENSG00000185339			11653	protein-coding gene	gene with protein product	"""macrocytic anemia"""	613441	"""transcobalamin II; macrocytic anemia"""			1708393, 7742531	Standard	NM_000355		Approved	D22S676, D22S750, TC2	uc003aip.2	P20062	OTTHUMG00000151095	ENST00000215838.3:c.1163C>T	22.37:g.31019011C>T	ENSP00000215838:p.Ala388Val	Somatic		Capture	Illumina HiSeq	Phase_I	29349011	NM_001184726	Q96FD4|Q9BVI8|Q9UCI5|Q9UCI6|Q9UDM0	Missense_Mutation	SNP	ENST00000215838.3	37	CCDS13881.1	.	.	.	.	.	.	.	.	.	.	C	4.635	0.118091	0.08881	.	.	ENSG00000185339	ENST00000215838;ENST00000405742;ENST00000407817	T;T;T	0.32272	1.46;1.46;1.46	5.51	-5.5	0.02576	.	0.983847	0.08343	N	0.960541	T	0.18800	0.0451	L	0.43923	1.385	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.002	B;B;B	0.04013	0.001;0.0;0.0	T	0.26538	-1.0100	10	0.33940	T	0.23	0.1717	2.814	0.05451	0.582:0.1717:0.1378:0.1085	.	361;384;388	Q96FD4;B5MBX2;P20062	.;.;TCO2_HUMAN	V	388;384;361	ENSP00000215838:A388V;ENSP00000385914:A384V;ENSP00000384914:A361V	ENSP00000215838:A388V	A	+	2	0	TCN2	29349011	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.728000	0.04925	-1.253000	0.02488	-1.377000	0.01181	GCG		0.562	TCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321282.2	NM_000355	
DUSP18	150290	broad.mit.edu	37	22	31059695	31059695	+	Missense_Mutation	SNP	C	C	T	rs200346696		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:31059695C>T	ENST00000334679.3	-	2	801	c.296G>A	c.(295-297)cGt>cAt	p.R99H	DUSP18_ENST00000404885.1_Missense_Mutation_p.R99H|DUSP18_ENST00000403268.1_Silent_p.P62P|DUSP18_ENST00000461301.1_Intron|DUSP18_ENST00000407308.1_Missense_Mutation_p.R99H	NM_152511.3	NP_689724.3	Q8NEJ0	DUS18_HUMAN	dual specificity phosphatase 18	99	Tyrosine-protein phosphatase.				peptidyl-tyrosine dephosphorylation (GO:0035335)	cytoplasm (GO:0005737)|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.R99H(1)		large_intestine(1)|lung(1)|prostate(1)|skin(1)	4						CAGCAAAGTACGGCCCTGCTT	0.577																																					p.R99H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G296A	22						.	C	HIS/ARG	0,4406		0,0,2203	145.0	108.0	121.0		296	5.4	1.0	22		121	1,8599	1.2+/-3.3	0,1,4299	no	missense	DUSP18	NM_152511.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	99/189	31059695	1,13005	2203	4300	6503	29389695	SO:0001583	missense	150290	exon2			AF461689	CCDS13883.1	22q12.1	2011-06-09				ENSG00000167065		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	18484	protein-coding gene	gene with protein product		611446				12408986	Standard	NM_152511		Approved	DUSP20	uc003aiw.1	Q8NEJ0		ENST00000334679.3:c.296G>A	22.37:g.31059695C>T	ENSP00000333917:p.Arg99His	Somatic		Capture	Illumina HiSeq	Phase_I	29389695	NM_152511	B3KPA4	Missense_Mutation	SNP	ENST00000334679.3	37	CCDS13883.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.387570	0.61956	0.0	1.16E-4	ENSG00000167065	ENST00000404885;ENST00000407308;ENST00000334679;ENST00000342474	T;T;T;T	0.61392	0.11;0.11;0.11;0.11	5.43	5.43	0.79202	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.100766	0.64402	N	0.000001	T	0.55386	0.1917	M	0.71296	2.17	0.80722	D	1	P	0.45428	0.858	B	0.33339	0.162	T	0.63580	-0.6605	10	0.45353	T	0.12	.	18.8532	0.92241	0.0:1.0:0.0:0.0	.	99	Q8NEJ0	DUS18_HUMAN	H	99	ENSP00000385463:R99H;ENSP00000386063:R99H;ENSP00000333917:R99H;ENSP00000340795:R99H	ENSP00000333917:R99H	R	-	2	0	DUSP18	29389695	1.000000	0.71417	0.998000	0.56505	0.708000	0.40852	1.523000	0.35932	2.547000	0.85894	0.655000	0.94253	CGT		0.577	DUSP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321400.1		
DRG1	4733	broad.mit.edu	37	22	31816335	31816335	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:31816335G>A	ENST00000331457.4	+	5	667	c.506G>A	c.(505-507)gGc>gAc	p.G169D	DRG1_ENST00000433341.1_3'UTR	NM_004147.3	NP_004138.1	Q9Y295	DRG1_HUMAN	developmentally regulated GTP binding protein 1	169	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|polysome (GO:0005844)	GTP binding (GO:0005525)|identical protein binding (GO:0042802)|transcription factor binding (GO:0008134)	p.G169D(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	11						GAAGGCTTTGGCATTCGCTTG	0.453																																					p.G169D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G506A	22						.						79.0	73.0	75.0					22																	31816335		2203	4300	6503	30146335	SO:0001583	missense	4733	exon5			AJ005940	CCDS13897.1	22q12.2	2010-02-26	2001-11-28		ENSG00000185721	ENSG00000185721			3029	protein-coding gene	gene with protein product		603952	"""developmentally regulated GTP-binding protein 1"""	NEDD3		7929244, 1449490	Standard	NM_004147		Approved		uc003aku.3	Q9Y295	OTTHUMG00000030792	ENST00000331457.4:c.506G>A	22.37:g.31816335G>A	ENSP00000329715:p.Gly169Asp	Somatic		Capture	Illumina HiSeq	Phase_I	30146335	NM_004147	B2RDS8|Q6FGP8|Q8WW69|Q9UGF2	Missense_Mutation	SNP	ENST00000331457.4	37	CCDS13897.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.816184	0.90790	.	.	ENSG00000185721	ENST00000331457	T	0.51574	0.7	5.2	5.2	0.72013	Small GTP-binding protein domain (1);GTP-binding domain, HSR1-related (1);	0.000000	0.85682	D	0.000000	T	0.65923	0.2738	L	0.54908	1.71	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.68176	-0.5478	10	0.87932	D	0	0.2803	18.0876	0.89462	0.0:0.0:1.0:0.0	.	169	Q9Y295	DRG1_HUMAN	D	169	ENSP00000329715:G169D	ENSP00000329715:G169D	G	+	2	0	DRG1	30146335	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.143000	0.94623	2.576000	0.86940	0.655000	0.94253	GGC		0.453	DRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075680.5	NM_004147	
EIF4ENIF1	56478	broad.mit.edu	37	22	31859873	31859873	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:31859873C>T	ENST00000397525.1	-	5	602	c.379G>A	c.(379-381)Gtg>Atg	p.V127M	RP11-247I13.11_ENST00000464523.1_RNA|EIF4ENIF1_ENST00000344710.5_Intron|RP11-247I13.8_ENST00000439588.1_RNA|EIF4ENIF1_ENST00000330125.5_Missense_Mutation_p.V127M|RP11-247I13.11_ENST00000483736.1_RNA|EIF4ENIF1_ENST00000397523.1_Missense_Mutation_p.V127M	NM_001164501.1	NP_001157973.1	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E nuclear import factor 1	127						cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)	p.V127M(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						GCGGCTGTCACGTGGCAGCCC	0.547																																					p.V127M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G379A	22						.						84.0	79.0	81.0					22																	31859873		2203	4300	6503	30189873	SO:0001583	missense	56478	exon5			AF240775	CCDS13898.1, CCDS54520.1	22q11.2	2007-01-16			ENSG00000184708	ENSG00000184708			16687	protein-coding gene	gene with protein product		607445				10856257	Standard	NM_019843		Approved	4E-T, FLJ21601, Clast4, 2610509L04Rik	uc003akz.2	Q9NRA8	OTTHUMG00000030793	ENST00000397525.1:c.379G>A	22.37:g.31859873C>T	ENSP00000380659:p.Val127Met	Somatic		Capture	Illumina HiSeq	Phase_I	30189873	NM_019843	B1AKL2|B1AKL3|B2RBF1|Q8NCF2|Q9H708	Missense_Mutation	SNP	ENST00000397525.1	37	CCDS13898.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.933454	0.92458	.	.	ENSG00000184708	ENST00000397525;ENST00000330125;ENST00000397523;ENST00000420671;ENST00000423097	.	.	.	5.56	5.56	0.83823	.	0.205916	0.42964	D	0.000638	T	0.75642	0.3877	L	0.52126	1.63	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.74674	-0.3586	9	0.51188	T	0.08	-13.245	18.8921	0.92408	0.0:1.0:0.0:0.0	.	127	Q9NRA8	4ET_HUMAN	M	127	.	ENSP00000328103:V127M	V	-	1	0	EIF4ENIF1	30189873	1.000000	0.71417	0.836000	0.33094	0.989000	0.77384	7.174000	0.77620	2.792000	0.96026	0.557000	0.71058	GTG		0.547	EIF4ENIF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127926.1	NM_019843	
TOM1	10043	broad.mit.edu	37	22	35729417	35729417	+	Silent	SNP	G	G	A	rs141753674	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:35729417G>A	ENST00000449058.2	+	10	1079	c.954G>A	c.(952-954)ccG>ccA	p.P318P	TOM1_ENST00000382034.5_3'UTR|TOM1_ENST00000436462.2_Silent_p.P280P|TOM1_ENST00000411850.1_Silent_p.P318P|MIR3909_ENST00000579518.1_RNA|TOM1_ENST00000447733.1_Silent_p.P285P|TOM1_ENST00000425375.1_Silent_p.P273P	NM_005488.2	NP_005479.1	O60784	TOM1_HUMAN	target of myb1 (chicken)	318					endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	clathrin binding (GO:0030276)	p.P318P(1)		NS(1)|breast(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)	19						AGGCCGAGCCGGCAGCTGACC	0.622													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18869	0.0		0.0	False		,,,				2504	0.0				p.P273P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G819A	22						.	G	,,,	9,4397	15.5+/-35.6	0,9,2194	43.0	42.0	42.0		855,819,954,954	-7.2	0.0	22	dbSNP_134	42	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TOM1	NM_001135729.1,NM_001135730.1,NM_001135732.1,NM_005488.2	,,,	0,9,6494	AA,AG,GG		0.0,0.2043,0.0692	,,,	285/461,273/448,318/494,318/493	35729417	9,12997	2203	4300	6503	34059417	SO:0001819	synonymous_variant	10043	exon9			AJ006973	CCDS13913.1, CCDS46696.1, CCDS46697.1, CCDS46698.1	22q13.1	2011-01-31	2001-11-28		ENSG00000100284	ENSG00000100284			11982	protein-coding gene	gene with protein product		604700	"""target of myb1 (chicken) homolog"""			10329004, 15047686	Standard	NM_005488		Approved		uc003anp.3	O60784	OTTHUMG00000150958	ENST00000449058.2:c.954G>A	22.37:g.35729417G>A		Somatic		Capture	Illumina HiSeq	Phase_I	34059417	NM_001135730	B4DEL9|B4DNA1|Q5TIJ6|Q86X74	Silent	SNP	ENST00000449058.2	37	CCDS13913.1																																																																																				0.622	TOM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320641.1	NM_005488	
NOL12	79159	broad.mit.edu	37	22	38087248	38087248	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:38087248C>T	ENST00000359114.4	+	6	617	c.547C>T	c.(547-549)Cgg>Tgg	p.R183W	NOL12_ENST00000493862.1_3'UTR	NM_024313.2	NP_077289.1	Q9UGY1	NOL12_HUMAN	nucleolar protein 12	183						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|rRNA binding (GO:0019843)	p.R183W(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)	8	Melanoma(58;0.0574)					ACATCCCCGACGGGCCCAGGA	0.602																																					p.R183W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C547T	22						.						72.0	67.0	69.0					22																	38087248		2203	4300	6503	36417194	SO:0001583	missense	11078	exon6			Z83844	CCDS13955.1	22q13.1	2012-05-02			ENSG00000256872	ENSG00000273899			28585	protein-coding gene	gene with protein product						12477932	Standard	NM_024313		Approved	MGC3731, Nop25, RRP17	uc003atp.3	Q9UGY1	OTTHUMG00000150660	ENST00000359114.4:c.547C>T	22.37:g.38087248C>T	ENSP00000352021:p.Arg183Trp	Somatic		Capture	Illumina HiSeq	Phase_I	36417194	NM_024313		De_novo_Start_OutOfFrame	SNP	ENST00000359114.4	37	CCDS13955.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.703963	0.30232	.	.	ENSG00000256872	ENST00000359114	D	0.83914	-1.78	6.08	5.06	0.68205	.	0.159698	0.56097	D	0.000040	T	0.79902	0.4526	L	0.59436	1.845	0.09310	N	0.999999	P	0.49635	0.926	B	0.39660	0.306	T	0.74112	-0.3770	10	0.46703	T	0.11	-5.3093	14.9439	0.71014	0.1431:0.8569:0.0:0.0	.	183	Q9UGY1	NOL12_HUMAN	W	183	ENSP00000352021:R183W	ENSP00000352021:R183W	R	+	1	2	Z83844.2	36417194	0.001000	0.12720	0.003000	0.11579	0.002000	0.02628	1.037000	0.30241	1.583000	0.49898	-0.230000	0.12252	CGG		0.602	NOL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319476.1	NM_024313	
TRIOBP	11078	broad.mit.edu	37	22	38120343	38120343	+	Missense_Mutation	SNP	A	A	G	rs71317067		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:38120343A>G	ENST00000406386.3	+	7	2035	c.1780A>G	c.(1780-1782)Aca>Gca	p.T594A		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	594					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.T594A(5)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CAATAGAGCTACACGAGACAA	0.572																																					p.T594A												.	.	5	Substitution - Missense(5)	skin(2)|large_intestine(1)|NS(1)|prostate(1)	c.A1780G	22						.						112.0	164.0	147.0					22																	38120343		1955	4165	6120	36450289	SO:0001583	missense	11078	exon7			AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1780A>G	22.37:g.38120343A>G	ENSP00000384312:p.Thr594Ala	None		Capture	Illumina HiSeq	Phase_I	36450289	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	-	7.079	0.569772	0.13560	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.20738	2.05	2.6	0.164	0.14990	.	.	.	.	.	T	0.11879	0.0289	L	0.28115	0.83	0.09310	N	0.999998	B	0.21381	0.055	B	0.12837	0.008	T	0.32745	-0.9895	9	0.26408	T	0.33	.	5.3198	0.15876	0.5376:0.0:0.0:0.4624	.	594	Q9H2D6	TARA_HUMAN	A	594	ENSP00000384312:T594A	ENSP00000384312:T594A	T	+	1	0	TRIOBP	36450289	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.521000	0.06245	-0.162000	0.10964	-1.765000	0.00666	ACA		0.572	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
BAIAP2L2	80115	broad.mit.edu	37	22	38493103	38493103	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:38493103C>T	ENST00000381669.3	-	7	692	c.548G>A	c.(547-549)cGc>cAc	p.R183H	BAIAP2L2_ENST00000332536.5_Missense_Mutation_p.R183H	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	183	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)	p.R183H(1)		large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					GAAGCGATAGCGCCGCTTCTC	0.617																																					p.R183H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G548A	22						.						32.0	40.0	38.0					22																	38493103		2073	4213	6286	36823049	SO:0001583	missense	80115	exon7			BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.548G>A	22.37:g.38493103C>T	ENSP00000371085:p.Arg183His	Somatic		Capture	Illumina HiSeq	Phase_I	36823049	NM_025045	B0QYE2|Q96BG7	Missense_Mutation	SNP	ENST00000381669.3	37	CCDS43018.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.021009	0.93462	.	.	ENSG00000128298	ENST00000381669;ENST00000402500;ENST00000332536	.	.	.	4.78	4.78	0.61160	IRSp53/MIM homology domain (IMD) (3);	0.000000	0.85682	D	0.000000	D	0.83004	0.5160	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85925	0.1448	9	0.87932	D	0	-11.9055	18.1737	0.89754	0.0:1.0:0.0:0.0	.	183	Q6UXY1	BI2L2_HUMAN	H	183	.	ENSP00000328876:R183H	R	-	2	0	BAIAP2L2	36823049	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	6.266000	0.72540	2.368000	0.80403	0.462000	0.41574	CGC		0.617	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045	
SUN2	25777	broad.mit.edu	37	22	39146336	39146336	+	Intron	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:39146336C>T	ENST00000405510.1	-	6	783				SUN2_ENST00000216064.4_Intron|SUN2_ENST00000405018.1_Silent_p.S159S|SUN2_ENST00000406622.1_Intron|SUN2_ENST00000411587.2_Intron|RP3-508I15.14_ENST00000416406.1_RNA	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2						centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						CTGCGGGGAACGAGGACACTG	0.602																																					p.S159S												.	.	0			c.G477A	22						.						45.0	41.0	42.0					22																	39146336		2203	4300	6503	37476282	SO:0001627	intron_variant	25777	exon5			AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"""unc-84 homolog B (C. elegans)"""	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.425-11G>A	22.37:g.39146336C>T		Somatic		Capture	Illumina HiSeq	Phase_I	37476282	NM_001199579	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	Silent	SNP	ENST00000405510.1	37	CCDS13978.1																																																																																				0.602	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332	
APOBEC3A	200315	broad.mit.edu	37	22	39357585	39357585	+	Missense_Mutation	SNP	G	G	A	rs150243518	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:39357585G>A	ENST00000402255.1	+	4	572	c.368G>A	c.(367-369)cGt>cAt	p.R123H	APOBEC3A_ENST00000249116.2_Missense_Mutation_p.R123H			P31941	ABC3A_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A	123					cellular response to xenobiotic stimulus (GO:0071466)|clearance of foreign intracellular DNA by conversion of DNA cytidine to uridine (GO:0044356)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|zinc ion binding (GO:0008270)	p.R123H(1)		large_intestine(1)|lung(2)|ovary(1)|skin(1)	5	Melanoma(58;0.04)					GTGAGACTGCGTATCTTCGCT	0.567																																					p.R123H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G368A	22						.	G	HIS/ARG	10,4246		2,6,2120	100.0	99.0	99.0		368	-5.0	0.0	22	dbSNP_134	99	4,8146		0,4,4071	no	missense	APOBEC3A	NM_145699.3	29	2,10,6191	AA,AG,GG		0.0491,0.235,0.1128		123/200	39357585	14,12392	2128	4075	6203	37687531	SO:0001583	missense	200315	exon3			U03891	CCDS13981.1	22q13.1-q13.2	2014-01-28			ENSG00000128383	ENSG00000128383		"""Apolipoprotein B mRNA editing enzymes"""	17343	protein-coding gene	gene with protein product	"""phorbolin I"""	607109				11863358, 10469298	Standard	NM_145699		Approved	ARP3, PHRBN		P31941	OTTHUMG00000151004	ENST00000402255.1:c.368G>A	22.37:g.39357585G>A	ENSP00000384359:p.Arg123His	Somatic		Capture	Illumina HiSeq	Phase_I	37687531	NM_145699	A0AVM1|Q12807|Q5JZ93|Q9UH18	Missense_Mutation	SNP	ENST00000402255.1	37	CCDS13981.1	.	.	.	.	.	.	.	.	.	.	.	3.686	-0.064611	0.07273	0.00235	4.91E-4	ENSG00000128383	ENST00000402255;ENST00000249116	T;T	0.65732	-0.17;-0.17	2.5	-4.99	0.03010	APOBEC-like, N-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.45955	0.1368	L	0.29908	0.895	0.09310	N	1	B;B	0.11235	0.003;0.004	B;B	0.11329	0.006;0.005	T	0.17319	-1.0373	9	0.38643	T	0.18	.	11.5223	0.50558	0.1583:0.1331:0.7086:0.0	.	105;123	B7ZLZ1;P31941	.;ABC3A_HUMAN	H	123	ENSP00000384359:R123H;ENSP00000249116:R123H	ENSP00000249116:R123H	R	+	2	0	APOBEC3A	37687531	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.387000	0.07361	-2.196000	0.00751	-2.593000	0.00164	CGT		0.567	APOBEC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320915.2	NM_145699	
TAB1	10454	broad.mit.edu	37	22	39811628	39811628	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:39811628C>T	ENST00000216160.6	+	3	356	c.294C>T	c.(292-294)gcC>gcT	p.A98A	TAB1_ENST00000331454.3_Silent_p.A98A	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	98	PP2C-like.				activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart morphogenesis (GO:0003007)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lung development (GO:0030324)|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)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|protein complex (GO:0043234)	catalytic activity (GO:0003824)|enzyme activator activity (GO:0008047)|kinase activator activity (GO:0019209)	p.A98A(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						CCGAGCACGCCGAGGCCGATG	0.652																																					p.A98A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C294T	22						.						50.0	45.0	47.0					22																	39811628		2203	4300	6503	38141574	SO:0001819	synonymous_variant	10454	exon3			U49928	CCDS13992.1, CCDS13993.1	22q13.1	2010-02-05	2010-02-05	2010-02-05	ENSG00000100324	ENSG00000100324			18157	protein-coding gene	gene with protein product	"""TAK1-binding protein 1"", ""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	602615	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	MAP3K7IP1		8638164, 10187861	Standard	NM_153497		Approved		uc003axt.3	Q15750	OTTHUMG00000151102	ENST00000216160.6:c.294C>T	22.37:g.39811628C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38141574	NM_153497	Q2PP09|Q8IZW2	Silent	SNP	ENST00000216160.6	37	CCDS13993.1	.	.	.	.	.	.	.	.	.	.	c	1.841	-0.467325	0.04476	.	.	ENSG00000100324	ENST00000462277;ENST00000480990	.	.	.	5.23	-10.5	0.00291	.	.	.	.	.	T	0.32585	0.0834	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69191	-0.5210	4	.	.	.	-13.5482	0.7505	0.00989	0.2535:0.1537:0.192:0.4008	.	.	.	.	L	26	.	.	P	+	2	0	TAB1	38141574	0.000000	0.05858	0.001000	0.08648	0.244000	0.25665	-5.429000	0.00123	-7.278000	0.00001	-1.088000	0.02184	CCG		0.652	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497	
CACNA1I	8911	broad.mit.edu	37	22	40075174	40075174	+	Silent	SNP	G	G	A	rs367902739		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:40075174G>A	ENST00000402142.3	+	32	5118	c.5118G>A	c.(5116-5118)tcG>tcA	p.S1706S	CACNA1I_ENST00000400164.3_Silent_p.S1671S|CACNA1I_ENST00000404898.1_Silent_p.S1671S|CACNA1I_ENST00000336649.4_Silent_p.S1712S|CACNA1I_ENST00000407673.1_Silent_p.S1671S|CACNA1I_ENST00000401624.1_Silent_p.S1706S	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	1706					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.S1671S(2)|p.S1706S(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	AGTTTGTGTCGCCGCTGTACT	0.632																																					p.S1706S												.	.	3	Substitution - coding silent(3)	endometrium(2)|large_intestine(1)	c.G5118A	22						.	G	,	1,4361		0,1,2180	21.0	24.0	23.0		5013,5118	0.1	1.0	22		23	0,8546		0,0,4273	no	coding-synonymous,coding-synonymous	CACNA1I	NM_001003406.1,NM_021096.3	,	0,1,6453	AA,AG,GG		0.0,0.0229,0.0077	,	1671/2189,1706/2224	40075174	1,12907	2181	4273	6454	38405120	SO:0001819	synonymous_variant	8911	exon32			AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.5118G>A	22.37:g.40075174G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38405120	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Silent	SNP	ENST00000402142.3	37	CCDS46710.1																																																																																				0.632	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	
EP300	2033	broad.mit.edu	37	22	41572357	41572357	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:41572357C>T	ENST00000263253.7	+	30	6105	c.4886C>T	c.(4885-4887)gCg>gTg	p.A1629V	RP1-85F18.5_ENST00000420537.1_RNA|RP1-85F18.6_ENST00000415054.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1629	Binding region for E1A adenovirus.|CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.				apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)	p.A1629V(2)		NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						GGTCGGGATGCGTTTCTCACG	0.582			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome																												p.A1629V			Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C4886T	22						.						119.0	100.0	106.0					22																	41572357		2203	4300	6503	39902303	SO:0001583	missense	2033	exon30	Familial Cancer Database	Broad Thumb-Hallux syndrome	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.4886C>T	22.37:g.41572357C>T	ENSP00000263253:p.Ala1629Val	Somatic		Capture	Illumina HiSeq	Phase_I	39902303	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.602581	0.66445	.	.	ENSG00000100393	ENST00000263253	D	0.86366	-2.11	5.03	5.03	0.67393	.	0.000000	0.48286	D	0.000193	D	0.94801	0.8321	M	0.90252	3.1	0.58432	D	0.999999	D	0.89917	1.0	D	0.78314	0.991	D	0.95684	0.8734	10	0.87932	D	0	-8.2919	18.7274	0.91718	0.0:1.0:0.0:0.0	.	1629	Q09472	EP300_HUMAN	V	1629	ENSP00000263253:A1629V	ENSP00000263253:A1629V	A	+	2	0	EP300	39902303	1.000000	0.71417	0.990000	0.47175	0.701000	0.40568	7.818000	0.86416	2.500000	0.84329	0.650000	0.86243	GCG		0.582	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
SEPT3	55964	broad.mit.edu	37	22	42383628	42383628	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:42383628G>T	ENST00000396426.3	+	5	671	c.416G>T	c.(415-417)tGg>tTg	p.W139L	SEPT3_ENST00000406029.1_Missense_Mutation_p.W75L|SEPT3_ENST00000291236.11_Missense_Mutation_p.W75L|SEPT3_ENST00000328414.8_Missense_Mutation_p.G69W|SEPT3_ENST00000396425.3_Missense_Mutation_p.W139L	NM_145733.2	NP_663786.2	Q9UH03	SEPT3_HUMAN	septin 3	139	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cell junction (GO:0030054)|septin complex (GO:0031105)|synapse (GO:0045202)	GTP binding (GO:0005525)	p.W139L(3)		breast(1)|kidney(3)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	17						CCCATCAGCTGGGAGCCCATT	0.488																																					p.W139L												.	.	3	Substitution - Missense(3)	lung(2)|large_intestine(1)	c.G416T	22						.						140.0	111.0	121.0					22																	42383628		2203	4300	6503	40713574	SO:0001583	missense	55964	exon5			AF285107	CCDS14026.2, CCDS14027.2	22q13.2	2013-01-21			ENSG00000100167	ENSG00000100167		"""Septins"""	10750	protein-coding gene	gene with protein product		608314		SEP3			Standard	NM_019106		Approved		uc003bbr.4	Q9UH03	OTTHUMG00000030494	ENST00000396426.3:c.416G>T	22.37:g.42383628G>T	ENSP00000379704:p.Trp139Leu	Somatic		Capture	Illumina HiSeq	Phase_I	40713574	NM_145733	B1AHR0|Q2NKJ7|Q59GF7|Q6IBZ6|Q8N3P3|Q9HD35	Missense_Mutation	SNP	ENST00000396426.3	37	CCDS14026.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.140205|5.140205	0.94560|0.94560	.|.	.|.	ENSG00000100167|ENSG00000100167	ENST00000328414|ENST00000449288;ENST00000396426;ENST00000406029;ENST00000396425;ENST00000291236	.|T;T;T;T;T	.|0.58797	.|0.31;0.31;0.31;0.31;0.31	5.13|5.13	5.13|5.13	0.70059|0.70059	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.79167|0.79167	0.4400|0.4400	M|M	0.83384|0.83384	2.64|2.64	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|0.997;1.0;0.996;0.997	.|D;D;D;D	.|0.97110	.|0.992;1.0;0.986;0.995	T|T	0.82368|0.82368	-0.0492|-0.0492	6|10	0.87932|0.87932	D|D	0|0	.|.	18.9591|18.9591	0.92671|0.92671	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|75;75;139;139	.|B7Z686;B1AHR1;Q9UH03-2;Q9UH03	.|.;.;.;SEPT3_HUMAN	W|L	69|126;139;75;139;75	.|ENSP00000391416:W126L;ENSP00000379704:W139L;ENSP00000383956:W75L;ENSP00000379703:W139L;ENSP00000291236:W75L	ENSP00000332866:G69W|ENSP00000291236:W75L	G|W	+|+	1|2	0|0	SEPT3|SEPT3	40713574|40713574	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.959000|0.959000	0.62525|0.62525	9.770000|9.770000	0.98971|0.98971	2.555000|2.555000	0.86185|0.86185	0.514000|0.514000	0.50259|0.50259	GGG|TGG		0.488	SEPT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322051.1	NM_145734	
FAM109B	150368	broad.mit.edu	37	22	42474012	42474012	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:42474012C>T	ENST00000321753.3	+	3	902	c.715C>T	c.(715-717)Cgg>Tgg	p.R239W	SMDT1_ENST00000331479.3_5'Flank|snoU13_ENST00000458891.1_RNA	NM_001002034.2	NP_001002034.2	Q6ICB4	SESQ2_HUMAN	family with sequence similarity 109, member B	239					endosome organization (GO:0007032)|receptor recycling (GO:0001881)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	protein homodimerization activity (GO:0042803)	p.R239W(1)		endometrium(2)|large_intestine(2)|liver(2)|lung(1)|prostate(1)	8						CGTGGAGCTGCGGCAGTGTTG	0.602																																					p.R239W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C715T	22						.						15.0	16.0	16.0					22																	42474012		2198	4297	6495	40803958	SO:0001583	missense	150368	exon3			BX648402	CCDS33655.1	22q13.2	2013-01-10			ENSG00000177096	ENSG00000177096		"""Pleckstrin homology (PH) domain containing"""	27161	protein-coding gene	gene with protein product		614240				12477932	Standard	NM_001002034		Approved	DKFZp686J07229	uc003bbz.3	Q6ICB4	OTTHUMG00000151285	ENST00000321753.3:c.715C>T	22.37:g.42474012C>T	ENSP00000312753:p.Arg239Trp	Somatic		Capture	Illumina HiSeq	Phase_I	40803958	NM_001002034	Q3SXQ3|Q8N6L9	Missense_Mutation	SNP	ENST00000321753.3	37	CCDS33655.1	.	.	.	.	.	.	.	.	.	.	C	12.95	2.090818	0.36855	.	.	ENSG00000177096	ENST00000321753	T	0.61158	0.13	5.13	-0.739	0.11120	.	0.000000	0.85682	D	0.000000	T	0.65647	0.2711	L	0.43152	1.355	0.37963	D	0.933025	D	0.89917	1.0	D	0.66351	0.943	T	0.71988	-0.4426	10	0.87932	D	0	-19.038	16.736	0.85447	0.3855:0.6145:0.0:0.0	.	239	Q6ICB4	SESQ2_HUMAN	W	239	ENSP00000312753:R239W	ENSP00000312753:R239W	R	+	1	2	FAM109B	40803958	1.000000	0.71417	0.995000	0.50966	0.004000	0.04260	1.780000	0.38634	-0.052000	0.13311	0.491000	0.48974	CGG		0.602	FAM109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322084.1	NM_001002034	
CYP2D6	1565	broad.mit.edu	37	22	42524349	42524349	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:42524349G>A	ENST00000360608.5	-	5	784	c.670C>T	c.(670-672)Ctg>Ttg	p.L224L	NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|CYP2D6_ENST00000389970.3_Silent_p.L224L|CYP2D6_ENST00000359033.4_Silent_p.L173L	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	224					alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)	p.L173L(1)		NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	ACAGCATTCAGCACCTACACC	0.592																																					p.L224L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C670T	22						.						58.0	52.0	54.0					22																	42524349		2198	4299	6497	40854293	SO:0001819	synonymous_variant	1565	exon5			M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.670C>T	22.37:g.42524349G>A		Somatic		Capture	Illumina HiSeq	Phase_I	40854293	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Silent	SNP	ENST00000360608.5	37	CCDS46721.1																																																																																				0.592	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
TCF20	6942	broad.mit.edu	37	22	42610028	42610028	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:42610028A>G	ENST00000359486.3	-	1	1420	c.1284T>C	c.(1282-1284)ccT>ccC	p.P428P	TCF20_ENST00000335626.4_Silent_p.P428P	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	428					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.P428P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						CATGAGAATTAGGACTGGGCA	0.483																																					p.P428P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1284C	22						.						128.0	127.0	127.0					22																	42610028		2203	4300	6503	40939972	SO:0001819	synonymous_variant	6942	exon1			U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"""stromelysin-1 platelet-derived growth factor-responsive element binding protein"""	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.1284T>C	22.37:g.42610028A>G		Somatic		Capture	Illumina HiSeq	Phase_I	40939972	NM_005650	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Silent	SNP	ENST00000359486.3	37	CCDS14033.1																																																																																				0.483	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492	
TTLL12	23170	broad.mit.edu	37	22	43579147	43579147	+	Silent	SNP	G	G	A	rs146360108		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:43579147G>A	ENST00000216129.6	-	2	249	c.186C>T	c.(184-186)gaC>gaT	p.D62D		NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	62					cellular protein modification process (GO:0006464)			p.D62D(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	13		Ovarian(80;0.221)|Glioma(61;0.222)				CTTCCCCAGCGTCGAAAACCT	0.642																																					p.D62D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C186T	22						.						114.0	118.0	116.0					22																	43579147		2203	4300	6503	41909091	SO:0001819	synonymous_variant	23170	exon2			D63487	CCDS14047.1	22q13.31	2013-02-14	2006-02-02		ENSG00000100304	ENSG00000100304		"""Tubulin tyrosine ligase-like family"""	28974	protein-coding gene	gene with protein product						15890843	Standard	NM_015140		Approved	KIAA0153	uc003bdp.3	Q14166	OTTHUMG00000150682	ENST00000216129.6:c.186C>T	22.37:g.43579147G>A		Somatic		Capture	Illumina HiSeq	Phase_I	41909091	NM_015140	Q20WK5|Q9UGU3	Silent	SNP	ENST00000216129.6	37	CCDS14047.1																																																																																				0.642	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140	
SCUBE1	80274	broad.mit.edu	37	22	43716038	43716038	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:43716038C>A	ENST00000360835.4	-	3	380	c.254G>T	c.(253-255)gGg>gTg	p.G85V	SCUBE1_ENST00000290460.7_Missense_Mutation_p.G85V	NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	85	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)	p.G85V(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				GACACAGCCCCCATTGTAGTA	0.542																																					p.G85V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G254T	22						.						204.0	158.0	174.0					22																	43716038		2203	4300	6503	42045982	SO:0001583	missense	80274	exon3				CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.254G>T	22.37:g.43716038C>A	ENSP00000354080:p.Gly85Val	Somatic		Capture	Illumina HiSeq	Phase_I	42045982	NM_173050	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	37	CCDS14048.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.742805	0.89573	.	.	ENSG00000159307	ENST00000360835;ENST00000434132;ENST00000290460	D;D	0.98455	-2.15;-4.94	5.2	5.2	0.72013	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.98789	0.9592	M	0.82056	2.57	0.80722	D	1	D;D	0.63046	0.992;0.963	P;P	0.61477	0.889;0.887	D	0.99797	1.1034	10	0.87932	D	0	.	18.9277	0.92552	0.0:1.0:0.0:0.0	.	85;85	B1AH90;Q8IWY4	.;SCUB1_HUMAN	V	85	ENSP00000354080:G85V;ENSP00000290460:G85V	ENSP00000290460:G85V	G	-	2	0	SCUBE1	42045982	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.733000	0.68571	2.702000	0.92279	0.462000	0.41574	GGG		0.542	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	
SAMM50	25813	broad.mit.edu	37	22	44386266	44386266	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:44386266G>T	ENST00000350028.4	+	14	1501	c.1344G>T	c.(1342-1344)atG>atT	p.M448I	SAMM50_ENST00000396202.3_Missense_Mutation_p.M238I	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	448					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrial sorting and assembly machinery complex (GO:0001401)|mitochondrion (GO:0005739)		p.M448I(1)		endometrium(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				GCGTCCCCATGGGAGTACAGA	0.488																																					p.M448I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1344T	22						.						142.0	106.0	119.0					22																	44386266		2203	4300	6503	42717599	SO:0001583	missense	25813	exon14			AK001087	CCDS14055.1	22q13.31	2013-08-21	2013-08-21	2005-11-20	ENSG00000100347	ENSG00000100347			24276	protein-coding gene	gene with protein product		612058	"""sorting and assembly machinery component 50 homolog (S. cerevisiae)"""			15644312	Standard	NM_015380		Approved	CGI-51, TRG-3, YNL026W, OMP85, TOB55	uc003bej.3	Q9Y512	OTTHUMG00000150557	ENST00000350028.4:c.1344G>T	22.37:g.44386266G>T	ENSP00000345445:p.Met448Ile	Somatic		Capture	Illumina HiSeq	Phase_I	42717599	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Missense_Mutation	SNP	ENST00000350028.4	37	CCDS14055.1	.	.	.	.	.	.	.	.	.	.	G	14.38	2.519586	0.44866	.	.	ENSG00000100347	ENST00000350028;ENST00000396202	T;T	0.37058	1.22;1.22	4.87	4.87	0.63330	Bacterial surface antigen (D15) (1);	0.000000	0.85682	D	0.000000	T	0.25901	0.0631	N	0.20685	0.6	0.80722	D	1	B;B	0.30146	0.137;0.27	B;B	0.28465	0.055;0.09	T	0.05209	-1.0899	10	0.25106	T	0.35	-36.4939	17.3474	0.87313	0.0:0.0:1.0:0.0	.	253;448	B3KUE6;Q9Y512	.;SAM50_HUMAN	I	448;238	ENSP00000345445:M448I;ENSP00000379505:M238I	ENSP00000345445:M448I	M	+	3	0	SAMM50	42717599	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	9.015000	0.93640	2.407000	0.81776	0.650000	0.86243	ATG		0.488	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380	
PARVB	29780	broad.mit.edu	37	22	44559756	44559756	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:44559756G>A	ENST00000338758.7	+	12	1027	c.964G>A	c.(964-966)Gcc>Acc	p.A322T	PARVB_ENST00000404989.1_Missense_Mutation_p.A285T|PARVB_ENST00000406477.3_Missense_Mutation_p.A355T	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	322	CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)		p.A355T(1)		NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				TGTGTCCTTCGCCTTTGAGCT	0.627																																					p.A355T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1063A	22						.						130.0	94.0	107.0					22																	44559756		2203	4300	6503	42891089	SO:0001583	missense	29780	exon13			AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"""Parvins"""	14653	protein-coding gene	gene with protein product	"""affixin"""	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.964G>A	22.37:g.44559756G>A	ENSP00000342492:p.Ala322Thr	Somatic		Capture	Illumina HiSeq	Phase_I	42891089	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Missense_Mutation	SNP	ENST00000338758.7	37	CCDS14056.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.176810	0.78564	.	.	ENSG00000188677	ENST00000406477;ENST00000338758;ENST00000404989	T;T;T	0.71579	-0.58;-0.58;-0.58	5.42	4.41	0.53225	Calponin homology domain (5);	0.050704	0.85682	D	0.000000	D	0.84325	0.5447	M	0.91090	3.175	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	P;D;D;D	0.71870	0.899;0.959;0.975;0.971	D	0.85234	0.1034	10	0.87932	D	0	-0.2485	6.9974	0.24791	0.0882:0.0:0.7402:0.1716	.	322;285;322;355	A6NG58;B0QYM8;Q9HBI1;Q9HBI1-2	.;.;PARVB_HUMAN;.	T	355;322;285	ENSP00000384515:A355T;ENSP00000342492:A322T;ENSP00000384353:A285T	ENSP00000342492:A322T	A	+	1	0	PARVB	42891089	1.000000	0.71417	0.892000	0.35008	0.965000	0.64279	3.890000	0.56220	1.290000	0.44636	0.491000	0.48974	GCC		0.627	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828	
FAM118A	55007	broad.mit.edu	37	22	45723845	45723845	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:45723845C>T	ENST00000216214.3	+	5	1257	c.423C>T	c.(421-423)ggC>ggT	p.G141G	FAM118A_ENST00000441876.2_Silent_p.G141G|FAM118A_ENST00000405673.1_Silent_p.G141G|FAM118A_ENST00000405548.3_5'Flank	NM_001104595.1	NP_001098065.1	Q9NWS6	F118A_HUMAN	family with sequence similarity 118, member A	141						integral component of membrane (GO:0016021)		p.G141G(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TGGACAGGGGCGCCATGGTCC	0.597																																					p.G141G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C423T	22						.						58.0	48.0	51.0					22																	45723845		2203	4300	6503	44102509	SO:0001819	synonymous_variant	55007	exon5			BC013696	CCDS14065.1	22q13.3	2006-04-26	2006-04-26	2006-04-26	ENSG00000100376	ENSG00000100376			1313	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 8"""	C22orf8		12477932	Standard	NM_001104595		Approved	FLJ20635, bK268H5.C22.4	uc003bga.4	Q9NWS6	OTTHUMG00000151338	ENST00000216214.3:c.423C>T	22.37:g.45723845C>T		Somatic		Capture	Illumina HiSeq	Phase_I	44102509	NM_001104595	B3KWG4|B4DY02|Q5TII5|Q96CY3	Silent	SNP	ENST00000216214.3	37	CCDS14065.1																																																																																				0.597	FAM118A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322260.1	NM_017911	
TTC38	55020	broad.mit.edu	37	22	46669805	46669805	+	Silent	SNP	C	C	T	rs371686823		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:46669805C>T	ENST00000381031.3	+	4	280	c.204C>T	c.(202-204)caC>caT	p.H68H	TTC38_ENST00000445282.2_Silent_p.H68H	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	68						extracellular vesicular exosome (GO:0070062)		p.H68H(1)		endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						TGATGGGCCACGCCATGGCTA	0.567																																					p.H68H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C204T	22						.						49.0	51.0	50.0					22																	46669805		2078	4215	6293	45048469	SO:0001819	synonymous_variant	55020	exon4				CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"""Tetratricopeptide (TTC) repeat domain containing"""	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.204C>T	22.37:g.46669805C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45048469	NM_017931	Q8WV27|Q9NWP8	Silent	SNP	ENST00000381031.3	37	CCDS43030.1																																																																																				0.567	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931	
CELSR1	9620	broad.mit.edu	37	22	46787147	46787147	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:46787147G>A	ENST00000262738.3	-	16	6185	c.6186C>T	c.(6184-6186)ggC>ggT	p.G2062G		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2062					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)	p.G2062G(1)		breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GCCACCAGATGCCGGCCTCAA	0.612											OREG0026656	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G2062G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C6186T	22						.						53.0	51.0	52.0					22																	46787147		2203	4300	6503	45165811	SO:0001819	synonymous_variant	9620	exon16			AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.6186C>T	22.37:g.46787147G>A		Somatic	941	Capture	Illumina HiSeq	Phase_I	45165811	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																				0.612	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
CELSR1	9620	broad.mit.edu	37	22	46790131	46790131	+	Missense_Mutation	SNP	A	A	C	rs199586660	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:46790131A>C	ENST00000262738.3	-	14	5871	c.5872T>G	c.(5872-5874)Tgg>Ggg	p.W1958G		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1958	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)	p.W1958G(3)		breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GGGTTCCCCCACCAGCCTCTG	0.567																																					p.W1958G												.	.	3	Substitution - Missense(3)	large_intestine(2)|ovary(1)	c.T5872G	22						.						45.0	41.0	42.0					22																	46790131		2203	4300	6503	45168795	SO:0001583	missense	9620	exon14			AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.5872T>G	22.37:g.46790131A>C	ENSP00000262738:p.Trp1958Gly	Somatic		Capture	Illumina HiSeq	Phase_I	45168795	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	A	17.58	3.425084	0.62733	.	.	ENSG00000075275	ENST00000262738	T	0.70164	-0.46	3.47	3.47	0.39725	.	0.000000	0.64402	U	0.000003	T	0.80270	0.4592	M	0.81112	2.525	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.70935	0.971;0.971	T	0.82940	-0.0208	10	0.87932	D	0	.	11.945	0.52924	1.0:0.0:0.0:0.0	.	279;1958	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	G	1958	ENSP00000262738:W1958G	ENSP00000262738:W1958G	W	-	1	0	CELSR1	45168795	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	8.638000	0.91019	1.360000	0.45960	0.379000	0.24179	TGG		0.567	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
TBC1D22A	25771	broad.mit.edu	37	22	47569211	47569211	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:47569211C>T	ENST00000337137.4	+	13	1662	c.1496C>T	c.(1495-1497)gCc>gTc	p.A499V	TBC1D22A_ENST00000407381.3_Missense_Mutation_p.A440V|TBC1D22A_ENST00000355704.3_Missense_Mutation_p.A421V|TBC1D22A_ENST00000406733.1_Missense_Mutation_p.A452V	NM_001284304.1|NM_001284305.1|NM_014346.2	NP_001271233.1|NP_001271234.1|NP_055161.1	Q8WUA7	TB22A_HUMAN	TBC1 domain family, member 22A	499							protein homodimerization activity (GO:0042803)|Rab GTPase activator activity (GO:0005097)	p.A499V(1)		breast(1)|endometrium(3)|large_intestine(10)|lung(5)|ovary(2)|prostate(1)	22		all_cancers(38;4.44e-05)|all_epithelial(38;0.000507)|Breast(42;0.0488)|all_lung(38;0.0682)|Ovarian(80;0.0731)|all_neural(38;0.0966)|Glioma(61;0.222)|Lung SC(80;0.236)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0347)|BRCA - Breast invasive adenocarcinoma(115;0.231)		CTGTTGCTGGCCGAGGCCTAC	0.617																																					p.A499V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1496T	22						.						102.0	98.0	99.0					22																	47569211		2203	4300	6503	45947875	SO:0001583	missense	25771	exon13			AK125705	CCDS14078.1, CCDS63511.1, CCDS63512.1, CCDS74877.1	22q13	2008-01-22	2005-01-05	2005-01-05	ENSG00000054611	ENSG00000054611			1309	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 4"""	C22orf4			Standard	XM_005261496		Approved		uc003bib.3	Q8WUA7	OTTHUMG00000150332	ENST00000337137.4:c.1496C>T	22.37:g.47569211C>T	ENSP00000336724:p.Ala499Val	Somatic		Capture	Illumina HiSeq	Phase_I	45947875	NM_014346	B0QYI2|B0QYI3|B9A6M3|Q5TE47|Q6ZUH2|Q92680|Q9BVD6|Q9UGG0|Q9UGT2|Q9UGU6|Q9UH25|Q9Y4W5	Missense_Mutation	SNP	ENST00000337137.4	37	CCDS14078.1	.	.	.	.	.	.	.	.	.	.	C	33	5.280017	0.95489	.	.	ENSG00000054611	ENST00000337137;ENST00000407381;ENST00000355704;ENST00000406733	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	5.21	5.21	0.72293	Rab-GAP/TBC domain (1);	0.000000	0.85682	D	0.000000	T	0.48857	0.1523	M	0.79475	2.455	0.80722	D	1	D;D;D;D	0.89917	0.987;1.0;1.0;0.987	P;D;D;P	0.91635	0.517;0.999;0.993;0.517	T	0.51379	-0.8713	10	0.62326	D	0.03	.	16.2362	0.82377	0.0:1.0:0.0:0.0	.	499;421;440;499	B9A6M3;Q8WUA7-2;B0QYI1;Q8WUA7	.;.;.;TB22A_HUMAN	V	499;440;421;452	ENSP00000336724:A499V;ENSP00000384036:A440V;ENSP00000347932:A421V;ENSP00000385634:A452V	ENSP00000336724:A499V	A	+	2	0	TBC1D22A	45947875	1.000000	0.71417	0.984000	0.44739	0.905000	0.53344	6.588000	0.74076	2.419000	0.82065	0.655000	0.94253	GCC		0.617	TBC1D22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317600.3	NM_014346	
BRD1	23774	broad.mit.edu	37	22	50170756	50170756	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:50170756G>A	ENST00000216267.8	-	9	3140	c.2654C>T	c.(2653-2655)aCg>aTg	p.T885M	BRD1_ENST00000457780.2_Missense_Mutation_p.R989C|BRD1_ENST00000342989.5_Missense_Mutation_p.T611M|BRD1_ENST00000404034.1_Missense_Mutation_p.T885M|BRD1_ENST00000404760.1_Missense_Mutation_p.T1016M|BRD1_ENST00000542442.1_Missense_Mutation_p.T573M	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	885					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)	p.T885M(2)		endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GTCCTCCAGCGTGTGCCGTCG	0.652																																					p.T885M												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.C2654T	22						.						80.0	77.0	78.0					22																	50170756		2203	4300	6503	48556760	SO:0001583	missense	23774	exon9			AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.2654C>T	22.37:g.50170756G>A	ENSP00000216267:p.Thr885Met	Somatic		Capture	Illumina HiSeq	Phase_I	48556760	NM_014577	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	37	CCDS14080.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.4|20.4	3.980639|3.980639	0.74474|0.74474	.|.	.|.	ENSG00000100425|ENSG00000100425	ENST00000457780|ENST00000216267;ENST00000404034;ENST00000404760;ENST00000542442;ENST00000342989;ENST00000419212	T|T;T;T;T;T	0.17213|0.29397	2.29|2.52;2.52;2.56;1.57;1.98	4.98|4.98	4.98|4.98	0.66077|0.66077	.|.	.|0.047425	.|0.85682	.|D	.|0.000000	T|T	0.53594|0.53594	0.1806|0.1806	M|M	0.63428|0.63428	1.95|1.95	0.51767|0.51767	D|D	0.999937|0.999937	.|D;D;D;D	.|0.89917	.|1.0;0.999;1.0;1.0	.|D;P;D;D	.|0.91635	.|0.998;0.859;0.931;0.999	T|T	0.49360|0.49360	-0.8948|-0.8948	7|10	0.87932|0.33940	D|T	0|0.23	.|.	18.245|18.245	0.89982|0.89982	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1016;611;885;1016	.|Q86X06;B7Z926;O95696;O95696-2	.|.;.;BRD1_HUMAN;.	C|M	989|885;885;1016;573;611;476	ENSP00000410042:R989C|ENSP00000216267:T885M;ENSP00000384076:T885M;ENSP00000385858:T1016M;ENSP00000437514:T573M;ENSP00000345886:T611M	ENSP00000410042:R989C|ENSP00000216267:T885M	R|T	-|-	1|2	0|0	BRD1|BRD1	48556760|48556760	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.950000|0.950000	0.60333|0.60333	9.110000|9.110000	0.94302|0.94302	2.300000|2.300000	0.77407|0.77407	0.655000|0.655000	0.94253|0.94253	CGC|ACG		0.652	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
MLC1	23209	broad.mit.edu	37	22	50515323	50515323	+	Missense_Mutation	SNP	C	C	T	rs537457768	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:50515323C>T	ENST00000311597.5	-	7	1150	c.544G>A	c.(544-546)Gcc>Acc	p.A182T	MLC1_ENST00000538737.1_Missense_Mutation_p.A148T|MLC1_ENST00000395876.2_Missense_Mutation_p.A182T|MLC1_ENST00000431262.2_Missense_Mutation_p.A152T|MLC1_ENST00000535444.1_Missense_Mutation_p.A103T|MLC1_ENST00000450140.2_Missense_Mutation_p.A130T	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	182					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.A182T(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)		AGAATGTTGGCGCTGTCAGAC	0.562													C|||	2	0.000399361	0.0	0.0	5008	,	,		17481	0.0		0.0	False		,,,				2504	0.002				p.A182T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G544A	22						.						106.0	108.0	107.0					22																	50515323		2203	4300	6503	48857450	SO:0001583	missense	23209	exon7			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.544G>A	22.37:g.50515323C>T	ENSP00000310375:p.Ala182Thr	Somatic		Capture	Illumina HiSeq	Phase_I	48857450	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Missense_Mutation	SNP	ENST00000311597.5	37	CCDS14083.1	.	.	.	.	.	.	.	.	.	.	C	0.337	-0.952470	0.02285	.	.	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000431262;ENST00000535444;ENST00000450140;ENST00000442311	D;D;D;D;D;D;D	0.87103	-2.21;-2.21;-2.21;-2.21;-2.21;-2.21;-2.21	5.02	-3.56	0.04626	.	0.681298	0.15288	N	0.270316	T	0.58018	0.2093	N	0.02916	-0.46	0.09310	N	1	B;B;B;B	0.15473	0.001;0.001;0.013;0.001	B;B;B;B	0.08055	0.001;0.002;0.003;0.002	T	0.57974	-0.7718	10	0.02654	T	1	-21.0386	3.5363	0.07795	0.3629:0.2222:0.0:0.4149	.	148;152;130;182	F5H1B9;B7Z659;B7Z1X1;Q15049	.;.;.;MLC1_HUMAN	T	182;182;148;152;103;130;152	ENSP00000379216:A182T;ENSP00000310375:A182T;ENSP00000445805:A148T;ENSP00000415877:A152T;ENSP00000438910:A103T;ENSP00000412448:A130T;ENSP00000401385:A152T	ENSP00000310375:A182T	A	-	1	0	MLC1	48857450	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.659000	0.01975	-0.750000	0.04740	-2.290000	0.00267	GCC		0.562	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
MOV10L1	54456	broad.mit.edu	37	22	50537979	50537979	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:50537979C>T	ENST00000262794.5	+	3	473	c.390C>T	c.(388-390)ggC>ggT	p.G130G	MOV10L1_ENST00000540615.1_Silent_p.G110G|MOV10L1_ENST00000395858.3_Silent_p.G130G|MOV10L1_ENST00000475190.1_3'UTR|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000545383.1_Silent_p.G130G	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	130					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.G130G(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TGGTGGAGGGCGCAGGCTGTA	0.527																																					p.G130G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C390T	22						.						123.0	97.0	106.0					22																	50537979		2203	4300	6503	48880106	SO:0001819	synonymous_variant	54456	exon3			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.390C>T	22.37:g.50537979C>T		Somatic		Capture	Illumina HiSeq	Phase_I	48880106	NM_001164104	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																				0.527	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
PLXNB2	23654	broad.mit.edu	37	22	50728412	50728412	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:50728412G>A	ENST00000449103.1	-	3	742	c.602C>T	c.(601-603)aCg>aTg	p.T201M	PLXNB2_ENST00000359337.4_Missense_Mutation_p.T201M			O15031	PLXB2_HUMAN	plexin B2	201	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)	p.T244M(1)		breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GGCGTGGTCCGTGTAGGCTTC	0.597																																					p.T201M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C602T	22						.						77.0	86.0	83.0					22																	50728412		2180	4268	6448	49070539	SO:0001583	missense	23654	exon2				CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.602C>T	22.37:g.50728412G>A	ENSP00000409171:p.Thr201Met	Somatic		Capture	Illumina HiSeq	Phase_I	49070539	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	37	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	G	19.26	3.793908	0.70452	.	.	ENSG00000196576	ENST00000449103;ENST00000359337;ENST00000414275;ENST00000432455	T;T;T	0.10960	2.82;2.82;2.82	4.51	4.51	0.55191	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.244797	0.28958	N	0.013583	T	0.17450	0.0419	L	0.55481	1.735	0.28105	N	0.931268	P	0.52463	0.953	P	0.50109	0.631	T	0.02574	-1.1139	10	0.44086	T	0.13	.	12.5034	0.55968	0.0:0.0:0.833:0.167	.	201	O15031	PLXB2_HUMAN	M	201	ENSP00000409171:T201M;ENSP00000352288:T201M;ENSP00000392620:T201M	ENSP00000352288:T201M	T	-	2	0	PLXNB2	49070539	0.974000	0.33945	0.997000	0.53966	0.922000	0.55478	5.163000	0.64948	2.335000	0.79485	0.462000	0.41574	ACG		0.597	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
TYMP	1890	broad.mit.edu	37	22	50967031	50967031	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr22:50967031C>T	ENST00000252029.3	-	4	588	c.426G>A	c.(424-426)atG>atA	p.M142I	SCO2_ENST00000395693.3_5'Flank|SCO2_ENST00000252785.3_5'Flank|SCO2_ENST00000543927.1_5'Flank|TYMP_ENST00000395681.1_Missense_Mutation_p.M142I|TYMP_ENST00000395678.3_Missense_Mutation_p.M142I|TYMP_ENST00000395680.1_Missense_Mutation_p.M142I|SCO2_ENST00000535425.1_5'Flank	NM_001113755.2|NM_001113756.2|NM_001257988.1|NM_001257989.1|NM_001953.4	NP_001107227.1|NP_001107228.1|NP_001244917.1|NP_001244918.1|NP_001944.1	P19971	TYPH_HUMAN	thymidine phosphorylase	142					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|chemotaxis (GO:0006935)|DNA replication (GO:0006260)|mitochondrial genome maintenance (GO:0000002)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphorylase activity (GO:0004645)|platelet-derived growth factor receptor binding (GO:0005161)|pyrimidine-nucleoside phosphorylase activity (GO:0016154)|thymidine phosphorylase activity (GO:0009032)|transferase activity, transferring pentosyl groups (GO:0016763)	p.M142I(1)		large_intestine(1)|lung(2)|ovary(1)|prostate(1)	5		all_cancers(38;4.58e-14)|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)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)	Capecitabine(DB01101)|Cidofovir(DB00369)|Floxuridine(DB00322)|Fluorouracil(DB00544)|Trifluridine(DB00432)	GTCCGCTGATCATTGGCACCT	0.592																																					p.M142I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G426A	22						.						100.0	74.0	83.0					22																	50967031		2203	4300	6503	49313897	SO:0001583	missense	1890	exon4			M63193	CCDS14096.1, CCDS58811.1	22q13	2014-09-17	2008-01-21	2008-01-21	ENSG00000025708	ENSG00000025708	2.4.2.4		3148	protein-coding gene	gene with protein product	"""gliostatin"""	131222	"""endothelial cell growth factor 1 (platelet-derived)"""	MNGIE, ECGF1		1590793, 11733540	Standard	NM_001113755		Approved		uc003bme.5	P19971	OTTHUMG00000150249	ENST00000252029.3:c.426G>A	22.37:g.50967031C>T	ENSP00000252029:p.Met142Ile	Somatic		Capture	Illumina HiSeq	Phase_I	49313897	NM_001953	A8MW15|H9KVA0|Q13390|Q8WVB7	Missense_Mutation	SNP	ENST00000252029.3	37	CCDS14096.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.327123	0.81690	.	.	ENSG00000025708	ENST00000395680;ENST00000395681;ENST00000252029;ENST00000395678	D;D;D;D	0.98329	-4.87;-4.87;-4.87;-4.87	4.66	2.54	0.30619	Glycosyl transferase, family 3 (3);	0.000000	0.85682	D	0.000000	D	0.98969	0.9649	H	0.94658	3.565	0.39649	D	0.970431	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.996;0.999;0.999	D	0.98903	1.0777	10	0.72032	D	0.01	-3.5304	7.4264	0.27102	0.1659:0.7446:0.0:0.0895	.	142;142;142	B4DVR2;E5KRG5;P19971	.;.;TYPH_HUMAN	I	142	ENSP00000379037:M142I;ENSP00000379038:M142I;ENSP00000252029:M142I;ENSP00000379036:M142I	ENSP00000252029:M142I	M	-	3	0	TYMP	49313897	1.000000	0.71417	0.964000	0.40570	0.984000	0.73092	2.895000	0.48648	0.574000	0.29417	0.555000	0.69702	ATG		0.592	TYMP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317081.1	NM_001953	
TTN	7273	broad.mit.edu	37	2	179447832	179447833	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179447832_179447833insT	ENST00000591111.1	-	263	60998_60999	c.60774_60775insA	c.(60772-60777)aaagatfs	p.D20259fs	TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Ins_p.D13027fs|TTN_ENST00000460472.2_Frame_Shift_Ins_p.D12835fs|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Ins_p.D19332fs|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Frame_Shift_Ins_p.D21900fs|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Ins_p.D12960fs			Q8WZ42	TITIN_HUMAN	titin	20259	Ig-like 111.				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.D12960fs*40(1)|p.D12835fs*40(1)|p.D13027fs*40(1)|p.D19330fs*40(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)			AGTGTGCCATCTTTTTTCCAAG	0.46																																					p.K12959fs												.	.	4	Insertion - Frameshift(4)	large_intestine(4)	c.38877_38878insA	2						.																																			179156079	SO:0001589	frameshift_variant	7273	exon142			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.60775dupA	2.37:g.179447838_179447838dupT	ENSP00000465570:p.Asp20259fs	Somatic		Capture	Illumina HiSeq	Phase_I	179156078	NM_133432	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	Frame_Shift_Ins	INS	ENST00000591111.1	37																																																																																					0.460	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
NPAS2	4862	broad.mit.edu	37	2	101604649	101604649	+	Missense_Mutation	SNP	G	G	A	rs368846782	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:101604649G>A	ENST00000335681.5	+	17	2023	c.1738G>A	c.(1738-1740)Ggg>Agg	p.G580R	NPAS2_ENST00000542504.1_Missense_Mutation_p.G645R	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	580					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.G580R(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						GCCCCAGCTCGGGGCGGGCCC	0.597													G|||	2	0.000399361	0.0	0.0	5008	,	,		19195	0.002		0.0	False		,,,				2504	0.0				p.G580R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1738A	2						.						61.0	67.0	65.0					2																	101604649		2203	4300	6503	100971081	SO:0001583	missense	4862	exon17			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.1738G>A	2.37:g.101604649G>A	ENSP00000338283:p.Gly580Arg	Somatic		Capture	Illumina HiSeq	Phase_I	100971081	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Missense_Mutation	SNP	ENST00000335681.5	37	CCDS2048.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	4.024|4.024	0.001861|0.001861	0.07819|0.07819	.|.	.|.	ENSG00000170485|ENSG00000170485	ENST00000335681;ENST00000542504|ENST00000433408	T;T|.	0.05081|.	3.53;3.5|.	5.43|5.43	3.62|3.62	0.41486|0.41486	.|.	4.083980|.	0.00857|.	N|.	0.001897|.	T|T	0.23094|0.23094	0.0558|0.0558	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B|.	0.23540|.	0.057;0.087|.	B;B|.	0.08055|.	0.003;0.002|.	T|T	0.18808|0.18808	-1.0325|-1.0325	10|5	0.51188|.	T|.	0.08|.	.|.	9.2423|9.2423	0.37504|0.37504	0.2208:0.0:0.7792:0.0|0.2208:0.0:0.7792:0.0	.|.	645;580|.	F5H027;Q99743|.	.;NPAS2_HUMAN|.	R|Q	580;645|78	ENSP00000338283:G580R;ENSP00000438428:G645R|.	ENSP00000338283:G580R|.	G|R	+|+	1|2	0|0	NPAS2|NPAS2	100971081|100971081	0.004000|0.004000	0.15560|0.15560	0.101000|0.101000	0.21167|0.21167	0.270000|0.270000	0.26580|0.26580	0.737000|0.737000	0.26144|0.26144	1.274000|1.274000	0.44362|0.44362	0.655000|0.655000	0.94253|0.94253	GGG|CGG		0.597	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3		
NPAS2	4862	broad.mit.edu	37	2	101606816	101606816	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:101606816G>A	ENST00000335681.5	+	18	2211	c.1926G>A	c.(1924-1926)ccG>ccA	p.P642P	NPAS2_ENST00000542504.1_Silent_p.P707P	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	642					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.P642P(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						CTGCGCTCCCGCCAAGTCTGA	0.612																																					p.P642P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1926A	2						.						53.0	56.0	55.0					2																	101606816		2203	4300	6503	100973248	SO:0001819	synonymous_variant	4862	exon18			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.1926G>A	2.37:g.101606816G>A		Somatic		Capture	Illumina HiSeq	Phase_I	100973248	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Silent	SNP	ENST00000335681.5	37	CCDS2048.1	.	.	.	.	.	.	.	.	.	.	G	9.101	1.004213	0.19199	.	.	ENSG00000170485	ENST00000433408	.	.	.	4.68	-6.88	0.01665	.	.	.	.	.	T	0.26629	0.0651	.	.	.	0.19300	N	0.999973	.	.	.	.	.	.	T	0.31052	-0.9957	4	.	.	.	.	7.86	0.29504	0.5538:0.2043:0.2418:0.0	.	.	.	.	T	141	.	.	A	+	1	0	NPAS2	100973248	0.000000	0.05858	0.001000	0.08648	0.393000	0.30537	-3.650000	0.00403	-1.449000	0.01938	0.455000	0.32223	GCC		0.612	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3		
TBC1D8	11138	broad.mit.edu	37	2	101666933	101666933	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:101666933G>A	ENST00000376840.4	-	5	756	c.757C>T	c.(757-759)Cga>Tga	p.R253*	TBC1D8_ENST00000409318.1_Nonsense_Mutation_p.R268*			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	253					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.R253*(1)		breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						AGCAGCCTTCGCAGCGTCACG	0.542																																					p.R253X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C757T	2						.						58.0	60.0	59.0					2																	101666933		2056	4204	6260	101033365	SO:0001587	stop_gained	11138	exon5			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.757C>T	2.37:g.101666933G>A	ENSP00000366036:p.Arg253*	Somatic		Capture	Illumina HiSeq	Phase_I	101033365	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Nonsense_Mutation	SNP	ENST00000376840.4	37	CCDS46375.1	.	.	.	.	.	.	.	.	.	.	G	35	5.541858	0.96474	.	.	ENSG00000204634	ENST00000376840;ENST00000409318	.	.	.	5.37	5.37	0.77165	.	0.000000	0.56097	D	0.000024	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.1158	14.0152	0.64519	0.0:0.0:0.8488:0.1511	.	.	.	.	X	253;268	.	ENSP00000366036:R253X	R	-	1	2	TBC1D8	101033365	1.000000	0.71417	0.591000	0.28745	0.779000	0.44077	4.362000	0.59467	2.511000	0.84671	0.561000	0.74099	CGA		0.542	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063	
CREG2	200407	broad.mit.edu	37	2	101971819	101971819	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:101971819G>A	ENST00000324768.5	-	3	758	c.621C>T	c.(619-621)atC>atT	p.I207I		NM_153836.3	NP_722578.1	Q8IUH2	CREG2_HUMAN	cellular repressor of E1A-stimulated genes 2	207						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	FMN binding (GO:0010181)|oxidoreductase activity (GO:0016491)	p.I207I(1)		endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						CCGGATCAACGATGTTTTTTC	0.393																																					p.I207I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C621T	2						.						52.0	53.0	52.0					2																	101971819		2203	4300	6503	101338251	SO:0001819	synonymous_variant	200407	exon3			AB046109	CCDS2052.1	2q12.1	2007-08-01			ENSG00000175874	ENSG00000175874			14272	protein-coding gene	gene with protein product						12408961	Standard	NM_153836		Approved		uc002tba.2	Q8IUH2	OTTHUMG00000130692	ENST00000324768.5:c.621C>T	2.37:g.101971819G>A		Somatic		Capture	Illumina HiSeq	Phase_I	101338251	NM_153836	Q86X03|Q8N540|Q8N9E3	Silent	SNP	ENST00000324768.5	37	CCDS2052.1																																																																																				0.393	CREG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253188.2	NM_153836	
MAP4K4	9448	broad.mit.edu	37	2	102486148	102486148	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:102486148C>T	ENST00000347699.4	+	20	2285	c.2285C>T	c.(2284-2286)aCg>aTg	p.T762M	MAP4K4_ENST00000425019.1_Missense_Mutation_p.T731M|MAP4K4_ENST00000413150.2_Missense_Mutation_p.T677M|MAP4K4_ENST00000498066.1_3'UTR|MAP4K4_ENST00000350198.4_Missense_Mutation_p.T681M|MAP4K4_ENST00000324219.4_Missense_Mutation_p.T843M|MAP4K4_ENST00000350878.4_Missense_Mutation_p.T738M|MAP4K4_ENST00000302217.5_Missense_Mutation_p.T565M|MAP4K4_ENST00000456652.1_Missense_Mutation_p.T561M	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	762					intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.T843M(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						CACAAAGTAACGGACTACTCC	0.557																																					p.T735M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2204T	2						.						38.0	41.0	40.0					2																	102486148		2044	4178	6222	101852580	SO:0001583	missense	9448	exon21			AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6866	protein-coding gene	gene with protein product	"""HPK/GCK-like kinase"", ""hepatocyte progenitor kinase-like/germinal center kinase-like kinase"""	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.2285C>T	2.37:g.102486148C>T	ENSP00000314363:p.Thr762Met	Somatic		Capture	Illumina HiSeq	Phase_I	101852580	NM_145687	O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	37	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.347188	0.82022	.	.	ENSG00000071054	ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699;ENST00000417294;ENST00000350878	D;D;D;D;D;D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87;-1.87	5.31	5.31	0.75309	.	0.057678	0.64402	D	0.000002	D	0.88459	0.6442	L	0.33293	1	0.80722	D	1	D;D;P;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.573;1.0;1.0;1.0;1.0;1.0;0.999;0.998	D;D;B;D;D;D;D;D;D;D	0.83275	0.99;0.99;0.079;0.99;0.996;0.98;0.995;0.996;0.921;0.954	D	0.85987	0.1486	10	0.25106	T	0.35	.	18.9824	0.92760	0.0:1.0:0.0:0.0	.	738;758;561;565;680;762;731;681;734;843	B7Z388;B7Z3V5;E7EX83;C9J840;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.;.;.;.;.;M4K4_HUMAN;.;.;.;.	M	731;843;681;565;677;561;762;693;738	ENSP00000392830:T731M;ENSP00000313644:T843M;ENSP00000281111:T681M;ENSP00000303600:T565M;ENSP00000389752:T677M;ENSP00000387370:T561M;ENSP00000314363:T762M;ENSP00000409720:T693M;ENSP00000343658:T738M	ENSP00000303600:T565M	T	+	2	0	MAP4K4	101852580	1.000000	0.71417	0.993000	0.49108	0.937000	0.57800	7.487000	0.81328	2.480000	0.83734	0.563000	0.77884	ACG		0.557	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	
IL1R1	3554	broad.mit.edu	37	2	102793205	102793205	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:102793205G>A	ENST00000410023.1	+	12	2014	c.1696G>A	c.(1696-1698)Gtg>Atg	p.V566M	IL1R1_ENST00000409589.1_Intron|IL1R1_ENST00000233946.3_Missense_Mutation_p.V566M|IL1R1_ENST00000409929.1_Missense_Mutation_p.V535M|AC007271.3_ENST00000428188.1_RNA|IL1R1_ENST00000424272.1_3'UTR			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	566					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)	p.V566M(2)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	AGAGGCTCACGTGCCTCTCGG	0.522																																					p.V566M												.	.	2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.G1696A	2						.						80.0	81.0	81.0					2																	102793205		2202	4300	6502	102159637	SO:0001583	missense	3554	exon11			M27492	CCDS2055.1, CCDS74547.1	2q12	2013-01-29			ENSG00000115594	ENSG00000115594		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5993	protein-coding gene	gene with protein product		147810		IL1R, IL1RA		1833184, 10191101	Standard	XM_005263929		Approved	D2S1473, CD121A	uc002tbr.3	P14778	OTTHUMG00000130783	ENST00000410023.1:c.1696G>A	2.37:g.102793205G>A	ENSP00000386380:p.Val566Met	Somatic		Capture	Illumina HiSeq	Phase_I	102159637	NM_000877	Q587I7	Missense_Mutation	SNP	ENST00000410023.1	37	CCDS2055.1	.	.	.	.	.	.	.	.	.	.	G	9.782	1.175469	0.21704	.	.	ENSG00000115594	ENST00000409929;ENST00000410023;ENST00000233946	T;T;T	0.02345	4.33;4.35;4.35	5.52	-4.89	0.03103	.	3.314520	0.00520	N	0.000189	T	0.02807	0.0084	L	0.44542	1.39	0.09310	N	1	B;B	0.19073	0.033;0.009	B;B	0.08055	0.003;0.003	T	0.43065	-0.9414	10	0.49607	T	0.09	.	1.2151	0.01913	0.3211:0.2862:0.2584:0.1343	.	535;566	B8ZZW4;P14778	.;IL1R1_HUMAN	M	535;566;566	ENSP00000386776:V535M;ENSP00000386380:V566M;ENSP00000233946:V566M	ENSP00000233946:V566M	V	+	1	0	IL1R1	102159637	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.679000	0.05203	-0.923000	0.03785	-1.289000	0.01358	GTG		0.522	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1		
SLC9A4	389015	broad.mit.edu	37	2	103142737	103142737	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:103142737G>A	ENST00000295269.4	+	11	2427	c.1970G>A	c.(1969-1971)cGc>cAc	p.R657H		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	657					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)	p.R657H(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						AAGAATATCCGCTACCTCTCC	0.512																																					p.R657H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1970A	2						.						137.0	130.0	133.0					2																	103142737		2203	4300	6503	102509169	SO:0001583	missense	389015	exon11				CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.1970G>A	2.37:g.103142737G>A	ENSP00000295269:p.Arg657His	Somatic		Capture	Illumina HiSeq	Phase_I	102509169	NM_001011552	Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	37	CCDS33264.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.465020	0.63513	.	.	ENSG00000180251	ENST00000295269	T	0.56103	0.48	5.8	5.8	0.92144	.	0.763894	0.12736	N	0.443447	T	0.47060	0.1425	L	0.45470	1.425	0.43412	D	0.995557	P	0.52463	0.953	B	0.37833	0.259	T	0.47886	-0.9082	10	0.33141	T	0.24	.	16.9798	0.86324	0.0:0.0:1.0:0.0	.	657	Q6AI14	SL9A4_HUMAN	H	657	ENSP00000295269:R657H	ENSP00000295269:R657H	R	+	2	0	SLC9A4	102509169	1.000000	0.71417	1.000000	0.80357	0.168000	0.22595	2.924000	0.48876	2.735000	0.93741	0.655000	0.94253	CGC		0.512	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
NOL10	79954	broad.mit.edu	37	2	10811713	10811713	+	Missense_Mutation	SNP	T	T	C	rs142968524	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:10811713T>C	ENST00000381685.5	-	6	536	c.431A>G	c.(430-432)tAt>tGt	p.Y144C	NOL10_ENST00000542668.1_Missense_Mutation_p.Y94C|NOL10_ENST00000538384.1_Missense_Mutation_p.Y118C|NOL10_ENST00000345985.3_Missense_Mutation_p.Y144C	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	144						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.Y144C(1)				Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		ACAGGATGGATAGTGGTAAGA	0.368																																					p.Y144C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A431G	2						.						106.0	104.0	105.0					2																	10811713		2203	4300	6503	10729164	SO:0001583	missense	79954	exon6			AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"""polyglutamine binding protein 5"""	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.431A>G	2.37:g.10811713T>C	ENSP00000371101:p.Tyr144Cys	Somatic		Capture	Illumina HiSeq	Phase_I	10729164	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Missense_Mutation	SNP	ENST00000381685.5	37	CCDS1673.2	.	.	.	.	.	.	.	.	.	.	T	16.85	3.237023	0.58886	.	.	ENSG00000115761	ENST00000345985;ENST00000381685;ENST00000542668;ENST00000538384;ENST00000431319	T;T;T;T;T	0.70516	2.3;2.78;-0.17;2.78;-0.49	5.52	5.52	0.82312	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.242356	0.43416	D	0.000578	T	0.76637	0.4015	L	0.54908	1.71	0.46774	D	0.99919	D;D;D	0.67145	0.983;0.983;0.996	P;P;P	0.56216	0.76;0.76;0.794	T	0.75431	-0.3320	10	0.34782	T	0.22	-13.9025	15.9347	0.79694	0.0:0.0:0.0:1.0	.	118;144;144	B4DLV0;Q9BSC4;Q9BSC4-2	.;NOL10_HUMAN;.	C	144;144;94;118;35	ENSP00000263837:Y144C;ENSP00000371101:Y144C;ENSP00000437625:Y94C;ENSP00000439663:Y118C;ENSP00000403170:Y35C	ENSP00000263837:Y144C	Y	-	2	0	NOL10	10729164	1.000000	0.71417	0.969000	0.41365	0.992000	0.81027	3.743000	0.55104	2.221000	0.72209	0.528000	0.53228	TAT		0.368	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894	
GPR45	11250	broad.mit.edu	37	2	105858848	105858848	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:105858848G>A	ENST00000258456.1	+	1	649	c.533G>A	c.(532-534)cGg>cAg	p.R178Q		NM_007227.3	NP_009158.3	Q9Y5Y3	GPR45_HUMAN	G protein-coupled receptor 45	178						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R178Q(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						GTGCCGGCGCGGGCCCCACAG	0.701																																					p.R178Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G533A	2						.						24.0	24.0	24.0					2																	105858848		2201	4298	6499	105225280	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.533G>A	2.37:g.105858848G>A	ENSP00000258456:p.Arg178Gln	Somatic		Capture	Illumina HiSeq	Phase_I	105225280	NM_007227	Q6NWS4|Q6NXU6	Missense_Mutation	SNP	ENST00000258456.1	37	CCDS2066.1	.	.	.	.	.	.	.	.	.	.	G	12.98	2.099720	0.37048	.	.	ENSG00000135973	ENST00000258456	T	0.37058	1.22	5.04	5.04	0.67666	GPCR, rhodopsin-like superfamily (1);	0.153445	0.44688	D	0.000433	T	0.24851	0.0603	N	0.17764	0.52	0.44771	D	0.997777	P	0.41673	0.759	B	0.37692	0.256	T	0.04041	-1.0982	10	0.15066	T	0.55	-25.5163	17.9759	0.89127	0.0:0.0:1.0:0.0	.	178	Q9Y5Y3	GPR45_HUMAN	Q	178	ENSP00000258456:R178Q	ENSP00000258456:R178Q	R	+	2	0	GPR45	105225280	1.000000	0.71417	0.988000	0.46212	0.272000	0.26649	6.388000	0.73195	2.337000	0.79520	0.462000	0.41574	CGG		0.701	GPR45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253348.1	NM_007227	
POLR1B	84172	broad.mit.edu	37	2	113331367	113331367	+	Missense_Mutation	SNP	G	G	A	rs553658068		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:113331367G>A	ENST00000263331.5	+	14	3080	c.2500G>A	c.(2500-2502)Ggg>Agg	p.G834R	POLR1B_ENST00000541869.1_Missense_Mutation_p.G872R|POLR1B_ENST00000417433.2_Missense_Mutation_p.G778R|POLR1B_ENST00000409894.3_Missense_Mutation_p.G651R|POLR1B_ENST00000537335.1_Missense_Mutation_p.G623R	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	834					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.G834R(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						CCTCAACACCGGGGAAAGTTT	0.438													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21629	0.0		0.0	False		,,,				2504	0.0				p.G778R	Ovarian(16;256 576 9537 23969 41147)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2332A	2						.						126.0	136.0	132.0					2																	113331367		2203	4300	6503	113047838	SO:0001583	missense	84172	exon13			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.2500G>A	2.37:g.113331367G>A	ENSP00000263331:p.Gly834Arg	Somatic		Capture	Illumina HiSeq	Phase_I	113047838	NM_001137604	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Missense_Mutation	SNP	ENST00000263331.5	37	CCDS2097.1	.	.	.	.	.	.	.	.	.	.	G	19.94	3.920664	0.73213	.	.	ENSG00000125630	ENST00000263331;ENST00000541869;ENST00000409894;ENST00000537335;ENST00000417433;ENST00000458012;ENST00000536096	T;T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62;-0.62	5.7	4.82	0.62117	DNA-directed RNA polymerase, subunit 2, domain 6 (1);	0.045272	0.85682	N	0.000000	T	0.74642	0.3743	L	0.31207	0.915	0.80722	D	1	D;B;P;D	0.89917	1.0;0.295;0.933;1.0	D;B;P;D	0.72338	0.977;0.089;0.5;0.975	T	0.73880	-0.3843	10	0.36615	T	0.2	-24.6548	13.7209	0.62725	0.0753:0.0:0.9247:0.0	.	872;651;778;834	F5GZX4;F8W898;Q9H9Y6-2;Q9H9Y6	.;.;.;RPA2_HUMAN	R	834;872;651;623;778;219;193	ENSP00000263331:G834R;ENSP00000444136:G872R;ENSP00000387143:G651R;ENSP00000437914:G623R;ENSP00000405358:G778R;ENSP00000394408:G219R	ENSP00000263331:G834R	G	+	1	0	POLR1B	113047838	1.000000	0.71417	0.100000	0.21137	0.652000	0.38707	9.365000	0.97139	1.412000	0.46977	0.555000	0.69702	GGG		0.438	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014	
CHCHD5	84269	broad.mit.edu	37	2	113343557	113343557	+	Silent	SNP	G	G	A	rs201426009		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:113343557G>A	ENST00000324913.5	+	2	216	c.9G>A	c.(7-9)gcG>gcA	p.A3A	CHCHD5_ENST00000489052.1_3'UTR|CHCHD5_ENST00000409719.1_Silent_p.A3A	NM_032309.2	NP_115685.1	Q9BSY4	CHCH5_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 5	3						mitochondrion (GO:0005739)		p.A3A(1)		NS(1)|endometrium(1)|large_intestine(4)|urinary_tract(1)	7						ACAGGCAGGCGGCCCTAGAGG	0.557																																					p.A3A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G9A	2						.						36.0	40.0	39.0					2																	113343557		2203	4300	6503	113060028	SO:0001819	synonymous_variant	84269	exon2			BC004498	CCDS2098.1	2q14.1	2012-10-15	2004-01-19	2004-01-21	ENSG00000125611	ENSG00000125611		"""Coiled-coil-helix-coiled-coil-helix domain containing"""	17840	protein-coding gene	gene with protein product	"""mitochondrial intermembrane space cysteine motif protein of 14 kDa homolog (S. cerevisiae)"""		"""chromosome 2 open reading frame 9"""	C2orf9		22842048	Standard	NM_032309		Approved	MGC11104, MIC14	uc002thz.1	Q9BSY4	OTTHUMG00000131312	ENST00000324913.5:c.9G>A	2.37:g.113343557G>A		Somatic		Capture	Illumina HiSeq	Phase_I	113060028	NM_032309	Q585T4|Q8N8C4	Silent	SNP	ENST00000324913.5	37	CCDS2098.1																																																																																				0.557	CHCHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254081.2	NM_032309	
CHCHD5	84269	broad.mit.edu	37	2	113346449	113346449	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:113346449C>T	ENST00000324913.5	+	4	523	c.316C>T	c.(316-318)Cca>Tca	p.P106S	CHCHD5_ENST00000409719.1_3'UTR|AC012442.5_ENST00000414784.1_RNA|AC012442.6_ENST00000436885.1_lincRNA	NM_032309.2	NP_115685.1	Q9BSY4	CHCH5_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 5	106						mitochondrion (GO:0005739)		p.P106S(1)		NS(1)|endometrium(1)|large_intestine(4)|urinary_tract(1)	7						ACAGGCACAGCCACTTCCTGC	0.592																																					p.P106S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C316T	2						.						88.0	72.0	78.0					2																	113346449		2203	4300	6503	113062920	SO:0001583	missense	84269	exon4			BC004498	CCDS2098.1	2q14.1	2012-10-15	2004-01-19	2004-01-21	ENSG00000125611	ENSG00000125611		"""Coiled-coil-helix-coiled-coil-helix domain containing"""	17840	protein-coding gene	gene with protein product	"""mitochondrial intermembrane space cysteine motif protein of 14 kDa homolog (S. cerevisiae)"""		"""chromosome 2 open reading frame 9"""	C2orf9		22842048	Standard	NM_032309		Approved	MGC11104, MIC14	uc002thz.1	Q9BSY4	OTTHUMG00000131312	ENST00000324913.5:c.316C>T	2.37:g.113346449C>T	ENSP00000325655:p.Pro106Ser	Somatic		Capture	Illumina HiSeq	Phase_I	113062920	NM_032309	Q585T4|Q8N8C4	Missense_Mutation	SNP	ENST00000324913.5	37	CCDS2098.1	.	.	.	.	.	.	.	.	.	.	C	10.83	1.462352	0.26248	.	.	ENSG00000125611	ENST00000324913	T	0.17370	2.28	4.07	3.2	0.36748	.	.	.	.	.	T	0.15305	0.0369	L	0.51422	1.61	0.80722	D	1	B	0.17038	0.02	B	0.13407	0.009	T	0.04467	-1.0949	9	0.42905	T	0.14	.	7.8358	0.29369	0.0:0.888:0.0:0.112	.	106	Q9BSY4	CHCH5_HUMAN	S	106	ENSP00000325655:P106S	ENSP00000325655:P106S	P	+	1	0	CHCHD5	113062920	0.901000	0.30685	0.750000	0.31169	0.587000	0.36485	1.585000	0.36600	1.324000	0.45282	-0.251000	0.11542	CCA		0.592	CHCHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254081.2	NM_032309	
IL1RN	3557	broad.mit.edu	37	2	113888724	113888724	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:113888724T>G	ENST00000409930.3	+	3	372	c.308T>G	c.(307-309)cTc>cGc	p.L103R	IL1RN_ENST00000361779.3_Missense_Mutation_p.L69R|IL1RN_ENST00000354115.2_Missense_Mutation_p.L85R|IL1RN_ENST00000409052.1_Missense_Mutation_p.L69R|IL1RN_ENST00000259206.5_Missense_Mutation_p.L106R	NM_173842.2	NP_776214.1	P18510	IL1RA_HUMAN	interleukin 1 receptor antagonist	103					acute-phase response (GO:0006953)|carboxylic acid metabolic process (GO:0019752)|chronic inflammatory response to antigenic stimulus (GO:0002439)|female pregnancy (GO:0007565)|fever generation (GO:0001660)|immune response (GO:0006955)|insulin secretion (GO:0030073)|lipid metabolic process (GO:0006629)|memory (GO:0007613)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of membrane potential (GO:0045837)|positive regulation of JUN kinase activity (GO:0043507)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to interleukin-4 (GO:0070670)|response to lipopolysaccharide (GO:0032496)|response to organonitrogen compound (GO:0010243)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	interleukin-1 receptor antagonist activity (GO:0005152)|interleukin-1 receptor binding (GO:0005149)|interleukin-1 Type I receptor antagonist activity (GO:0045352)|interleukin-1 Type II receptor antagonist activity (GO:0045353)|interleukin-1, Type I receptor binding (GO:0005150)|interleukin-1, Type II receptor binding (GO:0005151)	p.L106R(1)|p.L69R(1)		breast(1)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	10					Rilonacept(DB06372)	GAGACCAGACTCCAGCTGGAG	0.458									Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.L85R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T254G	2						.						112.0	100.0	104.0					2																	113888724		2203	4300	6503	113605195	SO:0001583	missense	3557	exon4	Familial Cancer Database	Lichen Sclerosis, Familial	M55646	CCDS2113.1, CCDS2114.1, CCDS2115.1, CCDS46396.1	2q14.2	2014-09-17			ENSG00000136689	ENSG00000136689		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	6000	protein-coding gene	gene with protein product	"""interleukin-1 receptor antagonist protein"", ""intracellular interleukin-1 receptor antagonist"""	147679				1386337, 8432529	Standard	NM_000577		Approved	IL1RA, ICIL-1RA, IL1F3, IRAP, IL-1RN, MGC10430	uc002tjb.3	P18510	OTTHUMG00000131341	ENST00000409930.3:c.308T>G	2.37:g.113888724T>G	ENSP00000387173:p.Leu103Arg	Somatic		Capture	Illumina HiSeq	Phase_I	113605195	NM_000577	A8K4G1|Q14628|Q53SC2|Q7RTZ4|Q96GD6|Q9UPC0	Missense_Mutation	SNP	ENST00000409930.3	37	CCDS46396.1	.	.	.	.	.	.	.	.	.	.	T	16.46	3.130165	0.56721	.	.	ENSG00000136689	ENST00000409052;ENST00000361779;ENST00000259206;ENST00000354115;ENST00000409930	T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46	5.19	5.19	0.71726	.	0.063429	0.64402	D	0.000007	T	0.64713	0.2623	H	0.94264	3.515	0.09310	N	0.999995	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.85130	0.978;0.994;0.997	T	0.65487	-0.6156	10	0.87932	D	0	-18.123	11.4417	0.50100	0.0:0.0:0.0:1.0	.	103;85;106	P18510;P18510-2;Q53SC2	IL1RA_HUMAN;.;.	R	69;69;106;85;103	ENSP00000387210:L69R;ENSP00000354816:L69R;ENSP00000259206:L106R;ENSP00000329072:L85R;ENSP00000387173:L103R	ENSP00000259206:L106R	L	+	2	0	IL1RN	113605195	0.937000	0.31787	0.093000	0.20910	0.849000	0.48306	3.865000	0.56033	1.964000	0.57103	0.533000	0.62120	CTC		0.458	IL1RN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330802.1	NM_173841	
NTSR2	23620	broad.mit.edu	37	2	11800212	11800212	+	Missense_Mutation	SNP	G	G	A	rs149468069		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:11800212G>A	ENST00000306928.5	-	3	980	c.946C>T	c.(946-948)Cgc>Tgc	p.R316C		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	316					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)	p.R316C(1)		breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	ATGAGCCTGCGGGCATGGTAC	0.577																																					p.R316C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C946T	2						.	G	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	103.0	88.0	93.0		946	2.4	1.0	2	dbSNP_134	93	1,8599	1.2+/-3.3	0,1,4299	no	missense	NTSR2	NM_012344.3	180	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	probably-damaging	316/411	11800212	3,13003	2203	4300	6503	11717663	SO:0001583	missense	23620	exon3			Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"""GPCR / Class A : Neurotensin receptors"""	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.946C>T	2.37:g.11800212G>A	ENSP00000303686:p.Arg316Cys	Somatic		Capture	Illumina HiSeq	Phase_I	11717663	NM_012344	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Missense_Mutation	SNP	ENST00000306928.5	37	CCDS1681.1	.	.	.	.	.	.	.	.	.	.	G	15.94	2.979720	0.53827	4.54E-4	1.16E-4	ENSG00000169006	ENST00000306928	T	0.72167	-0.63	3.33	2.41	0.29592	GPCR, rhodopsin-like superfamily (1);	0.127189	0.35525	N	0.003142	T	0.78168	0.4241	M	0.64567	1.98	0.46798	D	0.999204	D	0.89917	1.0	D	0.74674	0.984	T	0.77576	-0.2536	10	0.72032	D	0.01	-21.3479	8.0373	0.30499	0.0:0.0:0.5577:0.4423	.	316	O95665	NTR2_HUMAN	C	316	ENSP00000303686:R316C	ENSP00000303686:R316C	R	-	1	0	NTSR2	11717663	0.382000	0.25148	0.995000	0.50966	0.729000	0.41735	1.239000	0.32719	0.918000	0.36919	0.650000	0.86243	CGC		0.577	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1		
LPIN1	23175	broad.mit.edu	37	2	11911520	11911520	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:11911520C>T	ENST00000256720.2	+	4	404	c.311C>T	c.(310-312)gCc>gTc	p.A104V	LPIN1_ENST00000425416.2_Missense_Mutation_p.A110V|LPIN1_ENST00000396099.1_Missense_Mutation_p.A110V|LPIN1_ENST00000449576.2_Missense_Mutation_p.A153V|LPIN1_ENST00000396098.1_Missense_Mutation_p.A110V	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	104	N-LIP.				cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)	p.A104V(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		ATGCACCTGGCCACCTCCCCC	0.532																																					p.A104V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C311T	2						.						63.0	67.0	66.0					2																	11911520		2203	4300	6503	11828971	SO:0001583	missense	23175	exon4			D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.311C>T	2.37:g.11911520C>T	ENSP00000256720:p.Ala104Val	Somatic		Capture	Illumina HiSeq	Phase_I	11828971	NM_145693	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	C	33	5.267574	0.95399	.	.	ENSG00000134324	ENST00000449576;ENST00000396098;ENST00000396099;ENST00000425416;ENST00000256720	T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02	5.8	5.8	0.92144	Lipin, N-terminal (1);	0.046845	0.85682	D	0.000000	D	0.82518	0.5054	L	0.50333	1.59	0.80722	D	1	P;P;P	0.50272	0.709;0.798;0.933	P;P;P	0.53102	0.575;0.71;0.718	T	0.81833	-0.0751	10	0.49607	T	0.09	-25.2701	20.0609	0.97674	0.0:1.0:0.0:0.0	.	153;104;110	F5GY24;Q14693;A8MU38	.;LPIN1_HUMAN;.	V	153;110;110;110;104	ENSP00000397908:A153V;ENSP00000379405:A110V;ENSP00000379406:A110V;ENSP00000401522:A110V;ENSP00000256720:A104V	ENSP00000256720:A104V	A	+	2	0	LPIN1	11828971	1.000000	0.71417	1.000000	0.80357	0.701000	0.40568	7.395000	0.79876	2.755000	0.94549	0.655000	0.94253	GCC		0.532	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
LPIN1	23175	broad.mit.edu	37	2	11944621	11944621	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:11944621C>T	ENST00000256720.2	+	15	2071	c.1978C>T	c.(1978-1980)Cgc>Tgc	p.R660C	LPIN1_ENST00000425416.2_Missense_Mutation_p.R666C|LPIN1_ENST00000396099.1_Missense_Mutation_p.R702C|LPIN1_ENST00000449576.2_Missense_Mutation_p.R745C|LPIN1_ENST00000396097.1_Missense_Mutation_p.R390C|LPIN1_ENST00000404113.2_Missense_Mutation_p.R161C	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	660	C-LIP.				cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)	p.R660C(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		AGGCACGTGCCGCTGTGAGGG	0.473																																					p.R660C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1978T	2						.						118.0	104.0	109.0					2																	11944621		2203	4300	6503	11862072	SO:0001583	missense	23175	exon15			D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.1978C>T	2.37:g.11944621C>T	ENSP00000256720:p.Arg660Cys	Somatic		Capture	Illumina HiSeq	Phase_I	11862072	NM_145693	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.023958	0.93462	.	.	ENSG00000134324	ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097;ENST00000404113;ENST00000454151	D;D;D;D;T;T;T	0.82619	-1.63;-1.62;-1.6;-1.59;-1.43;-0.11;0.17	4.75	4.75	0.60458	.	0.046718	0.85682	D	0.000000	D	0.92107	0.7498	M	0.84948	2.725	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.912	D;D;B	0.97110	1.0;1.0;0.282	D	0.93266	0.6647	10	0.87932	D	0	-31.462	18.6476	0.91416	0.0:1.0:0.0:0.0	.	161;745;660	B4DET9;F5GY24;Q14693	.;.;LPIN1_HUMAN	C	745;702;666;660;390;161;187	ENSP00000397908:R745C;ENSP00000379406:R702C;ENSP00000401522:R666C;ENSP00000256720:R660C;ENSP00000379404:R390C;ENSP00000386120:R161C;ENSP00000413714:R187C	ENSP00000256720:R660C	R	+	1	0	LPIN1	11862072	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.386000	0.79775	2.586000	0.87340	0.655000	0.94253	CGC		0.473	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
DPP10	57628	broad.mit.edu	37	2	116485483	116485483	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:116485483T>C	ENST00000410059.1	+	8	1148	c.668T>C	c.(667-669)tTt>tCt	p.F223S	DPP10_ENST00000393147.2_Missense_Mutation_p.F227S|DPP10_ENST00000409163.1_Missense_Mutation_p.F173S|DPP10_ENST00000310323.8_Missense_Mutation_p.F216S|DPP10_ENST00000488208.1_3'UTR	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	223						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.F216S(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						GAAATAATTTTTAATGGGATT	0.289																																					p.F173S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T518C	2						.						45.0	49.0	47.0					2																	116485483		2203	4293	6496	116201953	SO:0001583	missense	57628	exon9			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.668T>C	2.37:g.116485483T>C	ENSP00000386565:p.Phe223Ser	Somatic		Capture	Illumina HiSeq	Phase_I	116201953	NM_001178036	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	T	19.02	3.745614	0.69418	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393146;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	5.73	5.73	0.89815	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.36635	0.0974	L	0.55481	1.735	0.80722	D	1	B;B;B;P	0.35307	0.439;0.051;0.299;0.494	B;B;B;B	0.41691	0.249;0.045;0.219;0.364	T	0.08868	-1.0701	10	0.32370	T	0.25	-6.9102	15.1915	0.73047	0.0:0.0:0.0:1.0	.	216;227;219;223	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	S	223;173;219;227;216;173	ENSP00000386565:F223S;ENSP00000387038:F173S;ENSP00000376854:F219S;ENSP00000376855:F227S;ENSP00000309066:F216S	ENSP00000309066:F216S	F	+	2	0	DPP10	116201953	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.845000	0.86875	2.196000	0.70406	0.482000	0.46254	TTT		0.289	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	
MARCO	8685	broad.mit.edu	37	2	119699907	119699907	+	Missense_Mutation	SNP	G	G	A	rs554794950		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:119699907G>A	ENST00000327097.4	+	1	166	c.31G>A	c.(31-33)Gag>Aag	p.E11K	MARCO_ENST00000541757.1_5'UTR	NM_006770.3	NP_006761.1	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	11					apoptotic cell clearance (GO:0043277)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)	collagen trimer (GO:0005581)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)	p.E11K(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(12)|lung(37)|ovary(4)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	70						CAAGGAGGACGAGCTCTTGAG	0.443													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17998	0.0		0.0	False		,,,				2504	0.0				p.E11K	GBM(8;18 374 7467 11269 32796)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G31A	2						.						93.0	92.0	92.0					2																	119699907		2203	4300	6503	119416377	SO:0001583	missense	8685	exon1			AF035819	CCDS2124.1	2q14.2	2011-10-11			ENSG00000019169	ENSG00000019169			6895	protein-coding gene	gene with protein product	"""scavenger receptor class A, member 2"""	604870				9468508, 7867067, 10331948	Standard	NM_006770		Approved	SCARA2	uc002tln.1	Q9UEW3	OTTHUMG00000131400	ENST00000327097.4:c.31G>A	2.37:g.119699907G>A	ENSP00000318916:p.Glu11Lys	Somatic		Capture	Illumina HiSeq	Phase_I	119416377	NM_006770	B4DW79|Q9Y5S3	Missense_Mutation	SNP	ENST00000327097.4	37	CCDS2124.1	.	.	.	.	.	.	.	.	.	.	G	10.26	1.301223	0.23650	.	.	ENSG00000019169	ENST00000327097;ENST00000410021	D	0.90324	-2.65	4.95	4.08	0.47627	.	0.777169	0.11789	N	0.529416	D	0.82572	0.5066	N	0.24115	0.695	0.26485	N	0.97505	B	0.21520	0.057	B	0.15484	0.013	T	0.69296	-0.5182	9	.	.	.	.	9.5976	0.39584	0.095:0.0:0.905:0.0	.	11	Q9UEW3	MARCO_HUMAN	K	11	ENSP00000318916:E11K	.	E	+	1	0	MARCO	119416377	0.085000	0.21516	0.006000	0.13384	0.011000	0.07611	1.040000	0.30278	1.448000	0.47680	-0.244000	0.11960	GAG		0.443	MARCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254190.2	NM_006770	
SCTR	6344	broad.mit.edu	37	2	120231030	120231030	+	Splice_Site	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:120231030C>T	ENST00000019103.5	-	4	671	c.404G>A	c.(403-405)cGg>cAg	p.R135Q	AC013275.2_ENST00000413602.1_RNA	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor	135					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.R135Q(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	CAGGCTTACCCGCTTCTCGTT	0.592																																					p.R135Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G404A	2						.						75.0	68.0	70.0					2																	120231030		2203	4300	6503	119947500	SO:0001630	splice_region_variant	6344	exon4				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	ENST00000019103.5:c.405+1G>A	2.37:g.120231030C>T		Somatic		Capture	Illumina HiSeq	Phase_I	119947500	NM_002980	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	37	CCDS2127.1	.	.	.	.	.	.	.	.	.	.	C	3.348	-0.133207	0.06711	.	.	ENSG00000080293	ENST00000019103	T	0.40476	1.03	5.04	4.16	0.48862	.	0.116768	0.37483	N	0.002070	T	0.18087	0.0434	N	0.05619	-0.005	0.38701	D	0.952998	B	0.06786	0.001	B	0.06405	0.002	T	0.13872	-1.0493	10	0.02654	T	1	.	9.0255	0.36227	0.0:0.8293:0.0:0.1707	.	135	P47872	SCTR_HUMAN	Q	135	ENSP00000019103:R135Q	ENSP00000019103:R135Q	R	-	2	0	SCTR	119947500	0.995000	0.38212	0.996000	0.52242	0.472000	0.32918	1.897000	0.39799	1.328000	0.45358	0.561000	0.74099	CGG		0.592	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2		Missense_Mutation
INHBB	3625	broad.mit.edu	37	2	121106693	121106693	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:121106693G>A	ENST00000295228.3	+	2	513	c.467G>A	c.(466-468)cGg>cAg	p.R156Q		NM_002193.2	NP_002184.2	P09529	INHBB_HUMAN	inhibin, beta B	156					activin receptor signaling pathway (GO:0032924)|cell differentiation (GO:0030154)|cellular response to insulin stimulus (GO:0032869)|cellular response to leptin stimulus (GO:0044320)|cellular response to starvation (GO:0009267)|defense response (GO:0006952)|fat cell differentiation (GO:0045444)|growth (GO:0040007)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of hepatocyte growth factor biosynthetic process (GO:0048178)|negative regulation of insulin secretion (GO:0046676)|oocyte development (GO:0048599)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|response to mechanical stimulus (GO:0009612)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|host cell surface receptor binding (GO:0046789)|protein homodimerization activity (GO:0042803)	p.R156Q(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(4)|pancreas(2)|skin(2)	15		Prostate(154;0.122)				GCCTCCTCCCGGGTCCGCCTA	0.557																																					p.R156Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G467A	2						.						53.0	58.0	56.0					2																	121106693		2203	4300	6503	120823163	SO:0001583	missense	3625	exon2				CCDS2132.1	2q14.2	2014-01-30	2007-07-30		ENSG00000163083	ENSG00000163083		"""Endogenous ligands"""	6067	protein-coding gene	gene with protein product		147390	"""inhibin, beta B (activin AB beta polypeptide)"""			3345731	Standard	NM_002193		Approved		uc002tmn.2	P09529	OTTHUMG00000131437	ENST00000295228.3:c.467G>A	2.37:g.121106693G>A	ENSP00000295228:p.Arg156Gln	Somatic		Capture	Illumina HiSeq	Phase_I	120823163	NM_002193	Q53T31|Q8N1D3	Missense_Mutation	SNP	ENST00000295228.3	37	CCDS2132.1	.	.	.	.	.	.	.	.	.	.	G	10.96	1.497539	0.26861	.	.	ENSG00000163083	ENST00000295228	T	0.66995	-0.24	5.09	5.09	0.68999	Transforming growth factor-beta, N-terminal (1);	0.555848	0.17053	N	0.188863	T	0.53850	0.1822	L	0.31664	0.95	0.33909	D	0.639429	B	0.24823	0.112	B	0.26094	0.066	T	0.59316	-0.7477	10	0.30854	T	0.27	-3.725	11.2497	0.49017	0.0848:0.0:0.9151:0.0	.	156	P09529	INHBB_HUMAN	Q	156	ENSP00000295228:R156Q	ENSP00000295228:R156Q	R	+	2	0	INHBB	120823163	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.966000	0.70395	2.804000	0.96469	0.655000	0.94253	CGG		0.557	INHBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254234.1		
CLASP1	23332	broad.mit.edu	37	2	122176216	122176216	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:122176216G>A	ENST00000263710.4	-	23	2691	c.2302C>T	c.(2302-2304)Cgg>Tgg	p.R768W	CLASP1_ENST00000541859.1_Intron|CLASP1_ENST00000541377.1_Intron|CLASP1_ENST00000545861.1_Intron|CLASP1_ENST00000455322.2_Intron|CLASP1_ENST00000409078.3_Intron|CLASP1_ENST00000397587.3_Intron	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	768	Interaction with microtubules, MAPRE1 and MAPRE3.				axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)	p.R768W(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					GGAAAGCCCCGAGCAGGGCTT	0.607																																					p.R768W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2302T	2						.						77.0	84.0	82.0					2																	122176216		2049	4198	6247	121892686	SO:0001583	missense	23332	exon23			AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"""multiple asters 1"""	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.2302C>T	2.37:g.122176216G>A	ENSP00000263710:p.Arg768Trp	Somatic		Capture	Illumina HiSeq	Phase_I	121892686	NM_015282	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	37		.	.	.	.	.	.	.	.	.	.	G	27.5	4.841515	0.91197	.	.	ENSG00000074054	ENST00000263710	T	0.23147	1.92	5.88	5.88	0.94601	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.56499	0.1989	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.65573	0.936	T	0.59852	-0.7376	10	0.87932	D	0	-9.9028	20.2314	0.98350	0.0:0.0:1.0:0.0	.	768	Q7Z460	CLAP1_HUMAN	W	768	ENSP00000263710:R768W	ENSP00000263710:R768W	R	-	1	2	CLASP1	121892686	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.922000	0.87538	2.789000	0.95967	0.591000	0.81541	CGG		0.607	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282	
MYO7B	4648	broad.mit.edu	37	2	128379644	128379644	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:128379644C>T	ENST00000409816.2	+	26	3567	c.3535C>T	c.(3535-3537)Cgt>Tgt	p.R1179C	MYO7B_ENST00000409090.1_Missense_Mutation_p.R32C|MYO7B_ENST00000389524.4_Missense_Mutation_p.R1179C|MYO7B_ENST00000428314.1_Missense_Mutation_p.R1179C			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1179	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R1179C(1)		breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CAATGGGGTGCGTGCGGAGCC	0.687																																					p.R1179C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3535T	2						.						15.0	16.0	16.0					2																	128379644		1667	3573	5240	128096114	SO:0001583	missense	4648	exon27				CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3535C>T	2.37:g.128379644C>T	ENSP00000386461:p.Arg1179Cys	Somatic		Capture	Illumina HiSeq	Phase_I	128096114	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	.	14.56	2.573328	0.45902	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000272666;ENST00000409816;ENST00000437387;ENST00000409090	D;D;D;T;T	0.98280	-4.84;-4.84;-4.84;-1.1;-1.1	5.06	4.09	0.47781	MyTH4 domain (3);	0.000000	0.85682	D	0.000000	D	0.99381	0.9782	H	0.98314	4.2	0.53005	D	0.999967	D	0.89917	1.0	D	0.97110	1.0	D	0.98093	1.0410	10	0.87932	D	0	.	15.4691	0.75426	0.2291:0.7709:0.0:0.0	.	1179	Q6PIF6	MYO7B_HUMAN	C	1179;1179;32;1179;32;32	ENSP00000374175:R1179C;ENSP00000415090:R1179C;ENSP00000386461:R1179C;ENSP00000404927:R32C;ENSP00000386850:R32C	ENSP00000272666:R32C	R	+	1	0	MYO7B	128096114	0.767000	0.28508	0.829000	0.32907	0.117000	0.20001	1.291000	0.33330	2.343000	0.79666	0.561000	0.74099	CGT		0.687	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
AMMECR1L	83607	broad.mit.edu	37	2	128627067	128627067	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:128627067G>A	ENST00000272647.5	-	6	945	c.685C>T	c.(685-687)Cgc>Tgc	p.R229C	AMMECR1L_ENST00000393001.1_Missense_Mutation_p.R229C	NM_001199140.1	NP_001186069.1	Q6DCA0	AMERL_HUMAN	AMMECR1-like	229	AMMECR1. {ECO:0000255|PROSITE- ProRule:PRU00467}.							p.R229C(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)		GTGGCTGTGCGTTTGACACCT	0.388																																					p.R229C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C685T	2						.						151.0	133.0	139.0					2																	128627067		2203	4300	6503	128343537	SO:0001583	missense	83607	exon6				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.685C>T	2.37:g.128627067G>A	ENSP00000272647:p.Arg229Cys	Somatic		Capture	Illumina HiSeq	Phase_I	128343537	NM_001199140	B4E276	Missense_Mutation	SNP	ENST00000272647.5	37	CCDS2152.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.547296	0.65311	.	.	ENSG00000144233	ENST00000272647;ENST00000393001	.	.	.	5.39	4.47	0.54385	AMMECR1 domain (2);	0.000000	0.64402	D	0.000001	T	0.70911	0.3278	M	0.85197	2.74	0.80722	D	1	B	0.18863	0.031	B	0.18263	0.021	T	0.72394	-0.4307	9	0.54805	T	0.06	-1.1185	16.1049	0.81213	0.0:0.0:0.8661:0.1339	.	229	Q6DCA0	AMERL_HUMAN	C	229	.	ENSP00000272647:R229C	R	-	1	0	AMMECR1L	128343537	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.498000	0.81546	2.702000	0.92279	0.650000	0.86243	CGC		0.388	AMMECR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254392.1	NM_031445	
IMP4	92856	broad.mit.edu	37	2	131103833	131103833	+	Missense_Mutation	SNP	G	G	A	rs151175528		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:131103833G>A	ENST00000259239.3	+	8	1457	c.749G>A	c.(748-750)cGc>cAc	p.R250H	IMP4_ENST00000409935.1_Intron	NM_033416.1	NP_219484.1	Q96G21	IMP4_HUMAN	IMP4, U3 small nucleolar ribonucleoprotein	250	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				rRNA processing (GO:0006364)	nucleolus (GO:0005730)|ribonucleoprotein complex (GO:0030529)		p.R250H(1)		central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	18	Colorectal(110;0.1)					GTCGGGCCCCGCTTTGAGCTG	0.622																																					p.R250H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G749A	2						.	G	HIS/ARG	0,4406		0,0,2203	93.0	81.0	85.0		749	5.6	1.0	2	dbSNP_134	85	1,8599	1.2+/-3.3	0,1,4299	no	missense	IMP4	NM_033416.1	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	250/292	131103833	1,13005	2203	4300	6503	130820303	SO:0001583	missense	92856	exon8			BC010042	CCDS2160.1	2q21.1	2014-02-19	2014-02-19		ENSG00000136718	ENSG00000136718			30856	protein-coding gene	gene with protein product		612981	"""IMP4, U3 small nucleolar ribonucleoprotein, homolog (yeast)"""			8619474, 9110174, 12655004	Standard	NM_033416		Approved	MGC19606, BXDC4	uc002tra.1	Q96G21	OTTHUMG00000131627	ENST00000259239.3:c.749G>A	2.37:g.131103833G>A	ENSP00000259239:p.Arg250His	Somatic		Capture	Illumina HiSeq	Phase_I	130820303	NM_033416	Q3ZTT3	Missense_Mutation	SNP	ENST00000259239.3	37	CCDS2160.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.9|25.9	4.685107|4.685107	0.88639|0.88639	0.0|0.0	1.16E-4|1.16E-4	ENSG00000136718|ENSG00000136718	ENST00000452955|ENST00000259239;ENST00000409649;ENST00000428740	.|T;T;T	.|0.34667	.|1.35;1.35;1.35	5.63|5.63	5.63|5.63	0.86233|0.86233	.|Brix domain (3);Anticodon-binding (1);	.|0.047786	.|0.85682	.|D	.|0.000000	T|T	0.76849|0.76849	0.4045|0.4045	H|H	0.98701|0.98701	4.305|4.305	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	D|D	0.86018|0.86018	0.1505|0.1505	5|10	.|0.87932	.|D	.|0	-24.9637|-24.9637	17.5424|17.5424	0.87852|0.87852	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|250	.|Q96G21	.|IMP4_HUMAN	T|H	239|250;165;195	.|ENSP00000259239:R250H;ENSP00000386716:R165H;ENSP00000389701:R195H	.|ENSP00000259239:R250H	A|R	+|+	1|2	0|0	IMP4|IMP4	130820303|130820303	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.684000|0.684000	0.39900|0.39900	7.679000|7.679000	0.84048|0.84048	2.825000|2.825000	0.97269|0.97269	0.655000|0.655000	0.94253|0.94253	GCT|CGC		0.622	IMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254520.2	NM_033416	
NCKAP5	344148	broad.mit.edu	37	2	133542554	133542554	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:133542554G>A	ENST00000409261.1	-	14	2203	c.1830C>T	c.(1828-1830)acC>acT	p.T610T	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Silent_p.T610T|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000405974.3_Intron	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	610								p.T610T(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						CGGACTTATCGGTGTCGGCAG	0.483																																					p.T610T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1830T	2						.						65.0	67.0	66.0					2																	133542554		1958	4145	6103	133259024	SO:0001819	synonymous_variant	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.1830C>T	2.37:g.133542554G>A		Somatic		Capture	Illumina HiSeq	Phase_I	133259024	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																				0.483	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
MGAT5	4249	broad.mit.edu	37	2	135185972	135185972	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:135185972G>T	ENST00000409645.1	+	15	2083	c.1831G>T	c.(1831-1833)Ggg>Tgg	p.G611W	MGAT5_ENST00000281923.2_Missense_Mutation_p.G611W			Q09328	MGT5A_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase	611					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)	p.G611W(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|liver(1)|lung(18)|ovary(3)|pancreas(1)|skin(3)	36				BRCA - Breast invasive adenocarcinoma(221;0.0964)		TACGTGCGAGGGGATGCTACA	0.458																																					p.G611W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1831T	2						.						223.0	188.0	200.0					2																	135185972		2203	4300	6503	134902442	SO:0001583	missense	4249	exon14			D17716	CCDS2171.1	2q21	2013-02-25			ENSG00000152127	ENSG00000152127	2.4.1.155	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7049	protein-coding gene	gene with protein product		601774				8292036	Standard	NM_002410		Approved	GNT-V	uc002ttw.4	Q09328	OTTHUMG00000131681	ENST00000409645.1:c.1831G>T	2.37:g.135185972G>T	ENSP00000386377:p.Gly611Trp	Somatic		Capture	Illumina HiSeq	Phase_I	134902442	NM_002410	D3DP70	Missense_Mutation	SNP	ENST00000409645.1	37	CCDS2171.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.696228	0.88830	.	.	ENSG00000152127	ENST00000409645;ENST00000281923	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.83746	0.5321	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84572	0.0656	9	0.87932	D	0	-19.0785	19.3915	0.94584	0.0:0.0:1.0:0.0	.	611	Q09328	MGT5A_HUMAN	W	611	.	ENSP00000281923:G611W	G	+	1	0	MGAT5	134902442	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.477000	0.90424	2.876000	0.98609	0.644000	0.83932	GGG		0.458	MGAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254584.3	NM_002410	
UBXN4	23190	broad.mit.edu	37	2	136536630	136536630	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:136536630C>T	ENST00000272638.9	+	11	1477	c.1166C>T	c.(1165-1167)gCt>gTt	p.A389V	UBXN4_ENST00000490163.1_3'UTR	NM_014607.3	NP_055422.1	Q92575	UBXN4_HUMAN	UBX domain protein 4	389	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.				response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)		p.A389V(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	24						GCCCCAAGCGCTTCGGTGGTA	0.353																																					p.A389V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1166T	2						.						115.0	112.0	113.0					2																	136536630		1822	4067	5889	136253100	SO:0001583	missense	23190	exon11			D87684	CCDS42761.1	2q21.3-q22.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000144224	ENSG00000144224		"""UBX domain containing"""	14860	protein-coding gene	gene with protein product	"""erasin"""	611216	"""UBX domain-containing 2"", ""UBX domain containing 2"""	UBXDC1, UBXD2		16968747	Standard	NM_014607		Approved	KIAA0242	uc002tur.3	Q92575	OTTHUMG00000153577	ENST00000272638.9:c.1166C>T	2.37:g.136536630C>T	ENSP00000272638:p.Ala389Val	Somatic		Capture	Illumina HiSeq	Phase_I	136253100	NM_014607	A8K9W4|Q4ZG56|Q8IYM5	Missense_Mutation	SNP	ENST00000272638.9	37	CCDS42761.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.011729	0.93346	.	.	ENSG00000144224	ENST00000272638;ENST00000430594	T	0.58652	0.32	5.1	5.1	0.69264	UBX (3);	0.000000	0.85682	D	0.000000	T	0.81226	0.4778	M	0.90019	3.08	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85139	0.0979	10	0.62326	D	0.03	.	18.5375	0.91015	0.0:1.0:0.0:0.0	.	389	Q92575	UBXN4_HUMAN	V	389;371	ENSP00000272638:A389V	ENSP00000272638:A389V	A	+	2	0	UBXN4	136253100	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.998000	0.76277	2.382000	0.81193	0.655000	0.94253	GCT		0.353	UBXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331696.1	NM_014607	
DARS	1615	broad.mit.edu	37	2	136719048	136719048	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:136719048G>T	ENST00000264161.4	-	4	453	c.238C>A	c.(238-240)Cta>Ata	p.L80I	DARS_ENST00000463008.1_5'UTR|DARS_ENST00000537273.1_5'UTR	NM_001349.2	NP_001340.2	P14868	SYDC_HUMAN	aspartyl-tRNA synthetase	80					aspartyl-tRNA aminoacylation (GO:0006422)|gene expression (GO:0010467)|protein complex assembly (GO:0006461)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacylase activity (GO:0004046)|aspartate-tRNA ligase activity (GO:0004815)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)	p.L80I(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(2)	15				BRCA - Breast invasive adenocarcinoma(221;0.168)	L-Aspartic Acid(DB00128)	TGCTGACGTAGGACTAAGAAG	0.413																																					p.L80I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C238A	2						.						89.0	70.0	76.0					2																	136719048		2203	4300	6503	136435518	SO:0001583	missense	1615	exon4			J05032	CCDS2180.1	2q21.3	2011-07-01			ENSG00000115866	ENSG00000115866	6.1.1.12	"""Aminoacyl tRNA synthetases / Class II"""	2678	protein-coding gene	gene with protein product	"""aspartate tRNA ligase 1, cytoplasmic"""	603084				2674137	Standard	NM_001349		Approved		uc002tux.1	P14868	OTTHUMG00000131741	ENST00000264161.4:c.238C>A	2.37:g.136719048G>T	ENSP00000264161:p.Leu80Ile	Somatic		Capture	Illumina HiSeq	Phase_I	136435518	NM_001349	A8K3J2|D3DP77|Q2TNI3|Q32Q69|Q53HV4|Q53YC5|Q68CR9|Q9BW52	Missense_Mutation	SNP	ENST00000264161.4	37	CCDS2180.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.331535	0.81690	.	.	ENSG00000115866	ENST00000264161;ENST00000441323;ENST00000456565;ENST00000449218	T;T;T;T	0.34275	1.37;1.37;1.37;1.37	5.72	4.84	0.62591	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);Nucleic acid binding, OB-fold, tRNA/helicase-type (1);	0.296137	0.33875	N	0.004473	T	0.47600	0.1454	M	0.80183	2.485	0.80722	D	1	B	0.14438	0.01	B	0.31686	0.134	T	0.50575	-0.8812	10	0.62326	D	0.03	-1.0051	14.9564	0.71116	0.0687:0.0:0.9313:0.0	.	80	P14868	SYDC_HUMAN	I	80;47;47;47	ENSP00000264161:L80I;ENSP00000389867:L47I;ENSP00000397616:L47I;ENSP00000388801:L47I	ENSP00000264161:L80I	L	-	1	2	DARS	136435518	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.425000	0.66470	1.432000	0.47375	0.650000	0.86243	CTA		0.413	DARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254660.5	NM_001349	
LRP1B	53353	broad.mit.edu	37	2	141299472	141299472	+	Silent	SNP	C	C	T	rs542052268		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:141299472C>T	ENST00000389484.3	-	44	8234	c.7263G>A	c.(7261-7263)tcG>tcA	p.S2421S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2421					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.S2421S(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)		TTCCCCAGTCCGACCAGAATA	0.388										TSP Lung(27;0.18)																											p.S2421S	Colon(99;50 2074 2507 20106)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G7263A	2						.						108.0	100.0	103.0					2																	141299472		2203	4299	6502	141015942	SO:0001819	synonymous_variant	53353	exon44			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.7263G>A	2.37:g.141299472C>T		Somatic		Capture	Illumina HiSeq	Phase_I	141015942	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																				0.388	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
TPO	7173	broad.mit.edu	37	2	1480920	1480920	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:1480920C>T	ENST00000345913.4	+	8	973	c.882C>T	c.(880-882)gcC>gcT	p.A294A	TPO_ENST00000349624.3_Intron|TPO_ENST00000346956.3_Silent_p.A294A|TPO_ENST00000337415.3_Silent_p.A294A|TPO_ENST00000329066.4_Silent_p.A294A|TPO_ENST00000497517.2_Intron|TPO_ENST00000382201.3_Silent_p.A294A|TPO_ENST00000382198.1_Intron	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	294					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.A294A(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)	GCTCTTCGGCCGCCTGCGGCA	0.706																																					p.A294A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C882T	2						.						11.0	14.0	13.0					2																	1480920		2191	4268	6459	1459927	SO:0001819	synonymous_variant	7173	exon7				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.882C>T	2.37:g.1480920C>T		Somatic		Capture	Illumina HiSeq	Phase_I	1459927	NM_175721	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	37	CCDS1643.1																																																																																				0.706	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
TPO	7173	broad.mit.edu	37	2	1491677	1491677	+	Missense_Mutation	SNP	C	C	T	rs200475577		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:1491677C>T	ENST00000345913.4	+	10	1773	c.1682C>T	c.(1681-1683)aCg>aTg	p.T561M	TPO_ENST00000349624.3_Missense_Mutation_p.T388M|TPO_ENST00000346956.3_Missense_Mutation_p.T561M|TPO_ENST00000337415.3_Missense_Mutation_p.T561M|TPO_ENST00000329066.4_Missense_Mutation_p.T561M|TPO_ENST00000497517.2_Intron|TPO_ENST00000382201.3_Intron|TPO_ENST00000382198.1_Missense_Mutation_p.T388M	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	561					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.T561M(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)	GAGGAGCTGACGGAAAGGCTC	0.567																																					p.T561M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1682T	2						.						141.0	118.0	126.0					2																	1491677		2203	4300	6503	1470684	SO:0001583	missense	7173	exon9				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.1682C>T	2.37:g.1491677C>T	ENSP00000318820:p.Thr561Met	Somatic		Capture	Illumina HiSeq	Phase_I	1470684	NM_175721	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	15.57	2.873780	0.51695	.	.	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382198;ENST00000422464	T;T;T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	D	0.87313	0.6146	M	0.93197	3.39	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.996;1.0;0.998	D	0.90191	0.4250	10	0.66056	D	0.02	-25.9928	13.5607	0.61788	0.0:0.844:0.156:0.0	.	561;388;561	P07202-4;P07202-5;P07202	.;.;PERT_HUMAN	M	561;561;561;388;561;388;490	ENSP00000337263:T561M;ENSP00000318820:T561M;ENSP00000263886:T561M;ENSP00000332044:T388M;ENSP00000329869:T561M;ENSP00000371633:T388M;ENSP00000405788:T490M	ENSP00000329869:T561M	T	+	2	0	TPO	1470684	1.000000	0.71417	0.927000	0.36925	0.324000	0.28378	5.740000	0.68629	2.191000	0.70037	0.591000	0.81541	ACG		0.567	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
ZEB2	9839	broad.mit.edu	37	2	145162528	145162528	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:145162528C>T	ENST00000558170.2	-	5	1651	c.467G>A	c.(466-468)cGc>cAc	p.R156H	ZEB2_ENST00000539609.3_Missense_Mutation_p.R132H|ZEB2_ENST00000409487.3_Missense_Mutation_p.R156H|ZEB2_ENST00000303660.4_Missense_Mutation_p.R156H	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	156					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)	p.R156H(2)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		ATGACCATCGCGTTCCTCCAG	0.473																																					p.R132H	Melanoma(33;1235 1264 5755 16332)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G395A	2						.						103.0	89.0	94.0					2																	145162528		2203	4300	6503	144878998	SO:0001583	missense	9839	exon4			AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	14881	protein-coding gene	gene with protein product	"""SMAD interacting protein 1"""	605802	"""zinc finger homeobox 1b"""	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.467G>A	2.37:g.145162528C>T	ENSP00000454157:p.Arg156His	Somatic		Capture	Illumina HiSeq	Phase_I	144878998	NM_001171653	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation	SNP	ENST00000558170.2	37	CCDS2186.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.00|13.00	2.105804|2.105804	0.37145|0.37145	.|.	.|.	ENSG00000169554|ENSG00000169554	ENST00000431672;ENST00000440875|ENST00000392860;ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902;ENST00000392861	.|T;T;T;T;T	.|0.76709	.|-1.04;-1.04;-1.04;-1.04;-1.04	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	.|0.097230	.|0.64402	.|D	.|0.000002	T|T	0.63558|0.63558	0.2521|0.2521	N|N	0.22421|0.22421	0.69|0.69	0.31834|0.31834	N|N	0.624343|0.624343	.|P;P;B;B	.|0.41643	.|0.758;0.733;0.431;0.431	.|B;B;B;B	.|0.24974	.|0.023;0.057;0.057;0.057	T|T	0.71735|0.71735	-0.4503|-0.4503	5|10	.|0.49607	.|T	.|0.09	-6.2093|-6.2093	20.0114|20.0114	0.97452|0.97452	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|132;21;155;156	.|F5H814;Q53TD9;A0JP08;O60315	.|.;.;.;ZEB2_HUMAN	T|H	122;143|151;132;156;156;156;156	.|ENSP00000443792:R132H;ENSP00000302501:R156H;ENSP00000386854:R156H;ENSP00000395496:R156H;ENSP00000376601:R156H	.|ENSP00000302501:R156H	A|R	-|-	1|2	0|0	ZEB2|ZEB2	144878998|144878998	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.863000|4.863000	0.62983|0.62983	2.795000|2.795000	0.96236|0.96236	0.655000|0.655000	0.94253|0.94253	GCG|CGC		0.473	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795	
KIF5C	3800	broad.mit.edu	37	2	149829956	149829956	+	Silent	SNP	C	C	T	rs369291063		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:149829956C>T	ENST00000435030.1	+	12	1592	c.1224C>T	c.(1222-1224)ggC>ggT	p.G408G	KIF5C_ENST00000414838.2_Silent_p.G313G|KIF5C_ENST00000397413.1_Silent_p.G176G|KIF5C_ENST00000464066.1_3'UTR			O60282	KIF5C_HUMAN	kinesin family member 5C	408					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.G311G(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		TTGTTGCTGGCATCTCTACAG	0.478																																					p.G384G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1152T	2						.						111.0	116.0	114.0					2																	149829956		1952	4154	6106	149538202	SO:0001819	synonymous_variant	3800	exon11			AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"""Kinesins"""	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.1224C>T	2.37:g.149829956C>T		Somatic		Capture	Illumina HiSeq	Phase_I	149538202	NM_004522	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																					0.478	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522	
RIF1	55183	broad.mit.edu	37	2	152321410	152321410	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:152321410T>C	ENST00000243326.5	+	29	5859	c.5376T>C	c.(5374-5376)caT>caC	p.H1792H	RIF1_ENST00000430328.2_Silent_p.H1792H|RIF1_ENST00000428287.2_Silent_p.H1792H|RIF1_ENST00000453091.2_Silent_p.H1792H|RIF1_ENST00000444746.2_Silent_p.H1792H			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.H1792H(1)		NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		ATGAACATCATAGTGTGAATT	0.323																																					p.H1792H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T5376C	2						.						72.0	79.0	77.0					2																	152321410		2202	4298	6500	152029656	SO:0001819	synonymous_variant	55183	exon30			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.5376T>C	2.37:g.152321410T>C		Somatic		Capture	Illumina HiSeq	Phase_I	152029656	NM_001177664	A0AVS0|Q9NS16	Silent	SNP	ENST00000243326.5	37	CCDS2194.1																																																																																				0.323	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		
NEB	4703	broad.mit.edu	37	2	152417136	152417136	+	Silent	SNP	G	G	A	rs201005449	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:152417136G>A	ENST00000172853.10	-	96	14328	c.14181C>T	c.(14179-14181)caC>caT	p.H4727H	NEB_ENST00000409198.1_Silent_p.H4727H|NEB_ENST00000603639.1_Silent_p.H6428H|NEB_ENST00000427231.2_Silent_p.H6428H|NEB_ENST00000604864.1_Silent_p.H6428H|NEB_ENST00000397345.3_Silent_p.H6428H			P20929	NEBU_HUMAN	nebulin	4727					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.H4727H(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)		GGTTCTTGGCGTGTGTCAGGG	0.522													G|||	3	0.000599042	0.0008	0.0029	5008	,	,		15660	0.0		0.0	False		,,,				2504	0.0				p.H6428H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C19284T	2						.	G	,,	2,4046		0,2,2022	100.0	105.0	103.0		19284,19284,14181	-6.3	0.9	2		103	0,8370		0,0,4185	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	0,2,6207	AA,AG,GG		0.0,0.0494,0.0161	,,	6428/8526,6428/8526,4727/6670	152417136	2,12416	2024	4185	6209	152125382	SO:0001819	synonymous_variant	4703	exon124			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.14181C>T	2.37:g.152417136G>A		Somatic		Capture	Illumina HiSeq	Phase_I	152125382	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																					0.522	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
NEB	4703	broad.mit.edu	37	2	152507181	152507181	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:152507181G>A	ENST00000172853.10	-	53	7281	c.7134C>T	c.(7132-7134)gaC>gaT	p.D2378D	NEB_ENST00000409198.1_Silent_p.D2378D|NEB_ENST00000603639.1_Silent_p.D2378D|NEB_ENST00000427231.2_Silent_p.D2378D|NEB_ENST00000604864.1_Silent_p.D2378D|NEB_ENST00000397345.3_Silent_p.D2378D			P20929	NEBU_HUMAN	nebulin	2378					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.D2378D(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)		TGTAGTCCACGTCACTAACCA	0.453																																					p.D2378D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C7134T	2						.						258.0	259.0	259.0					2																	152507181		2033	4187	6220	152215427	SO:0001819	synonymous_variant	4703	exon53			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.7134C>T	2.37:g.152507181G>A		Somatic		Capture	Illumina HiSeq	Phase_I	152215427	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																					0.453	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
NR4A2	4929	broad.mit.edu	37	2	157182439	157182439	+	Silent	SNP	G	G	A	rs550135305		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:157182439G>A	ENST00000339562.4	-	8	1976	c.1614C>T	c.(1612-1614)caC>caT	p.H538H	NR4A2_ENST00000409108.2_Missense_Mutation_p.R504C|NR4A2_ENST00000409572.1_Silent_p.H538H|NR4A2_ENST00000539077.1_Silent_p.H549H|NR4A2_ENST00000426264.1_Silent_p.H475H|NR4A2_ENST00000429376.1_Missense_Mutation_p.R441C	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	538					adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.H538H(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						TGAAAGTCACGTGGTCTTTGA	0.463													G|||	1	0.000199681	0.0	0.0	5008	,	,		20346	0.001		0.0	False		,,,				2504	0.0				p.H538H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1614T	2						.						125.0	125.0	125.0					2																	157182439		2203	4300	6503	156890685	SO:0001819	synonymous_variant	4929	exon8			X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"""Nuclear hormone receptors"""	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.1614C>T	2.37:g.157182439G>A		Somatic		Capture	Illumina HiSeq	Phase_I	156890685	NM_006186	Q16311|Q53RZ2|Q6NXU0	Silent	SNP	ENST00000339562.4	37	CCDS2201.1	.	.	.	.	.	.	.	.	.	.	G	8.487	0.861184	0.17178	.	.	ENSG00000153234	ENST00000409108;ENST00000429376	D;D	0.92911	-3.13;-3.07	6.06	-8.49	0.00931	.	.	.	.	.	D	0.93766	0.8007	.	.	.	0.80722	D	1	.	.	.	.	.	.	D	0.92765	0.6227	6	0.87932	D	0	.	17.8477	0.88736	0.7497:0.0:0.2503:0.0	.	.	.	.	C	504;441	ENSP00000386993:R504C;ENSP00000410952:R441C	ENSP00000386993:R504C	R	-	1	0	NR4A2	156890685	0.043000	0.20138	0.781000	0.31783	0.996000	0.88848	-0.483000	0.06536	-1.422000	0.02004	-0.238000	0.12139	CGT		0.463	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2		
PKP4	8502	broad.mit.edu	37	2	159519587	159519587	+	Missense_Mutation	SNP	C	C	T	rs370420292		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:159519587C>T	ENST00000389759.3	+	14	2502	c.2390C>T	c.(2389-2391)cCg>cTg	p.P797L	PKP4_ENST00000495123.1_3'UTR|PKP4_ENST00000389757.3_Missense_Mutation_p.P797L|AC005042.4_ENST00000342892.4_RNA	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	797					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)		p.P797L(1)		breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						AAGAGGACTCCGCAAGAAGAT	0.378										HNSCC(62;0.18)																											p.P797L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2390T	2						.	C	LEU/PRO,LEU/PRO	2,4394		0,2,2196	24.0	27.0	26.0		2390,2390	5.7	1.0	2		26	0,8596		0,0,4298	no	missense,missense	PKP4	NM_001005476.1,NM_003628.3	98,98	0,2,6494	TT,TC,CC		0.0,0.0455,0.0154	benign,benign	797/1150,797/1193	159519587	2,12990	2198	4298	6496	159227833	SO:0001583	missense	8502	exon14			X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"""Armadillo repeat containing"""	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.2390C>T	2.37:g.159519587C>T	ENSP00000374409:p.Pro797Leu	Somatic		Capture	Illumina HiSeq	Phase_I	159227833	NM_003628	Q86W91	Missense_Mutation	SNP	ENST00000389759.3	37	CCDS33305.1	.	.	.	.	.	.	.	.	.	.	C	8.217	0.801709	0.16397	4.55E-4	0.0	ENSG00000144283	ENST00000389757;ENST00000389759	T;T	0.78481	-1.18;-1.18	5.72	5.72	0.89469	Armadillo-like helical (1);Armadillo-type fold (1);	0.385358	0.27572	N	0.018767	T	0.60869	0.2302	N	0.03154	-0.405	0.50039	D	0.999847	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.55159	-0.8184	10	0.32370	T	0.25	-11.6004	19.8968	0.96969	0.0:1.0:0.0:0.0	.	752;797;797	Q4W5T8;Q99569-2;Q99569	.;.;PKP4_HUMAN	L	797	ENSP00000374407:P797L;ENSP00000374409:P797L	ENSP00000374407:P797L	P	+	2	0	PKP4	159227833	0.868000	0.29978	0.978000	0.43139	0.985000	0.73830	3.885000	0.56182	2.691000	0.91804	0.655000	0.94253	CCG		0.378	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1		
TANC1	85461	broad.mit.edu	37	2	160050911	160050911	+	Silent	SNP	C	C	T	rs200783758		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:160050911C>T	ENST00000263635.6	+	17	3123	c.2886C>T	c.(2884-2886)gaC>gaT	p.D962D	TANC1_ENST00000454300.1_Silent_p.D856D	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	962					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.D962D(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						CCTGCCTGGACGGAACGTCAG	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		20544	0.001		0.0	False		,,,				2504	0.0				p.D962D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2886T	2						.						69.0	72.0	71.0					2																	160050911		2119	4232	6351	159759157	SO:0001819	synonymous_variant	85461	exon17			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.2886C>T	2.37:g.160050911C>T		Somatic		Capture	Illumina HiSeq	Phase_I	159759157	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																				0.552	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
ITGB6	3694	broad.mit.edu	37	2	161029145	161029145	+	Missense_Mutation	SNP	C	C	T	rs576531469		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:161029145C>T	ENST00000283249.2	-	6	1093	c.856G>A	c.(856-858)Gtc>Atc	p.V286I	ITGB6_ENST00000409872.1_Missense_Mutation_p.V286I|ITGB6_ENST00000485635.1_5'UTR|ITGB6_ENST00000409967.2_Missense_Mutation_p.V286I|ITGB6_ENST00000428609.2_Missense_Mutation_p.V244I	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	286	VWFA.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|multicellular organismal development (GO:0007275)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	virus receptor activity (GO:0001618)	p.V286I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23						TTAGGAATGACGATGCCTGCT	0.473													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19161	0.0		0.0	False		,,,				2504	0.0				p.V286I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G856A	2						.						164.0	150.0	155.0					2																	161029145		2203	4300	6503	160737391	SO:0001583	missense	3694	exon6				CCDS2212.1, CCDS63040.1, CCDS74596.1, CCDS74597.1	2q24.2	2010-03-23			ENSG00000115221	ENSG00000115221		"""Integrins"""	6161	protein-coding gene	gene with protein product		147558				1729173, 8120056	Standard	NM_001282353		Approved		uc002ubh.2	P18564	OTTHUMG00000132026	ENST00000283249.2:c.856G>A	2.37:g.161029145C>T	ENSP00000283249:p.Val286Ile	Somatic		Capture	Illumina HiSeq	Phase_I	160737391	NM_000888	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Missense_Mutation	SNP	ENST00000283249.2	37	CCDS2212.1	.	.	.	.	.	.	.	.	.	.	C	35	5.462673	0.96240	.	.	ENSG00000115221	ENST00000283249;ENST00000428609;ENST00000409967;ENST00000409872	D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23	5.49	5.49	0.81192	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	D	0.95686	0.8597	L	0.52011	1.625	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	D	0.94962	0.8109	10	0.45353	T	0.12	.	19.7273	0.96170	0.0:1.0:0.0:0.0	.	244;286	E9PEE8;P18564	.;ITB6_HUMAN	I	286;244;286;286	ENSP00000283249:V286I;ENSP00000408024:V244I;ENSP00000386828:V286I;ENSP00000386367:V286I	ENSP00000283249:V286I	V	-	1	0	ITGB6	160737391	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.718000	0.92993	0.655000	0.94253	GTC		0.473	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888	
RBMS1	5937	broad.mit.edu	37	2	161135122	161135122	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:161135122G>A	ENST00000348849.3	-	11	1429	c.999C>T	c.(997-999)ccC>ccT	p.P333P	RBMS1_ENST00000409289.2_Silent_p.P297P|RBMS1_ENST00000392753.3_Silent_p.P346P|RBMS1_ENST00000409972.1_Silent_p.P297P|RBMS1_ENST00000409075.1_Silent_p.P297P|RBMS1_ENST00000474820.1_5'UTR	NM_002897.4|NM_016836.3	NP_002888.1|NP_058520.1	P29558	RBMS1_HUMAN	RNA binding motif, single stranded interacting protein 1	333					DNA replication (GO:0006260)|RNA processing (GO:0006396)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.P333P(1)	PLA2R1/RBMS1(2)								TCATTGATGCGGGCTGTAGTG	0.493											OREG0015036	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P330P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C990T	2						.						114.0	97.0	103.0					2																	161135122		2203	4298	6501	160843368	SO:0001819	synonymous_variant	5937	exon11			D28482	CCDS2213.1	2q24.2	2013-02-12			ENSG00000153250	ENSG00000153250		"""RNA binding motif (RRM) containing"""	9907	protein-coding gene	gene with protein product	"""suppressor of cdc 2 (cdc13) with RNA binding motif 2"", ""c-myc gene single strand binding protein 2"""	602310	"""chromosome 2 open reading frame 12"""	C2orf12		8041632, 8134115, 7838710	Standard	NM_016836		Approved	SCR2, MSSP-1, MSSP-2, MSSP-3, YC1, HCC-4, DKFZp564H0764	uc002ubo.3	P29558	OTTHUMG00000132031	ENST00000348849.3:c.999C>T	2.37:g.161135122G>A		Somatic	1814	Capture	Illumina HiSeq	Phase_I	160843368	NM_002897	Q14869|Q15433|Q53P46|Q53QX8|Q53RG6|Q8WV20	Silent	SNP	ENST00000348849.3	37	CCDS2213.1																																																																																				0.493	RBMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255043.4	NM_016836	
PXDN	7837	broad.mit.edu	37	2	1664726	1664726	+	Silent	SNP	G	G	A	rs558268059		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:1664726G>A	ENST00000252804.4	-	14	1814	c.1764C>T	c.(1762-1764)gaC>gaT	p.D588D		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	588	Ig-like C2-type 4.				extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)	p.D588D(2)		breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		AGCGACCTGCGTCTGCAGGGC	0.527													G|||	1	0.000199681	0.0	0.0	5008	,	,		20076	0.001		0.0	False		,,,				2504	0.0				p.D588D												.	.	2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	c.C1764T	2						.						98.0	102.0	101.0					2																	1664726		2039	4181	6220	1643733	SO:0001819	synonymous_variant	7837	exon14			AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"""Immunoglobulin superfamily / I-set domain containing"""	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.1764C>T	2.37:g.1664726G>A		Somatic		Capture	Illumina HiSeq	Phase_I	1643733	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	37	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	G	0.068	-1.207619	0.01568	.	.	ENSG00000130508	ENST00000433670	.	.	.	5.05	-6.55	0.01854	.	.	.	.	.	T	0.62196	0.2408	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65319	-0.6197	4	.	.	.	-25.229	15.011	0.71550	0.725:0.0:0.275:0.0	.	.	.	.	M	584	.	.	T	-	2	0	PXDN	1643733	0.003000	0.15002	0.002000	0.10522	0.012000	0.07955	-0.830000	0.04410	-1.250000	0.02497	-0.229000	0.12294	ACG		0.527	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
SLC4A10	57282	broad.mit.edu	37	2	162799395	162799395	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:162799395C>T	ENST00000446997.1	+	16	2184	c.2091C>T	c.(2089-2091)aaC>aaT	p.N697N	SLC4A10_ENST00000421911.1_Silent_p.N697N|SLC4A10_ENST00000375514.5_Silent_p.N678N|SLC4A10_ENST00000272716.5_Silent_p.N667N|SLC4A10_ENST00000415876.2_Silent_p.N667N	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	697					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.N667N(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)	TTTGGGAGAACCTAACTGTGT	0.363																																					p.N678N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2034T	2						.						68.0	65.0	66.0					2																	162799395		1866	4092	5958	162507641	SO:0001819	synonymous_variant	57282	exon16				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.2091C>T	2.37:g.162799395C>T		Somatic		Capture	Illumina HiSeq	Phase_I	162507641	NM_001178016	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Silent	SNP	ENST00000446997.1	37	CCDS54411.1																																																																																				0.363	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058	
GALNT3	2591	broad.mit.edu	37	2	166606373	166606373	+	Missense_Mutation	SNP	C	C	T	rs201855584		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:166606373C>T	ENST00000392701.3	-	10	2433	c.1658G>A	c.(1657-1659)cGg>cAg	p.R553Q	GALNT3_ENST00000409882.1_Missense_Mutation_p.R291Q	NM_004482.3	NP_004473.2	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	553	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.R553Q(1)		NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(1)	20						GATGTTGTGCCGAATTTCATG	0.408																																					p.R553Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1658A	2						.						178.0	151.0	160.0					2																	166606373		2203	4299	6502	166314619	SO:0001583	missense	2591	exon10				CCDS2226.1	2q24-q31	2014-03-13	2014-03-13		ENSG00000115339	ENSG00000115339	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4125	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 3"""	601756	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)"""			9592121, 15133511	Standard	NM_004482		Approved	GalNAc-T3, HHS, HFTC	uc010fph.1	Q14435	OTTHUMG00000132157	ENST00000392701.3:c.1658G>A	2.37:g.166606373C>T	ENSP00000376465:p.Arg553Gln	Somatic		Capture	Illumina HiSeq	Phase_I	166314619	NM_004482	Q53TG9|Q7Z476	Missense_Mutation	SNP	ENST00000392701.3	37	CCDS2226.1	.	.	.	.	.	.	.	.	.	.	C	35	5.501445	0.96371	.	.	ENSG00000115339	ENST00000392701;ENST00000409882	T;T	0.80123	-1.34;-1.34	5.43	5.43	0.79202	Ricin B-related lectin (1);Ricin B lectin (3);	0.270197	0.35124	N	0.003430	D	0.90521	0.7030	M	0.90759	3.145	0.58432	D	0.999996	D	0.57571	0.98	P	0.58077	0.832	D	0.92089	0.5679	10	0.66056	D	0.02	.	19.2459	0.93902	0.0:1.0:0.0:0.0	.	553	Q14435	GALT3_HUMAN	Q	553;291	ENSP00000376465:R553Q;ENSP00000386955:R291Q	ENSP00000376465:R553Q	R	-	2	0	GALNT3	166314619	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	7.814000	0.86154	2.551000	0.86045	0.655000	0.94253	CGG		0.408	GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255205.2	NM_004482	
GALNT3	2591	broad.mit.edu	37	2	166613620	166613620	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:166613620C>T	ENST00000392701.3	-	7	2104	c.1329G>A	c.(1327-1329)tgG>tgA	p.W443*	GALNT3_ENST00000409882.1_Nonsense_Mutation_p.W181*	NM_004482.3	NP_004473.2	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	443					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.W443*(1)		NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(1)	20						ATTCATCCATCCAGACTTCTG	0.368																																					p.W443X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1329A	2						.						95.0	91.0	92.0					2																	166613620		2203	4300	6503	166321866	SO:0001587	stop_gained	2591	exon7				CCDS2226.1	2q24-q31	2014-03-13	2014-03-13		ENSG00000115339	ENSG00000115339	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4125	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 3"""	601756	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)"""			9592121, 15133511	Standard	NM_004482		Approved	GalNAc-T3, HHS, HFTC	uc010fph.1	Q14435	OTTHUMG00000132157	ENST00000392701.3:c.1329G>A	2.37:g.166613620C>T	ENSP00000376465:p.Trp443*	Somatic		Capture	Illumina HiSeq	Phase_I	166321866	NM_004482	Q53TG9|Q7Z476	Nonsense_Mutation	SNP	ENST00000392701.3	37	CCDS2226.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.475265	0.84640	.	.	ENSG00000115339	ENST00000392701;ENST00000409882;ENST00000412248	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.8609	0.96783	0.0:1.0:0.0:0.0	.	.	.	.	X	443;181;443	.	ENSP00000376465:W443X	W	-	3	0	GALNT3	166321866	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.700000	0.92200	0.650000	0.86243	TGG		0.368	GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255205.2	NM_004482	
GALNT3	2591	broad.mit.edu	37	2	166615966	166615966	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:166615966T>G	ENST00000392701.3	-	5	1728	c.953A>C	c.(952-954)aAa>aCa	p.K318T	GALNT3_ENST00000409882.1_Missense_Mutation_p.K56T	NM_004482.3	NP_004473.2	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	318					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(1)	20						AGGAGAAGGTTTGTTGAATTC	0.438																																					p.K318T												.	.	0			c.A953C	2						.						90.0	89.0	90.0					2																	166615966		2203	4300	6503	166324212	SO:0001583	missense	2591	exon5				CCDS2226.1	2q24-q31	2014-03-13	2014-03-13		ENSG00000115339	ENSG00000115339	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4125	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 3"""	601756	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)"""			9592121, 15133511	Standard	NM_004482		Approved	GalNAc-T3, HHS, HFTC	uc010fph.1	Q14435	OTTHUMG00000132157	ENST00000392701.3:c.953A>C	2.37:g.166615966T>G	ENSP00000376465:p.Lys318Thr	Germline		Capture	Illumina HiSeq	Phase_I	166324212	NM_004482	Q53TG9|Q7Z476	Missense_Mutation	SNP	ENST00000392701.3	37	CCDS2226.1	.	.	.	.	.	.	.	.	.	.	T	18.19	3.568608	0.65651	.	.	ENSG00000115339	ENST00000392701;ENST00000409882;ENST00000412248	T;T;T	0.62105	0.05;0.2;0.05	5.56	5.56	0.83823	Glycosyl transferase, family 2 (1);	0.000000	0.41712	U	0.000837	T	0.54208	0.1844	L	0.28649	0.875	0.58432	D	0.999998	B	0.28258	0.205	B	0.35971	0.215	T	0.50004	-0.8878	10	0.19147	T	0.46	.	15.7175	0.77681	0.0:0.0:0.0:1.0	.	318	Q14435	GALT3_HUMAN	T	318;56;318	ENSP00000376465:K318T;ENSP00000386955:K56T;ENSP00000412643:K318T	ENSP00000376465:K318T	K	-	2	0	GALNT3	166324212	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	8.005000	0.88553	2.109000	0.64355	0.460000	0.39030	AAA		0.438	GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255205.2	NM_004482	
SCN1A	6323	broad.mit.edu	37	2	166847987	166847987	+	Missense_Mutation	SNP	C	C	T	rs556893466|rs587780446	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:166847987C>T	ENST00000303395.4	-	26	5797	c.5798G>A	c.(5797-5799)cGa>cAa	p.R1933Q	AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000423058.2_Missense_Mutation_p.R1933Q|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.R1922Q|SCN1A_ENST00000409050.1_Missense_Mutation_p.R1905Q			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1933	IQ.				adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)	p.R1922Q(1)		NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTTTACAGTTCGCTTTAAAAG	0.353																																					p.R1905Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5714A	2						.						83.0	80.0	81.0					2																	166847987		2203	4300	6503	166556233	SO:0001583	missense	6323	exon26			AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.5798G>A	2.37:g.166847987C>T	ENSP00000303540:p.Arg1933Gln	Somatic		Capture	Illumina HiSeq	Phase_I	166556233	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	C	9.117	1.008118	0.19199	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.96522	-4.04;-4.04;-3.99;-3.99	5.76	5.76	0.90799	.	0.000000	0.52532	D	0.000074	D	0.88377	0.6420	N	0.04655	-0.195	0.29128	N	0.879821	B	0.12013	0.005	B	0.08055	0.003	T	0.78247	-0.2278	10	0.17832	T	0.49	.	10.3785	0.44096	0.0:0.8557:0.0:0.1443	.	1922	P35498-2	.	Q	1933;1933;1922;1905	ENSP00000407030:R1933Q;ENSP00000303540:R1933Q;ENSP00000364554:R1922Q;ENSP00000386312:R1905Q	ENSP00000303540:R1933Q	R	-	2	0	SCN1A	166556233	0.921000	0.31238	1.000000	0.80357	0.994000	0.84299	0.597000	0.24059	2.719000	0.93026	0.555000	0.69702	CGA		0.353	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
SCN7A	6332	broad.mit.edu	37	2	167262919	167262919	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:167262919T>G	ENST00000409855.1	-	25	4346	c.4220A>C	c.(4219-4221)aAa>aCa	p.K1407T		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1407					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.K1407T(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	TCCAGCTTCTTTTTTAACATA	0.373																																					p.K1407T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4220C	2						.						132.0	130.0	130.0					2																	167262919		1923	4165	6088	166971165	SO:0001583	missense	6332	exon25			M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.4220A>C	2.37:g.167262919T>G	ENSP00000386796:p.Lys1407Thr	Somatic		Capture	Illumina HiSeq	Phase_I	166971165	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.962751	0.74016	.	.	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.98474	-4.95	4.99	4.99	0.66335	Ion transport (1);	0.000000	0.64402	D	0.000005	D	0.98466	0.9489	L	0.61218	1.895	0.40962	D	0.984637	D	0.89917	1.0	D	0.87578	0.998	D	0.99804	1.1037	10	0.72032	D	0.01	.	12.9411	0.58345	0.0:0.0:0.0:1.0	.	1407	Q01118	SCN7A_HUMAN	T	1407	ENSP00000386796:K1407T	ENSP00000259060:K1407T	K	-	2	0	SCN7A	166971165	0.981000	0.34729	1.000000	0.80357	0.993000	0.82548	2.415000	0.44635	2.226000	0.72624	0.482000	0.46254	AAA		0.373	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
SPC25	57405	broad.mit.edu	37	2	169746017	169746017	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:169746017C>T	ENST00000282074.2	-	2	154	c.13G>A	c.(13-15)Gaa>Aaa	p.E5K	SPC25_ENST00000472216.2_5'UTR	NM_020675.3	NP_065726.1	Q9HBM1	SPC25_HUMAN	SPC25, NDC80 kinetochore complex component	5	Interaction with the N-terminus of SPBC24.|Interaction with the NDC80-NUF2 subcomplex.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)	condensed chromosome kinetochore (GO:0000777)|cytosol (GO:0005829)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)		p.E5K(1)		central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(1)	9						AGTGCCAGTTCGTCCTCTACC	0.363																																					p.E5K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G13A	2						.						55.0	51.0	53.0					2																	169746017		2203	4300	6503	169454263	SO:0001583	missense	57405	exon2			AF225416	CCDS2229.1	2q31.1	2013-06-05	2013-06-05	2007-03-02	ENSG00000152253	ENSG00000152253			24031	protein-coding gene	gene with protein product		609395	"""spindle pole body component 25 homolog (S. cerevisiae)"", ""SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae)"""	SPBC25		12477932	Standard	NM_020675		Approved	MGC22228, AD024	uc002uel.3	Q9HBM1	OTTHUMG00000132181	ENST00000282074.2:c.13G>A	2.37:g.169746017C>T	ENSP00000282074:p.Glu5Lys	Somatic		Capture	Illumina HiSeq	Phase_I	169454263	NM_020675	A8K4X8|D3DPC0	Missense_Mutation	SNP	ENST00000282074.2	37	CCDS2229.1	.	.	.	.	.	.	.	.	.	.	C	10.33	1.319099	0.23994	.	.	ENSG00000152253	ENST00000282074;ENST00000451987	.	.	.	6.16	5.28	0.74379	.	0.198673	0.52532	D	0.000075	T	0.35828	0.0945	L	0.34521	1.04	0.33383	D	0.57512	P	0.45902	0.868	B	0.37833	0.259	T	0.52388	-0.8582	9	0.37606	T	0.19	-13.641	13.6064	0.62050	0.0:0.8449:0.1551:0.0	.	5	Q9HBM1	SPC25_HUMAN	K	5	.	ENSP00000282074:E5K	E	-	1	0	SPC25	169454263	0.971000	0.33674	0.168000	0.22838	0.015000	0.08874	2.481000	0.45215	1.604000	0.50143	-0.182000	0.12963	GAA		0.363	SPC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255233.2	NM_020675	
DHRS9	10170	broad.mit.edu	37	2	169939950	169939950	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:169939950T>C	ENST00000327239.4	+	6	1929	c.425T>C	c.(424-426)aTc>aCc	p.I142T	DHRS9_ENST00000602501.1_Missense_Mutation_p.I142T|DHRS9_ENST00000432060.2_Missense_Mutation_p.I202T|DHRS9_ENST00000421653.1_5'UTR|DHRS9_ENST00000357546.2_Missense_Mutation_p.I142T|DHRS9_ENST00000436483.2_Missense_Mutation_p.I142T|DHRS9_ENST00000428522.1_Missense_Mutation_p.I142T|DHRS9_ENST00000412271.1_Missense_Mutation_p.I142T	NM_005771.4	NP_005762.2	Q9BPW9	DHRS9_HUMAN	dehydrogenase/reductase (SDR family) member 9	142					9-cis-retinoic acid biosynthetic process (GO:0042904)|androgen metabolic process (GO:0008209)|epithelial cell differentiation (GO:0030855)|progesterone metabolic process (GO:0042448)|retinol metabolic process (GO:0042572)	integral component of endoplasmic reticulum membrane (GO:0030176)	alcohol dehydrogenase (NAD) activity (GO:0004022)|racemase and epimerase activity (GO:0016854)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)	p.I142T(1)		breast(1)|endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						TTTGGACTCATCAGTGTGACA	0.493																																					p.I142T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T425C	2						.						151.0	139.0	143.0					2																	169939950		2203	4300	6503	169648196	SO:0001583	missense	10170	exon4			AF067174	CCDS2231.1, CCDS74600.1	2q31.1	2011-09-14			ENSG00000073737	ENSG00000073737		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	16888	protein-coding gene	gene with protein product	"""NADP-dependent retinol dehydrogenase/reductase"", ""3-alpha hydroxysteroid dehydrogenase"", ""retinol dehydrogenase homolog"", ""short chain dehydrogenase/reductase family 9C, member 4"""	612131				11304534, 11294878, 19027726	Standard	NM_001142270		Approved	RDHL, 3alpha-HSD, RETSDR8, RDH15, SDR9C4	uc010zde.2	Q9BPW9	OTTHUMG00000132180	ENST00000327239.4:c.425T>C	2.37:g.169939950T>C	ENSP00000316670:p.Ile142Thr	Somatic		Capture	Illumina HiSeq	Phase_I	169648196	NM_001142270	B7Z416|D3DPC1|Q5RKX1|Q9NRA9|Q9NRB0	Missense_Mutation	SNP	ENST00000327239.4	37	CCDS2231.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.839615	0.91117	.	.	ENSG00000073737	ENST00000327239;ENST00000357546;ENST00000432060;ENST00000428522;ENST00000436483;ENST00000412271	D;D;D;D;D;D	0.89810	-2.57;-2.57;-2.57;-2.57;-2.57;-2.57	5.93	5.93	0.95920	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.94414	0.8203	M	0.89968	3.075	0.58432	D	0.999999	P;D	0.55385	0.951;0.971	P;P	0.56278	0.596;0.795	D	0.95167	0.8286	10	0.66056	D	0.02	.	16.0558	0.80805	0.0:0.0:0.0:1.0	.	202;142	B7Z416;Q9BPW9	.;DHRS9_HUMAN	T	142;142;202;142;142;142	ENSP00000316670:I142T;ENSP00000350154:I142T;ENSP00000389241:I202T;ENSP00000388564:I142T;ENSP00000407167:I142T;ENSP00000407747:I142T	ENSP00000316670:I142T	I	+	2	0	DHRS9	169648196	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.797000	0.85911	2.281000	0.76405	0.533000	0.62120	ATC		0.493	DHRS9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333612.3	NM_005771	
LRP2	4036	broad.mit.edu	37	2	170009432	170009432	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:170009432C>T	ENST00000263816.3	-	67	12623	c.12338G>A	c.(12337-12339)gGt>gAt	p.G4113D		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4113					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.G4113D(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)"""	TTTGATAGCACCAAACCTAGA	0.468																																					p.G4113D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G12338A	2						.						235.0	230.0	232.0					2																	170009432		2203	4300	6503	169717678	SO:0001583	missense	4036	exon67				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.12338G>A	2.37:g.170009432C>T	ENSP00000263816:p.Gly4113Asp	Somatic		Capture	Illumina HiSeq	Phase_I	169717678	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.047731	0.93740	.	.	ENSG00000081479	ENST00000263816	D	0.89270	-2.49	5.59	5.59	0.84812	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	D	0.94145	0.8122	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90843	0.4725	10	0.10636	T	0.68	.	19.9507	0.97198	0.0:1.0:0.0:0.0	.	4113	P98164	LRP2_HUMAN	D	4113	ENSP00000263816:G4113D	ENSP00000263816:G4113D	G	-	2	0	LRP2	169717678	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.772000	0.85439	2.763000	0.94921	0.655000	0.94253	GGT		0.468	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
LRP2	4036	broad.mit.edu	37	2	170134349	170134349	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:170134349C>T	ENST00000263816.3	-	13	1963	c.1678G>A	c.(1678-1680)Gct>Act	p.A560T	LRP2_ENST00000443831.1_Intron	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	560					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.A560T(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)"""	GTTACCCCAGCAGGCCATCCC	0.453																																					p.A560T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1678A	2						.						145.0	141.0	142.0					2																	170134349		2203	4300	6503	169842595	SO:0001583	missense	4036	exon13				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.1678G>A	2.37:g.170134349C>T	ENSP00000263816:p.Ala560Thr	Somatic		Capture	Illumina HiSeq	Phase_I	169842595	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	11.92	1.783762	0.31593	.	.	ENSG00000081479	ENST00000263816	D	0.95949	-3.86	5.7	4.81	0.61882	Six-bladed beta-propeller, TolB-like (1);	0.152106	0.64402	D	0.000020	D	0.92179	0.7520	N	0.04724	-0.175	0.80722	D	1	P	0.48230	0.907	P	0.53809	0.735	D	0.91426	0.5162	10	0.25106	T	0.35	.	15.9158	0.79517	0.1365:0.8635:0.0:0.0	.	560	P98164	LRP2_HUMAN	T	560	ENSP00000263816:A560T	ENSP00000263816:A560T	A	-	1	0	LRP2	169842595	1.000000	0.71417	1.000000	0.80357	0.025000	0.11179	4.822000	0.62686	1.366000	0.46076	0.555000	0.69702	GCT		0.453	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
LRP2	4036	broad.mit.edu	37	2	170147367	170147367	+	Missense_Mutation	SNP	C	C	T	rs570052630		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:170147367C>T	ENST00000263816.3	-	8	1195	c.910G>A	c.(910-912)Gga>Aga	p.G304R	LRP2_ENST00000443831.1_Missense_Mutation_p.G304R	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	304	LDL-receptor class A 7. {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.G304R(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)"""	CAGTATTTTCCGGTACTAGTG	0.393																																					p.G304R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G910A	2						.						122.0	114.0	117.0					2																	170147367		2203	4300	6503	169855613	SO:0001583	missense	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.910G>A	2.37:g.170147367C>T	ENSP00000263816:p.Gly304Arg	Somatic		Capture	Illumina HiSeq	Phase_I	169855613	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.952356	0.53293	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.87887	-2.31;-2.31	5.42	2.55	0.30701	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (1);	0.339049	0.34156	N	0.004203	D	0.88735	0.6517	L	0.45228	1.405	0.09310	N	0.999999	D;D	0.76494	0.999;0.999	D;D	0.69307	0.963;0.948	T	0.80480	-0.1364	9	.	.	.	.	10.4984	0.44791	0.0:0.6792:0.2516:0.0692	.	304;304	E9PC35;P98164	.;LRP2_HUMAN	R	304	ENSP00000263816:G304R;ENSP00000409813:G304R	.	G	-	1	0	LRP2	169855613	0.002000	0.14202	0.000000	0.03702	0.009000	0.06853	1.037000	0.30241	0.314000	0.23086	0.655000	0.94253	GGA		0.393	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
UBR3	130507	broad.mit.edu	37	2	170857895	170857895	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:170857895T>G	ENST00000272793.5	+	27	4050	c.4000T>G	c.(4000-4002)Tgt>Ggt	p.C1334G	UBR3_ENST00000392631.1_Missense_Mutation_p.C155G|UBR3_ENST00000418381.1_Missense_Mutation_p.C1334G			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1334					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.C1334G(1)|p.C187G(1)		breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						ACATATAGATTGTCATAAATC	0.318																																					p.C1334G												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T4000G	2						.						122.0	117.0	118.0					2																	170857895		2203	4299	6502	170566141	SO:0001583	missense	130507	exon27			AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.4000T>G	2.37:g.170857895T>G	ENSP00000272793:p.Cys1334Gly	Somatic		Capture	Illumina HiSeq	Phase_I	170566141	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Missense_Mutation	SNP	ENST00000272793.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	21.0|21.0	4.076020|4.076020	0.76415|0.76415	.|.	.|.	ENSG00000144357|ENSG00000144357	ENST00000272793;ENST00000442603;ENST00000418381;ENST00000392631;ENST00000439681|ENST00000392632	D;D;D;D|.	0.99701|.	-6.45;-6.45;-6.45;-2.82|.	5.05|5.05	5.05|5.05	0.67936|0.67936	Zinc finger, RING/FYVE/PHD-type (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80518|0.80518	0.4638|0.4638	M|M	0.89214|0.89214	3.015|3.015	0.53005|0.53005	D|D	0.999964|0.999964	D;D;P|.	0.69078|.	0.995;0.997;0.932|.	D;D;D|.	0.78314|.	0.979;0.991;0.916|.	D|D	0.84317|0.84317	0.0514|0.0514	10|5	0.87932|.	D|.	0|.	.|.	15.1045|15.1045	0.72310|0.72310	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1334;155;1334|.	Q6ZT12;Q6ZT12-2;E7EVK3|.	UBR3_HUMAN;.;.|.	G|M	1334;1334;1334;155;5|391	ENSP00000272793:C1334G;ENSP00000396068:C1334G;ENSP00000376408:C155G;ENSP00000389097:C5G|.	ENSP00000272793:C1334G|.	C|I	+|+	1|3	0|3	UBR3|UBR3	170566141|170566141	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.970000|0.970000	0.65996|0.65996	7.652000|7.652000	0.83633|0.83633	2.036000|2.036000	0.60181|0.60181	0.248000|0.248000	0.18094|0.18094	TGT|ATT		0.318	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
GAD1	2571	broad.mit.edu	37	2	171702021	171702021	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:171702021G>A	ENST00000358196.3	+	8	1307	c.757G>A	c.(757-759)Gcc>Acc	p.A253T		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	253					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)	p.A253T(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						GACAGGGGGCGCCATATCCAA	0.512																																					p.A253T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G757A	2						.						97.0	97.0	97.0					2																	171702021		2203	4300	6503	171410267	SO:0001583	missense	2571	exon8				CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"""glutamate decarboxylase 1 (brain, 67kD)"""	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.757G>A	2.37:g.171702021G>A	ENSP00000350928:p.Ala253Thr	Somatic		Capture	Illumina HiSeq	Phase_I	171410267	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	37	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.171083	0.78452	.	.	ENSG00000128683	ENST00000358196	T	0.25414	1.8	5.67	5.67	0.87782	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.15435	0.0372	N	0.11313	0.125	0.80722	D	1	P	0.44344	0.833	B	0.34536	0.185	T	0.05241	-1.0897	10	0.46703	T	0.11	-17.3197	19.7657	0.96340	0.0:0.0:1.0:0.0	.	253	Q99259	DCE1_HUMAN	T	253	ENSP00000350928:A253T	ENSP00000350928:A253T	A	+	1	0	GAD1	171410267	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.476000	0.97823	2.649000	0.89929	0.655000	0.94253	GCC		0.512	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2		
GAD1	2571	broad.mit.edu	37	2	171705836	171705836	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:171705836G>A	ENST00000358196.3	+	12	1710	c.1160G>A	c.(1159-1161)cGc>cAc	p.R387H		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	387					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)	p.R387H(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						AGGAAGCACCGCCATAAACTC	0.542																																					p.R387H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1160A	2						.						80.0	70.0	73.0					2																	171705836		2203	4300	6503	171414082	SO:0001583	missense	2571	exon12				CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"""glutamate decarboxylase 1 (brain, 67kD)"""	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1160G>A	2.37:g.171705836G>A	ENSP00000350928:p.Arg387His	Somatic		Capture	Illumina HiSeq	Phase_I	171414082	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	37	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.917002	0.92249	.	.	ENSG00000128683	ENST00000358196	T	0.49720	0.77	5.76	5.76	0.90799	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.049890	0.85682	D	0.000000	T	0.69061	0.3069	M	0.88775	2.98	0.80722	D	1	D	0.56035	0.974	P	0.52598	0.703	T	0.75739	-0.3212	10	0.87932	D	0	-12.8832	19.9857	0.97347	0.0:0.0:1.0:0.0	.	387	Q99259	DCE1_HUMAN	H	387	ENSP00000350928:R387H	ENSP00000350928:R387H	R	+	2	0	GAD1	171414082	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.074000	0.64401	2.706000	0.92434	0.655000	0.94253	CGC		0.542	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2		
SLC25A12	8604	broad.mit.edu	37	2	172650181	172650181	+	Missense_Mutation	SNP	C	C	T	rs143128415	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:172650181C>T	ENST00000422440.2	-	14	1439	c.1402G>A	c.(1402-1404)Gcc>Acc	p.A468T	SLC25A12_ENST00000392592.4_Missense_Mutation_p.A361T	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	468					aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)	p.A468T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	ACATTCAGGGCGCTGACTCTG	0.458																																					p.A468T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1402A	2						.	C	THR/ALA	0,4406		0,0,2203	81.0	82.0	81.0		1402	5.3	1.0	2	dbSNP_134	81	3,8597	3.0+/-9.4	0,3,4297	no	missense	SLC25A12	NM_003705.3	58	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	468/679	172650181	3,13003	2203	4300	6503	172358427	SO:0001583	missense	8604	exon14			Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"""Solute carriers"", ""EF-hand domain containing"""	10982	protein-coding gene	gene with protein product		603667	"""solute carrier family 25 (mitochondrial carrier, Aralar), member 12"""			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.1402G>A	2.37:g.172650181C>T	ENSP00000388658:p.Ala468Thr	Somatic		Capture	Illumina HiSeq	Phase_I	172358427	NM_003705	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	37	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	C	35	5.552784	0.96501	0.0	3.49E-4	ENSG00000115840	ENST00000422440;ENST00000392592	T;T	0.79033	-1.23;-1.23	5.31	5.31	0.75309	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.88687	0.6504	M	0.76938	2.355	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	D	0.89738	0.3931	10	0.72032	D	0.01	-11.9914	18.9718	0.92718	0.0:1.0:0.0:0.0	.	361;468	B3KR64;O75746	.;CMC1_HUMAN	T	468;361	ENSP00000388658:A468T;ENSP00000376371:A361T	ENSP00000376371:A361T	A	-	1	0	SLC25A12	172358427	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.792000	0.85828	2.480000	0.83734	0.655000	0.94253	GCC		0.458	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705	
WIPF1	7456	broad.mit.edu	37	2	175436640	175436640	+	Missense_Mutation	SNP	G	G	A	rs575913592		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:175436640G>A	ENST00000392547.2	-	5	992	c.893C>T	c.(892-894)cCg>cTg	p.P298L	AC018890.6_ENST00000442996.1_RNA|WIPF1_ENST00000409415.3_Missense_Mutation_p.P298L|WIPF1_ENST00000392546.2_Missense_Mutation_p.P298L|AC018890.6_ENST00000412835.1_RNA|WIPF1_ENST00000272746.5_Missense_Mutation_p.P298L|WIPF1_ENST00000359761.3_Missense_Mutation_p.P298L|WIPF1_ENST00000409891.1_Missense_Mutation_p.P298L|WIPF1_ENST00000467149.1_5'Flank	NM_003387.4	NP_003378.3	O43516	WIPF1_HUMAN	WAS/WASL interacting protein family, member 1	298	Pro-rich.				actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|response to other organism (GO:0051707)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	actin binding (GO:0003779)|profilin binding (GO:0005522)	p.P298L(1)		NS(1)|breast(1)|endometrium(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)	32						CGAAGGCCGCGGAGTGGAAGG	0.677													G|||	1	0.000199681	0.0	0.0	5008	,	,		13796	0.0		0.001	False		,,,				2504	0.0				p.P298L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C893T	2						.						26.0	32.0	30.0					2																	175436640		2203	4300	6503	175144886	SO:0001583	missense	7456	exon5			AF031588	CCDS2260.1	2q31.2	2014-09-17	2006-10-12	2006-10-12	ENSG00000115935	ENSG00000115935			12736	protein-coding gene	gene with protein product		602357	"""Wiskott-Aldrich syndrome protein interacting protein"""	WASPIP		9405671	Standard	NM_001077269		Approved	WIP	uc002uiz.3	O43516	OTTHUMG00000132334	ENST00000392547.2:c.893C>T	2.37:g.175436640G>A	ENSP00000376330:p.Pro298Leu	Somatic		Capture	Illumina HiSeq	Phase_I	175144886	NM_001077269	B8ZZM1|D3DPE4|Q15220|Q53TA9|Q6MZU9|Q9BU37|Q9UNP1	Missense_Mutation	SNP	ENST00000392547.2	37	CCDS2260.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.610036	0.46527	.	.	ENSG00000115935	ENST00000392547;ENST00000272746;ENST00000359761;ENST00000392546;ENST00000409891;ENST00000409415	T;T;T;T;T;T	0.46063	1.55;1.54;1.55;1.55;0.9;0.88	4.53	4.53	0.55603	.	0.060005	0.64402	D	0.000002	T	0.36220	0.0959	L	0.55103	1.725	0.80722	D	1	B;B;B;B	0.31989	0.35;0.238;0.35;0.238	B;B;B;B	0.28385	0.089;0.041;0.089;0.041	T	0.22941	-1.0202	10	0.38643	T	0.18	.	11.5147	0.50513	0.089:0.0:0.911:0.0	.	298;298;298;298	O43516-3;E9PB87;O43516-2;O43516	.;.;.;WIPF1_HUMAN	L	298	ENSP00000376330:P298L;ENSP00000272746:P298L;ENSP00000352802:P298L;ENSP00000376329:P298L;ENSP00000386431:P298L;ENSP00000387150:P298L	ENSP00000272746:P298L	P	-	2	0	WIPF1	175144886	1.000000	0.71417	0.971000	0.41717	0.143000	0.21401	4.078000	0.57606	2.070000	0.61991	0.430000	0.28490	CCG		0.677	WIPF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255453.1	NM_003387	
HOXD3	3232	broad.mit.edu	37	2	177036295	177036295	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:177036295C>T	ENST00000468418.3	+	4	2682	c.592C>T	c.(592-594)Cgc>Tgc	p.R198C	HOXD3_ENST00000410016.1_Missense_Mutation_p.R198C|HOXD-AS1_ENST00000416928.2_RNA|HOXD3_ENST00000249440.3_Missense_Mutation_p.R198C			P31249	HXD3_HUMAN	homeobox D3	198					anterior/posterior pattern specification (GO:0009952)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|embryonic skeletal system morphogenesis (GO:0048704)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron differentiation (GO:0045666)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R198C(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(11)|prostate(1)|upper_aerodigestive_tract(2)	23			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.247)		CAAGCGGGTACGCACGGCATA	0.657																																					p.R198C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C592T	2						.						44.0	45.0	44.0					2																	177036295		2203	4300	6503	176744541	SO:0001583	missense	3232	exon3				CCDS2270.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128652	ENSG00000128652		"""Homeoboxes / ANTP class : HOXL subclass"""	5137	protein-coding gene	gene with protein product		142980	"""homeo box D3"""	HOX4A, HOX4, HOX1D		1973146, 1358459	Standard	NM_006898		Approved		uc002ukt.1	P31249	OTTHUMG00000132517	ENST00000468418.3:c.592C>T	2.37:g.177036295C>T	ENSP00000424734:p.Arg198Cys	Somatic		Capture	Illumina HiSeq	Phase_I	176744541	NM_006898	Q99955|Q9BSC5	Missense_Mutation	SNP	ENST00000468418.3	37	CCDS2270.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.039012	0.75617	.	.	ENSG00000128652	ENST00000468418;ENST00000410016;ENST00000249440	D;D;D	0.99186	-5.53;-5.53;-5.53	5.36	5.36	0.76844	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99641	0.9868	H	0.98542	4.26	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97454	1.0030	10	0.87932	D	0	.	19.0654	0.93108	0.0:1.0:0.0:0.0	.	198	P31249	HXD3_HUMAN	C	198	ENSP00000424734:R198C;ENSP00000386498:R198C;ENSP00000249440:R198C	ENSP00000249440:R198C	R	+	1	0	HOXD3	176744541	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	6.113000	0.71553	2.504000	0.84457	0.561000	0.74099	CGC		0.657	HOXD3-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334246.4		
PDE11A	50940	broad.mit.edu	37	2	178936708	178936708	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:178936708G>A	ENST00000286063.6	-	1	774	c.457C>T	c.(457-459)Cga>Tga	p.R153*	PDE11A_ENST00000358450.4_Intron	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	153					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)	p.R153*(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	GCCCTCCGTCGTACACTACTC	0.587									Primary Pigmented Nodular Adrenocortical Disease, Familial																												p.R153X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C457T	2						.						78.0	75.0	76.0					2																	178936708		2203	4300	6503	178644954	SO:0001587	stop_gained	50940	exon1	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"""Phosphodiesterases"""	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.457C>T	2.37:g.178936708G>A	ENSP00000286063:p.Arg153*	Somatic		Capture	Illumina HiSeq	Phase_I	178644954	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Nonsense_Mutation	SNP	ENST00000286063.6	37	CCDS33334.1	.	.	.	.	.	.	.	.	.	.	G	40	8.081797	0.98643	.	.	ENSG00000128655	ENST00000286063	.	.	.	5.04	4.06	0.47325	.	0.504890	0.20822	N	0.085054	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.6094	0.62068	0.0:0.0:0.7542:0.2457	.	.	.	.	X	153	.	ENSP00000286063:R153X	R	-	1	2	PDE11A	178644954	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.726000	0.38085	2.341000	0.79615	0.655000	0.94253	CGA		0.587	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		
OSBPL6	114880	broad.mit.edu	37	2	179201089	179201089	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179201089C>T	ENST00000190611.4	+	9	1095	c.719C>T	c.(718-720)aCg>aTg	p.T240M	OSBPL6_ENST00000315022.2_Missense_Mutation_p.T219M|OSBPL6_ENST00000357080.4_Missense_Mutation_p.T240M|OSBPL6_ENST00000409045.3_Missense_Mutation_p.T240M|OSBPL6_ENST00000409631.1_Missense_Mutation_p.T240M|OSBPL6_ENST00000359685.3_Missense_Mutation_p.T240M|OSBPL6_ENST00000392505.2_Missense_Mutation_p.T240M	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	240					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)	p.T240M(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			CTCCCTGCAACGTGCACAACT	0.507																																					p.T240M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C719T	2						.						193.0	190.0	191.0					2																	179201089		2203	4300	6503	178909335	SO:0001583	missense	114880	exon9			AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"""Oxysterol binding proteins"""	16388	protein-coding gene	gene with protein product	"""OSBP-related protein 6"""	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.719C>T	2.37:g.179201089C>T	ENSP00000190611:p.Thr240Met	Somatic		Capture	Illumina HiSeq	Phase_I	178909335	NM_032523	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	37	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.805849	0.70682	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000361154;ENST00000357080;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T;T	0.12569	2.68;2.69;2.67;2.68;2.69;2.69;2.69	5.57	4.68	0.58851	.	0.245860	0.42420	D	0.000709	T	0.24586	0.0596	L	0.29908	0.895	0.50467	D	0.999879	B;D;D;D;D;D	0.76494	0.427;0.998;0.979;0.998;0.997;0.999	B;P;P;P;P;P	0.62184	0.145;0.899;0.616;0.899;0.714;0.804	T	0.02533	-1.1145	10	0.62326	D	0.03	-4.824	16.6855	0.85304	0.0:0.8703:0.1297:0.0	.	240;219;240;240;240;240	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3;Q86V84	.;.;.;.;OSBL6_HUMAN;.	M	240;240;25;240;240;240;240;219	ENSP00000376293:T240M;ENSP00000352713:T240M;ENSP00000349591:T240M;ENSP00000387248:T240M;ENSP00000190611:T240M;ENSP00000386885:T240M;ENSP00000318723:T219M	ENSP00000190611:T240M	T	+	2	0	OSBPL6	178909335	1.000000	0.71417	0.925000	0.36789	0.532000	0.34746	4.265000	0.58865	1.448000	0.47680	0.655000	0.94253	ACG		0.507	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523	
TTN	7273	broad.mit.edu	37	2	179421757	179421757	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179421757C>T	ENST00000591111.1	-	280	83425	c.83201G>A	c.(83200-83202)cGt>cAt	p.R27734H	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R20502H|TTN_ENST00000460472.2_Missense_Mutation_p.R20310H|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R26807H|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R29375H|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R20435H			Q8WZ42	TITIN_HUMAN	titin	27734	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.R20310H(1)|p.R26805H(1)|p.R20502H(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)			TGGAAGGTCACGTCTCTCAAC	0.443																																					p.V20310M												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G60928A	2						.						86.0	88.0	87.0					2																	179421757		1996	4150	6146	179130003	SO:0001583	missense	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.83201G>A	2.37:g.179421757C>T	ENSP00000465570:p.Arg27734His	Somatic		Capture	Illumina HiSeq	Phase_I	179130003	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		.	.	.	.	.	.	.	.	.	.	C	13.12	2.142263	0.37825	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.59502	0.26;0.26;0.26;0.26	5.87	4.99	0.66335	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.63046	0.2478	M	0.88979	2.995	0.49051	D	0.999746	B;B;B;B	0.20671	0.047;0.047;0.047;0.047	B;B;B;B	0.17433	0.018;0.018;0.018;0.018	T	0.66064	-0.6016	9	0.87932	D	0	.	10.7632	0.46277	0.0:0.8004:0.131:0.0685	.	20310;20435;20502;27734	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	26807;20310;20502;20435;20307	ENSP00000343764:R26807H;ENSP00000434586:R20310H;ENSP00000340554:R20502H;ENSP00000352154:R20435H	ENSP00000340554:R20502H	R	-	2	0	TTN	179130003	1.000000	0.71417	0.996000	0.52242	0.422000	0.31414	2.567000	0.45956	1.621000	0.50320	0.655000	0.94253	CGT		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179439065	179439065	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179439065C>T	ENST00000591111.1	-	276	67095	c.66871G>A	c.(66871-66873)Gta>Ata	p.V22291I	TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V15059I|TTN_ENST00000460472.2_Missense_Mutation_p.V14867I|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V21364I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V23932I|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V14992I			Q8WZ42	TITIN_HUMAN	titin	22291	Fibronectin type-III 62. {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.V14867I(1)|p.V15059I(1)|p.V21362I(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)			TTTAGAGGTACTGGTTTTCCA	0.428																																					p.Q14866Q												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G44598A	2						.						96.0	96.0	96.0					2																	179439065		1874	4100	5974	179147311	SO:0001583	missense	7273	exon154			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.66871G>A	2.37:g.179439065C>T	ENSP00000465570:p.Val22291Ile	Somatic		Capture	Illumina HiSeq	Phase_I	179147311	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		.	.	.	.	.	.	.	.	.	.	C	4.826	0.153618	0.09185	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	5.44	-3.22	0.05125	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.43277	0.1240	L	0.41124	1.26	0.21802	N	0.999536	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.12156	0.002;0.002;0.004;0.007	T	0.45629	-0.9248	9	0.87932	D	0	.	13.9811	0.64306	0.0:0.45:0.0:0.55	.	14867;14992;15059;22291	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	21364;14867;15059;14992;14865	ENSP00000343764:V21364I;ENSP00000434586:V14867I;ENSP00000340554:V15059I;ENSP00000352154:V14992I	ENSP00000340554:V15059I	V	-	1	0	TTN	179147311	0.000000	0.05858	0.618000	0.29105	0.538000	0.34931	-0.145000	0.10265	-0.483000	0.06772	-1.360000	0.01215	GTA		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179442501	179442501	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179442501A>G	ENST00000591111.1	-	273	63953	c.63729T>C	c.(63727-63729)ccT>ccC	p.P21243P	TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342175.6_Silent_p.P14011P|TTN_ENST00000460472.2_Silent_p.P13819P|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000342992.6_Silent_p.P20316P|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Silent_p.P22884P|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.P13944P			Q8WZ42	TITIN_HUMAN	titin	21243	Fibronectin type-III 54. {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.P20314P(1)|p.P14011P(1)|p.P13819P(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)			AAGACTTCGAAGGTAGATCTC	0.388																																					p.L13819P												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.T41456C	2						.						159.0	140.0	146.0					2																	179442501		1920	4134	6054	179150747	SO:0001819	synonymous_variant	7273	exon151			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.63729T>C	2.37:g.179442501A>G		Somatic		Capture	Illumina HiSeq	Phase_I	179150747	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																																																																																					0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179458950	179458950	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179458950G>A	ENST00000591111.1	-	247	53471	c.53247C>T	c.(53245-53247)ctC>ctT	p.L17749L	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342175.6_Silent_p.L10517L|TTN_ENST00000460472.2_Silent_p.L10325L|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Silent_p.L16822L|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Silent_p.L19390L|TTN_ENST00000359218.5_Silent_p.L10450L			Q8WZ42	TITIN_HUMAN	titin	17749	Ig-like 104.				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.L16820L(1)|p.L10325L(1)|p.L10517L(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)			CTCTGAAGTCGAGGTGAAGCG	0.403																																					p.S10325L												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C30974T	2						.						61.0	58.0	59.0					2																	179458950		1886	4113	5999	179167196	SO:0001819	synonymous_variant	7273	exon125			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.53247C>T	2.37:g.179458950G>A		Somatic		Capture	Illumina HiSeq	Phase_I	179167196	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																																																																																					0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179462332	179462332	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179462332G>A	ENST00000591111.1	-	244	52778	c.52554C>T	c.(52552-52554)ggC>ggT	p.G17518G	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342175.6_Silent_p.G10286G|TTN_ENST00000460472.2_Silent_p.G10094G|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000342992.6_Silent_p.G16591G|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Silent_p.G19159G|TTN_ENST00000359218.5_Silent_p.G10219G			Q8WZ42	TITIN_HUMAN	titin	17518	Ig-like 103.				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.G10286G(1)|p.G16589G(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)			GAGAATAGACGCCTTGATGGC	0.403																																					p.G10094G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C30282T	2						.						112.0	100.0	104.0					2																	179462332		1889	4115	6004	179170577	SO:0001819	synonymous_variant	7273	exon122			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.52554C>T	2.37:g.179462332G>A		Somatic		Capture	Illumina HiSeq	Phase_I	179170577	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																																																																																					0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179484992	179484992	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179484992G>A	ENST00000591111.1	-	198	41557	c.41333C>T	c.(41332-41334)gCc>gTc	p.A13778V	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A6546V|TTN_ENST00000460472.2_Missense_Mutation_p.A6354V|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A12851V|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000604956.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A15419V|TTN_ENST00000359218.5_Missense_Mutation_p.A6479V			Q8WZ42	TITIN_HUMAN	titin	13778	Ig-like 94.				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.A6546V(1)|p.A12851V(1)|p.A6354V(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)			TTTTACATTGGCTTTCTCTCT	0.398																																					p.A6354V												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.C19061T	2						.						81.0	79.0	80.0					2																	179484992		1863	4110	5973	179193237	SO:0001583	missense	7273	exon76			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.41333C>T	2.37:g.179484992G>A	ENSP00000465570:p.Ala13778Val	Somatic		Capture	Illumina HiSeq	Phase_I	179193237	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	15.61	2.884328	0.51908	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2	6.06	6.06	0.98353	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.56543	0.1992	L	0.35288	1.05	0.58432	D	0.999997	B;B;B;B	0.29162	0.235;0.235;0.235;0.235	B;B;B;B	0.33568	0.103;0.103;0.103;0.166	T	0.57347	-0.7827	9	0.87932	D	0	.	15.6679	0.77247	0.0668:0.0:0.9332:0.0	.	6354;6479;6546;13778	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	12851;6354;6546;6479;6354	ENSP00000343764:A12851V;ENSP00000434586:A6354V;ENSP00000340554:A6546V;ENSP00000352154:A6479V	ENSP00000340554:A6546V	A	-	2	0	TTN	179193237	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.958000	0.87877	2.882000	0.98803	0.655000	0.94253	GCC		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179574312	179574312	+	Silent	SNP	C	C	T	rs369319371		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179574312C>T	ENST00000591111.1	-	97	28007	c.27783G>A	c.(27781-27783)acG>acA	p.T9261T	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342992.6_Silent_p.T8334T|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000589042.1_Silent_p.T9578T|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	13384	Ig-like 75.				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.T8334T(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)			CGATTGAAGACGTGCACAGAG	0.448																																					p.T8334T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G25002A	2						.	T	,,,	1,4079		0,1,2039	139.0	137.0	137.0		,25002,,	-8.3	0.7	2		137	0,8398		0,0,4199	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,1,6238	TT,TC,CC		0.0,0.0245,0.0080	,,,	,8334/33424,,	179574312	1,12477	2040	4199	6239	179282557	SO:0001819	synonymous_variant	7273	exon96			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.27783G>A	2.37:g.179574312C>T		Somatic		Capture	Illumina HiSeq	Phase_I	179282557	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	Silent	SNP	ENST00000591111.1	37																																																																																					0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179590692	179590692	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179590692C>A	ENST00000591111.1	-	68	19630	c.19406G>T	c.(19405-19407)gGa>gTa	p.G6469V	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.G5542V|TTN_ENST00000589042.1_Missense_Mutation_p.G6786V|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	12071	Ig-like 46.				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.G5542V(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)			CGGTGGTGTTCCCGAAAGTTC	0.413																																					p.G5542V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G16625T	2						.						90.0	86.0	87.0					2																	179590692		1892	4123	6015	179298937	SO:0001583	missense	7273	exon67			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.19406G>T	2.37:g.179590692C>A	ENSP00000465570:p.Gly6469Val	Somatic		Capture	Illumina HiSeq	Phase_I	179298937	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	15.94	2.981725	0.53827	.	.	ENSG00000155657	ENST00000342992	T	0.79940	-1.32	5.87	5.87	0.94306	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.94308	0.8171	H	0.97918	4.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95465	0.8546	9	0.87932	D	0	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	6469	Q8WZ42	TITIN_HUMAN	V	5542	ENSP00000343764:G5542V	ENSP00000343764:G5542V	G	-	2	0	TTN	179298937	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	7.758000	0.85224	2.941000	0.99782	0.655000	0.94253	GGA		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179595812	179595812	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179595812G>T	ENST00000591111.1	-	58	16853	c.16629C>A	c.(16627-16629)ggC>ggA	p.G5543G	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342992.6_Silent_p.G4616G|TTN_ENST00000589042.1_Silent_p.G5860G|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	12360	Ig-like 36.				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.G4616G(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)			TCAGTTCTTGGCCATCTTTAA	0.393																																					p.G4616G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C13848A	2						.						121.0	114.0	116.0					2																	179595812		1846	4096	5942	179304057	SO:0001819	synonymous_variant	7273	exon57			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.16629C>A	2.37:g.179595812G>T		Somatic		Capture	Illumina HiSeq	Phase_I	179304057	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	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	179639791	179639791	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179639791T>G	ENST00000591111.1	-	29	6871	c.6647A>C	c.(6646-6648)gAg>gCg	p.E2216A	TTN-AS1_ENST00000585451.1_RNA|RP11-88L24.4_ENST00000582038.2_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E2170A|TTN_ENST00000460472.2_Missense_Mutation_p.E2170A|TTN_ENST00000360870.5_Missense_Mutation_p.E2216A|TTN_ENST00000342992.6_Missense_Mutation_p.E2216A|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E2216A|TTN_ENST00000359218.5_Missense_Mutation_p.E2170A			Q8WZ42	TITIN_HUMAN	titin	12542	Ig-like 11.				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.E2170A(3)|p.E2216A(2)		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)			TTTATCTCCCTCATGAACCTC	0.403																																					p.E2216A												.	.	5	Substitution - Missense(5)	large_intestine(5)	c.A6647C	2						.						182.0	170.0	174.0					2																	179639791		2203	4300	6503	179348036	SO:0001583	missense	7273	exon29			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.6647A>C	2.37:g.179639791T>G	ENSP00000465570:p.Glu2216Ala	Somatic		Capture	Illumina HiSeq	Phase_I	179348036	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	9.864	1.197144	0.22037	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3	5.42	-1.45	0.08828	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.44623	0.1302	N	0.04880	-0.145	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	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.29792	-1.0000	9	0.87932	D	0	.	12.5625	0.56291	0.0:0.0992:0.3885:0.5123	.	2170;2170;2170;2216;2216	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	A	2216;2170;2170;2170;2170;2216	ENSP00000343764:E2216A;ENSP00000434586:E2170A;ENSP00000340554:E2170A;ENSP00000352154:E2170A;ENSP00000354117:E2216A	ENSP00000340554:E2170A	E	-	2	0	TTN	179348036	0.809000	0.29036	0.000000	0.03702	0.738000	0.42128	4.069000	0.57541	-0.653000	0.05401	-0.472000	0.04984	GAG		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179641995	179641995	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179641995G>A	ENST00000591111.1	-	27	4919	c.4695C>T	c.(4693-4695)gtC>gtT	p.V1565V	TTN-AS1_ENST00000585451.1_RNA|RP11-88L24.4_ENST00000582038.2_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342175.6_Silent_p.V1519V|TTN_ENST00000460472.2_Silent_p.V1519V|TTN_ENST00000360870.5_Silent_p.V1565V|TTN_ENST00000342992.6_Silent_p.V1565V|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000589042.1_Silent_p.V1565V|TTN_ENST00000359218.5_Silent_p.V1519V			Q8WZ42	TITIN_HUMAN	titin	12422	Ig-like 7.				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.V1519V(3)|p.V1565V(2)		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)			CCTTTATATTGACATTTTTCA	0.403																																					p.V1565V												.	.	5	Substitution - coding silent(5)	large_intestine(5)	c.C4695T	2						.						125.0	117.0	120.0					2																	179641995		2203	4300	6503	179350240	SO:0001819	synonymous_variant	7273	exon27			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.4695C>T	2.37:g.179641995G>A		Somatic		Capture	Illumina HiSeq	Phase_I	179350240	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CCDC141	285025	broad.mit.edu	37	2	179702128	179702128	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179702128G>A	ENST00000420890.2	-	23	3935	c.3818C>T	c.(3817-3819)gCg>gTg	p.A1273V	CCDC141_ENST00000295723.5_Missense_Mutation_p.A698V|CCDC141_ENST00000480419.1_5'UTR	NM_173648.3	NP_775919.3	Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	1273								p.A698V(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)			GCATGCATCCGCAAAGGCAAC	0.527																																					p.A1273V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3818T	2						.						79.0	81.0	80.0					2																	179702128		2203	4300	6503	179410373	SO:0001583	missense	285025	exon23			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.3818C>T	2.37:g.179702128G>A	ENSP00000395995:p.Ala1273Val	Somatic		Capture	Illumina HiSeq	Phase_I	179410373	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000420890.2	37		.	.	.	.	.	.	.	.	.	.	G	15.98	2.993136	0.54041	.	.	ENSG00000163492	ENST00000420890;ENST00000343876;ENST00000295723	T;T;T	0.55588	0.51;1.06;1.05	5.56	3.42	0.39159	.	0.211473	0.32719	N	0.005733	T	0.46014	0.1371	L	0.53249	1.67	0.24368	N	0.994843	D;D	0.55605	0.972;0.972	B;B	0.40864	0.342;0.342	T	0.48958	-0.8988	10	0.72032	D	0.01	-2.3557	11.2844	0.49214	0.0743:0.2404:0.6853:0.0	.	698;698	Q6ZP82;Q6ZP82-2	CC141_HUMAN;.	V	1273;717;698	ENSP00000395995:A1273V;ENSP00000344627:A717V;ENSP00000295723:A698V	ENSP00000295723:A698V	A	-	2	0	CCDC141	179410373	1.000000	0.71417	0.900000	0.35374	0.969000	0.65631	3.149000	0.50655	1.322000	0.45245	0.650000	0.86243	GCG		0.527	CCDC141-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173648	
CERKL	375298	broad.mit.edu	37	2	182413572	182413572	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:182413572A>C	ENST00000339098.5	-	8	985	c.986T>G	c.(985-987)cTg>cGg	p.L329R	CERKL_ENST00000409440.3_Missense_Mutation_p.L285R|CERKL_ENST00000410087.3_Missense_Mutation_p.L303R|CERKL_ENST00000374969.2_Missense_Mutation_p.L190R|CERKL_ENST00000479558.1_5'UTR|CERKL_ENST00000374970.2_Missense_Mutation_p.L234R			Q49MI3	CERKL_HUMAN	ceramide kinase-like	329	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				negative regulation of apoptotic process (GO:0043066)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)	p.L303R(1)		NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(13)|ovary(3)|skin(3)	32			OV - Ovarian serous cystadenocarcinoma(117;0.088)			GACGTCGACCAGCTGTACATG	0.423																																					p.L303R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T908G	2						.						57.0	61.0	60.0					2																	182413572		2203	4300	6503	182121817	SO:0001583	missense	375298	exon7			BC020465	CCDS33340.1, CCDS33341.1, CCDS42789.1, CCDS46466.1, CCDS54425.1	2q31.3	2005-01-04			ENSG00000188452	ENSG00000188452			21699	protein-coding gene	gene with protein product			"""retinitis pigmentosa 26 (autosomal recessive)"""	RP26		14681825	Standard	NR_027689		Approved		uc002uny.3	Q49MI3	OTTHUMG00000154315	ENST00000339098.5:c.986T>G	2.37:g.182413572A>C	ENSP00000341159:p.Leu329Arg	Somatic		Capture	Illumina HiSeq	Phase_I	182121817	NM_201548	B2RPL2|B4DEY1|Q49MH9|Q49MI0|Q49MI1|Q49MI2|Q5DVJ2|Q5DVJ4|Q5DVJ5|Q6UZF6|Q6ZP59	Missense_Mutation	SNP	ENST00000339098.5	37	CCDS42789.1	.	.	.	.	.	.	.	.	.	.	A	10.85	1.465991	0.26335	.	.	ENSG00000188452	ENST00000410087;ENST00000409440;ENST00000374969;ENST00000339098;ENST00000374970	T;T;T;T;T	0.13196	2.61;2.61;2.61;2.61;2.61	5.53	1.44	0.22558	Diacylglycerol kinase, catalytic domain (2);	0.402127	0.28067	N	0.016730	T	0.05364	0.0142	N	0.02916	-0.46	0.09310	N	1	B;B;B;B;B	0.24882	0.005;0.018;0.113;0.002;0.005	B;B;B;B;B	0.21917	0.02;0.017;0.037;0.004;0.011	T	0.35025	-0.9805	10	0.42905	T	0.14	.	9.2621	0.37619	0.0759:0.0:0.6816:0.2425	.	285;190;234;303;329	B4DEY1;Q49MI3-4;Q49MI3-3;Q49MI3-2;Q49MI3	.;.;.;.;CERKL_HUMAN	R	303;285;190;329;234	ENSP00000386725:L303R;ENSP00000387080:L285R;ENSP00000364108:L190R;ENSP00000341159:L329R;ENSP00000364109:L234R	ENSP00000341159:L329R	L	-	2	0	CERKL	182121817	0.995000	0.38212	0.000000	0.03702	0.059000	0.15707	2.881000	0.48538	-0.025000	0.13918	-0.256000	0.11100	CTG		0.423	CERKL-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334811.1		
MYT1L	23040	broad.mit.edu	37	2	1893072	1893072	+	Missense_Mutation	SNP	C	C	T	rs201961477	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:1893072C>T	ENST00000399161.2	-	16	3208	c.2461G>A	c.(2461-2463)Gta>Ata	p.V821I	MYT1L_ENST00000428368.2_Missense_Mutation_p.V819I	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	821					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.V821I(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)		GTGTAGTCTACGGGCAAGTCC	0.557													C|||	2	0.000399361	0.0	0.0	5008	,	,		15407	0.002		0.0	False		,,,				2504	0.0				p.V819I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2455A	2						.	C	ILE/VAL	2,4004		0,2,2001	86.0	90.0	89.0		2455	4.8	0.6	2		89	0,8278		0,0,4139	yes	missense	MYT1L	NM_015025.2	29	0,2,6140	TT,TC,CC		0.0,0.0499,0.0163	possibly-damaging	819/1185	1893072	2,12282	2003	4139	6142	1872079	SO:0001583	missense	23040	exon16			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.2461G>A	2.37:g.1893072C>T	ENSP00000382114:p.Val821Ile	Somatic		Capture	Illumina HiSeq	Phase_I	1872079	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	37		2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	c	12.40	1.927467	0.34002	4.99E-4	0.0	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.42513	0.97;0.97	4.77	4.77	0.60923	Myelin transcription factor 1 (1);	0.000000	0.85682	D	0.000000	T	0.45155	0.1328	N	0.25890	0.77	0.58432	D	0.999999	D;D	0.71674	0.998;0.997	D;P	0.64321	0.924;0.835	T	0.20075	-1.0286	10	0.02654	T	1	-24.9726	17.7539	0.88444	0.0:1.0:0.0:0.0	.	821;819	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	I	821;767;819	ENSP00000382114:V821I;ENSP00000396103:V819I	ENSP00000295067:V767I	V	-	1	0	MYT1L	1872079	1.000000	0.71417	0.617000	0.29091	0.959000	0.62525	4.805000	0.62561	2.365000	0.80145	0.586000	0.80456	GTA		0.557	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025	
MYT1L	23040	broad.mit.edu	37	2	1915834	1915834	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:1915834G>A	ENST00000399161.2	-	12	2414	c.1667C>T	c.(1666-1668)aCg>aTg	p.T556M	MYT1L_ENST00000428368.2_Missense_Mutation_p.T554M	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	556					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.T556M(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)		CCCGCGCCCCGTGCAGCCCGG	0.597																																					p.T554M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1661T	2						.						46.0	48.0	47.0					2																	1915834		2045	4222	6267	1894841	SO:0001583	missense	23040	exon12			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.1667C>T	2.37:g.1915834G>A	ENSP00000382114:p.Thr556Met	Somatic		Capture	Illumina HiSeq	Phase_I	1894841	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	37		.	.	.	.	.	.	.	.	.	.	G	31	5.081081	0.94050	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.52295	0.68;0.67	5.24	5.24	0.73138	.	0.046027	0.85682	D	0.000000	T	0.67239	0.2872	M	0.68952	2.095	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.65010	0.926;0.931	T	0.70346	-0.4897	10	0.87932	D	0	-23.6239	19.1783	0.93612	0.0:0.0:1.0:0.0	.	556;554	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	M	556;502;554	ENSP00000382114:T556M;ENSP00000396103:T554M	ENSP00000295067:T502M	T	-	2	0	MYT1L	1894841	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.685000	0.84117	2.595000	0.87683	0.561000	0.74099	ACG		0.597	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025	
ZNF804A	91752	broad.mit.edu	37	2	185803240	185803240	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:185803240A>T	ENST00000302277.6	+	4	3711	c.3117A>T	c.(3115-3117)gaA>gaT	p.E1039D		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	1039							metal ion binding (GO:0046872)	p.E1039D(1)		NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						TCCCACTAGAAAACCATGACA	0.423																																					p.E1039D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3117T	2						.						72.0	70.0	70.0					2																	185803240		2203	4300	6503	185511485	SO:0001583	missense	91752	exon4			AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.3117A>T	2.37:g.185803240A>T	ENSP00000303252:p.Glu1039Asp	Somatic		Capture	Illumina HiSeq	Phase_I	185511485	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	A	13.14	2.149519	0.37923	.	.	ENSG00000170396	ENST00000302277	T	0.09911	2.93	5.09	5.09	0.68999	.	0.000000	0.47093	D	0.000250	T	0.09113	0.0225	L	0.46157	1.445	0.29412	N	0.861165	B	0.24920	0.114	B	0.28638	0.092	T	0.15983	-1.0418	10	0.32370	T	0.25	-21.8498	2.3096	0.04183	0.5989:0.1616:0.0847:0.1548	.	1039	Q7Z570	Z804A_HUMAN	D	1039	ENSP00000303252:E1039D	ENSP00000303252:E1039D	E	+	3	2	ZNF804A	185511485	0.996000	0.38824	1.000000	0.80357	0.798000	0.45092	0.787000	0.26858	1.907000	0.55213	0.383000	0.25322	GAA		0.423	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
ASNSD1	54529	broad.mit.edu	37	2	190532578	190532578	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:190532578T>C	ENST00000260952.4	+	5	1966	c.1553T>C	c.(1552-1554)tTg>tCg	p.L518S	ASNSD1_ENST00000607062.1_Missense_Mutation_p.L37S	NM_019048.2	NP_061921	Q9NWL6	ASND1_HUMAN	asparagine synthetase domain containing 1	518	Asparagine synthetase.				asparagine biosynthetic process (GO:0006529)|glutamine metabolic process (GO:0006541)		asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)	p.L518S(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(3)	25			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0449)|all cancers(119;0.118)			CTGGAAGGATTGAATAAGGAA	0.423																																					p.L518S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1553C	2						.						126.0	129.0	128.0					2																	190532578		2203	4300	6503	190240823	SO:0001583	missense	54529	exon5			AY116969	CCDS2300.1	2q32.2	2012-09-20			ENSG00000138381	ENSG00000138381			24910	protein-coding gene	gene with protein product							Standard	NM_019048		Approved	NS3TP1, FLJ20752, NBLA00058	uc002uqt.3	Q9NWL6	OTTHUMG00000132665	ENST00000260952.4:c.1553T>C	2.37:g.190532578T>C	ENSP00000260952:p.Leu518Ser	Somatic		Capture	Illumina HiSeq	Phase_I	190240823	NM_019048	D3DPH6|Q3LIC3|Q4ZG45	Missense_Mutation	SNP	ENST00000260952.4	37	CCDS2300.1	.	.	.	.	.	.	.	.	.	.	T	16.46	3.129114	0.56721	.	.	ENSG00000138381	ENST00000260952;ENST00000420250	T;T	0.45276	0.9;0.9	5.33	4.15	0.48705	Rossmann-like alpha/beta/alpha sandwich fold (1);Asparagine synthase (1);	0.070349	0.64402	D	0.000020	T	0.73048	0.3537	H	0.95816	3.725	0.51767	D	0.999937	D	0.89917	1.0	D	0.85130	0.997	T	0.79916	-0.1601	10	0.87932	D	0	-4.3629	12.3845	0.55325	0.0:0.0:0.141:0.859	.	518	Q9NWL6	ASND1_HUMAN	S	518	ENSP00000260952:L518S;ENSP00000406790:L518S	ENSP00000260952:L518S	L	+	2	0	ASNSD1	190240823	1.000000	0.71417	0.098000	0.21074	0.928000	0.56348	7.698000	0.84413	0.838000	0.34948	-0.466000	0.05196	TTG		0.423	ASNSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255919.3	NM_019048	
STAT1	6772	broad.mit.edu	37	2	191851606	191851606	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:191851606T>C	ENST00000361099.3	-	14	1582	c.1195A>G	c.(1195-1197)Agt>Ggt	p.S399G	STAT1_ENST00000409465.1_Missense_Mutation_p.S399G|STAT1_ENST00000540176.1_3'UTR|STAT1_ENST00000392322.3_Missense_Mutation_p.S399G|STAT1_ENST00000392323.2_Missense_Mutation_p.S401G	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	399					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.S399G(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)			GCCGCCAGACTGCCATTGGTG	0.438																																					p.S399G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1195G	2						.						249.0	259.0	256.0					2																	191851606		2203	4300	6503	191559851	SO:0001583	missense	6772	exon14				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.1195A>G	2.37:g.191851606T>C	ENSP00000354394:p.Ser399Gly	Somatic		Capture	Illumina HiSeq	Phase_I	191559851	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	37	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.723773	0.48728	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000392322;ENST00000392323	D;D;D;D	0.88509	-2.39;-2.39;-2.39;-2.39	5.49	5.49	0.81192	STAT transcription factor, DNA-binding, subdomain (1);STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);	0.078947	0.85682	D	0.000000	D	0.89733	0.6800	L	0.39147	1.195	0.80722	D	1	D;B	0.69078	0.997;0.035	P;B	0.59056	0.851;0.049	D	0.86955	0.2088	10	0.18276	T	0.48	-27.4222	15.7623	0.78096	0.0:0.0:0.0:1.0	.	399;399	P42224-2;P42224	.;STAT1_HUMAN	G	399;399;399;401	ENSP00000354394:S399G;ENSP00000386244:S399G;ENSP00000376136:S399G;ENSP00000376137:S401G	ENSP00000354394:S399G	S	-	1	0	STAT1	191559851	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	3.682000	0.54656	2.311000	0.77944	0.533000	0.62120	AGT		0.438	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315	
OSR1	130497	broad.mit.edu	37	2	19553462	19553462	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:19553462C>T	ENST00000272223.2	-	2	449	c.105G>A	c.(103-105)tcG>tcA	p.S35S	OSR1_ENST00000536433.1_Silent_p.S35S	NM_145260.2	NP_660303.1	Q8TAX0	OSR1_HUMAN	odd-skipped related transciption factor 1	35					cell differentiation (GO:0030154)|cell proliferation involved in kidney development (GO:0072111)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal joint morphogenesis (GO:0060272)|embryonic skeletal limb joint morphogenesis (GO:0036023)|gonad development (GO:0008406)|heart development (GO:0007507)|intermediate mesoderm development (GO:0048389)|mesangial cell development (GO:0072143)|mesonephric duct morphogenesis (GO:0072180)|mesonephros development (GO:0001823)|metanephric cap mesenchymal cell proliferation involved in metanephros development (GO:0090094)|metanephric epithelium development (GO:0072207)|metanephric glomerulus vasculature development (GO:0072239)|metanephric interstitial fibroblast development (GO:0072259)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephric nephron tubule development (GO:0072234)|metanephric smooth muscle tissue development (GO:0072208)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of nephron tubule epithelial cell differentiation (GO:0072183)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis (GO:0042476)|palate development (GO:0060021)|pattern specification involved in metanephros development (GO:0072268)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gastrulation (GO:2000543)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posterior mesonephric tubule development (GO:0072166)|pronephros development (GO:0048793)|renal vesicle progenitor cell differentiation (GO:0072184)|specification of anterior mesonephric tubule identity (GO:0072168)|specification of posterior mesonephric tubule identity (GO:0072169)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)|ureter urothelium development (GO:0072190)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.S35S(1)		breast(1)|large_intestine(2)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.197)	Acute lymphoblastic leukemia(84;0.221)				GCAGATGGTCCGAAGGCACTG	0.617																																					p.S35S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G105A	2						.						49.0	46.0	47.0					2																	19553462		2203	4300	6503	19416943	SO:0001819	synonymous_variant	130497	exon2			BC025712	CCDS1694.1	2p24.1	2013-10-17	2013-10-17	2004-11-26	ENSG00000143867	ENSG00000143867		"""Zinc fingers, C2H2-type"""	8111	protein-coding gene	gene with protein product		608891	"""odd-skipped (Drosophila) homolog"", ""odd-skipped related 1 (Drosophila)"""	ODD		2120051, 12119563	Standard	XM_006711942		Approved		uc002rdc.3	Q8TAX0	OTTHUMG00000088793	ENST00000272223.2:c.105G>A	2.37:g.19553462C>T		Somatic		Capture	Illumina HiSeq	Phase_I	19416943	NM_145260	B3KV97|D6W521	Silent	SNP	ENST00000272223.2	37	CCDS1694.1																																																																																				0.617	OSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000201432.2	NM_145260	
MYO1B	4430	broad.mit.edu	37	2	192256913	192256913	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:192256913C>T	ENST00000392318.3	+	19	2309	c.2062C>T	c.(2062-2064)Cga>Tga	p.R688*	MYO1B_ENST00000339514.4_Nonsense_Mutation_p.R688*|MYO1B_ENST00000439065.2_5'UTR|MYO1B_ENST00000304164.4_Nonsense_Mutation_p.R688*|MYO1B_ENST00000392316.1_Nonsense_Mutation_p.R688*	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	688	Myosin motor.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.R688*(1)		NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			GATATTCATCCGAAACCCAAG	0.303																																					p.R688X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2062T	2						.						58.0	65.0	62.0					2																	192256913		2203	4298	6501	191965158	SO:0001587	stop_gained	4430	exon19			L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"""Myosins / Myosin superfamily : Class I"""	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.2062C>T	2.37:g.192256913C>T	ENSP00000376132:p.Arg688*	Somatic		Capture	Illumina HiSeq	Phase_I	191965158	NM_012223	O43794|Q7Z6L5	Nonsense_Mutation	SNP	ENST00000392318.3	37	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	C	41	8.566635	0.98866	.	.	ENSG00000128641	ENST00000339514;ENST00000392318;ENST00000304164;ENST00000392316	.	.	.	5.71	3.83	0.44106	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8571	0.63534	0.3986:0.6014:0.0:0.0	.	.	.	.	X	688	.	ENSP00000306382:R688X	R	+	1	2	MYO1B	191965158	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.903000	0.39858	1.404000	0.46819	0.557000	0.71058	CGA		0.303	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223	
DNAH7	56171	broad.mit.edu	37	2	196664076	196664076	+	Missense_Mutation	SNP	C	C	T	rs146114466	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:196664076C>T	ENST00000312428.6	-	55	10397	c.10297G>A	c.(10297-10299)Gtg>Atg	p.V3433M		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3433	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.V3433M(1)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						GGAGAGAGCACGAAAATCAGT	0.418													C|||	5	0.000998403	0.0038	0.0	5008	,	,		15075	0.0		0.0	False		,,,				2504	0.0				p.V3433M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G10297A	2						.	C	MET/VAL	8,3808		0,8,1900	126.0	130.0	129.0		10297	3.4	0.6	2	dbSNP_134	129	1,8249		0,1,4124	yes	missense	DNAH7	NM_018897.2	21	0,9,6024	TT,TC,CC		0.0121,0.2096,0.0746	probably-damaging	3433/4025	196664076	9,12057	1908	4125	6033	196372321	SO:0001583	missense	56171	exon55			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.10297G>A	2.37:g.196664076C>T	ENSP00000311273:p.Val3433Met	Somatic		Capture	Illumina HiSeq	Phase_I	196372321	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	17.42	3.385982	0.61956	0.002096	1.21E-4	ENSG00000118997	ENST00000312428	T	0.10763	2.84	5.2	3.4	0.38934	Dynein heavy chain (1);	0.132781	0.51477	D	0.000097	T	0.37839	0.1018	M	0.92604	3.325	0.80722	D	1	D	0.54772	0.968	D	0.66084	0.941	T	0.39840	-0.9594	10	0.62326	D	0.03	.	10.9503	0.47325	0.0:0.8479:0.0:0.1521	.	3433	Q8WXX0	DYH7_HUMAN	M	3433	ENSP00000311273:V3433M	ENSP00000311273:V3433M	V	-	1	0	DNAH7	196372321	0.497000	0.26067	0.596000	0.28811	0.875000	0.50365	0.999000	0.29757	0.759000	0.33084	0.650000	0.86243	GTG		0.418	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
PGAP1	80055	broad.mit.edu	37	2	197706002	197706002	+	Missense_Mutation	SNP	C	C	T	rs77720656		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:197706002C>T	ENST00000354764.4	-	27	2839	c.2725G>A	c.(2725-2727)Gtc>Atc	p.V909I		NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	909					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)	p.V909I(1)		breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						GGAATGAAGACAAAGCATGGA	0.368																																					p.V909I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2725A	2						.						105.0	98.0	101.0					2																	197706002		2203	4300	6503	197414247	SO:0001583	missense	80055	exon27				CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"""GPI inositol-deacylase"""	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.2725G>A	2.37:g.197706002C>T	ENSP00000346809:p.Val909Ile	Somatic		Capture	Illumina HiSeq	Phase_I	197414247	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.962403	0.34659	.	.	ENSG00000197121	ENST00000354764;ENST00000422444	.	.	.	4.89	4.89	0.63831	.	0.168141	0.40908	D	0.000999	T	0.30541	0.0768	N	0.12182	0.205	0.80722	D	1	B;B	0.12013	0.005;0.002	B;B	0.10450	0.002;0.005	T	0.13872	-1.0493	9	0.18710	T	0.47	-2.0589	9.0499	0.36369	0.0:0.8383:0.0:0.1617	.	735;909	Q75T13-2;Q75T13	.;PGAP1_HUMAN	I	909;146	.	ENSP00000346809:V909I	V	-	1	0	PGAP1	197414247	0.989000	0.36119	1.000000	0.80357	0.801000	0.45260	1.037000	0.30241	2.558000	0.86282	0.585000	0.79938	GTC		0.368	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989	
PLCL1	5334	broad.mit.edu	37	2	198949573	198949573	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:198949573C>T	ENST00000428675.1	+	2	1730	c.1332C>T	c.(1330-1332)ctC>ctT	p.L444L	PLCL1_ENST00000437704.2_Silent_p.L346L	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	444	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.L346L(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	GCGTTGAACTCGATGTAAGTG	0.398																																					p.L444L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1332T	2						.						61.0	58.0	59.0					2																	198949573		2203	4300	6503	198657818	SO:0001819	synonymous_variant	5334	exon2			D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"""phospholipase C related, but catalytically inactive protein"", ""protein phosphatase 1, regulatory subunit 127"""	600597	"""phospholipase C, epsilon"""	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.1332C>T	2.37:g.198949573C>T		Somatic		Capture	Illumina HiSeq	Phase_I	198657818	NM_006226	Q3MJ90|Q53SD3|Q7Z3S3	Silent	SNP	ENST00000428675.1	37	CCDS2326.2																																																																																				0.398	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226	
SPATS2L	26010	broad.mit.edu	37	2	201337621	201337621	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:201337621C>T	ENST00000358677.5	+	12	1374	c.1127C>T	c.(1126-1128)gCg>gTg	p.A376V	SPATS2L_ENST00000409385.1_Missense_Mutation_p.A316V|SPATS2L_ENST00000409140.3_Missense_Mutation_p.A376V|SPATS2L_ENST00000409755.3_Missense_Mutation_p.A406V|SPATS2L_ENST00000409151.1_Missense_Mutation_p.A384V|SPATS2L_ENST00000451764.2_Missense_Mutation_p.A376V|SPATS2L_ENST00000460095.1_3'UTR|SPATS2L_ENST00000360760.5_Missense_Mutation_p.A307V|SPATS2L_ENST00000409988.3_Missense_Mutation_p.A376V|SPATS2L_ENST00000409718.1_Missense_Mutation_p.A376V	NM_001282735.1|NM_001282743.1|NM_001282744.1|NM_015535.2	NP_001269664.1|NP_001269672.1|NP_001269673.1|NP_056350.2	Q9NUQ6	SPS2L_HUMAN	spermatogenesis associated, serine-rich 2-like	376						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)	poly(A) RNA binding (GO:0044822)	p.A406V(2)|p.A376V(1)		endometrium(1)|kidney(1)|lung(4)|ovary(2)|pancreas(1)|prostate(1)	10						CTGCTGAATGCGCACGCAGCA	0.488																																					p.A376V												.	.	3	Substitution - Missense(3)	prostate(2)|large_intestine(1)	c.C1127T	2						.						82.0	87.0	86.0					2																	201337621		1989	4175	6164	201045866	SO:0001583	missense	26010	exon12			AF193059	CCDS46483.1, CCDS46484.1, CCDS74621.1, CCDS74622.1	2q33.1	2009-06-12			ENSG00000196141	ENSG00000196141			24574	protein-coding gene	gene with protein product	"""DNA polymerase transactivated protein 6"""	613817				11230166	Standard	NM_001100422		Approved	DNAPTP6	uc002uvr.4	Q9NUQ6	OTTHUMG00000154589	ENST00000358677.5:c.1127C>T	2.37:g.201337621C>T	ENSP00000351503:p.Ala376Val	Somatic		Capture	Illumina HiSeq	Phase_I	201045866	NM_015535	A8K381|B4DRE6|B4DT67|B7WNZ7|Q53T22|Q8WV53|Q8WYG1|Q9NTW4	Missense_Mutation	SNP	ENST00000358677.5	37	CCDS46483.1	.	.	.	.	.	.	.	.	.	.	C	3.986	-0.005526	0.07773	.	.	ENSG00000196141	ENST00000409718;ENST00000358677;ENST00000409988;ENST00000409385;ENST00000451764;ENST00000360760;ENST00000409140;ENST00000409755;ENST00000409151	.	.	.	5.39	3.62	0.41486	.	0.796492	0.11604	N	0.547497	T	0.27866	0.0686	N	0.22421	0.69	0.09310	N	1	B;B;B	0.26975	0.041;0.165;0.016	B;B;B	0.21546	0.002;0.035;0.002	T	0.15925	-1.0420	9	0.33141	T	0.24	0.062	8.9058	0.35523	0.0:0.7731:0.0:0.2269	.	406;307;376	B4DT67;Q9NUQ6-2;Q9NUQ6	.;.;SPS2L_HUMAN	V	376;376;376;316;376;307;376;406;384	.	ENSP00000351503:A376V	A	+	2	0	SPATS2L	201045866	0.001000	0.12720	0.001000	0.08648	0.009000	0.06853	1.143000	0.31553	0.855000	0.35359	-0.812000	0.03155	GCG		0.488	SPATS2L-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336208.3	NM_015535	
AOX1	316	broad.mit.edu	37	2	201457926	201457926	+	Splice_Site	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:201457926C>T	ENST00000374700.2	+	2	344	c.103C>T	c.(103-105)Ctt>Ttt	p.L35F		NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	35	2Fe-2S ferredoxin-type. {ECO:0000255|PROSITE-ProRule:PRU00465}.				inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)	p.L35F(1)		breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	GAGGAAGAAGCGTATCCTTTT	0.328																																					p.L35F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C103T	2						.						282.0	239.0	253.0					2																	201457926		2203	4300	6503	201166171	SO:0001630	splice_region_variant	316	exon2			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.103+1C>T	2.37:g.201457926C>T		Somatic		Capture	Illumina HiSeq	Phase_I	201166171	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	37	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.881333	0.51801	.	.	ENSG00000138356	ENST00000374700;ENST00000454629	T;T	0.58940	1.45;0.3	5.22	3.43	0.39272	Beta-grasp fold, ferredoxin-type (1);Ferredoxin (3);	0.156801	0.42821	N	0.000651	T	0.58424	0.2121	M	0.76727	2.345	0.54753	D	0.999981	B	0.25772	0.134	B	0.30782	0.12	T	0.60188	-0.7312	10	0.87932	D	0	-5.2863	10.7283	0.46081	0.0:0.8429:0.0:0.1571	.	35	Q06278	ADO_HUMAN	F	35;10	ENSP00000363832:L35F;ENSP00000392485:L10F	ENSP00000363832:L35F	L	+	1	0	AOX1	201166171	0.865000	0.29922	0.456000	0.27044	0.987000	0.75469	1.034000	0.30204	0.776000	0.33473	0.591000	0.81541	CTT		0.328	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	Missense_Mutation
AOX1	316	broad.mit.edu	37	2	201527662	201527662	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:201527662T>C	ENST00000374700.2	+	31	3754	c.3513T>C	c.(3511-3513)gtT>gtC	p.V1171V	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	1171					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)	p.V1171V(1)		breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	GTTCCGAGGTTGAAATAGACT	0.478																																					p.V1171V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3513C	2						.						141.0	131.0	135.0					2																	201527662		2203	4300	6503	201235907	SO:0001819	synonymous_variant	316	exon31			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.3513T>C	2.37:g.201527662T>C		Somatic		Capture	Illumina HiSeq	Phase_I	201235907	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Silent	SNP	ENST00000374700.2	37	CCDS33360.1																																																																																				0.478	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	
NIF3L1	60491	broad.mit.edu	37	2	201768297	201768297	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:201768297C>T	ENST00000409020.1	+	7	1324	c.1030C>T	c.(1030-1032)Cga>Tga	p.R344*	NIF3L1_ENST00000409357.1_Nonsense_Mutation_p.R344*|NIF3L1_ENST00000409588.1_3'UTR|NIF3L1_ENST00000416651.1_Nonsense_Mutation_p.R344*|NIF3L1_ENST00000359683.4_Nonsense_Mutation_p.R317*			Q9GZT8	GTPC1_HUMAN	NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae)	344					7,8-dihydroneopterin 3'-triphosphate biosynthetic process (GO:0035998)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTP cyclohydrolase I activity (GO:0003934)|metal ion binding (GO:0046872)|transcription factor binding (GO:0008134)	p.R317*(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(2)	13						CAACACTGAACGAGGCTTTCT	0.438																																					p.R317X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C949T	2						.						154.0	145.0	148.0					2																	201768297		1889	4116	6005	201476542	SO:0001587	stop_gained	60491	exon7			AB038949	CCDS42797.1, CCDS46485.1, CCDS46486.1	2q33	2011-11-10	2011-11-10		ENSG00000196290	ENSG00000196290			13390	protein-coding gene	gene with protein product		605778	"""NIF3 (Ngg1 interacting factor 3, S.pombe homolog)-like 1"", ""NIF3 NGG1 interacting factor 3-like 1 (S. pombe)"""	ALS2CR1		11124544, 11161814, 12522100	Standard	NM_001136039		Approved	CALS-7, MDS015	uc002uwm.2	Q9GZT8	OTTHUMG00000154588	ENST00000409020.1:c.1030C>T	2.37:g.201768297C>T	ENSP00000386394:p.Arg344*	Somatic		Capture	Illumina HiSeq	Phase_I	201476542	NM_021824	Q53TX4|Q6X735|Q9H2D2|Q9HC18	Nonsense_Mutation	SNP	ENST00000409020.1	37	CCDS46485.1	.	.	.	.	.	.	.	.	.	.	C	32	5.173245	0.94807	.	.	ENSG00000196290	ENST00000416651;ENST00000409020;ENST00000359683;ENST00000409357	.	.	.	5.33	3.48	0.39840	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.6632	10.0426	0.42166	0.1417:0.7862:0.0:0.0721	.	.	.	.	X	344;344;317;344	.	ENSP00000352711:R317X	R	+	1	2	NIF3L1	201476542	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.713000	0.37951	0.692000	0.31613	0.557000	0.71058	CGA		0.438	NIF3L1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336201.1	NM_021824	
CASP8	841	broad.mit.edu	37	2	202150030	202150030	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:202150030C>T	ENST00000432109.2	+	9	1483	c.1294C>T	c.(1294-1296)Cga>Tga	p.R432*	CASP8_ENST00000264274.9_Nonsense_Mutation_p.R348*|CASP8_ENST00000392266.3_3'UTR|CASP8_ENST00000264275.5_Nonsense_Mutation_p.R449*|CASP8_ENST00000323492.7_Nonsense_Mutation_p.R417*|CASP8_ENST00000358485.4_Nonsense_Mutation_p.R491*|CASP8_ENST00000392259.2_3'UTR	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase	432					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|heart development (GO:0007507)|hepatocyte apoptotic process (GO:0097284)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|macrophage differentiation (GO:0030225)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|natural killer cell activation (GO:0030101)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of necroptotic process (GO:0060546)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|protein heterooligomerization (GO:0051291)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of thymocyte apoptotic process (GO:0070243)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to cold (GO:0009409)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell activation (GO:0042110)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|Noc1p-Noc2p complex (GO:0030690)|nucleus (GO:0005634)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|peptidase activity (GO:0008233)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)	p.R449*(2)|p.R491*(2)		breast(5)|cervix(2)|endometrium(6)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(9)|urinary_tract(3)	52						CCTGAGAGAGCGATGTCCTCG	0.507										HNSCC(4;0.00038)																											p.R417X	Melanoma(82;831 1348 20716 36952 40159)											.	.	4	Substitution - Nonsense(4)	large_intestine(4)	c.C1249T	2						.						88.0	79.0	82.0					2																	202150030		2203	4300	6503	201858275	SO:0001587	stop_gained	841	exon7			U60520	CCDS2342.1, CCDS2343.1, CCDS2345.1, CCDS42798.1, CCDS42799.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000064012	ENSG00000064012		"""Caspases"""	1509	protein-coding gene	gene with protein product		601763	"""caspase 8, apoptosis-related cysteine protease"""			8681376, 8681377	Standard	NM_033355		Approved	MCH5, MACH, FLICE, Casp-8	uc002uxt.1	Q14790	OTTHUMG00000132821	ENST00000432109.2:c.1294C>T	2.37:g.202150030C>T	ENSP00000412523:p.Arg432*	Somatic		Capture	Illumina HiSeq	Phase_I	201858275	NM_033356	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Nonsense_Mutation	SNP	ENST00000432109.2	37	CCDS2342.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.854011	0.91355	.	.	ENSG00000064012	ENST00000392263;ENST00000264274;ENST00000432109;ENST00000264275;ENST00000358485;ENST00000323492;ENST00000444430	.	.	.	5.37	-0.0641	0.13774	.	0.491720	0.23362	N	0.049019	.	.	.	.	.	.	0.33432	D	0.581203	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.7959	0.08738	0.4714:0.3404:0.0731:0.1151	.	.	.	.	X	417;348;432;449;491;417;211	.	ENSP00000264274:R348X	R	+	1	2	CASP8	201858275	0.981000	0.34729	0.997000	0.53966	0.724000	0.41520	0.848000	0.27710	0.348000	0.23949	-0.314000	0.08810	CGA		0.507	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228	
ALS2	57679	broad.mit.edu	37	2	202580551	202580551	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:202580551C>T	ENST00000264276.6	-	25	4220	c.3848G>A	c.(3847-3849)gGa>gAa	p.G1283E	ALS2_ENST00000457679.2_3'UTR	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	1283					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.G1283E(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						TGCCAGGTTTCCTAGCTTCCT	0.433																																					p.G1283E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3848A	2						.						176.0	169.0	171.0					2																	202580551		1866	4095	5961	202288796	SO:0001583	missense	57679	exon25			AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"""Rho guanine nucleotide exchange factors"""	443	protein-coding gene	gene with protein product	"""alsin"""	606352	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"""	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.3848G>A	2.37:g.202580551C>T	ENSP00000264276:p.Gly1283Glu	Somatic		Capture	Illumina HiSeq	Phase_I	202288796	NM_020919	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Missense_Mutation	SNP	ENST00000264276.6	37	CCDS42800.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.887510	0.91814	.	.	ENSG00000003393	ENST00000264276	T	0.60920	0.15	5.28	5.28	0.74379	.	0.050980	0.85682	D	0.000000	T	0.74906	0.3778	M	0.76574	2.34	0.80722	D	1	P	0.45827	0.867	P	0.58873	0.847	T	0.76963	-0.2764	10	0.62326	D	0.03	.	18.9003	0.92440	0.0:1.0:0.0:0.0	.	1283	Q96Q42	ALS2_HUMAN	E	1283	ENSP00000264276:G1283E	ENSP00000264276:G1283E	G	-	2	0	ALS2	202288796	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	7.594000	0.82698	2.456000	0.83038	0.491000	0.48974	GGA		0.433	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919	
ALS2	57679	broad.mit.edu	37	2	202591432	202591432	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:202591432T>A	ENST00000264276.6	-	18	3509	c.3137A>T	c.(3136-3138)gAt>gTt	p.D1046V	ALS2_ENST00000457679.2_Missense_Mutation_p.D358V	NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	1046					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.D1046V(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						ATAGGTGGCATCCTTTAGGCG	0.478																																					p.D1046V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3137T	2						.						95.0	93.0	94.0					2																	202591432		1956	4149	6105	202299677	SO:0001583	missense	57679	exon18			AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"""Rho guanine nucleotide exchange factors"""	443	protein-coding gene	gene with protein product	"""alsin"""	606352	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"""	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.3137A>T	2.37:g.202591432T>A	ENSP00000264276:p.Asp1046Val	Somatic		Capture	Illumina HiSeq	Phase_I	202299677	NM_020919	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Missense_Mutation	SNP	ENST00000264276.6	37	CCDS42800.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.753614	0.89753	.	.	ENSG00000003393	ENST00000264276;ENST00000457679	T;T	0.78816	0.28;-1.21	5.72	5.72	0.89469	.	0.207562	0.52532	D	0.000078	D	0.86814	0.6023	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;0.992	D;P	0.73380	0.98;0.899	D	0.87960	0.2729	10	0.72032	D	0.01	.	16.3035	0.82836	0.0:0.0:0.0:1.0	.	1046;1046	Q6IQ41;Q96Q42	.;ALS2_HUMAN	V	1046;358	ENSP00000264276:D1046V;ENSP00000394823:D358V	ENSP00000264276:D1046V	D	-	2	0	ALS2	202299677	1.000000	0.71417	0.994000	0.49952	0.892000	0.51952	7.655000	0.83696	2.299000	0.77371	0.528000	0.53228	GAT		0.478	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919	
ICA1L	130026	broad.mit.edu	37	2	203679474	203679474	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:203679474C>T	ENST00000392237.2	-	9	974	c.817G>A	c.(817-819)Gac>Aac	p.D273N	ICA1L_ENST00000358299.2_Missense_Mutation_p.D273N	NM_138468.4	NP_612477.3	Q8NDH6	ICA1L_HUMAN	islet cell autoantigen 1,69kDa-like	273								p.D273N(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TCTTTATTGTCTTCACTAATC	0.348																																					p.D273N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G817A	2						.						209.0	186.0	194.0					2																	203679474		2202	4300	6502	203387719	SO:0001583	missense	130026	exon9			AB053317	CCDS2354.1, CCDS74632.1	2q33	2008-02-05	2006-05-26	2006-05-26	ENSG00000163596	ENSG00000163596			14442	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 15"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 14"""	ALS2CR15, ALS2CR14		11586298	Standard	NM_138468		Approved		uc002uzh.1	Q8NDH6	OTTHUMG00000132856	ENST00000392237.2:c.817G>A	2.37:g.203679474C>T	ENSP00000376070:p.Asp273Asn	Somatic		Capture	Illumina HiSeq	Phase_I	203387719	NM_138468	B3KRW6|Q53P45|Q53QZ4|Q53T97|Q96N47|Q96Q32|Q9BVQ2	Missense_Mutation	SNP	ENST00000392237.2	37	CCDS2354.1	.	.	.	.	.	.	.	.	.	.	C	10.90	1.481449	0.26598	.	.	ENSG00000163596	ENST00000392237;ENST00000358299	.	.	.	5.79	4.9	0.64082	Islet cell autoantigen Ica1, C-terminal (1);	0.599918	0.17940	N	0.156892	T	0.55577	0.1929	L	0.54323	1.7	0.80722	D	1	B	0.17038	0.02	B	0.18871	0.023	T	0.49466	-0.8937	9	0.27785	T	0.31	.	11.2704	0.49136	0.0:0.9135:0.0:0.0865	.	273	Q8NDH6	ICA1L_HUMAN	N	273	.	ENSP00000351047:D273N	D	-	1	0	ICA1L	203387719	0.997000	0.39634	0.985000	0.45067	0.024000	0.10985	1.330000	0.33781	2.735000	0.93741	0.655000	0.94253	GAC		0.348	ICA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256330.1	NM_138468	
NBEAL1	65065	broad.mit.edu	37	2	204067431	204067431	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:204067431C>T	ENST00000449802.1	+	50	7679	c.7346C>T	c.(7345-7347)aCa>aTa	p.T2449I		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2449								p.T2449I(1)|p.T1159I(1)		NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						TGCTTAGCTACAGATTACTGT	0.308																																					p.T2449I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C7346T	2						.						125.0	119.0	120.0					2																	204067431		1852	4086	5938	203775676	SO:0001583	missense	65065	exon50			AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.7346C>T	2.37:g.204067431C>T	ENSP00000399903:p.Thr2449Ile	Somatic		Capture	Illumina HiSeq	Phase_I	203775676	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	37	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.906617	0.33628	.	.	ENSG00000144426	ENST00000449802;ENST00000340268;ENST00000414576	T;T	0.57907	0.37;0.37	5.98	5.11	0.69529	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.087245	0.85682	N	0.000000	T	0.32041	0.0816	N	0.11154	0.105	0.40968	D	0.984672	B;B	0.11235	0.004;0.002	B;B	0.20384	0.016;0.029	T	0.14062	-1.0486	10	0.25106	T	0.35	.	9.9248	0.41485	0.0:0.8061:0.0:0.1939	.	2449;2438	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	I	2449;2380;464	ENSP00000399903:T2449I;ENSP00000388466:T464I	ENSP00000344985:T2380I	T	+	2	0	NBEAL1	203775676	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.385000	0.44371	1.530000	0.49136	0.591000	0.81541	ACA		0.308	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
NRP2	8828	broad.mit.edu	37	2	206607961	206607961	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:206607961A>G	ENST00000357785.5	+	9	1357	c.1326A>G	c.(1324-1326)tcA>tcG	p.S442S	NRP2_ENST00000272849.3_Silent_p.S442S|NRP2_ENST00000357118.4_Silent_p.S442S|NRP2_ENST00000540841.1_Silent_p.S442S|NRP2_ENST00000360409.3_Silent_p.S442S|NRP2_ENST00000412873.2_Silent_p.S442S|NRP2_ENST00000355117.4_Silent_p.S442S|NRP2_ENST00000540178.1_Silent_p.S442S|NRP2_ENST00000417189.1_Silent_p.S442S			Q99435	NELL2_HUMAN	neuropilin 2	0	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.S442S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						GGATGCTCTCAGGCCTCATTG	0.607																																					p.S442S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1326G	2						.						165.0	175.0	171.0					2																	206607961		2203	4300	6503	206316206	SO:0001819	synonymous_variant	8828	exon9			AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.1326A>G	2.37:g.206607961A>G		Somatic		Capture	Illumina HiSeq	Phase_I	206316206	NM_201266	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Silent	SNP	ENST00000357785.5	37	CCDS46496.1																																																																																				0.607	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1		
NRP2	8828	broad.mit.edu	37	2	206659615	206659615	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:206659615G>A	ENST00000357785.5	+	17	2645	c.2614G>A	c.(2614-2616)Gtc>Atc	p.V872I	NRP2_ENST00000540841.1_Missense_Mutation_p.V855I|NRP2_ENST00000360409.3_Missense_Mutation_p.V877I|NRP2_ENST00000412873.2_Missense_Mutation_p.V855I|NRP2_ENST00000540178.1_Missense_Mutation_p.V872I			Q99435	NELL2_HUMAN	neuropilin 2	0						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.V877I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						CTCACTGGGCGTCCTCCTGGG	0.602																																					p.V877I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2629A	2						.						101.0	90.0	94.0					2																	206659615		2203	4300	6503	206367860	SO:0001583	missense	8828	exon17			AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.2614G>A	2.37:g.206659615G>A	ENSP00000350432:p.Val872Ile	Somatic		Capture	Illumina HiSeq	Phase_I	206367860	NM_201266	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000357785.5	37	CCDS46496.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.158035	0.78114	.	.	ENSG00000118257	ENST00000360409;ENST00000540178;ENST00000540841;ENST00000357785;ENST00000412873	D;D;D;D;D	0.91351	-2.64;-2.7;-2.82;-2.75;-2.83	6.17	5.28	0.74379	Neuropilin-1, C-terminal (1);	0.170766	0.51477	D	0.000100	D	0.94598	0.8259	M	0.63843	1.955	0.80722	D	1	D;D;P	0.89917	1.0;1.0;0.937	D;D;B	0.85130	0.997;0.997;0.196	D	0.95105	0.8233	10	0.87932	D	0	-40.6739	17.419	0.87510	0.0:0.1245:0.8754:0.0	.	855;872;877	O60462-2;O60462-3;O60462	.;.;NRP2_HUMAN	I	877;872;855;872;855	ENSP00000353582:V877I;ENSP00000439658:V872I;ENSP00000439261:V855I;ENSP00000350432:V872I;ENSP00000407626:V855I	ENSP00000350432:V872I	V	+	1	0	NRP2	206367860	1.000000	0.71417	0.917000	0.36280	0.608000	0.37181	7.979000	0.88103	1.585000	0.49928	0.655000	0.94253	GTC		0.602	NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1		
ZDBF2	57683	broad.mit.edu	37	2	207172772	207172772	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:207172772C>T	ENST00000374423.3	+	5	3906	c.3520C>T	c.(3520-3522)Cga>Tga	p.R1174*		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1174							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R1174*(1)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AATAGTCAATCGACCTCAAAT	0.373																																					p.R1174X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C3520T	2						.						106.0	102.0	103.0					2																	207172772		1884	4103	5987	206881017	SO:0001587	stop_gained	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.3520C>T	2.37:g.207172772C>T	ENSP00000363545:p.Arg1174*	Somatic		Capture	Illumina HiSeq	Phase_I	206881017	NM_020923	Q6ZNP7|Q6ZSN8	Nonsense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	C	41	9.102261	0.99066	.	.	ENSG00000204186	ENST00000374423	.	.	.	4.1	3.22	0.36961	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.061	0.42275	0.0:0.7961:0.2039:0.0	.	.	.	.	X	1174	.	ENSP00000363545:R1174X	R	+	1	2	ZDBF2	206881017	0.111000	0.22076	0.072000	0.20136	0.021000	0.10359	3.018000	0.49625	1.296000	0.44742	-0.172000	0.13284	CGA		0.373	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
MDH1B	130752	broad.mit.edu	37	2	207619823	207619823	+	Missense_Mutation	SNP	G	G	A	rs545659170		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:207619823G>A	ENST00000374412.3	-	5	1095	c.820C>T	c.(820-822)Cgc>Tgc	p.R274C	MDH1B_ENST00000449792.1_Missense_Mutation_p.R176C|MDH1B_ENST00000454776.2_Missense_Mutation_p.R274C|MDH1B_ENST00000392214.2_Intron	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	274					carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)	p.R274C(1)		NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		TGTGCAATGCGTGGGGCATAT	0.473													G|||	1	0.000199681	0.0	0.0	5008	,	,		19983	0.0		0.0	False		,,,				2504	0.001				p.R274C	Pancreas(76;29 1355 28675 37177 51207)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C820T	2						.						123.0	109.0	114.0					2																	207619823		2203	4300	6503	207328068	SO:0001583	missense	130752	exon5				CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.820C>T	2.37:g.207619823G>A	ENSP00000363533:p.Arg274Cys	Somatic		Capture	Illumina HiSeq	Phase_I	207328068	NM_001039845	A8K8M1|Q53TK9|Q8IV51	Missense_Mutation	SNP	ENST00000374412.3	37	CCDS33365.1	.	.	.	.	.	.	.	.	.	.	G	16.41	3.114777	0.56505	.	.	ENSG00000138400	ENST00000374412;ENST00000449792;ENST00000454776	T;T;T	0.07114	3.22;3.22;3.22	5.49	-0.661	0.11417	NAD(P)-binding domain (1);	0.623994	0.18753	N	0.132136	T	0.05318	0.0141	N	0.08118	0	0.09310	N	1	D;D	0.56521	0.976;0.959	P;P	0.52710	0.707;0.513	T	0.29671	-1.0004	10	0.87932	D	0	-0.7766	0.9488	0.01371	0.3283:0.0913:0.227:0.3533	.	274;274	Q5I0G3-2;Q5I0G3	.;MDH1B_HUMAN	C	274;176;274	ENSP00000363533:R274C;ENSP00000416577:R176C;ENSP00000389916:R274C	ENSP00000363533:R274C	R	-	1	0	MDH1B	207328068	0.050000	0.20438	0.002000	0.10522	0.002000	0.02628	2.765000	0.47621	0.108000	0.17862	-0.262000	0.10625	CGC		0.473	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845	
PIKFYVE	200576	broad.mit.edu	37	2	209195376	209195376	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:209195376G>A	ENST00000264380.4	+	23	4079	c.3921G>A	c.(3919-3921)caG>caA	p.Q1307Q		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1307					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)	p.Q1307Q(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						CTGGATATCAGCATACAATTC	0.383																																					p.Q1307Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3921A	2						.						176.0	176.0	176.0					2																	209195376		2203	4300	6503	208903621	SO:0001819	synonymous_variant	200576	exon23			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.3921G>A	2.37:g.209195376G>A		Somatic		Capture	Illumina HiSeq	Phase_I	208903621	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	37	CCDS2382.1																																																																																				0.383	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
PIKFYVE	200576	broad.mit.edu	37	2	209204148	209204148	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:209204148G>A	ENST00000264380.4	+	30	4837	c.4679G>A	c.(4678-4680)cGc>cAc	p.R1560H		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1560					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)	p.R1560H(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						TTAGAGGATCGCTTCTTAACA	0.413																																					p.R1560H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4679A	2						.						126.0	125.0	125.0					2																	209204148		2203	4300	6503	208912393	SO:0001583	missense	200576	exon30			AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.4679G>A	2.37:g.209204148G>A	ENSP00000264380:p.Arg1560His	Somatic		Capture	Illumina HiSeq	Phase_I	208912393	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.825795	0.90955	.	.	ENSG00000115020	ENST00000264380	T	0.29655	1.56	6.16	6.16	0.99307	.	0.061291	0.64402	D	0.000004	T	0.46580	0.1400	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.27806	-1.0063	10	0.49607	T	0.09	-13.0904	20.8598	0.99761	0.0:0.0:1.0:0.0	.	1560	Q9Y2I7	FYV1_HUMAN	H	1560	ENSP00000264380:R1560H	ENSP00000264380:R1560H	R	+	2	0	PIKFYVE	208912393	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.093000	0.64517	2.937000	0.99478	0.650000	0.86243	CGC		0.413	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
ERBB4	2066	broad.mit.edu	37	2	212566887	212566887	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:212566887G>T	ENST00000342788.4	-	12	1604	c.1294C>A	c.(1294-1296)Ctg>Atg	p.L432M	ERBB4_ENST00000436443.1_Missense_Mutation_p.L432M|ERBB4_ENST00000402597.1_Missense_Mutation_p.L432M	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	432					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.L432M(1)		NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	AGCAAGGACAGGCCACTAAGG	0.428										TSP Lung(8;0.080)																											p.L432M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1294A	2						.						97.0	91.0	93.0					2																	212566887		2203	4300	6503	212275132	SO:0001583	missense	2066	exon12			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.1294C>A	2.37:g.212566887G>T	ENSP00000342235:p.Leu432Met	Somatic		Capture	Illumina HiSeq	Phase_I	212275132	NM_005235	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	G	16.20	3.055159	0.55325	.	.	ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597	T;T;T	0.44482	0.92;0.92;0.92	5.71	5.71	0.89125	EGF receptor, L domain (1);	0.052531	0.85682	D	0.000000	T	0.46268	0.1384	L	0.31578	0.945	0.43830	D	0.996408	P;P;P;P;P	0.51240	0.896;0.657;0.943;0.896;0.915	P;P;P;P;P	0.62649	0.846;0.599;0.792;0.846;0.905	T	0.30119	-0.9989	10	0.33141	T	0.24	.	9.0523	0.36383	0.0731:0.0:0.7792:0.1476	.	432;432;291;432;432	Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303	.;.;.;.;ERBB4_HUMAN	M	432	ENSP00000342235:L432M;ENSP00000403204:L432M;ENSP00000385565:L432M	ENSP00000342235:L432M	L	-	1	2	ERBB4	212275132	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.881000	0.63114	2.712000	0.92718	0.650000	0.86243	CTG		0.428	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	
BARD1	580	broad.mit.edu	37	2	215634028	215634028	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:215634028T>C	ENST00000260947.4	-	5	1457	c.1323A>G	c.(1321-1323)atA>atG	p.I441M	BARD1_ENST00000449967.2_Missense_Mutation_p.I297M	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	441					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.I441M(1)		NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CAACAGAAGGTATGTCGCCCT	0.333									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.I441M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1323G	2						.						81.0	76.0	77.0					2																	215634028		2203	4300	6503	215342273	SO:0001583	missense	580	exon5	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"""Ankyrin repeat domain containing"""	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.1323A>G	2.37:g.215634028T>C	ENSP00000260947:p.Ile441Met	Somatic		Capture	Illumina HiSeq	Phase_I	215342273	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	37	CCDS2397.1	.	.	.	.	.	.	.	.	.	.	T	11.12	1.546048	0.27652	.	.	ENSG00000138376	ENST00000260947;ENST00000449967	T;T	0.66280	-0.2;-0.2	5.01	-6.88	0.01665	Ankyrin repeat-containing domain (3);	0.944178	0.08874	N	0.881021	T	0.52533	0.1740	L	0.55834	1.745	0.09310	N	1	B;P	0.45768	0.142;0.866	B;P	0.48654	0.156;0.585	T	0.50466	-0.8825	10	0.56958	D	0.05	-0.1221	0.4361	0.00479	0.2856:0.1922:0.2939:0.2283	.	297;441	E7EUI3;Q99728	.;BARD1_HUMAN	M	441;297	ENSP00000260947:I441M;ENSP00000406752:I297M	ENSP00000260947:I441M	I	-	3	3	BARD1	215342273	0.002000	0.14202	0.006000	0.13384	0.112000	0.19704	-0.264000	0.08658	-0.983000	0.03511	-0.256000	0.11100	ATA		0.333	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465	
SMARCAL1	50485	broad.mit.edu	37	2	217311825	217311825	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:217311825C>T	ENST00000357276.4	+	11	2125	c.1795C>T	c.(1795-1797)Cca>Tca	p.P599S	SMARCAL1_ENST00000358207.5_Missense_Mutation_p.P599S	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	599	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)	p.P599S(1)		NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		CGCAGTCAAGCCAACTTTCTT	0.537									Schimke Immuno-Osseous Dysplasia																												p.P599S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1795T	2						.						169.0	156.0	160.0					2																	217311825		2203	4300	6503	217020070	SO:0001583	missense	50485	exon11	Familial Cancer Database	SIOD	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"""HepA-related protein"", ""ATP-driven annealing helicase"""	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.1795C>T	2.37:g.217311825C>T	ENSP00000349823:p.Pro599Ser	Somatic		Capture	Illumina HiSeq	Phase_I	217020070	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Missense_Mutation	SNP	ENST00000357276.4	37	CCDS2403.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.855671	0.91355	.	.	ENSG00000138375	ENST00000357276;ENST00000358207;ENST00000392128	D;D;D	0.95001	-3.51;-3.51;-3.58	5.5	5.5	0.81552	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.97012	0.9024	M	0.83692	2.655	0.80722	D	1	P	0.46706	0.883	P	0.58130	0.833	D	0.97231	0.9884	10	0.62326	D	0.03	-16.3277	18.3826	0.90455	0.0:1.0:0.0:0.0	.	599	Q9NZC9	SMAL1_HUMAN	S	599;599;441	ENSP00000349823:P599S;ENSP00000350940:P599S;ENSP00000375974:P441S	ENSP00000349823:P599S	P	+	1	0	SMARCAL1	217020070	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.761000	0.85260	2.581000	0.87130	0.655000	0.94253	CCA		0.537	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2		
TNS1	7145	broad.mit.edu	37	2	218682918	218682918	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:218682918G>T	ENST00000171887.4	-	24	4277	c.3825C>A	c.(3823-3825)caC>caA	p.H1275Q	TNS1_ENST00000419504.1_Missense_Mutation_p.H1262Q|TNS1_ENST00000430930.1_Missense_Mutation_p.H1254Q	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1275					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)	p.H1275Q(1)		breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GAGCCCCAGGGTGCCGGCCCA	0.667																																					p.H1275Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3825A	2						.						17.0	20.0	19.0					2																	218682918		2194	4280	6474	218391163	SO:0001583	missense	7145	exon24			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.3825C>A	2.37:g.218682918G>T	ENSP00000171887:p.His1275Gln	Somatic		Capture	Illumina HiSeq	Phase_I	218391163	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	G	9.465	1.094198	0.20471	.	.	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	D;T;D;D	0.90444	-2.67;2.38;-2.66;-2.67	4.11	-0.367	0.12541	.	0.798927	0.10219	N	0.701100	D	0.90820	0.7117	L	0.52573	1.65	0.28316	N	0.922464	B;D;P	0.71674	0.15;0.998;0.539	B;D;B	0.77557	0.027;0.99;0.204	T	0.80739	-0.1248	10	0.27785	T	0.31	.	2.7988	0.05409	0.226:0.1213:0.5286:0.124	.	1275;1254;1262	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	Q	1275;413;1262;1254	ENSP00000171887:H1275Q;ENSP00000394171:H413Q;ENSP00000408724:H1262Q;ENSP00000406016:H1254Q	ENSP00000171887:H1275Q	H	-	3	2	TNS1	218391163	0.973000	0.33851	0.954000	0.39281	0.818000	0.46254	0.252000	0.18278	0.218000	0.20820	0.563000	0.77884	CAC		0.667	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
ZNF142	7701	broad.mit.edu	37	2	219509497	219509497	+	Missense_Mutation	SNP	C	C	T	rs573181948		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:219509497C>T	ENST00000449707.1	-	8	2163	c.1742G>A	c.(1741-1743)cGc>cAc	p.R581H	ZNF142_ENST00000411696.2_Missense_Mutation_p.R581H	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	581					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.R418H(1)		breast(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GCTGAAGGTGCGGTAGTCACA	0.577													C|||	1	0.000199681	0.0008	0.0	5008	,	,		23181	0.0		0.0	False		,,,				2504	0.0				p.R581H	Colon(170;867 1942 8995 15834 18053)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1742A	2						.						95.0	106.0	102.0					2																	219509497		2201	4298	6499	219217741	SO:0001583	missense	7701	exon8			U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"""Zinc fingers, C2H2-type"""	12927	protein-coding gene	gene with protein product		604083	"""zinc finger protein 142 (clone pHZ-49)"""				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.1742G>A	2.37:g.219509497C>T	ENSP00000408643:p.Arg581His	Somatic		Capture	Illumina HiSeq	Phase_I	219217741	NM_001105537	Q92510	Missense_Mutation	SNP	ENST00000449707.1	37	CCDS42817.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.941870	0.53079	.	.	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.12672	2.66;2.66	5.95	5.03	0.67393	Zinc finger, C2H2-like (1);	0.282378	0.42294	D	0.000735	T	0.32882	0.0844	M	0.82433	2.59	0.27796	N	0.942654	D;D	0.71674	0.998;0.992	P;P	0.60886	0.796;0.88	T	0.18745	-1.0327	10	0.36615	T	0.2	-22.1332	10.0624	0.42284	0.0:0.7906:0.1386:0.0709	.	581;418	P52746;A8MWU9	ZN142_HUMAN;.	H	581	ENSP00000408643:R581H;ENSP00000398798:R581H	ENSP00000398798:R581H	R	-	2	0	ZNF142	219217741	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.456000	0.44997	2.824000	0.97209	0.655000	0.94253	CGC		0.577	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081	
BCS1L	617	broad.mit.edu	37	2	219526635	219526635	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:219526635T>C	ENST00000431802.1	+	4	1313	c.614T>C	c.(613-615)gTc>gCc	p.V205A	BCS1L_ENST00000392109.1_Missense_Mutation_p.V205A|BCS1L_ENST00000359273.3_Missense_Mutation_p.V205A|BCS1L_ENST00000392110.2_Missense_Mutation_p.V205A|ZNF142_ENST00000449707.1_5'Flank|BCS1L_ENST00000439945.1_Missense_Mutation_p.V205A|ZNF142_ENST00000411696.2_5'Flank|BCS1L_ENST00000392111.2_Missense_Mutation_p.V205A|BCS1L_ENST00000412366.1_Missense_Mutation_p.V205A			Q9Y276	BCS1_HUMAN	BC1 (ubiquinol-cytochrome c reductase) synthesis-like	205					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex III assembly (GO:0034551)|mitochondrial respiratory chain complex IV assembly (GO:0033617)|mitochondrion organization (GO:0007005)	mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.V205A(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	8		Renal(207;0.0474)		Epithelial(149;7.12e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTCAGAGACGTCCAGGAATTC	0.527																																					p.V205A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T614C	2						.						55.0	58.0	57.0					2																	219526635		2203	4300	6503	219234879	SO:0001583	missense	617	exon5			AF026849	CCDS2419.1	2q35	2014-09-17	2012-10-12		ENSG00000074582	ENSG00000074582		"""ATPases / AAA-type"", ""Mitochondrial respiratory chain complex assembly factors"""	1020	protein-coding gene	gene with protein product	"""GRACILE syndrome"", ""Bjornstad syndrome"""	603647	"""BCS1 (yeast homolog)-like"", ""BCS1-like (yeast)"", ""BCS1-like (S. cerevisiae)"""			9878253, 17314340	Standard	NM_001079866		Approved	Hs.6719, BCS, h-BCS, BJS	uc002viq.3	Q9Y276	OTTHUMG00000133114	ENST00000431802.1:c.614T>C	2.37:g.219526635T>C	ENSP00000413908:p.Val205Ala	Somatic		Capture	Illumina HiSeq	Phase_I	219234879	NM_004328	B3KTW9|Q7Z2V7	Missense_Mutation	SNP	ENST00000431802.1	37	CCDS2419.1	.	.	.	.	.	.	.	.	.	.	T	17.89	3.500441	0.64298	.	.	ENSG00000074582	ENST00000430322;ENST00000456050;ENST00000443791;ENST00000359273;ENST00000392109;ENST00000392110;ENST00000392111;ENST00000412366;ENST00000439945;ENST00000431802	D;D;D;D;D;D;D;D;D;D	0.97041	-4.22;-4.22;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43	5.86	5.86	0.93980	.	0.290510	0.36972	N	0.002304	D	0.95373	0.8498	L	0.56124	1.755	0.53688	D	0.999974	B	0.09022	0.002	B	0.08055	0.003	D	0.92680	0.6157	10	0.35671	T	0.21	-5.7317	16.2513	0.82489	0.0:0.0:0.0:1.0	.	205	Q9Y276	BCS1_HUMAN	A	205;205;85;205;205;205;205;205;205;205	ENSP00000398957:V205A;ENSP00000395440:V205A;ENSP00000412729:V85A;ENSP00000352219:V205A;ENSP00000375957:V205A;ENSP00000375958:V205A;ENSP00000375959:V205A;ENSP00000406494:V205A;ENSP00000404999:V205A;ENSP00000413908:V205A	ENSP00000352219:V205A	V	+	2	0	BCS1L	219234879	1.000000	0.71417	0.650000	0.29550	0.722000	0.41435	8.005000	0.88553	2.239000	0.73571	0.528000	0.53228	GTC		0.527	BCS1L-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336756.1	NM_004328	
TTLL4	9654	broad.mit.edu	37	2	219603867	219603867	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:219603867T>C	ENST00000392102.1	+	3	1808	c.1468T>C	c.(1468-1470)Tca>Cca	p.S490P	TTLL4_ENST00000442769.1_Missense_Mutation_p.S490P|TTLL4_ENST00000258398.4_Missense_Mutation_p.S490P|TTLL4_ENST00000457313.1_Missense_Mutation_p.S325P	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	490					protein polyglutamylation (GO:0018095)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)|tubulin binding (GO:0015631)	p.S490P(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	39		Renal(207;0.0915)		Epithelial(149;5.03e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0101)		GGAGCTGGACTCATCTGATAG	0.507																																					p.S490P	GBM(172;1818 2053 15407 20943 49753)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1468C	2						.						53.0	54.0	54.0					2																	219603867		2202	4298	6500	219312111	SO:0001583	missense	9654	exon3				CCDS2422.1	2p24.3-p24.1	2013-02-14			ENSG00000135912	ENSG00000135912		"""Tubulin tyrosine ligase-like family"""	28976	protein-coding gene	gene with protein product						11054573	Standard	NM_014640		Approved	KIAA0173	uc002viy.3	Q14679	OTTHUMG00000133081	ENST00000392102.1:c.1468T>C	2.37:g.219603867T>C	ENSP00000375951:p.Ser490Pro	Somatic		Capture	Illumina HiSeq	Phase_I	219312111	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	37	CCDS2422.1	.	.	.	.	.	.	.	.	.	.	T	1.038	-0.679605	0.03353	.	.	ENSG00000135912	ENST00000457313;ENST00000392102;ENST00000442769;ENST00000258398	T;T;T;T	0.04917	3.8;4.04;3.53;4.04	4.87	2.43	0.29744	.	4.776960	0.00508	N	0.000170	T	0.07324	0.0185	L	0.29908	0.895	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.35992	-0.9766	10	0.59425	D	0.04	.	7.2442	0.26114	0.0:0.2878:0.0:0.7122	.	325;490;490	E9PH58;E7EX20;Q14679	.;.;TTLL4_HUMAN	P	325;490;490;490	ENSP00000393332:S325P;ENSP00000375951:S490P;ENSP00000396555:S490P;ENSP00000258398:S490P	ENSP00000258398:S490P	S	+	1	0	TTLL4	219312111	0.555000	0.26530	0.108000	0.21378	0.079000	0.17450	1.447000	0.35101	0.337000	0.23665	-0.366000	0.07423	TCA		0.507	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640	
CCDC108	255101	broad.mit.edu	37	2	219892467	219892467	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:219892467G>A	ENST00000341552.5	-	13	2199	c.2116C>T	c.(2116-2118)Ccc>Tcc	p.P706S	CCDC108_ENST00000410037.1_Missense_Mutation_p.P641S|CCDC108_ENST00000453220.1_Missense_Mutation_p.P706S|CCDC108_ENST00000441968.1_Missense_Mutation_p.P706S|CCDC108_ENST00000409865.3_Missense_Mutation_p.P695S	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	706						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.P706S(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)		TTGAGTGGGGGCACGTCGCAG	0.602																																					p.P706S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2116T	2						.						74.0	72.0	73.0					2																	219892467		2203	4300	6503	219600711	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.2116C>T	2.37:g.219892467G>A	ENSP00000340776:p.Pro706Ser	Somatic		Capture	Illumina HiSeq	Phase_I	219600711	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	G	14.25	2.478584	0.44044	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220;ENST00000545086;ENST00000409865;ENST00000410037;ENST00000441164	T;T;T;T;T	0.07688	3.43;3.43;3.43;3.17;3.17	5.18	5.18	0.71444	.	0.000000	0.46442	D	0.000298	T	0.27731	0.0682	M	0.69823	2.125	0.80722	D	1	D;D;D	0.62365	0.981;0.991;0.991	P;D;D	0.64506	0.866;0.926;0.926	T	0.00303	-1.1833	10	0.37606	T	0.19	-31.0748	18.8819	0.92358	0.0:0.0:1.0:0.0	.	695;640;706	E9PG25;B4DYZ8;Q6ZU64	.;.;CC108_HUMAN	S	706;706;706;182;695;641;640	ENSP00000340776:P706S;ENSP00000413377:P706S;ENSP00000409117:P706S;ENSP00000386945:P695S;ENSP00000386258:P641S	ENSP00000340776:P706S	P	-	1	0	CCDC108	219600711	1.000000	0.71417	1.000000	0.80357	0.064000	0.16182	3.654000	0.54453	2.688000	0.91661	0.655000	0.94253	CCC		0.602	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
ABCB6	10058	broad.mit.edu	37	2	220078004	220078004	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:220078004G>A	ENST00000265316.3	-	12	2080	c.1764C>T	c.(1762-1764)ggC>ggT	p.G588G	ABCB6_ENST00000439002.2_Silent_p.G542G	NM_005689.2	NP_005680.1	Q9NP58	ABCB6_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 6 (Langereis blood group)	588					brain development (GO:0007420)|cellular iron ion homeostasis (GO:0006879)|heme transport (GO:0015886)|porphyrin-containing compound biosynthetic process (GO:0006779)|skin development (GO:0043588)|transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial envelope (GO:0005740)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|efflux transmembrane transporter activity (GO:0015562)|heme binding (GO:0020037)|heme transporter activity (GO:0015232)|heme-transporting ATPase activity (GO:0015439)	p.G588G(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	34		Renal(207;0.0474)		Epithelial(149;1.22e-06)|all cancers(144;0.000201)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ACTCAATACGGCCCTTCTGAA	0.532																																					p.G588G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1764T	2						.						106.0	110.0	109.0					2																	220078004		2203	4300	6503	219786248	SO:0001819	synonymous_variant	10058	exon12			AF070598	CCDS2436.1	2q36	2014-08-27	2014-08-27		ENSG00000115657	ENSG00000115657		"""ATP binding cassette transporters / subfamily B"""	47	protein-coding gene	gene with protein product	"""ATP-binding cassette half-transporter"""	605452	"""ATP-binding cassette, sub-family B (MDR/TAP), member 6"""			8894702, 9110174	Standard	NM_005689		Approved	EST45597, umat, MTABC3	uc002vkc.2	Q9NP58	OTTHUMG00000133131	ENST00000265316.3:c.1764C>T	2.37:g.220078004G>A		Somatic		Capture	Illumina HiSeq	Phase_I	219786248	NM_005689	O75542|Q49A66|Q59GQ5|Q6ZME6|Q96ME8|Q9HAQ6|Q9HAQ7	Silent	SNP	ENST00000265316.3	37	CCDS2436.1	.	.	.	.	.	.	.	.	.	.	G	7.823	0.718128	0.15372	.	.	ENSG00000115657	ENST00000295750	.	.	.	4.7	2.73	0.32206	.	.	.	.	.	T	0.44726	0.1307	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34850	-0.9812	4	.	.	.	-17.3593	2.7954	0.05400	0.0958:0.1291:0.4405:0.3346	.	.	.	.	V	436	.	.	A	-	2	0	ABCB6	219786248	0.994000	0.37717	0.942000	0.38095	0.757000	0.42996	0.947000	0.29082	1.193000	0.43086	0.609000	0.83330	GCC		0.532	ABCB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256820.2	NM_005689	
ATG9A	79065	broad.mit.edu	37	2	220089026	220089026	+	Missense_Mutation	SNP	C	C	T	rs570750110		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:220089026C>T	ENST00000409618.1	-	8	1506	c.1067G>A	c.(1066-1068)cGt>cAt	p.R356H	ATG9A_ENST00000361242.4_Missense_Mutation_p.R356H|ATG9A_ENST00000409422.1_Missense_Mutation_p.R295H|ATG9A_ENST00000396761.2_Missense_Mutation_p.R356H|AC068946.1_ENST00000408417.1_RNA|ATG9A_ENST00000488833.1_5'Flank			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	356					autophagic vacuole assembly (GO:0000045)|late nucleophagy (GO:0044805)|mitochondrion degradation (GO:0000422)|piecemeal microautophagy of nucleus (GO:0034727)|protein localization to pre-autophagosomal structure (GO:0034497)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)		p.R356H(1)		endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(1)	13		Renal(207;0.0474)		Epithelial(149;1.37e-06)|all cancers(144;0.000222)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTTGTAGCCACGGTTGAGGCG	0.607																																					p.R356H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1067A	2						.						55.0	63.0	60.0					2																	220089026		2124	4239	6363	219797270	SO:0001583	missense	79065	exon7			AK021732	CCDS42820.1	2q35	2014-02-12	2012-06-06	2005-09-11	ENSG00000198925	ENSG00000198925			22408	protein-coding gene	gene with protein product		612204	"""APG9 autophagy 9-like 1 (S. cerevisiae)"", ""ATG9 autophagy related 9 homolog A (S. cerevisiae)"""	APG9L1			Standard	NM_024085		Approved	FLJ22169	uc002vkf.1	Q7Z3C6	OTTHUMG00000154557	ENST00000409618.1:c.1067G>A	2.37:g.220089026C>T	ENSP00000386710:p.Arg356His	Somatic		Capture	Illumina HiSeq	Phase_I	219797270	NM_024085	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Missense_Mutation	SNP	ENST00000409618.1	37	CCDS42820.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.393005	0.42410	.	.	ENSG00000198925	ENST00000396761;ENST00000409618;ENST00000361242;ENST00000409422	T;T;T;T	0.33865	1.8;1.8;1.8;1.39	5.0	5.0	0.66597	.	0.113037	0.53938	D	0.000056	T	0.48660	0.1512	M	0.87758	2.905	0.45648	D	0.998574	P	0.47350	0.894	P	0.46585	0.521	T	0.55982	-0.8054	10	0.52906	T	0.07	-7.2088	10.0266	0.42074	0.0:0.8737:0.0:0.1263	.	356	Q7Z3C6	ATG9A_HUMAN	H	356;356;356;295	ENSP00000379983:R356H;ENSP00000386710:R356H;ENSP00000355173:R356H;ENSP00000386535:R295H	ENSP00000355173:R356H	R	-	2	0	ATG9A	219797270	0.998000	0.40836	0.890000	0.34922	0.355000	0.29361	3.288000	0.51739	2.485000	0.83878	0.585000	0.79938	CGT		0.607	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085	
DES	1674	broad.mit.edu	37	2	220284997	220284997	+	Missense_Mutation	SNP	C	C	T	rs374687448		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:220284997C>T	ENST00000373960.3	+	3	750	c.664C>T	c.(664-666)Cgc>Tgc	p.R222C		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	222	Coil 1B.|Rod.				cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)	p.R222C(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		TACTCTAGCTCGCATTGACCT	0.572																																					p.R222C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C664T	2						.	C	CYS/ARG	0,4406		0,0,2203	71.0	65.0	67.0		664	3.5	0.9	2		67	1,8599	1.2+/-3.3	0,1,4299	no	missense	DES	NM_001927.3	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	222/471	220284997	1,13005	2203	4300	6503	219993241	SO:0001583	missense	1674	exon3			AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"""Intermediate filaments type III"""	2770	protein-coding gene	gene with protein product	"""intermediate filament protein"""	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	ENST00000373960.3:c.664C>T	2.37:g.220284997C>T	ENSP00000363071:p.Arg222Cys	Somatic		Capture	Illumina HiSeq	Phase_I	219993241	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Missense_Mutation	SNP	ENST00000373960.3	37	CCDS33383.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.269477	0.80469	0.0	1.16E-4	ENSG00000175084	ENST00000373960	D	0.91740	-2.9	4.38	3.49	0.39957	Filament (1);	0.000000	0.42053	D	0.000769	D	0.96911	0.8991	H	0.94925	3.6	0.58432	D	0.999995	D	0.89917	1.0	D	0.83275	0.996	D	0.97569	1.0103	10	0.87932	D	0	.	13.6808	0.62484	0.1557:0.8443:0.0:0.0	.	222	P17661	DESM_HUMAN	C	222	ENSP00000363071:R222C	ENSP00000363071:R222C	R	+	1	0	DES	219993241	0.971000	0.33674	0.906000	0.35671	0.976000	0.68499	2.406000	0.44557	1.032000	0.39892	0.655000	0.94253	CGC		0.572	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927	
SPEG	10290	broad.mit.edu	37	2	220329280	220329280	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:220329280C>T	ENST00000312358.7	+	9	2963	c.2831C>T	c.(2830-2832)gCg>gTg	p.A944V	SPEG_ENST00000396698.1_Missense_Mutation_p.A840V|SPEG_ENST00000396686.1_Missense_Mutation_p.A95V|SPEG_ENST00000396689.2_Missense_Mutation_p.A95V|SPEG_ENST00000396695.2_Missense_Mutation_p.A152V|SPEG_ENST00000485813.1_3'UTR|SPEG_ENST00000396688.1_Missense_Mutation_p.A95V	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	944	Ig-like 3.				cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A944V(2)		breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		ACTTGCAAAGCGGTCAATGAG	0.632																																					p.A95V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C284T	2						.						90.0	100.0	97.0					2																	220329280		2167	4277	6444	220037524	SO:0001583	missense	10290	exon4			BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.2831C>T	2.37:g.220329280C>T	ENSP00000311684:p.Ala944Val	Somatic		Capture	Illumina HiSeq	Phase_I	220037524	NM_001173476	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.587831	0.66105	.	.	ENSG00000072195	ENST00000312358;ENST00000265327;ENST00000396698;ENST00000396695;ENST00000396688;ENST00000396686;ENST00000396689	T;T;T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66;-0.66;-0.66	5.28	5.28	0.74379	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.41823	D	0.000815	D	0.83954	0.5366	M	0.80616	2.505	0.39815	D	0.972754	D;D;D	0.69078	0.997;0.988;0.997	P;P;D	0.68039	0.766;0.654;0.955	D	0.86029	0.1512	10	0.52906	T	0.07	.	16.7035	0.85365	0.0:1.0:0.0:0.0	.	944;152;840	Q15772;Q15772-3;B9ZVR7	SPEG_HUMAN;.;.	V	944;944;840;152;95;95;95	ENSP00000311684:A944V;ENSP00000379926:A840V;ENSP00000379923:A152V;ENSP00000379919:A95V;ENSP00000379917:A95V;ENSP00000379920:A95V	ENSP00000265327:A944V	A	+	2	0	SPEG	220037524	1.000000	0.71417	0.799000	0.32177	0.005000	0.04900	5.326000	0.65875	2.484000	0.83849	0.561000	0.74099	GCG		0.632	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
ASIC4	55515	broad.mit.edu	37	2	220400009	220400009	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:220400009C>A	ENST00000347842.3	+	5	1530	c.1516C>A	c.(1516-1518)Ctg>Atg	p.L506M	ASIC4_ENST00000358078.4_Missense_Mutation_p.L525M	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	506					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)	p.L525M(2)									AGCCCGGTACCTGGCGAGGAA	0.607																																					p.L525M												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C1573A	2						.						55.0	42.0	46.0					2																	220400009		2203	4300	6503	220108253	SO:0001583	missense	55515	exon6			AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	21263	protein-coding gene	gene with protein product		606715	"""amiloride-sensitive cation channel 4, pituitary"", ""amiloride-sensitive cation channel family member 4, pituitary"""	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.1516C>A	2.37:g.220400009C>A	ENSP00000326627:p.Leu506Met	Somatic		Capture	Illumina HiSeq	Phase_I	220108253	NM_018674	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Missense_Mutation	SNP	ENST00000347842.3	37	CCDS2442.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.950127	0.73787	.	.	ENSG00000072182	ENST00000347842;ENST00000358078	T;T	0.68624	-0.34;-0.34	4.67	3.8	0.43715	.	0.000000	0.85682	D	0.000000	T	0.80287	0.4595	M	0.81239	2.535	0.51767	D	0.99993	D;D	0.76494	0.999;0.993	D;D	0.91635	0.999;0.925	T	0.81767	-0.0782	10	0.66056	D	0.02	-11.7996	10.3069	0.43685	0.0:0.841:0.0:0.159	.	506;525	Q96FT7;Q96FT7-4	ACCN4_HUMAN;.	M	506;525	ENSP00000326627:L506M;ENSP00000350786:L525M	ENSP00000326627:L506M	L	+	1	2	ACCN4	220108253	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.905000	0.56333	1.341000	0.45600	0.650000	0.86243	CTG		0.607	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674	
TMEM198	130612	broad.mit.edu	37	2	220414516	220414516	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:220414516C>T	ENST00000344458.2	+	6	1608	c.1023C>T	c.(1021-1023)gaC>gaT	p.D341D	RP11-256I23.1_ENST00000596829.1_RNA|MIR3132_ENST00000581997.1_RNA|TMEM198_ENST00000373883.3_Silent_p.D341D			Q66K66	TM198_HUMAN	transmembrane protein 198	341					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.D341D(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)		CAGATGCGGACTATGAGTATG	0.597																																					p.D341D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1023T	2						.						57.0	64.0	62.0					2																	220414516		2203	4300	6503	220122760	SO:0001819	synonymous_variant	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.1023C>T	2.37:g.220414516C>T		Somatic		Capture	Illumina HiSeq	Phase_I	220122760	NM_001005209		Silent	SNP	ENST00000344458.2	37	CCDS33385.1																																																																																				0.597	TMEM198-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131063.1	NM_001005209	
PAX3	5077	broad.mit.edu	37	2	223085051	223085051	+	Silent	SNP	G	G	A	rs374429328		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:223085051G>A	ENST00000350526.4	-	7	1117	c.981C>T	c.(979-981)acC>acT	p.T327T	PAX3_ENST00000409551.3_Silent_p.T326T|PAX3_ENST00000392070.2_Silent_p.T327T|PAX3_ENST00000464706.1_5'UTR|PAX3_ENST00000336840.6_Silent_p.T327T|PAX3_ENST00000344493.4_Silent_p.T327T|PAX3_ENST00000392069.2_Silent_p.T327T	NM_181457.3	NP_852122.1	P23760	PAX3_HUMAN	paired box 3	327					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|mammary gland specification (GO:0060594)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of somitogenesis (GO:0014807)|sensory perception of sound (GO:0007605)|spinal cord association neuron differentiation (GO:0021527)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|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)	p.T327T(1)	PAX3/NCOA2(4)|PAX3/NCOA1(8)|PAX3/FOXO1(749)	NS(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(13)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	38		Renal(207;0.0183)		Epithelial(121;4.13e-10)|all cancers(144;1.85e-07)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTCTGTGAACGGTGCTGCTGG	0.507			T	"""FOXO1A, NCOA1"""	alveolar rhabdomyosarcoma		Waardenburg syndrome; craniofacial-deafness-hand syndrome																														p.T327T			Dom	yes		2	2q35	5077	paired box gene 3	yes	M	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C981T	2						.	G	,,,,,	0,4406		0,0,2203	216.0	180.0	192.0		978,981,981,981,981,981	-9.2	0.6	2		192	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PAX3	NM_001127366.2,NM_181457.3,NM_181458.3,NM_181459.3,NM_181460.3,NM_181461.3	,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,	326/484,327/480,327/485,327/506,327/408,327/404	223085051	1,13005	2203	4300	6503	222793295	SO:0001819	synonymous_variant	5077	exon7				CCDS2449.1, CCDS2450.1, CCDS2451.1, CCDS42825.1, CCDS2448.1, CCDS42826.1, CCDS46522.1, CCDS46523.1	2q36.1	2011-06-20	2007-07-12		ENSG00000135903	ENSG00000135903		"""Paired boxes"", ""Homeoboxes / PRD class"""	8617	protein-coding gene	gene with protein product		606597	"""Waardenburg syndrome 1"", ""paired box gene 3 (Waardenburg syndrome 1)"""	WS1		1347149	Standard	NM_181461		Approved	HUP2	uc002vmt.2	P23760	OTTHUMG00000133157	ENST00000350526.4:c.981C>T	2.37:g.223085051G>A		Somatic		Capture	Illumina HiSeq	Phase_I	222793295	NM_181461	G5E9C1|Q16448|Q494Z3|Q494Z4|Q53T90|Q6GSJ9|Q86UQ2|Q86UQ3	Silent	SNP	ENST00000350526.4	37	CCDS42826.1																																																																																				0.507	PAX3-006	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328670.1		
FAM124B	79843	broad.mit.edu	37	2	225266032	225266032	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:225266032C>T	ENST00000409685.3	-	1	719	c.454G>A	c.(454-456)Gcc>Acc	p.A152T	FAM124B_ENST00000243806.2_Missense_Mutation_p.A152T|FAM124B_ENST00000389874.3_Missense_Mutation_p.A152T	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	152								p.A152T(2)		endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		AGTCTGATGGCGTCTTCATAG	0.522																																					p.A152T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G454A	2						.						89.0	84.0	86.0					2																	225266032		2203	4300	6503	224974276	SO:0001583	missense	79843	exon1			AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.454G>A	2.37:g.225266032C>T	ENSP00000386895:p.Ala152Thr	Somatic		Capture	Illumina HiSeq	Phase_I	224974276	NM_001122779	A6NNC7|Q8NBZ4|Q8TAV7	Missense_Mutation	SNP	ENST00000409685.3	37	CCDS46527.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972974	0.74246	.	.	ENSG00000124019	ENST00000389874;ENST00000409685;ENST00000243806	T;T;T	0.44083	0.93;0.93;0.93	5.64	4.76	0.60689	.	0.101330	0.64402	D	0.000002	T	0.53286	0.1787	M	0.65320	2	0.43734	D	0.996226	D;D	0.76494	0.999;0.997	P;P	0.61201	0.885;0.818	T	0.55431	-0.8142	10	0.02654	T	1	-20.6537	15.9002	0.79369	0.1365:0.8635:0.0:0.0	.	152;152	Q9H5Z6;Q9H5Z6-2	F124B_HUMAN;.	T	152	ENSP00000374524:A152T;ENSP00000386895:A152T;ENSP00000243806:A152T	ENSP00000243806:A152T	A	-	1	0	FAM124B	224974276	1.000000	0.71417	0.885000	0.34714	0.708000	0.40852	4.429000	0.59901	1.361000	0.45981	0.655000	0.94253	GCC		0.522	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785	
COL4A4	1286	broad.mit.edu	37	2	227917093	227917093	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:227917093C>T	ENST00000396625.3	-	32	3103	c.2896G>A	c.(2896-2898)Gct>Act	p.A966T	COL4A4_ENST00000329662.7_Missense_Mutation_p.A966T	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	966	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)	p.A966T(1)		breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GAAATGATAGCCATTTCTCCT	0.408																																					p.A966T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2896A	2						.						116.0	113.0	114.0					2																	227917093		1846	4093	5939	227625337	SO:0001583	missense	1286	exon32				CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.2896G>A	2.37:g.227917093C>T	ENSP00000379866:p.Ala966Thr	Somatic		Capture	Illumina HiSeq	Phase_I	227625337	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	.	.	.	.	.	.	.	.	.	.	C	10.41	1.342305	0.24339	.	.	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.93488	-3.23;-3.23	5.55	3.58	0.41010	.	.	.	.	.	T	0.80486	0.4632	N	0.01874	-0.695	0.09310	N	1	B	0.10296	0.003	B	0.16289	0.015	T	0.70883	-0.4751	9	0.72032	D	0.01	.	3.9108	0.09202	0.2392:0.5621:0.0:0.1987	.	966	P53420	CO4A4_HUMAN	T	966	ENSP00000379866:A966T;ENSP00000328553:A966T	ENSP00000328553:A966T	A	-	1	0	COL4A4	227625337	0.000000	0.05858	0.004000	0.12327	0.756000	0.42949	0.543000	0.23237	1.345000	0.45676	0.557000	0.71058	GCT		0.408	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
SLC16A14	151473	broad.mit.edu	37	2	230911277	230911277	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:230911277T>C	ENST00000295190.4	-	4	1023	c.565A>G	c.(565-567)Agg>Ggg	p.R189G		NM_152527.4	NP_689740.2	Q7RTX9	MOT14_HUMAN	solute carrier family 16, member 14	189						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)	p.R189G(1)		NS(1)|cervix(1)|endometrium(7)|large_intestine(7)|lung(3)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Renal(207;0.025)|all_hematologic(139;0.122)|all_lung(227;0.149)|Acute lymphoblastic leukemia(138;0.164)		Epithelial(121;7.31e-13)|all cancers(144;5.1e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00948)		ATGGCATTCCTCCAGCCGTAC	0.592																																					p.R189G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A565G	2						.						91.0	90.0	90.0					2																	230911277		2203	4300	6503	230619521	SO:0001583	missense	151473	exon4			BN000146	CCDS2473.1	2q37.1	2013-07-18	2013-07-18		ENSG00000163053	ENSG00000163053		"""Solute carriers"""	26417	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 14"""		"""solute carrier family 16 (monocarboxylic acid transporters), member 14"""				Standard	NM_152527		Approved	FLJ30794, MCT14	uc002vqd.2	Q7RTX9	OTTHUMG00000133205	ENST00000295190.4:c.565A>G	2.37:g.230911277T>C	ENSP00000295190:p.Arg189Gly	Somatic		Capture	Illumina HiSeq	Phase_I	230619521	NM_152527	A8KA08|Q53R92|Q96NI7	Missense_Mutation	SNP	ENST00000295190.4	37	CCDS2473.1	.	.	.	.	.	.	.	.	.	.	T	12.83	2.055474	0.36277	.	.	ENSG00000163053	ENST00000295190;ENST00000457406;ENST00000412034	T;T;T	0.63096	-0.02;-0.02;-0.02	4.94	3.02	0.34903	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.097964	0.43919	D	0.000504	T	0.73040	0.3536	M	0.85630	2.765	0.54753	D	0.999988	P;P	0.42649	0.645;0.786	P;P	0.49502	0.516;0.613	T	0.78687	-0.2107	10	0.59425	D	0.04	.	13.6955	0.62578	0.0:0.0:0.5223:0.4777	.	189;189	E7EMG7;Q7RTX9	.;MOT14_HUMAN	G	189	ENSP00000295190:R189G;ENSP00000400352:R189G;ENSP00000395775:R189G	ENSP00000295190:R189G	R	-	1	2	SLC16A14	230619521	0.998000	0.40836	0.988000	0.46212	0.333000	0.28666	0.769000	0.26604	1.274000	0.44362	-0.213000	0.12676	AGG		0.592	SLC16A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256918.2	NM_152527	
ALPI	248	broad.mit.edu	37	2	233322995	233322995	+	Missense_Mutation	SNP	G	G	A	rs151137290		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:233322995G>A	ENST00000295463.3	+	9	1137	c.1060G>A	c.(1060-1062)Gac>Aac	p.D354N		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	354					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.D354N(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)		GGTCATGTTCGACGACGCCAT	0.622													G|||	1	0.000199681	0.0	0.0	5008	,	,		17253	0.0		0.0	False		,,,				2504	0.001				p.D354N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1060A	2						.	G	ASN/ASP	3,4403	6.2+/-15.9	0,3,2200	83.0	74.0	77.0		1060	3.6	0.0	2	dbSNP_134	77	0,8600		0,0,4300	no	missense	ALPI	NM_001631.3	23	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	probably-damaging	354/529	233322995	3,13003	2203	4300	6503	233031239	SO:0001583	missense	248	exon9			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.1060G>A	2.37:g.233322995G>A	ENSP00000295463:p.Asp354Asn	Somatic		Capture	Illumina HiSeq	Phase_I	233031239	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Missense_Mutation	SNP	ENST00000295463.3	37	CCDS2492.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.278894	0.80692	6.81E-4	0.0	ENSG00000163295	ENST00000295463	D	0.98075	-4.7	4.46	3.58	0.41010	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.98629	0.9541	M	0.89030	3	0.52099	D	0.999945	D	0.89917	1.0	D	0.79784	0.993	D	0.99177	1.0866	10	0.87932	D	0	.	11.3549	0.49609	0.0877:0.0:0.9123:0.0	.	354	P09923	PPBI_HUMAN	N	354	ENSP00000295463:D354N	ENSP00000295463:D354N	D	+	1	0	ALPI	233031239	1.000000	0.71417	0.020000	0.16555	0.006000	0.05464	7.763000	0.85283	1.105000	0.41606	0.561000	0.74099	GAC		0.622	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631	
ECEL1	9427	broad.mit.edu	37	2	233347169	233347169	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:233347169C>T	ENST00000304546.1	-	12	1965	c.1755G>A	c.(1753-1755)gcG>gcA	p.A585A	ECEL1_ENST00000409941.1_Silent_p.A583A	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	585					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)	p.A585A(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		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;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		GCAGGATGCCCGCGGGGAACA	0.607																																					p.A585A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1755A	2						.						141.0	143.0	143.0					2																	233347169		2203	4300	6503	233055413	SO:0001819	synonymous_variant	9427	exon12			Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"""damage induced neuronal endopeptidase"""	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.1755G>A	2.37:g.233347169C>T		Somatic		Capture	Illumina HiSeq	Phase_I	233055413	NM_004826	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Silent	SNP	ENST00000304546.1	37	CCDS2493.1																																																																																				0.607	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826	
DGKD	8527	broad.mit.edu	37	2	234356769	234356769	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:234356769G>A	ENST00000264057.2	+	13	1468	c.1456G>A	c.(1456-1458)Gcc>Acc	p.A486T	DGKD_ENST00000409813.3_Missense_Mutation_p.A442T	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	486					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.A486T(1)		central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	CTCGGTTGCAGCCCACCTTTC	0.577																																					p.A486T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1456A	2						.						108.0	95.0	99.0					2																	234356769		2203	4300	6503	234021508	SO:0001583	missense	8527	exon13			D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2851	protein-coding gene	gene with protein product	"""diglyceride kinase"""	601826	"""diacylglycerol kinase, delta (130kD)"""			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.1456G>A	2.37:g.234356769G>A	ENSP00000264057:p.Ala486Thr	Somatic		Capture	Illumina HiSeq	Phase_I	234021508	NM_152879	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	37	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.844544	0.32606	.	.	ENSG00000077044	ENST00000264057;ENST00000409813	T;T	0.79653	-1.13;-1.29	4.22	4.22	0.49857	.	0.000000	0.85682	D	0.000000	T	0.76169	0.3950	L	0.29908	0.895	0.49798	D	0.999824	B;D;B	0.56287	0.007;0.975;0.007	B;P;B	0.50570	0.009;0.644;0.009	T	0.71945	-0.4439	10	0.11794	T	0.64	.	17.146	0.86767	0.0:0.0:1.0:0.0	.	370;442;486	Q53SE4;Q16760-2;Q16760	.;.;DGKD_HUMAN	T	486;442	ENSP00000264057:A486T;ENSP00000386455:A442T	ENSP00000264057:A486T	A	+	1	0	DGKD	234021508	1.000000	0.71417	0.582000	0.28627	0.986000	0.74619	6.503000	0.73699	2.373000	0.80994	0.491000	0.48974	GCC		0.577	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648	
DGKD	8527	broad.mit.edu	37	2	234375783	234375783	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:234375783G>A	ENST00000264057.2	+	28	3370	c.3358G>A	c.(3358-3360)Gtg>Atg	p.V1120M	DGKD_ENST00000409813.3_Missense_Mutation_p.V1076M	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	1120					blood coagulation (GO:0007596)|cell growth (GO:0016049)|diacylglycerol metabolic process (GO:0046339)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|multicellular organismal development (GO:0007275)|platelet activation (GO:0030168)|protein homooligomerization (GO:0051260)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein transport (GO:0015031)|response to organic substance (GO:0010033)|second-messenger-mediated signaling (GO:0019932)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol binding (GO:0019992)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.V1120M(1)		central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(13)|lung(15)|ovary(1)|pancreas(1)|skin(1)	38		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0538)		Epithelial(121;1.31e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000416)|Lung(119;0.00285)|LUSC - Lung squamous cell carcinoma(224;0.00655)	Phosphatidylserine(DB00144)	ATTCCGCCTCGTGACCAAGTT	0.522																																					p.V1120M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3358A	2						.						129.0	141.0	137.0					2																	234375783		2203	4300	6503	234040522	SO:0001583	missense	8527	exon28			D63479	CCDS2504.1, CCDS46546.1	2q37	2013-01-10	2002-08-29		ENSG00000077044	ENSG00000077044		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2851	protein-coding gene	gene with protein product	"""diglyceride kinase"""	601826	"""diacylglycerol kinase, delta (130kD)"""			8626538, 12810723	Standard	NM_003648		Approved	KIAA0145, DGKdelta	uc002vui.1	Q16760	OTTHUMG00000133290	ENST00000264057.2:c.3358G>A	2.37:g.234375783G>A	ENSP00000264057:p.Val1120Met	Somatic		Capture	Illumina HiSeq	Phase_I	234040522	NM_152879	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	37	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.899222	0.91962	.	.	ENSG00000077044	ENST00000264057;ENST00000409813	T;T	0.80824	-1.26;-1.42	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000012	D	0.88005	0.6321	L	0.60455	1.87	0.58432	D	0.999991	D;D	0.89917	1.0;0.999	D;D	0.76071	0.987;0.927	D	0.87228	0.2258	10	0.46703	T	0.11	.	18.8253	0.92115	0.0:0.0:1.0:0.0	.	1076;1120	Q16760-2;Q16760	.;DGKD_HUMAN	M	1120;1076	ENSP00000264057:V1120M;ENSP00000386455:V1076M	ENSP00000264057:V1120M	V	+	1	0	DGKD	234040522	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.419000	0.97397	2.749000	0.94314	0.655000	0.94253	GTG		0.522	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648	
UGT1A9	54600	broad.mit.edu	37	2	234581344	234581344	+	Missense_Mutation	SNP	C	C	T	rs368960201		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:234581344C>T	ENST00000354728.4	+	1	846	c.764C>T	c.(763-765)aCg>aTg	p.T255M	UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A1_ENST00000609637.1_Missense_Mutation_p.T255M|UGT1A1_ENST00000373450.4_Intron			O60656	UD19_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A9	255					cellular glucuronidation (GO:0052695)|cellular lipid metabolic process (GO:0044255)|drug metabolic process (GO:0017144)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|metabolic process (GO:0008152)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of fatty acid metabolic process (GO:0045922)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)	p.T255M(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	37		Breast(86;0.000766)|all_lung(227;0.00269)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0331)|Lung NSC(271;0.0459)|Lung SC(224;0.128)		Epithelial(121;1.26e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000436)|Lung(119;0.00347)|LUSC - Lung squamous cell carcinoma(224;0.00757)	Acetaminophen(DB00316)|Buprenorphine(DB00921)|Canagliflozin(DB08907)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Entacapone(DB00494)|Etodolac(DB00749)|Ezogabine(DB04953)|Flurbiprofen(DB00712)|Haloperidol(DB00502)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ketobemidone(DB06738)|Lumiracoxib(DB01283)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Nateglinide(DB00731)|Niflumic Acid(DB04552)|Oxazepam(DB00842)|Propofol(DB00818)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sulfamethoxazole(DB01015)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zileuton(DB00744)	TTGTTGCGAACGGACTTTGTT	0.433																																					p.T255M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C764T	2						.	C	,,MET/THR	1,4405	2.1+/-5.4	0,1,2202	241.0	231.0	234.0		,,764	-1.5	0.1	2		234	0,8600		0,0,4300	no	intron,intron,missense	UGT1A10,UGT1A8,UGT1A9	NM_019075.2,NM_019076.4,NM_021027.2	,,81	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,	,,255/531	234581344	1,13005	2203	4300	6503	234246083	SO:0001583	missense	54600	exon1			AF056188	CCDS2505.1	2q37	2010-03-05	2005-07-20		ENSG00000241119	ENSG00000241119		"""UDP glucuronosyltransferases"""	12541	other	complex locus constituent		606434	"""UDP glycosyltransferase 1 family, polypeptide A9"""			9295054, 1910331	Standard	NM_021027		Approved	HLUGP4, LUGP4, UGT1AI		O60656	OTTHUMG00000059124	ENST00000354728.4:c.764C>T	2.37:g.234581344C>T	ENSP00000346768:p.Thr255Met	Somatic		Capture	Illumina HiSeq	Phase_I	234246083	NM_021027	B8K285|P36509|Q9HAX0	Missense_Mutation	SNP	ENST00000354728.4	37	CCDS2505.1	.	.	.	.	.	.	.	.	.	.	C	0.300	-0.974559	0.02215	2.27E-4	0.0	ENSG00000241119	ENST00000354728	T	0.67345	-0.26	3.26	-1.47	0.08772	.	.	.	.	.	T	0.63129	0.2485	M	0.84326	2.69	0.09310	N	1	B;B	0.22983	0.078;0.078	B;B	0.29785	0.107;0.107	T	0.59413	-0.7459	9	0.52906	T	0.07	.	1.1185	0.01719	0.4618:0.1791:0.1183:0.2408	.	255;255	Q5DSZ5;O60656	.;UD19_HUMAN	M	255	ENSP00000346768:T255M	ENSP00000346768:T255M	T	+	2	0	UGT1A9	234246083	0.000000	0.05858	0.079000	0.20413	0.149000	0.21700	-5.063000	0.00155	-0.482000	0.06782	-0.398000	0.06409	ACG		0.433	UGT1A9-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130995.1	NM_021027	
TRPM8	79054	broad.mit.edu	37	2	234891862	234891862	+	Missense_Mutation	SNP	G	G	A	rs199993016		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:234891862G>A	ENST00000324695.4	+	20	2795	c.2755G>A	c.(2755-2757)Gtg>Atg	p.V919M	TRPM8_ENST00000433712.2_Missense_Mutation_p.V497M	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	919					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.V919M(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)	GCCCAGTGACGTGGATGGTAA	0.587																																					p.V919M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2755A	2						.						72.0	67.0	69.0					2																	234891862		2203	4300	6503	234556601	SO:0001583	missense	79054	exon20			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.2755G>A	2.37:g.234891862G>A	ENSP00000323926:p.Val919Met	Somatic		Capture	Illumina HiSeq	Phase_I	234556601	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	37	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.546112	0.86022	.	.	ENSG00000144481	ENST00000324695;ENST00000433712;ENST00000456930	D;D;D	0.98028	-4.67;-4.67;-4.67	5.69	5.69	0.88448	Ion transport (1);	0.199018	0.35124	N	0.003428	D	0.97763	0.9266	L	0.33668	1.02	0.31570	N	0.656427	D;D	0.89917	1.0;0.994	D;P	0.79108	0.992;0.874	D	0.97096	0.9794	10	0.62326	D	0.03	-29.3916	18.3913	0.90484	0.0:0.0:1.0:0.0	.	497;919	A0AVG2;Q7Z2W7	.;TRPM8_HUMAN	M	919;497;180	ENSP00000323926:V919M;ENSP00000404423:V497M;ENSP00000414198:V180M	ENSP00000323926:V919M	V	+	1	0	TRPM8	234556601	0.998000	0.40836	0.994000	0.49952	0.941000	0.58515	3.119000	0.50422	2.684000	0.91462	0.650000	0.86243	GTG		0.587	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
SH3BP4	23677	broad.mit.edu	37	2	235961300	235961300	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:235961300G>A	ENST00000409212.1	+	5	3080	c.2573G>A	c.(2572-2574)cGg>cAg	p.R858Q	SH3BP4_ENST00000392011.2_Missense_Mutation_p.R858Q|SH3BP4_ENST00000344528.4_Missense_Mutation_p.R858Q			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	858					cellular response to amino acid stimulus (GO:0071230)|endocytosis (GO:0006897)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of GTPase activity (GO:0034260)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|protein localization to lysosome (GO:0061462)|regulation of catalytic activity (GO:0050790)	coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|identical protein binding (GO:0042802)|Ras GTPase binding (GO:0017016)	p.R858Q(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(6)|stomach(3)|urinary_tract(2)	44		Breast(86;0.000332)|Renal(207;0.00339)|all_lung(227;0.00458)|all_hematologic(139;0.0296)|Lung NSC(271;0.0419)		Epithelial(121;7.66e-20)|BRCA - Breast invasive adenocarcinoma(100;0.000402)|Lung(119;0.00299)|LUSC - Lung squamous cell carcinoma(224;0.00645)|GBM - Glioblastoma multiforme(43;0.237)		CAGCGCTGGCGGGAGCTGGCT	0.637																																					p.R858Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2573A	2						.						34.0	30.0	32.0					2																	235961300		2196	4292	6488	235626039	SO:0001583	missense	23677	exon5			AF147747	CCDS2513.1	2q37.1-q37.2	2008-05-15			ENSG00000130147	ENSG00000130147			10826	protein-coding gene	gene with protein product		605611				10644451	Standard	NM_014521		Approved		uc002vvp.3	Q9P0V3	OTTHUMG00000133292	ENST00000409212.1:c.2573G>A	2.37:g.235961300G>A	ENSP00000386862:p.Arg858Gln	Somatic		Capture	Illumina HiSeq	Phase_I	235626039	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	37	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	G	31	5.085761	0.94100	.	.	ENSG00000130147	ENST00000392011;ENST00000409212;ENST00000344528;ENST00000538289	T;T;T	0.39592	1.07;1.07;1.07	5.72	4.85	0.62838	.	0.089465	0.85682	D	0.000000	T	0.62085	0.2399	M	0.71206	2.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	T	0.63377	-0.6651	10	0.45353	T	0.12	-32.8849	13.4232	0.61009	0.0755:0.0:0.9245:0.0	.	858;858	A8K594;Q9P0V3	.;SH3B4_HUMAN	Q	858;858;858;96	ENSP00000375867:R858Q;ENSP00000386862:R858Q;ENSP00000340237:R858Q	ENSP00000340237:R858Q	R	+	2	0	SH3BP4	235626039	1.000000	0.71417	0.997000	0.53966	0.828000	0.46876	9.549000	0.98106	1.421000	0.47157	0.655000	0.94253	CGG		0.637	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
AGAP1	116987	broad.mit.edu	37	2	236945285	236945285	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:236945285C>T	ENST00000304032.8	+	14	2306	c.1726C>T	c.(1726-1728)Cgg>Tgg	p.R576W	AGAP1_ENST00000336665.5_Missense_Mutation_p.R523W|AGAP1_ENST00000409538.1_Missense_Mutation_p.R788W|RNU7-127P_ENST00000458845.1_RNA|AGAP1_ENST00000428334.2_Missense_Mutation_p.R415W	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	576	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)	p.R576W(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						GTATGAGGAGCGGGACGCCTG	0.542																																					p.R576W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1726T	2						.						106.0	111.0	110.0					2																	236945285		2203	4300	6503	236610024	SO:0001583	missense	116987	exon14			AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.1726C>T	2.37:g.236945285C>T	ENSP00000307634:p.Arg576Trp	Somatic		Capture	Illumina HiSeq	Phase_I	236610024	NM_001037131	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	37	CCDS33408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.5|23.5	4.418968|4.418968	0.83559|0.83559	.|.	.|.	ENSG00000157985|ENSG00000157985	ENST00000448025;ENST00000418654|ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334	.|T;T;T;T	.|0.20200	.|2.09;2.09;2.09;2.09	4.75|4.75	1.44|1.44	0.22558|0.22558	.|Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.|0.135579	.|0.47093	.|D	.|0.000246	T|T	0.42921|0.42921	0.1224|0.1224	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.996;0.999	T|T	0.43327|0.43327	-0.9398|-0.9398	5|10	.|0.72032	.|D	.|0.01	.|.	13.1019|13.1019	0.59224|0.59224	0.6576:0.3424:0.0:0.0|0.6576:0.3424:0.0:0.0	.|.	.|523;576	.|Q9UPQ3-2;Q9UPQ3	.|.;AGAP1_HUMAN	V|W	234;128|576;523;788;415	.|ENSP00000307634:R576W;ENSP00000338378:R523W;ENSP00000386897:R788W;ENSP00000411824:R415W	.|ENSP00000307634:R576W	A|R	+|+	2|1	0|2	AGAP1|AGAP1	236610024|236610024	1.000000|1.000000	0.71417|0.71417	0.922000|0.922000	0.36590|0.36590	0.980000|0.980000	0.70556|0.70556	1.278000|1.278000	0.33179|0.33179	0.456000|0.456000	0.26937|0.26937	0.655000|0.655000	0.94253|0.94253	GCG|CGG		0.542	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914	
IQCA1	79781	broad.mit.edu	37	2	237374169	237374169	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:237374169C>T	ENST00000409907.3	-	6	1179	c.905G>A	c.(904-906)cGg>cAg	p.R302Q	IQCA1_ENST00000309507.5_Missense_Mutation_p.R298Q|IQCA1_ENST00000431676.2_Missense_Mutation_p.R302Q	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	302							ATP binding (GO:0005524)	p.R302Q(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						GAACCAATGCCGGATCTGGTC	0.443																																					p.R302Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G905A	2						.						156.0	145.0	149.0					2																	237374169		1989	4164	6153	237038908	SO:0001583	missense	79781	exon6			AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"""ATPases / AAA-type"""	26195	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 11"""		"""IQ motif containing with AAA domain"""	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.905G>A	2.37:g.237374169C>T	ENSP00000387347:p.Arg302Gln	Somatic		Capture	Illumina HiSeq	Phase_I	237038908	NM_024726	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Missense_Mutation	SNP	ENST00000409907.3	37	CCDS46549.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417578	0.62622	.	.	ENSG00000132321	ENST00000409907;ENST00000457693;ENST00000309507;ENST00000431676;ENST00000412437	D;D;D	0.96522	-3.62;-3.62;-4.04	5.43	5.43	0.79202	.	0.000000	0.52532	D	0.000063	D	0.98005	0.9343	M	0.88640	2.97	0.44789	D	0.997795	D;D;D	0.76494	0.999;0.993;0.996	P;P;P	0.59424	0.857;0.621;0.714	D	0.98720	1.0708	10	0.72032	D	0.01	.	16.2733	0.82630	0.0:0.8678:0.1322:0.0	.	302;309;302	E7EWQ0;E9PH78;Q86XH1	.;.;IQCA1_HUMAN	Q	302;309;298;302;298	ENSP00000387347:R302Q;ENSP00000311951:R298Q;ENSP00000407213:R302Q	ENSP00000254653:R302Q	R	-	2	0	IQCA1	237038908	0.998000	0.40836	0.999000	0.59377	0.162000	0.22319	4.097000	0.57741	2.551000	0.86045	0.563000	0.77884	CGG		0.443	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726	
IQCA1	79781	broad.mit.edu	37	2	237405855	237405855	+	Missense_Mutation	SNP	G	G	A	rs201684914	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:237405855G>A	ENST00000409907.3	-	2	561	c.287C>T	c.(286-288)aCg>aTg	p.T96M	IQCA1_ENST00000309507.5_Missense_Mutation_p.T92M|IQCA1_ENST00000431676.2_Missense_Mutation_p.T96M	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	96							ATP binding (GO:0005524)	p.T96M(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						ATGGAACTCCGTGAGTTCCAG	0.473													G|||	3	0.000599042	0.0008	0.0014	5008	,	,		18083	0.0		0.001	False		,,,				2504	0.0				p.T96M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C287T	2						.	G	MET/THR	3,3903		0,3,1950	41.0	41.0	41.0		287	4.6	0.0	2		41	1,8281		0,1,4140	no	missense	IQCA1	NM_024726.3	81	0,4,6090	AA,AG,GG		0.0121,0.0768,0.0328	benign	96/823	237405855	4,12184	1953	4141	6094	237070594	SO:0001583	missense	79781	exon2			AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"""ATPases / AAA-type"""	26195	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 11"""		"""IQ motif containing with AAA domain"""	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.287C>T	2.37:g.237405855G>A	ENSP00000387347:p.Thr96Met	Somatic		Capture	Illumina HiSeq	Phase_I	237070594	NM_024726	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Missense_Mutation	SNP	ENST00000409907.3	37	CCDS46549.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	11.51	1.659210	0.29515	7.68E-4	1.21E-4	ENSG00000132321	ENST00000409907;ENST00000457693;ENST00000309507;ENST00000431676;ENST00000412437	D;D;D	0.94457	-3.31;-3.31;-3.43	5.51	4.62	0.57501	.	0.545556	0.17922	N	0.157451	D	0.95242	0.8457	L	0.49640	1.575	0.19300	N	0.999975	B;D;B	0.61080	0.403;0.989;0.403	B;P;B	0.56088	0.047;0.791;0.068	D	0.90237	0.4283	10	0.66056	D	0.02	.	16.2637	0.82563	0.0:0.1327:0.8673:0.0	.	96;103;96	E7EWQ0;E9PH78;Q86XH1	.;.;IQCA1_HUMAN	M	96;103;92;96;92	ENSP00000387347:T96M;ENSP00000311951:T92M;ENSP00000407213:T96M	ENSP00000254653:T96M	T	-	2	0	IQCA1	237070594	1.000000	0.71417	0.002000	0.10522	0.262000	0.26303	4.660000	0.61511	1.288000	0.44600	0.650000	0.86243	ACG		0.473	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726	
COL6A3	1293	broad.mit.edu	37	2	238277492	238277492	+	Silent	SNP	G	G	A	rs199759398		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:238277492G>A	ENST00000295550.4	-	10	5066	c.4614C>T	c.(4612-4614)gaC>gaT	p.D1538D	COL6A3_ENST00000409809.1_Silent_p.D1332D|COL6A3_ENST00000472056.1_Silent_p.D931D|COL6A3_ENST00000353578.4_Silent_p.D1332D|COL6A3_ENST00000346358.4_Silent_p.D1338D|COL6A3_ENST00000347401.3_Silent_p.D1337D	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1538	Nonhelical region.|VWFA 8. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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.D1538D(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)		GGGGCACCCCGTCTTCTATGC	0.577													G|||	1	0.000199681	0.0	0.0	5008	,	,		18167	0.001		0.0	False		,,,				2504	0.0				p.D931D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2793T	2						.						77.0	77.0	77.0					2																	238277492		2203	4300	6503	237942231	SO:0001819	synonymous_variant	1293	exon7			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.4614C>T	2.37:g.238277492G>A		Somatic		Capture	Illumina HiSeq	Phase_I	237942231	NM_057166	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.577	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
COL6A3	1293	broad.mit.edu	37	2	238280871	238280871	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:238280871G>A	ENST00000295550.4	-	9	4241	c.3789C>T	c.(3787-3789)gaC>gaT	p.D1263D	COL6A3_ENST00000409809.1_Silent_p.D1057D|COL6A3_ENST00000472056.1_Silent_p.D656D|COL6A3_ENST00000392003.2_Silent_p.D856D|COL6A3_ENST00000353578.4_Silent_p.D1057D|COL6A3_ENST00000392004.3_Silent_p.D1057D|COL6A3_ENST00000346358.4_Silent_p.D1063D|COL6A3_ENST00000347401.3_Silent_p.D1062D	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1263	Nonhelical region.|VWFA 7. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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.D1263D(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)		CAAAGCCCACGTCCAGGTAGT	0.577																																					p.D656D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1968T	2						.						51.0	47.0	48.0					2																	238280871		2203	4300	6503	237945610	SO:0001819	synonymous_variant	1293	exon6			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.3789C>T	2.37:g.238280871G>A		Somatic		Capture	Illumina HiSeq	Phase_I	237945610	NM_057166	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.577	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
COL6A3	1293	broad.mit.edu	37	2	238289832	238289832	+	Silent	SNP	G	G	A	rs114144694		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:238289832G>A	ENST00000295550.4	-	5	2075	c.1623C>T	c.(1621-1623)gcC>gcT	p.A541A	COL6A3_ENST00000409809.1_Silent_p.A335A|COL6A3_ENST00000472056.1_Silent_p.A134A|COL6A3_ENST00000392003.2_Silent_p.A134A|COL6A3_ENST00000353578.4_Silent_p.A335A|COL6A3_ENST00000392004.3_Silent_p.A335A|COL6A3_ENST00000346358.4_Silent_p.A541A|COL6A3_ENST00000347401.3_Silent_p.A340A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	541	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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.A541A(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)		CCCGGTAGCCGGCTGAACTCG	0.552													G|||	1	0.000199681	0.0	0.0	5008	,	,		18563	0.0		0.001	False		,,,				2504	0.0				p.A134A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C402T	2						.	G	,,,,	0,4406		0,0,2203	66.0	76.0	73.0		1623,402,1005,402,1005	-9.3	0.0	2	dbSNP_132	73	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	,,,,	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	,,,,	541/3178,134/1037,335/1238,134/2571,335/2972	238289832	3,13003	2203	4300	6503	237954571	SO:0001819	synonymous_variant	1293	exon3			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.1623C>T	2.37:g.238289832G>A		Somatic		Capture	Illumina HiSeq	Phase_I	237954571	NM_057166	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																				0.552	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
SCLY	51540	broad.mit.edu	37	2	238990799	238990799	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:238990799C>T	ENST00000555827.1	+	6	790	c.726C>T	c.(724-726)cgC>cgT	p.R242R	SCLY_ENST00000409736.2_Silent_p.R242R|SCLY_ENST00000429612.2_Intron|SCLY_ENST00000373332.3_Silent_p.R160R|SCLY_ENST00000422984.2_Silent_p.R148R|SCLY_ENST00000254663.6_Silent_p.R250R			Q96I15	SCLY_HUMAN	selenocysteine lyase	242					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)	p.R242R(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|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;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		GGAAGCAGCGCGTGGATGTGG	0.612																																					p.R242R	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C726T	2						.						83.0	76.0	78.0					2																	238990799		2203	4300	6503	238655538	SO:0001819	synonymous_variant	51540	exon6			AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"""putative selenocysteine lyase"""	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.726C>T	2.37:g.238990799C>T		Somatic		Capture	Illumina HiSeq	Phase_I	238655538	NM_016510	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Silent	SNP	ENST00000555827.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.43|13.43	2.236158|2.236158	0.39498|0.39498	.|.	.|.	ENSG00000132330|ENSG00000132330	ENST00000431487|ENST00000437134;ENST00000440143	.|D	.|0.87103	.|-2.21	5.48|5.48	-8.59|-8.59	0.00893|0.00893	.|.	.|0.247981	.|0.42821	.|D	.|0.000652	D|D	0.82926|0.82926	0.5143|0.5143	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.76119|0.76119	-0.3076|-0.3076	4|7	.|0.87932	.|D	.|0	-2.7019|-2.7019	3.0991|3.0991	0.06319|0.06319	0.2338:0.1184:0.1253:0.5224|0.2338:0.1184:0.1253:0.5224	.|.	.|.	.|.	.|.	V|C	88|86;20	.|ENSP00000404444:R86C	.|ENSP00000404444:R86C	A|R	+|+	2|1	0|0	SCLY|SCLY	238655538|238655538	0.000000|0.000000	0.05858|0.05858	0.650000|0.650000	0.29550|0.29550	0.742000|0.742000	0.42306|0.42306	-1.500000|-1.500000	0.02283|0.02283	-1.196000|-1.196000	0.02676|0.02676	-0.768000|-0.768000	0.03414|0.03414	GCG|CGT		0.612	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510	
ASB1	51665	broad.mit.edu	37	2	239353086	239353086	+	Missense_Mutation	SNP	G	G	A	rs150540319	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:239353086G>A	ENST00000264607.4	+	4	845	c.598G>A	c.(598-600)Gca>Aca	p.A200T	ASB1_ENST00000409297.1_Missense_Mutation_p.A99T	NM_001040445.1	NP_001035535.1	Q9Y576	ASB1_HUMAN	ankyrin repeat and SOCS box containing 1	200					intracellular signal transduction (GO:0035556)|male genitalia development (GO:0030539)|negative regulation of cytokine biosynthetic process (GO:0042036)|protein ubiquitination (GO:0016567)	intracellular (GO:0005622)		p.A200T(1)		breast(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	8		all_epithelial(40;2.65e-14)|Breast(86;7.61e-05)|Renal(207;0.00183)|all_lung(227;0.0283)|Ovarian(221;0.0365)|Lung NSC(271;0.0941)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)		GTACATCAGCGCAGCCTACCA	0.597																																					p.A200T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G598A	2						.	G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	63.0	50.0	54.0		598	5.0	0.3	2	dbSNP_134	54	1,8599	1.2+/-3.3	0,1,4299	no	missense	ASB1	NM_001040445.1	58	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	200/336	239353086	2,13004	2203	4300	6503	239017825	SO:0001583	missense	51665	exon4			AF156777	CCDS33416.1	2q37	2013-01-10	2011-01-25		ENSG00000065802	ENSG00000065802		"""Ankyrin repeat domain containing"""	16011	protein-coding gene	gene with protein product		605758	"""ankyrin repeat and SOCS box-containing 1"""				Standard	XR_241235		Approved	ASB-1	uc002vyg.3	Q9Y576	OTTHUMG00000152866	ENST00000264607.4:c.598G>A	2.37:g.239353086G>A	ENSP00000264607:p.Ala200Thr	Somatic		Capture	Illumina HiSeq	Phase_I	239017825	NM_001040445	A6NL50|Q4ZG29|Q9ULS4	Missense_Mutation	SNP	ENST00000264607.4	37	CCDS33416.1	.	.	.	.	.	.	.	.	.	.	G	31	5.089541	0.94149	2.27E-4	1.16E-4	ENSG00000065802	ENST00000264607;ENST00000409297	T;T	0.71817	0.23;-0.6	5.91	5.03	0.67393	Ankyrin repeat-containing domain (3);	0.099244	0.64402	N	0.000001	T	0.77961	0.4209	M	0.67953	2.075	0.80722	D	1	D	0.63046	0.992	P	0.54856	0.762	T	0.78732	-0.2089	9	.	.	.	.	14.7309	0.69379	0.0686:0.0:0.9314:0.0	.	200	Q9Y576	ASB1_HUMAN	T	200;99	ENSP00000264607:A200T;ENSP00000387025:A99T	.	A	+	1	0	ASB1	239017825	1.000000	0.71417	0.347000	0.25668	0.933000	0.57130	9.068000	0.93961	1.502000	0.48669	0.655000	0.94253	GCA		0.597	ASB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328294.1	NM_001040445	
MFSD2B	388931	broad.mit.edu	37	2	24239740	24239740	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:24239740G>A	ENST00000406420.3	+	4	389	c.373G>A	c.(373-375)Gcc>Acc	p.A125T	MFSD2B_ENST00000338315.4_Missense_Mutation_p.A125T	NM_001080473.1	NP_001073942.1	A6NFX1	MFS2B_HUMAN	major facilitator superfamily domain containing 2B	125					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.A125T(1)		cervix(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10						CCCCTTCATCGCCCTGGCCTA	0.662																																					p.A125T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G373A	2						.						58.0	64.0	62.0					2																	24239740		2063	4180	6243	24093244	SO:0001583	missense	388931	exon4				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.373G>A	2.37:g.24239740G>A	ENSP00000385527:p.Ala125Thr	Somatic		Capture	Illumina HiSeq	Phase_I	24093244	NM_001080473	B5MC32	Missense_Mutation	SNP	ENST00000406420.3	37	CCDS46228.1	.	.	.	.	.	.	.	.	.	.	G	9.100	1.003795	0.19199	.	.	ENSG00000205639	ENST00000406420;ENST00000338315	D;D	0.82255	-1.59;-1.59	4.87	-1.44	0.08856	Major facilitator superfamily domain, general substrate transporter (1);	0.322034	0.28135	U	0.016475	T	0.69548	0.3123	L	0.40543	1.245	0.09310	N	1	B	0.27416	0.178	B	0.21708	0.036	T	0.59048	-0.7527	10	0.59425	D	0.04	-2.0905	5.5405	0.17036	0.4582:0.0:0.4114:0.1303	.	125	A6NFX1	MFS2B_HUMAN	T	125	ENSP00000385527:A125T;ENSP00000342501:A125T	ENSP00000342501:A125T	A	+	1	0	MFSD2B	24093244	0.003000	0.15002	0.000000	0.03702	0.071000	0.16799	0.380000	0.20602	-0.280000	0.09154	0.511000	0.50034	GCC		0.662	MFSD2B-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000324307.1	NM_001080473	
PRR21	643905	broad.mit.edu	37	2	240981996	240981996	+	Missense_Mutation	SNP	G	G	C	rs568535538|rs78477080	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:240981996G>C	ENST00000408934.1	-	1	403	c.404C>G	c.(403-405)cCt>cGt	p.P135R		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	135	Pro-rich.							p.P135R(4)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GAGGCATGGAGGAAGGGCCGT	0.642																																					p.P135R												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.C404G	2						.						3.0	3.0	3.0					2																	240981996		1158	2510	3668	240630669	SO:0001583	missense	643905	exon1			AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.404C>G	2.37:g.240981996G>C	ENSP00000386166:p.Pro135Arg	None		Capture	Illumina HiSeq	Phase_I	240630669	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	N	0.004	-2.241787	0.00274	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.13307	2.6;2.6	1.73	-3.46	0.04767	.	.	.	.	.	T	0.06280	0.0162	N	0.08118	0	0.09310	N	1	B	0.16802	0.019	B	0.22753	0.041	T	0.44283	-0.9338	9	0.13853	T	0.58	.	11.1434	0.48415	0.0:0.0:0.7795:0.2205	.	135	Q8WXC7	PRR21_HUMAN	R	135	ENSP00000386166:P135R;ENSP00000418240:P135R	ENSP00000386166:P135R	P	-	2	0	PRR21	240630669	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-2.073000	0.00878	-1.240000	0.01540	CCT		0.642	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
GPC1	2817	broad.mit.edu	37	2	241402839	241402839	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:241402839G>A	ENST00000264039.2	+	4	1041	c.793G>A	c.(793-795)Gcc>Acc	p.A265T		NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	265					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|myelin assembly (GO:0032288)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|phototransduction, visible light (GO:0007603)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|retinoid metabolic process (GO:0001523)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|fibroblast growth factor binding (GO:0017134)|laminin binding (GO:0043236)	p.A265T(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	9		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)		AGTCCCCGGCGCCAGGCCCTG	0.662																																					p.A265T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G793A	2						.						73.0	77.0	76.0					2																	241402839		2202	4300	6502	241051512	SO:0001583	missense	2817	exon4			AK095397	CCDS2534.1	2q35-q37	2008-02-05			ENSG00000063660	ENSG00000063660		"""Proteoglycans / Cell Surface : Glypicans"""	4449	protein-coding gene	gene with protein product	"""glypican proteoglycan 1"""	600395				7774946	Standard	NM_002081		Approved	glypican	uc002vyw.4	P35052	OTTHUMG00000133349	ENST00000264039.2:c.793G>A	2.37:g.241402839G>A	ENSP00000264039:p.Ala265Thr	Somatic		Capture	Illumina HiSeq	Phase_I	241051512	NM_002081	B3KTD1|Q53QM4	Missense_Mutation	SNP	ENST00000264039.2	37	CCDS2534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.55|17.55	3.416418|3.416418	0.62511|0.62511	.|.	.|.	ENSG00000063660|ENSG00000063660	ENST00000264039|ENST00000420138;ENST00000455111	T|.	0.48201|.	0.82|.	3.88|3.88	2.91|2.91	0.33838|0.33838	Glypican, conserved site (1);|.	0.442501|.	0.24611|.	N|.	0.037058|.	T|T	0.42314|0.42314	0.1197|0.1197	L|L	0.60455|0.60455	1.87|1.87	0.21878|0.21878	N|N	0.999496|0.999496	B|.	0.33379|.	0.41|.	B|.	0.33392|.	0.163|.	T|T	0.30822|0.30822	-0.9965|-0.9965	10|5	0.66056|.	D|.	0.02|.	-29.5322|-29.5322	5.0111|5.0111	0.14313|0.14313	0.1192:0.2165:0.6643:0.0|0.1192:0.2165:0.6643:0.0	.|.	265|.	P35052|.	GPC1_HUMAN|.	T|H	265|304;9	ENSP00000264039:A265T|.	ENSP00000264039:A265T|.	A|R	+|+	1|2	0|0	GPC1|GPC1	241051512|241051512	1.000000|1.000000	0.71417|0.71417	0.964000|0.964000	0.40570|0.40570	0.646000|0.646000	0.38490|0.38490	3.514000|3.514000	0.53422|0.53422	2.176000|2.176000	0.68965|0.68965	0.484000|0.484000	0.47621|0.47621	GCC|CGC		0.662	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
CAPN10	11132	broad.mit.edu	37	2	241530409	241530409	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:241530409C>A	ENST00000391984.2	+	3	647	c.451C>A	c.(451-453)Ctg>Atg	p.L151M	CAPN10_ENST00000352879.4_Intron|CAPN10_ENST00000270364.7_Intron|CAPN10_ENST00000354082.4_Missense_Mutation_p.L151M|CAPN10_ENST00000404753.3_Missense_Mutation_p.L151M|CAPN10_ENST00000391982.2_Missense_Mutation_p.L151M	NM_023083.3	NP_075571	Q9HC96	CAN10_HUMAN	calpain 10	151	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				actin cytoskeleton reorganization (GO:0031532)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to insulin stimulus (GO:0032869)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin secretion (GO:0032024)|positive regulation of intracellular transport (GO:0032388)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteolysis (GO:0006508)|type B pancreatic cell apoptotic process (GO:0097050)	cell (GO:0005623)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cytoskeletal protein binding (GO:0008092)|SNARE binding (GO:0000149)	p.L151M(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|urinary_tract(1)	27		all_epithelial(40;1.72e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.13e-31)|all cancers(36;3.24e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.82e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.1e-06)|Lung(119;0.00168)|Colorectal(34;0.00495)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.032)		GCTCCCCTTACTGGAAAAGGT	0.637																																					p.L151M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C451A	2						.						69.0	62.0	65.0					2																	241530409		2203	4300	6503	241179082	SO:0001583	missense	11132	exon3			AF089088	CCDS33420.1, CCDS42838.1	2q37.3	2008-05-22			ENSG00000142330	ENSG00000142330			1477	protein-coding gene	gene with protein product		605286				11017071, 11018080	Standard	NM_023083		Approved		uc002vzk.2	Q9HC96	OTTHUMG00000133358	ENST00000391984.2:c.451C>A	2.37:g.241530409C>A	ENSP00000375844:p.Leu151Met	Somatic		Capture	Illumina HiSeq	Phase_I	241179082	NM_023085	A8MVS7|Q4ZFV1|Q8NCD4|Q96IG4|Q96JI2|Q9HC89|Q9HC90|Q9HC91|Q9HC92|Q9HC93|Q9HC94|Q9HC95	Nonsense_Mutation	SNP	ENST00000391984.2	37	CCDS42838.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.028149	0.54790	.	.	ENSG00000142330	ENST00000391984;ENST00000391982;ENST00000404753;ENST00000354082	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	4.65	2.83	0.33086	Peptidase C2, calpain, catalytic domain (3);	0.000000	0.64402	D	0.000006	T	0.55513	0.1925	M	0.86953	2.85	0.43014	D	0.994555	D;D;D	0.89917	1.0;0.997;0.995	D;P;D	0.91635	0.999;0.902;0.984	T	0.58918	-0.7551	10	0.62326	D	0.03	.	8.3126	0.32080	0.0:0.8037:0.0:0.1963	.	151;151;151	B7Z6G3;Q9HC96-3;Q9HC96	.;.;CAN10_HUMAN	M	151	ENSP00000375844:L151M;ENSP00000375842:L151M;ENSP00000384422:L151M;ENSP00000270362:L151M	ENSP00000270361:L151M	L	+	1	2	CAPN10	241179082	0.754000	0.28360	0.999000	0.59377	0.863000	0.49368	0.537000	0.23144	0.947000	0.37659	-0.291000	0.09656	CTG		0.637	CAPN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257191.3	NM_023083	
CAPN10	11132	broad.mit.edu	37	2	241533370	241533370	+	Missense_Mutation	SNP	C	C	T	rs372639976		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:241533370C>T	ENST00000391984.2	+	5	932	c.736C>T	c.(736-738)Cgg>Tgg	p.R246W	CAPN10_ENST00000352879.4_Intron|CAPN10_ENST00000270364.7_Intron|CAPN10_ENST00000354082.4_Missense_Mutation_p.R246W|CAPN10_ENST00000404753.3_Missense_Mutation_p.R246W|CAPN10_ENST00000391982.2_Missense_Mutation_p.R246W	NM_023083.3	NP_075571	Q9HC96	CAN10_HUMAN	calpain 10	246	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				actin cytoskeleton reorganization (GO:0031532)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to insulin stimulus (GO:0032869)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin secretion (GO:0032024)|positive regulation of intracellular transport (GO:0032388)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|proteolysis (GO:0006508)|type B pancreatic cell apoptotic process (GO:0097050)	cell (GO:0005623)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cytoskeletal protein binding (GO:0008092)|SNARE binding (GO:0000149)	p.R246W(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|urinary_tract(1)	27		all_epithelial(40;1.72e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.13e-31)|all cancers(36;3.24e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.82e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;5.1e-06)|Lung(119;0.00168)|Colorectal(34;0.00495)|LUSC - Lung squamous cell carcinoma(224;0.00813)|COAD - Colon adenocarcinoma(134;0.032)		CTCGGACCTGCGGGAGCTCCA	0.667																																					p.R246W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C736T	2						.	C	TRP/ARG,TRP/ARG	0,4406		0,0,2203	92.0	97.0	96.0		736,736	3.6	0.0	2		96	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CAPN10	NM_023083.3,NM_023085.3	101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	246/673,246/518	241533370	1,13005	2203	4300	6503	241182043	SO:0001583	missense	11132	exon5			AF089088	CCDS33420.1, CCDS42838.1	2q37.3	2008-05-22			ENSG00000142330	ENSG00000142330			1477	protein-coding gene	gene with protein product		605286				11017071, 11018080	Standard	NM_023083		Approved		uc002vzk.2	Q9HC96	OTTHUMG00000133358	ENST00000391984.2:c.736C>T	2.37:g.241533370C>T	ENSP00000375844:p.Arg246Trp	Somatic		Capture	Illumina HiSeq	Phase_I	241182043	NM_023085	A8MVS7|Q4ZFV1|Q8NCD4|Q96IG4|Q96JI2|Q9HC89|Q9HC90|Q9HC91|Q9HC92|Q9HC93|Q9HC94|Q9HC95	Missense_Mutation	SNP	ENST00000391984.2	37	CCDS42838.1	.	.	.	.	.	.	.	.	.	.	C	11.13	1.548215	0.27652	0.0	1.16E-4	ENSG00000142330	ENST00000391984;ENST00000391982;ENST00000404753;ENST00000354082	D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31	4.52	3.63	0.41609	Peptidase C2, calpain, catalytic domain (3);	0.764929	0.11420	N	0.565871	D	0.92532	0.7628	M	0.80508	2.5	0.09310	N	0.999999	D;D;D;D	0.89917	1.0;0.998;0.995;0.997	D;P;P;P	0.63033	0.91;0.809;0.711;0.849	D	0.83484	0.0066	10	0.87932	D	0	.	11.5895	0.50938	0.1799:0.8201:0.0:0.0	.	246;246;246;246	B7Z6G3;B7WPF5;Q9HC96-3;Q9HC96	.;.;.;CAN10_HUMAN	W	246	ENSP00000375844:R246W;ENSP00000375842:R246W;ENSP00000384422:R246W;ENSP00000270362:R246W	ENSP00000270362:R246W	R	+	1	2	CAPN10	241182043	0.004000	0.15560	0.029000	0.17559	0.830000	0.47004	0.024000	0.13555	0.877000	0.35895	0.655000	0.94253	CGG		0.667	CAPN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257191.3	NM_023083	
THAP4	51078	broad.mit.edu	37	2	242545755	242545755	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:242545755G>A	ENST00000407315.1	-	3	1805	c.1374C>T	c.(1372-1374)caC>caT	p.H458H	THAP4_ENST00000402545.1_Silent_p.H46H|THAP4_ENST00000402136.1_Silent_p.H46H	NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN	THAP domain containing 4	458							DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H458H(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)		GCTGGCCCACGTGGGAGATGT	0.597																																					p.H46H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C138T	2						.						67.0	45.0	53.0					2																	242545755		2188	4286	6474	242194428	SO:0001819	synonymous_variant	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.1374C>T	2.37:g.242545755G>A		Somatic		Capture	Illumina HiSeq	Phase_I	242194428	NM_001164356	Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	Silent	SNP	ENST00000407315.1	37	CCDS2551.1																																																																																				0.597	THAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257267.3	NM_015963	
TSSC1	7260	broad.mit.edu	37	2	3261194	3261194	+	Missense_Mutation	SNP	C	C	T	rs200794439		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:3261194C>T	ENST00000382125.4	-	4	484	c.292G>A	c.(292-294)Gtg>Atg	p.V98M	TSSC1_ENST00000443925.2_Missense_Mutation_p.V98M|TSSC1_ENST00000478754.1_5'UTR|TSSC1_ENST00000398659.4_Missense_Mutation_p.V125M	NM_003310.2	NP_003301.1	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1	98								p.V98M(1)|p.V98L(1)		breast(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		ATCCTCCACACGGCTGCACAT	0.537																																					p.V98M	Colon(140;1261 1762 4183 34270 49743)											.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G292A	2						.						97.0	88.0	91.0					2																	3261194		2203	4300	6503	3240201	SO:0001583	missense	7260	exon4			AF019952	CCDS1651.1	2p25.3	2013-01-10			ENSG00000032389	ENSG00000032389		"""WD repeat domain containing"""	12383	protein-coding gene	gene with protein product		608998				9403053, 9925925	Standard	NM_003310		Approved		uc002qxj.2	Q53HC9	OTTHUMG00000090329	ENST00000382125.4:c.292G>A	2.37:g.3261194C>T	ENSP00000371559:p.Val98Met	Somatic		Capture	Illumina HiSeq	Phase_I	3240201	NM_003310	D6W4Y1|O43179|Q53S19|Q53SG2	Missense_Mutation	SNP	ENST00000382125.4	37	CCDS1651.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.964578	0.92791	.	.	ENSG00000032389	ENST00000382125;ENST00000398659;ENST00000443925;ENST00000444776	T;D;T	0.85484	2.22;-1.99;2.22	5.44	5.44	0.79542	WD40/YVTN repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.89522	0.6739	M	0.64567	1.98	0.80722	D	1	D	0.69078	0.997	P	0.56042	0.79	D	0.90068	0.4161	10	0.59425	D	0.04	-13.0679	18.2929	0.90136	0.0:1.0:0.0:0.0	.	98	Q53HC9	TSSC1_HUMAN	M	98;125;98;132	ENSP00000371559:V98M;ENSP00000381652:V125M;ENSP00000389080:V98M	ENSP00000371559:V98M	V	-	1	0	TSSC1	3240201	1.000000	0.71417	0.992000	0.48379	0.999000	0.98932	5.930000	0.70104	2.549000	0.85964	0.650000	0.86243	GTG		0.537	TSSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206694.2	NM_003310	
TRAPPC12	51112	broad.mit.edu	37	2	3391570	3391570	+	Missense_Mutation	SNP	C	C	T	rs372611768		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:3391570C>T	ENST00000324266.5	+	2	371	c.176C>T	c.(175-177)gCg>gTg	p.A59V	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.A59V	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	59					vesicle-mediated transport (GO:0016192)			p.A59V(1)									AGTCCTCTCGCGGACAAGCTG	0.607																																					p.A59V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C176T	2						.	C	VAL/ALA	0,4406		0,0,2203	56.0	47.0	50.0		176	-7.7	0.0	2		50	1,8599	1.2+/-3.3	0,1,4299	no	missense	TTC15	NM_016030.5	64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	59/736	3391570	1,13005	2203	4300	6503	3370577	SO:0001583	missense	51112	exon2			BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.176C>T	2.37:g.3391570C>T	ENSP00000324318:p.Ala59Val	Somatic		Capture	Illumina HiSeq	Phase_I	3370577	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	.	.	.	.	.	.	.	.	.	.	C	0.446	-0.896307	0.02472	0.0	1.16E-4	ENSG00000171853	ENST00000382110;ENST00000304601;ENST00000324266	T;T	0.55588	0.51;0.51	5.21	-7.72	0.01250	.	1.553890	0.03552	N	0.225647	T	0.21881	0.0527	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.04013	0.0;0.0;0.001	T	0.14924	-1.0455	10	0.20046	T	0.44	.	7.1552	0.25632	0.0:0.3379:0.3534:0.3087	.	42;59;59	E7ENL7;Q8WVT3;Q53S18	.;TPC12_HUMAN;.	V	59;42;59	ENSP00000371544:A59V;ENSP00000324318:A59V	ENSP00000303612:A42V	A	+	2	0	TTC15	3370577	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.617000	0.24359	-1.606000	0.01591	-1.432000	0.01085	GCG		0.607	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
RNF144A	9781	broad.mit.edu	37	2	7160638	7160638	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:7160638G>A	ENST00000320892.6	+	6	778	c.336G>A	c.(334-336)ccG>ccA	p.P112P	RNF144A_ENST00000467276.1_3'UTR	NM_014746.3	NP_055561.2	P50876	R144A_HUMAN	ring finger protein 144A	112					protein ubiquitination (GO:0016567)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.P112P(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)	25	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)		CTTGGTGCCCGGCGTCCACCT	0.567																																					p.P112P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G336A	2						.						74.0	68.0	70.0					2																	7160638		2203	4300	6503	7078089	SO:0001819	synonymous_variant	9781	exon6			D79983	CCDS1657.1	2p25.2	2008-02-05	2007-08-20	2007-08-20	ENSG00000151692	ENSG00000151692		"""RING-type (C3HC4) zinc fingers"""	20457	protein-coding gene	gene with protein product			"""ring finger protein 144"""	RNF144		8724849, 10431818	Standard	NM_014746		Approved	UBCE7IP4, KIAA0161	uc002qys.3	P50876	OTTHUMG00000090353	ENST00000320892.6:c.336G>A	2.37:g.7160638G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7078089	NM_014746	D6W4Y6|Q585H5	Silent	SNP	ENST00000320892.6	37	CCDS1657.1	.	.	.	.	.	.	.	.	.	.	G	5.368	0.253115	0.10185	.	.	ENSG00000151692	ENST00000432850	.	.	.	5.24	-10.5	0.00291	.	.	.	.	.	T	0.33818	0.0876	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43750	-0.9372	4	.	.	.	.	2.9863	0.05969	0.2803:0.0754:0.3693:0.275	.	.	.	.	Q	108	.	.	R	+	2	0	RNF144A	7078089	0.000000	0.05858	0.079000	0.20413	0.741000	0.42261	-2.105000	0.01339	-2.973000	0.00285	-2.069000	0.00389	CGG		0.567	RNF144A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206725.2	NM_014746	
KIDINS220	57498	broad.mit.edu	37	2	8936948	8936948	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:8936948C>T	ENST00000256707.3	-	11	1232	c.1051G>A	c.(1051-1053)Gtg>Atg	p.V351M	KIDINS220_ENST00000418530.1_Missense_Mutation_p.V309M|KIDINS220_ENST00000427284.1_Missense_Mutation_p.V351M|KIDINS220_ENST00000319688.5_Missense_Mutation_p.V352M|KIDINS220_ENST00000473731.1_Missense_Mutation_p.V351M	NM_020738.2	NP_065789.1	Q9ULH0	KDIS_HUMAN	kinase D-interacting substrate, 220kDa	351					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.V351M(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)					AGCAGCTCCACCACTTCAATG	0.438																																					p.V351M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1051A	2						.						266.0	263.0	264.0					2																	8936948		1988	4177	6165	8854399	SO:0001583	missense	57498	exon11			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.1051G>A	2.37:g.8936948C>T	ENSP00000256707:p.Val351Met	Somatic		Capture	Illumina HiSeq	Phase_I	8854399	NM_020738	A1L4N4|Q4VC08|Q6MZU2|Q9H889|Q9H9E4|Q9NT37|Q9UF42	Missense_Mutation	SNP	ENST00000256707.3	37	CCDS42650.1	.	.	.	.	.	.	.	.	.	.	C	17.12	3.308845	0.60305	.	.	ENSG00000134313	ENST00000496383;ENST00000541927;ENST00000256707;ENST00000427284;ENST00000418530;ENST00000473731;ENST00000489024;ENST00000319688	T;T;T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55	5.11	5.11	0.69529	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.84023	0.5381	M	0.71296	2.17	0.80722	D	1	P;D;D;D	0.89917	0.911;1.0;1.0;1.0	P;D;D;D	0.97110	0.776;1.0;0.999;1.0	D	0.85748	0.1341	10	0.87932	D	0	.	18.879	0.92350	0.0:1.0:0.0:0.0	.	352;352;309;351	B4DK94;E9PH70;Q9ULH0-2;Q9ULH0	.;.;.;KDIS_HUMAN	M	98;35;351;351;309;351;352;352	ENSP00000420364:V98M;ENSP00000256707:V351M;ENSP00000411849:V351M;ENSP00000414923:V309M;ENSP00000418974:V351M;ENSP00000419964:V352M;ENSP00000319947:V352M	ENSP00000256707:V351M	V	-	1	0	KIDINS220	8854399	1.000000	0.71417	0.092000	0.20876	0.087000	0.18053	7.398000	0.79919	2.540000	0.85666	0.591000	0.81541	GTG		0.438	KIDINS220-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323408.2	NM_020738	
ITSN2	50618	broad.mit.edu	37	2	24536387	24536387	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:24536387G>A	ENST00000355123.4	-	4	573	c.130C>T	c.(130-132)Caa>Taa	p.Q44*	ITSN2_ENST00000407704.1_5'UTR|ITSN2_ENST00000406921.3_Nonsense_Mutation_p.Q44*|ITSN2_ENST00000361999.3_Nonsense_Mutation_p.Q44*	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	44	EH 1. {ECO:0000255|PROSITE- ProRule:PRU00077}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)	p.Q43*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTACGTGCTTGATCACCTGGA	0.328																																					p.Q44X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C130T	2						.						54.0	55.0	55.0					2																	24536387		2203	4300	6503	24389891	SO:0001587	stop_gained	50618	exon4			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.130C>T	2.37:g.24536387G>A	ENSP00000347244:p.Gln44*	Somatic		Capture	Illumina HiSeq	Phase_I	24389891	NM_019595	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Nonsense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	.	.	.	.	.	.	.	.	.	.	G	38	6.672218	0.97751	.	.	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868;ENST00000445614;ENST00000406921;ENST00000412011;ENST00000443927	.	.	.	4.94	4.94	0.65067	.	0.000000	0.34386	U	0.004005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	18.7361	0.91755	0.0:0.0:1.0:0.0	.	.	.	.	X	44;44;44;43;44;44;30	.	ENSP00000347244:Q44X	Q	-	1	0	ITSN2	24389891	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	9.208000	0.95075	2.727000	0.93392	0.591000	0.81541	CAA		0.328	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
NCOA1	8648	broad.mit.edu	37	2	24881613	24881613	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:24881613C>T	ENST00000406961.1	+	5	719	c.67C>T	c.(67-69)Cca>Tca	p.P23S	NCOA1_ENST00000538539.1_Missense_Mutation_p.P23S|NCOA1_ENST00000288599.5_Missense_Mutation_p.P23S|NCOA1_ENST00000348332.3_Missense_Mutation_p.P23S|NCOA1_ENST00000407230.1_5'UTR|NCOA1_ENST00000405141.1_Missense_Mutation_p.P23S|NCOA1_ENST00000395856.3_Missense_Mutation_p.P23S			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	23	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				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.P23S(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)					GAAAGGATCGCCATGTGACAC	0.453			T	PAX3	alveolar rhadomyosarcoma																																p.P23S			Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C67T	2						.						93.0	75.0	81.0					2																	24881613		2203	4300	6503	24735117	SO:0001583	missense	8648	exon3			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.67C>T	2.37:g.24881613C>T	ENSP00000385216:p.Pro23Ser	Somatic		Capture	Illumina HiSeq	Phase_I	24735117	NM_003743	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	37	CCDS1712.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.244590	0.79912	.	.	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	D;D;D;D;D;D	0.97256	-4.31;-4.31;-4.31;-4.31;-4.31;-4.31	5.65	5.65	0.86999	Helix-loop-helix DNA-binding (2);	0.000000	0.85682	D	0.000000	D	0.97005	0.9022	N	0.22421	0.69	0.80722	D	1	D;B;P	0.89917	1.0;0.391;0.899	D;B;P	0.87578	0.998;0.362;0.661	D	0.96562	0.9416	10	0.38643	T	0.18	.	19.5069	0.95121	0.0:1.0:0.0:0.0	.	23;23;23	Q15788-3;Q15788;Q15788-2	.;NCOA1_HUMAN;.	S	23	ENSP00000385216:P23S;ENSP00000385097:P23S;ENSP00000444039:P23S;ENSP00000320940:P23S;ENSP00000288599:P23S;ENSP00000379197:P23S	ENSP00000288599:P23S	P	+	1	0	NCOA1	24735117	0.851000	0.29673	1.000000	0.80357	0.997000	0.91878	1.574000	0.36482	2.941000	0.99782	0.655000	0.94253	CCA		0.453	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223	
ADCY3	109	broad.mit.edu	37	2	25141680	25141680	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:25141680C>T	ENST00000260600.5	-	1	1028	c.177G>A	c.(175-177)ccG>ccA	p.P59P		NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	59					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)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.P59P(1)		NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					CCAAGGACTCCGGCACGAAAG	0.627																																					p.P59P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G177A	2						.						53.0	57.0	56.0					2																	25141680		2203	4300	6503	24995184	SO:0001819	synonymous_variant	109	exon1			AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"""Adenylate cyclases"""	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.177G>A	2.37:g.25141680C>T		Somatic		Capture	Illumina HiSeq	Phase_I	24995184	NM_004036	B3KT86|Q53T54|Q9UDB1	Silent	SNP	ENST00000260600.5	37	CCDS1715.1																																																																																				0.627	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2		
DRC1	92749	broad.mit.edu	37	2	26652585	26652585	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:26652585G>T	ENST00000288710.2	+	5	704	c.630G>T	c.(628-630)caG>caT	p.Q210H		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	210					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)		p.Q210H(1)									TGGAAGAACAGGTGAAGAATG	0.458																																					p.Q210H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G630T	2						.						120.0	119.0	119.0					2																	26652585		2203	4300	6503	26506089	SO:0001583	missense	92749	exon5			AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"""chromosome 2 open reading frame 39"", ""coiled-coil domain containing 164"", ""dynein regulatory complex subunit 1 homolog (Chlamydomonas)"""	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.630G>T	2.37:g.26652585G>T	ENSP00000288710:p.Gln210His	Somatic		Capture	Illumina HiSeq	Phase_I	26506089	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	37	CCDS1723.1	.	.	.	.	.	.	.	.	.	.	G	18.29	3.591108	0.66219	.	.	ENSG00000157856	ENST00000288710	T	0.21543	2.0	5.35	-6.19	0.02078	.	0.057805	0.64402	D	0.000001	T	0.44993	0.1320	M	0.87180	2.865	0.39469	D	0.967699	D	0.69078	0.997	D	0.65684	0.937	T	0.61691	-0.7011	10	0.62326	D	0.03	-20.7866	18.2488	0.89996	0.2324:0.0:0.7676:0.0	.	210	Q96MC2	CC164_HUMAN	H	210	ENSP00000288710:Q210H	ENSP00000288710:Q210H	Q	+	3	2	CCDC164	26506089	0.982000	0.34865	0.391000	0.26233	0.925000	0.55904	-0.017000	0.12590	-1.330000	0.02255	-0.471000	0.05019	CAG		0.458	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038	
DRC1	92749	broad.mit.edu	37	2	26653672	26653672	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:26653672C>T	ENST00000288710.2	+	6	771	c.697C>T	c.(697-699)Cgc>Tgc	p.R233C	DRC1_ENST00000483675.1_3'UTR	NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	233					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)		p.R233C(1)									TGAGGTGGAACGCCAAGAGCT	0.468																																					p.R233C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C697T	2						.						153.0	158.0	156.0					2																	26653672		2203	4300	6503	26507176	SO:0001583	missense	92749	exon6			AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"""chromosome 2 open reading frame 39"", ""coiled-coil domain containing 164"", ""dynein regulatory complex subunit 1 homolog (Chlamydomonas)"""	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.697C>T	2.37:g.26653672C>T	ENSP00000288710:p.Arg233Cys	Somatic		Capture	Illumina HiSeq	Phase_I	26507176	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	37	CCDS1723.1	.	.	.	.	.	.	.	.	.	.	C	19.39	3.817864	0.71028	.	.	ENSG00000157856	ENST00000288710;ENST00000442810	T	0.24723	1.84	5.71	4.83	0.62350	.	0.184196	0.37906	N	0.001895	T	0.51517	0.1679	M	0.78916	2.43	0.54753	D	0.999983	D	0.89917	1.0	D	0.91635	0.999	T	0.56044	-0.8044	10	0.62326	D	0.03	-12.3036	13.3391	0.60535	0.1583:0.8417:0.0:0.0	.	233	Q96MC2	CC164_HUMAN	C	233;62	ENSP00000288710:R233C	ENSP00000288710:R233C	R	+	1	0	CCDC164	26507176	0.999000	0.42202	0.253000	0.24343	0.978000	0.69477	2.406000	0.44557	1.412000	0.46977	0.655000	0.94253	CGC		0.468	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038	
CENPA	1058	broad.mit.edu	37	2	27015671	27015671	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:27015671G>A	ENST00000335756.4	+	3	458	c.258G>A	c.(256-258)tgG>tgA	p.W86*	CENPA_ENST00000233505.8_Intron|CENPA_ENST00000475662.1_Intron	NM_001809.3	NP_001800.1	P49450	CENPA_HUMAN	centromere protein A	86	CATD.|H3-like.				CENP-A containing nucleosome assembly (GO:0034080)|establishment of mitotic spindle orientation (GO:0000132)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|protein localization to chromosome, centromeric region (GO:0071459)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|condensed chromosome inner kinetochore (GO:0000939)|condensed nuclear chromosome kinetochore (GO:0000778)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.W86*(1)		endometrium(1)|large_intestine(3)|lung(3)|urinary_tract(1)	8	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACTTCAATTGGCAAGCCCAGG	0.512																																					p.W86X	Pancreas(28;769 878 30250 30578 41330)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G258A	2						.						86.0	86.0	86.0					2																	27015671		2203	4300	6503	26869175	SO:0001587	stop_gained	1058	exon3			U14518	CCDS1729.1, CCDS42662.1	2p23.3	2013-11-05	2006-06-16		ENSG00000115163	ENSG00000115163			1851	protein-coding gene	gene with protein product	"""centromere-specific histone"", ""histone H3-like centromeric protein A"""	117139	"""centromere protein A (17kD)"", ""centromere protein A, 17kDa"""				Standard	NM_001042426		Approved	CENP-A, CenH3	uc002rhr.3	P49450	OTTHUMG00000097073	ENST00000335756.4:c.258G>A	2.37:g.27015671G>A	ENSP00000336868:p.Trp86*	Somatic		Capture	Illumina HiSeq	Phase_I	26869175	NM_001809	D6W544|Q53T74|Q9BVW2	Nonsense_Mutation	SNP	ENST00000335756.4	37	CCDS1729.1	.	.	.	.	.	.	.	.	.	.	G	36	5.704935	0.96812	.	.	ENSG00000115163	ENST00000335756	.	.	.	5.44	5.44	0.79542	.	0.000000	0.45867	U	0.000333	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-13.9844	14.6328	0.68668	0.0:0.0:1.0:0.0	.	.	.	.	X	86	.	ENSP00000336868:W86X	W	+	3	0	CENPA	26869175	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.883000	0.69721	2.831000	0.97527	0.650000	0.86243	TGG		0.512	CENPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214190.2	NM_001809	
GTF3C2	2976	broad.mit.edu	37	2	27560424	27560424	+	Splice_Site	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:27560424G>A	ENST00000359541.2	-	6	1381	c.952C>T	c.(952-954)Cga>Tga	p.R318*	AC109828.1_ENST00000592265.1_RNA|GTF3C2_ENST00000264720.3_Splice_Site_p.R318*|AC109828.1_ENST00000585326.1_RNA|AC109828.1_ENST00000590754.1_RNA|AC109828.1_ENST00000585645.1_RNA|AC109828.1_ENST00000590383.1_RNA|AC109828.1_ENST00000587586.1_RNA|AC109828.1_ENST00000608473.1_RNA|AC109828.1_ENST00000588707.1_RNA|AC109828.1_ENST00000589853.1_RNA|AC109828.1_ENST00000589232.1_RNA|AC109828.1_ENST00000416453.2_RNA			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	318					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)		p.R318*(1)		central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCTGCTCTCGGCTGGAGAAA	0.443																																					p.R318X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C952T	2						.						52.0	50.0	51.0					2																	27560424		2203	4300	6503	27413928	SO:0001630	splice_region_variant	2976	exon6			D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"""General transcription factors"", ""WD repeat domain containing"""	4665	protein-coding gene	gene with protein product		604883	"""general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"""			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.951-1C>T	2.37:g.27560424G>A		Somatic		Capture	Illumina HiSeq	Phase_I	27413928	NM_001035521	D6W557|Q16632|Q9BWI7	Nonsense_Mutation	SNP	ENST00000359541.2	37	CCDS1749.1	.	.	.	.	.	.	.	.	.	.	G	39	7.502747	0.98322	.	.	ENSG00000115207	ENST00000359541;ENST00000264720	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.3479	12.4845	0.55863	0.0:0.0:0.8331:0.1669	.	.	.	.	X	318	.	ENSP00000264720:R318X	R	-	1	2	GTF3C2	27413928	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	3.764000	0.55264	2.753000	0.94483	0.557000	0.71058	CGA		0.443	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2		Nonsense_Mutation
FNDC4	64838	broad.mit.edu	37	2	27717222	27717222	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:27717222T>C	ENST00000264703.3	-	3	636	c.245A>G	c.(244-246)cAg>cGg	p.Q82R	GCKR_ENST00000264717.2_5'Flank|GCKR_ENST00000424318.2_5'Flank	NM_022823.2	NP_073734.1	Q9H6D8	FNDC4_HUMAN	fibronectin type III domain containing 4	82	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.Q82R(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|prostate(1)|skin(1)	9	Acute lymphoblastic leukemia(172;0.155)					TCATACTTGCTGGGAAATGGA	0.542																																					p.Q82R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A245G	2						.						81.0	75.0	77.0					2																	27717222		2203	4300	6503	27570726	SO:0001583	missense	64838	exon3			AK026015	CCDS1756.1	2p23.3	2013-02-11			ENSG00000115226	ENSG00000115226		"""Fibronectin type III domain containing"""	20239	protein-coding gene	gene with protein product		611905				12384288	Standard	NM_022823		Approved	FLJ22362, FRCP1	uc002rkx.3	Q9H6D8	OTTHUMG00000097787	ENST00000264703.3:c.245A>G	2.37:g.27717222T>C	ENSP00000264703:p.Gln82Arg	Somatic		Capture	Illumina HiSeq	Phase_I	27570726	NM_022823	D6W560	Missense_Mutation	SNP	ENST00000264703.3	37	CCDS1756.1	.	.	.	.	.	.	.	.	.	.	T	17.09	3.299141	0.60195	.	.	ENSG00000115226	ENST00000264703	T	0.56103	0.48	5.16	5.16	0.70880	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.057193	0.64402	D	0.000001	T	0.47451	0.1446	L	0.39245	1.2	0.80722	D	1	P	0.35468	0.503	B	0.39617	0.305	T	0.42632	-0.9440	10	0.31617	T	0.26	-18.0268	13.7926	0.63150	0.0:0.0:0.0:1.0	.	82	Q9H6D8	FNDC4_HUMAN	R	82	ENSP00000264703:Q82R	ENSP00000264703:Q82R	Q	-	2	0	FNDC4	27570726	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.664000	0.46783	1.939000	0.56221	0.379000	0.24179	CAG		0.542	FNDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215031.1	NM_022823	
GCKR	2646	broad.mit.edu	37	2	27726484	27726484	+	Missense_Mutation	SNP	G	G	A	rs374489109		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:27726484G>A	ENST00000264717.2	+	9	811	c.748G>A	c.(748-750)Ggg>Agg	p.G250R	GCKR_ENST00000424318.2_Missense_Mutation_p.G60R	NM_001486.3	NP_001477.2	Q14397	GCKR_HUMAN	glucokinase (hexokinase 4) regulator	250	SIS 1. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|negative regulation of glucokinase activity (GO:0033132)|positive regulation of glucokinase activity (GO:0033133)|protein import into nucleus, translocation (GO:0000060)|regulation of glucose transport (GO:0010827)|response to fructose (GO:0009750)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|triglyceride homeostasis (GO:0070328)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	carbohydrate binding (GO:0030246)|enzyme inhibitor activity (GO:0004857)|fructose-6-phosphate binding (GO:0070095)	p.G250R(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(2)	29	Acute lymphoblastic leukemia(172;0.155)					TCCTGCCATCGGGGTAGGGCC	0.483																																					p.G250R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G748A	2						.						107.0	81.0	90.0					2																	27726484		2203	4300	6503	27579988	SO:0001583	missense	2646	exon9			Z48475	CCDS1757.1	2p23	2008-05-21	2004-05-20		ENSG00000084734	ENSG00000084734			4196	protein-coding gene	gene with protein product		600842	"""glucokinase (hexokinase 4) regulatory protein"""			9570959, 8662230	Standard	NM_001486		Approved		uc002rky.3	Q14397	OTTHUMG00000128426	ENST00000264717.2:c.748G>A	2.37:g.27726484G>A	ENSP00000264717:p.Gly250Arg	Somatic		Capture	Illumina HiSeq	Phase_I	27579988	NM_001486	A1L4C2|B4DPQ2|Q53RY6|Q99522	Missense_Mutation	SNP	ENST00000264717.2	37	CCDS1757.1	.	.	.	.	.	.	.	.	.	.	G	18.33	3.599500	0.66332	.	.	ENSG00000084734	ENST00000264717;ENST00000424318	D;T	0.86956	-2.19;-0.17	3.92	3.04	0.35103	Glucokinase regulatory, conserved site (1);Sugar isomerase (SIS) (1);	0.072882	0.53938	N	0.000052	D	0.91998	0.7465	M	0.83483	2.645	0.35265	D	0.779903	D;D;D	0.76494	0.995;0.999;0.997	P;D;D	0.66602	0.894;0.928;0.945	D	0.93698	0.7013	10	0.87932	D	0	-8.6496	9.2504	0.37551	0.1083:0.0:0.8917:0.0	.	60;250;250	F5H1P6;A8K731;Q14397	.;.;GCKR_HUMAN	R	250;60	ENSP00000264717:G250R;ENSP00000409109:G60R	ENSP00000264717:G250R	G	+	1	0	GCKR	27579988	0.997000	0.39634	0.496000	0.27539	0.357000	0.29423	2.898000	0.48672	0.865000	0.35603	0.462000	0.41574	GGG		0.483	GCKR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250214.1	NM_001486	
C2orf16	84226	broad.mit.edu	37	2	27803421	27803421	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:27803421G>T	ENST00000408964.2	+	1	4033	c.3982G>T	c.(3982-3984)Gga>Tga	p.G1328*	ZNF512_ENST00000556601.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000379717.1_5'Flank|ZNF512_ENST00000416005.2_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000355467.4_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1328						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.G1328*(1)		breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GAAGAGGATTGGAGCAACTCA	0.423																																					p.G1328X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G3982T	2						.						67.0	64.0	65.0					2																	27803421		1874	4103	5977	27656925	SO:0001587	stop_gained	84226	exon1			AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.3982G>T	2.37:g.27803421G>T	ENSP00000386190:p.Gly1328*	Somatic		Capture	Illumina HiSeq	Phase_I	27656925	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Nonsense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	G	39	7.535440	0.98345	.	.	ENSG00000221843	ENST00000408964	.	.	.	5.31	2.52	0.30459	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	7.3558	0.26719	0.2781:0.0:0.7219:0.0	.	.	.	.	X	1328	.	ENSP00000386190:G1328X	G	+	1	0	C2orf16	27656925	0.004000	0.15560	0.001000	0.08648	0.740000	0.42216	0.506000	0.22658	0.228000	0.21019	0.563000	0.77884	GGA		0.423	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
MRPL33	9553	broad.mit.edu	37	2	27997371	27997371	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:27997371T>C	ENST00000296102.3	+	3	183	c.122T>C	c.(121-123)cTg>cCg	p.L41P	MRPL33_ENST00000379666.3_Intron|MRPL33_ENST00000483992.1_Intron	NM_004891.3	NP_004882.1	O75394	RM33_HUMAN	mitochondrial ribosomal protein L33	41					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)	p.L41P(1)		breast(1)|large_intestine(1)	2	Acute lymphoblastic leukemia(172;0.155)					CGGGAAAAACTGACTCTTTTG	0.463																																					p.L41P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T122C	2						.						109.0	112.0	111.0					2																	27997371		2203	4300	6503	27850875	SO:0001583	missense	9553	exon3			AB051623	CCDS1761.1, CCDS33167.1	2p21	2012-09-13			ENSG00000243147	ENSG00000243147		"""Mitochondrial ribosomal proteins / large subunits"""	14487	protein-coding gene	gene with protein product		610059		C2orf1			Standard	NM_145330		Approved	RPL33L	uc002rlm.1	O75394	OTTHUMG00000097795	ENST00000296102.3:c.122T>C	2.37:g.27997371T>C	ENSP00000296102:p.Leu41Pro	Somatic		Capture	Illumina HiSeq	Phase_I	27850875	NM_004891	Q53RZ6|Q5FVE3|Q96Q50	Missense_Mutation	SNP	ENST00000296102.3	37	CCDS1761.1	.	.	.	.	.	.	.	.	.	.	T	14.66	2.603112	0.46423	.	.	ENSG00000243147	ENST00000296102	.	.	.	5.75	5.75	0.90469	Ribosomal protein, zinc-binding domain (1);	0.099133	0.45126	D	0.000391	T	0.77791	0.4183	.	.	.	0.80722	D	1	D	0.71674	0.998	D	0.69654	0.965	T	0.80804	-0.1219	8	0.87932	D	0	-11.951	12.5729	0.56347	0.0:0.0:0.1385:0.8615	.	41	O75394	RM33_HUMAN	P	41	.	ENSP00000296102:L41P	L	+	2	0	MRPL33	27850875	1.000000	0.71417	1.000000	0.80357	0.007000	0.05969	5.867000	0.69597	2.194000	0.70268	0.533000	0.62120	CTG		0.463	MRPL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215049.1	NM_004891	
FAM179A	165186	broad.mit.edu	37	2	29247232	29247232	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:29247232G>A	ENST00000379558.4	+	13	2196	c.1845G>A	c.(1843-1845)gcG>gcA	p.A615A	FAM179A_ENST00000465300.1_3'UTR|FAM179A_ENST00000403861.2_Silent_p.A560A	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	615								p.A615A(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						TCACCTCGGCGGGTGTCTAGT	0.612																																					p.A615A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1845A	2						.						31.0	31.0	31.0					2																	29247232		2002	4185	6187	29100736	SO:0001819	synonymous_variant	165186	exon13			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.1845G>A	2.37:g.29247232G>A		Somatic		Capture	Illumina HiSeq	Phase_I	29100736	NM_199280	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																				0.612	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	29606701	29606701	+	Silent	SNP	G	G	A	rs371642412		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:29606701G>A	ENST00000389048.3	-	5	2085	c.1179C>T	c.(1177-1179)atC>atT	p.I393I	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	393	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.I393I(1)	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)	CTGGACGCCCGATTCTTCCCT	0.498			"""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.I393I		yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1179T	2						.	G		0,4406		0,0,2203	111.0	107.0	108.0		1179	0.4	1.0	2		108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ALK	NM_004304.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		393/1621	29606701	1,13005	2203	4300	6503	29460205	SO:0001819	synonymous_variant	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.1179C>T	2.37:g.29606701G>A		Somatic		Capture	Illumina HiSeq	Phase_I	29460205	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																				0.498	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
EHD3	30845	broad.mit.edu	37	2	31457617	31457617	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:31457617G>A	ENST00000322054.5	+	1	415	c.130G>A	c.(130-132)Gag>Aag	p.E44K	EHD3_ENST00000541626.1_Missense_Mutation_p.E44K	NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	44					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.E44K(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)					CCGCTTCCACGAGTTCCACTC	0.587																																					p.E44K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G130A	2						.						107.0	101.0	103.0					2																	31457617		2203	4300	6503	31311121	SO:0001583	missense	30845	exon1			AF181264	CCDS1774.1	2p21	2013-01-10			ENSG00000013016	ENSG00000013016		"""EF-hand domain containing"""	3244	protein-coding gene	gene with protein product		605891		PAST3		10673336	Standard	NM_014600		Approved		uc002rnu.3	Q9NZN3	OTTHUMG00000099365	ENST00000322054.5:c.130G>A	2.37:g.31457617G>A	ENSP00000327116:p.Glu44Lys	Somatic		Capture	Illumina HiSeq	Phase_I	31311121	NM_014600	B4DFR5|D6W574|Q8N514|Q9NZB3	Missense_Mutation	SNP	ENST00000322054.5	37	CCDS1774.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.456198	0.84209	.	.	ENSG00000013016	ENST00000541626;ENST00000322054	T;T	0.32023	1.47;2.22	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.32376	0.0827	M	0.68317	2.08	0.80722	D	1	P;B	0.39326	0.668;0.351	B;B	0.29942	0.109;0.069	T	0.33292	-0.9874	10	0.52906	T	0.07	-50.6122	18.4785	0.90802	0.0:0.0:1.0:0.0	.	44;44	B4DFR5;Q9NZN3	.;EHD3_HUMAN	K	44	ENSP00000440685:E44K;ENSP00000327116:E44K	ENSP00000327116:E44K	E	+	1	0	EHD3	31311121	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.996000	0.70639	2.600000	0.87896	0.561000	0.74099	GAG		0.587	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216810.1	NM_014600	
EHD3	30845	broad.mit.edu	37	2	31467290	31467290	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:31467290C>T	ENST00000322054.5	+	2	663	c.378C>T	c.(376-378)aaC>aaT	p.N126N	EHD3_ENST00000541626.1_Silent_p.N126N	NM_014600.2	NP_055415.1	Q9NZN3	EHD3_HUMAN	EH-domain containing 3	126	Dynamin-type G.				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.N126N(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|skin(3)	33	Acute lymphoblastic leukemia(172;0.155)					GGAAACTCAACGCCTTTGGCA	0.527																																					p.N126N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C378T	2						.						121.0	95.0	104.0					2																	31467290		2203	4300	6503	31320794	SO:0001819	synonymous_variant	30845	exon2			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.378C>T	2.37:g.31467290C>T		Somatic		Capture	Illumina HiSeq	Phase_I	31320794	NM_014600	B4DFR5|D6W574|Q8N514|Q9NZB3	Silent	SNP	ENST00000322054.5	37	CCDS1774.1																																																																																				0.527	EHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216810.1	NM_014600	
SPAST	6683	broad.mit.edu	37	2	32362003	32362003	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:32362003G>A	ENST00000315285.3	+	11	1504	c.1379G>A	c.(1378-1380)cGc>cAc	p.R460H	SPAST_ENST00000345662.1_Missense_Mutation_p.R428H	NM_014946.3	NP_055761.2			spastin									p.R460H(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GCTAGTAGACGCCTAAAAACT	0.328																																					p.R428H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1283A	2	GRCh37	CD090671|CM000438|CM090413	SPAST	D|M		.						106.0	116.0	112.0					2																	32362003		2203	4300	6503	32215507	SO:0001583	missense	6683	exon10			AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"""ATPases / AAA-type"""	11233	protein-coding gene	gene with protein product		604277	"""spastic paraplegia 4 (autosomal dominant; spastin)"""	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.1379G>A	2.37:g.32362003G>A	ENSP00000320885:p.Arg460His	Somatic		Capture	Illumina HiSeq	Phase_I	32215507	NM_199436		Missense_Mutation	SNP	ENST00000315285.3	37	CCDS1778.1	.	.	.	.	.	.	.	.	.	.	G	33	5.214085	0.95104	.	.	ENSG00000021574	ENST00000345662;ENST00000315285	D;D	0.94046	-3.34;-3.34	5.63	5.63	0.86233	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.97263	0.9105	M	0.87038	2.855	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.97475	1.0043	10	0.87932	D	0	-37.9795	19.6351	0.95728	0.0:0.0:1.0:0.0	.	428;460	E5KRP6;Q9UBP0	.;SPAST_HUMAN	H	428;460	ENSP00000340817:R428H;ENSP00000320885:R460H	ENSP00000320885:R460H	R	+	2	0	SPAST	32215507	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.987000	0.93497	2.805000	0.96524	0.655000	0.94253	CGC		0.328	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436	
BIRC6	57448	broad.mit.edu	37	2	32667199	32667199	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:32667199delA	ENST00000421745.2	+	18	4145	c.4011delA	c.(4009-4011)agafs	p.R1337fs		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1337					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.T1339fs*21(1)|p.T1311fs*21(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CTCTTTGCAGAAAAACAGATG	0.388																																					p.R1337fs	Pancreas(94;175 1509 16028 18060 45422)											.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.4011delA	2						.						59.0	62.0	61.0					2																	32667199		2203	4300	6503	32520703	SO:0001589	frameshift_variant	57448	exon18			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.4011delA	2.37:g.32667199delA	ENSP00000393596:p.Arg1337fs	Somatic		Capture	Illumina HiSeq	Phase_I	32520703	NM_016252	Q9ULD1	Frame_Shift_Del	DEL	ENST00000421745.2	37	CCDS33175.2																																																																																				0.388	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
BIRC6	57448	broad.mit.edu	37	2	32689791	32689791	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:32689791T>C	ENST00000421745.2	+	25	5290	c.5156T>C	c.(5155-5157)gTg>gCg	p.V1719A		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1719					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.V1691A(1)|p.V1719A(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					GTTTCCGTTGTGATTAATGCC	0.438																																					p.V1719A	Pancreas(94;175 1509 16028 18060 45422)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T5156C	2						.						142.0	135.0	137.0					2																	32689791		2203	4300	6503	32543295	SO:0001583	missense	57448	exon25			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.5156T>C	2.37:g.32689791T>C	ENSP00000393596:p.Val1719Ala	Somatic		Capture	Illumina HiSeq	Phase_I	32543295	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	T	7.285	0.609927	0.14066	.	.	ENSG00000115760	ENST00000421745	T	0.72942	-0.7	5.84	5.84	0.93424	.	0.066394	0.64402	D	0.000012	T	0.49729	0.1574	N	0.04508	-0.205	0.48135	D	0.999594	B	0.02656	0.0	B	0.04013	0.001	T	0.47018	-0.9149	10	0.20046	T	0.44	.	16.2302	0.82332	0.0:0.0:0.0:1.0	.	1719	Q9NR09	BIRC6_HUMAN	A	1719	ENSP00000393596:V1719A	ENSP00000393596:V1719A	V	+	2	0	BIRC6	32543295	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.789000	0.69029	2.228000	0.72767	0.533000	0.62120	GTG		0.438	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
LTBP1	4052	broad.mit.edu	37	2	33525616	33525616	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:33525616T>C	ENST00000404816.2	+	21	3687	c.3334T>C	c.(3334-3336)Tcg>Ccg	p.S1112P	LTBP1_ENST00000498013.1_3'UTR|LTBP1_ENST00000402934.1_Missense_Mutation_p.S733P|LTBP1_ENST00000354476.3_Missense_Mutation_p.S1113P|LTBP1_ENST00000404525.1_Missense_Mutation_p.S733P|LTBP1_ENST00000272273.5_Missense_Mutation_p.S52P|LTBP1_ENST00000390003.4_Missense_Mutation_p.S787P|LTBP1_ENST00000407925.1_Missense_Mutation_p.S786P|LTBP1_ENST00000418533.2_Missense_Mutation_p.S786P			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1112	EGF-like 9; calcium-binding. {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.S1113P(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)				GTACCAGCTGTCGGCAGCTAA	0.468																																					p.S786P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2356C	2						.						79.0	79.0	79.0					2																	33525616		2203	4300	6503	33379120	SO:0001583	missense	4052	exon17				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.3334T>C	2.37:g.33525616T>C	ENSP00000386043:p.Ser1112Pro	Somatic		Capture	Illumina HiSeq	Phase_I	33379120	NM_000627	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	T	20.1	3.937195	0.73557	.	.	ENSG00000049323	ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273	D;D;D;D;D;D;D;D	0.92348	-3.02;-3.02;-3.02;-3.02;-3.02;-3.02;-3.02;-3.02	5.39	5.39	0.77823	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.94361	0.8187	M	0.63208	1.945	0.48236	D	0.999617	P;D;D;P;D;D;D	0.67145	0.59;0.996;0.978;0.694;0.993;0.987;0.995	B;D;P;B;D;P;D	0.70935	0.391;0.971;0.762;0.328;0.917;0.88;0.951	D	0.94134	0.7391	9	0.54805	T	0.06	.	10.5608	0.45144	0.0:0.0:0.1618:0.8382	.	52;1112;786;733;786;787;1113	E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	.;LTBP1_HUMAN;.;.;.;.;.	P	1112;1113;787;786;733;733;786;52	ENSP00000386043:S1112P;ENSP00000346467:S1113P;ENSP00000374653:S787P;ENSP00000393057:S786P;ENSP00000384373:S733P;ENSP00000385359:S733P;ENSP00000384091:S786P;ENSP00000272273:S52P	ENSP00000272273:S52P	S	+	1	0	LTBP1	33379120	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	3.720000	0.54933	2.049000	0.60858	0.454000	0.30748	TCG		0.468	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
CRIM1	51232	broad.mit.edu	37	2	36669808	36669808	+	Missense_Mutation	SNP	G	G	A	rs560635455		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:36669808G>A	ENST00000280527.2	+	4	1166	c.799G>A	c.(799-801)Gcg>Acg	p.A267T		NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	267					insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.A267T(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				TCAGCAGACCGCGTGTCCCCC	0.473													G|||	1	0.000199681	0.0	0.0	5008	,	,		21007	0.0		0.0	False		,,,				2504	0.001				p.A267T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G799A	2						.						169.0	150.0	156.0					2																	36669808		2203	4300	6503	36523312	SO:0001583	missense	51232	exon4			AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"""cysteine-rich motor neuron 1"""	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.799G>A	2.37:g.36669808G>A	ENSP00000280527:p.Ala267Thr	Somatic		Capture	Illumina HiSeq	Phase_I	36523312	NM_016441	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Missense_Mutation	SNP	ENST00000280527.2	37	CCDS1783.1	.	.	.	.	.	.	.	.	.	.	G	9.495	1.101710	0.20632	.	.	ENSG00000150938	ENST00000280527;ENST00000426856	T	0.04156	3.69	5.24	4.37	0.52481	.	0.538606	0.18772	N	0.131566	T	0.02267	0.0070	N	0.03608	-0.345	0.20307	N	0.999917	B	0.24426	0.103	B	0.11329	0.006	T	0.47275	-0.9130	10	0.20046	T	0.44	-2.6072	9.393	0.38386	0.162:0.0:0.838:0.0	.	267	Q9NZV1	CRIM1_HUMAN	T	267;159	ENSP00000280527:A267T	ENSP00000280527:A267T	A	+	1	0	CRIM1	36523312	0.996000	0.38824	1.000000	0.80357	0.609000	0.37215	2.369000	0.44231	1.358000	0.45922	0.555000	0.69702	GCG		0.473	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441	
CRIM1	51232	broad.mit.edu	37	2	36706764	36706764	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:36706764C>T	ENST00000280527.2	+	7	1666	c.1299C>T	c.(1297-1299)tgC>tgT	p.C433C		NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	433	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.			C -> F (in Ref. 2; BAD92376). {ECO:0000305}.	insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.C433C(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				AACGCCACTGCGTTGCGACCG	0.592																																					p.C433C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1299T	2						.						136.0	128.0	131.0					2																	36706764		2203	4300	6503	36560268	SO:0001819	synonymous_variant	51232	exon7			AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"""cysteine-rich motor neuron 1"""	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.1299C>T	2.37:g.36706764C>T		Somatic		Capture	Illumina HiSeq	Phase_I	36560268	NM_016441	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Silent	SNP	ENST00000280527.2	37	CCDS1783.1																																																																																				0.592	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441	
CRIM1	51232	broad.mit.edu	37	2	36744653	36744653	+	Missense_Mutation	SNP	G	G	A	rs145410862		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:36744653G>A	ENST00000280527.2	+	12	2541	c.2174G>A	c.(2173-2175)cGc>cAc	p.R725H		NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	725	VWFC 4. {ECO:0000255|PROSITE- ProRule:PRU00220}.				insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.R725H(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				AACCCCTCACGCACCCAGGAT	0.592																																					p.R725H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2174A	2						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	74.0	68.0	70.0		2174	5.6	1.0	2	dbSNP_134	70	0,8600		0,0,4300	no	missense	CRIM1	NM_016441.2	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	725/1037	36744653	1,13005	2203	4300	6503	36598157	SO:0001583	missense	51232	exon12			AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"""cysteine-rich motor neuron 1"""	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.2174G>A	2.37:g.36744653G>A	ENSP00000280527:p.Arg725His	Somatic		Capture	Illumina HiSeq	Phase_I	36598157	NM_016441	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Missense_Mutation	SNP	ENST00000280527.2	37	CCDS1783.1	.	.	.	.	.	.	.	.	.	.	G	34	5.307103	0.95629	2.27E-4	0.0	ENSG00000150938	ENST00000280527;ENST00000413985	T;T	0.72051	-0.62;-0.62	5.56	5.56	0.83823	von Willebrand factor, type C (4);	0.000000	0.85682	D	0.000000	T	0.75280	0.3828	N	0.21324	0.655	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72130	-0.4383	10	0.25751	T	0.34	-34.4884	18.5257	0.90971	0.0:0.0:1.0:0.0	.	725	Q9NZV1	CRIM1_HUMAN	H	725;87	ENSP00000280527:R725H;ENSP00000403120:R87H	ENSP00000280527:R725H	R	+	2	0	CRIM1	36598157	1.000000	0.71417	0.987000	0.45799	0.995000	0.86356	9.504000	0.97986	2.620000	0.88729	0.655000	0.94253	CGC		0.592	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441	
VIT	5212	broad.mit.edu	37	2	36982145	36982145	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:36982145C>T	ENST00000389975.3	+	5	659	c.357C>T	c.(355-357)aaC>aaT	p.N119N	VIT_ENST00000404084.1_Silent_p.N97N|VIT_ENST00000497382.1_5'UTR|VIT_ENST00000457137.2_Silent_p.N119N|VIT_ENST00000401530.1_Silent_p.N119N|VIT_ENST00000379242.3_Silent_p.N119N|VIT_ENST00000379241.3_Silent_p.N119N	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	119	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)	p.N119N(1)		autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				GTTATTCCAACGGTGTCCAAT	0.428																																					p.N119N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C357T	2						.						164.0	144.0	151.0					2																	36982145		2203	4300	6503	36835649	SO:0001819	synonymous_variant	5212	exon5			AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.357C>T	2.37:g.36982145C>T		Somatic		Capture	Illumina HiSeq	Phase_I	36835649	NM_001177972	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Silent	SNP	ENST00000389975.3	37	CCDS54347.1																																																																																				0.428	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			
STRN	6801	broad.mit.edu	37	2	37126774	37126774	+	Silent	SNP	G	G	A	rs548893424		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:37126774G>A	ENST00000263918.4	-	6	695	c.687C>T	c.(685-687)tcC>tcT	p.S229S	STRN_ENST00000379213.2_Silent_p.S217S	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein	229					dendrite development (GO:0016358)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|tight junction assembly (GO:0070830)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|estrogen receptor binding (GO:0030331)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)	p.S229S(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33		Ovarian(717;0.0129)|all_hematologic(82;0.21)				TATCCAGCACGGAGGCAGAAT	0.358																																					p.S229S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C687T	2						.						64.0	62.0	62.0					2																	37126774		2202	4299	6501	36980278	SO:0001819	synonymous_variant	6801	exon6			AJ223814	CCDS1784.1	2p22.2	2013-01-10	2001-11-28		ENSG00000115808	ENSG00000115808		"""WD repeat domain containing"""	11424	protein-coding gene	gene with protein product		614765	"""striatin, calmodulin-binding protein"""			9693043, 8769426	Standard	NM_003162		Approved	SG2NA	uc002rpn.3	O43815	OTTHUMG00000100959	ENST00000263918.4:c.687C>T	2.37:g.37126774G>A		Somatic		Capture	Illumina HiSeq	Phase_I	36980278	NM_003162	Q3KP65|Q53TQ8|Q9NP38	Silent	SNP	ENST00000263918.4	37	CCDS1784.1																																																																																				0.358	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1		
GPATCH11	253635	broad.mit.edu	37	2	37315546	37315546	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:37315546G>A	ENST00000608836.1	+	2	155	c.10G>A	c.(10-12)Gaa>Aaa	p.E4K	GPATCH11_ENST00000281932.5_5'UTR|GPATCH11_ENST00000409774.1_Missense_Mutation_p.E30K	NM_174931.2	NP_777591.3	Q8N954	GPT11_HUMAN	G patch domain containing 11	4							nucleic acid binding (GO:0003676)	p.E4K(1)									CATGGCAGAAGAAGAGGACTA	0.303																																					p.E4K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G10A	2						.						71.0	69.0	70.0					2																	37315546		2203	4300	6503	37169050	SO:0001583	missense	253635	exon2			AK095667	CCDS1785.2, CCDS62891.1, CCDS1785.3	2p22.2	2013-11-05	2013-01-28	2013-01-28	ENSG00000152133	ENSG00000152133		"""G patch domain containing"""	26768	protein-coding gene	gene with protein product	"""centromere protein Y"""		"""coiled-coil domain containing 75"""	CCDC75			Standard	NM_001278505		Approved	FLJ38348, CENPY, CENP-Y	uc010ezz.3	Q8N954	OTTHUMG00000128469	ENST00000608836.1:c.10G>A	2.37:g.37315546G>A	ENSP00000476383:p.Glu4Lys	Somatic		Capture	Illumina HiSeq	Phase_I	37169050	NM_174931	A8K0D9|B7Z2G4|B8ZZ44	Missense_Mutation	SNP	ENST00000608836.1	37	CCDS1785.2	.	.	.	.	.	.	.	.	.	.	G	32	5.183747	0.94885	.	.	ENSG00000152133	ENST00000409774	T	0.49720	0.77	5.42	5.42	0.78866	.	0.218437	0.46442	D	0.000289	T	0.73377	0.3579	M	0.85859	2.78	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	T	0.77739	-0.2475	10	0.72032	D	0.01	-17.6402	18.8167	0.92079	0.0:0.0:1.0:0.0	.	4	Q8N954	CCD75_HUMAN	K	4	ENSP00000386772:E4K	ENSP00000386772:E4K	E	+	1	0	CCDC75	37169050	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.566000	0.82347	2.537000	0.85549	0.561000	0.74099	GAA		0.303	GPATCH11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_174931	
GALM	130589	broad.mit.edu	37	2	38903075	38903075	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:38903075A>G	ENST00000272252.5	+	2	464	c.212A>G	c.(211-213)tAc>tGc	p.Y71C	GALM_ENST00000410063.1_Intron	NM_138801.2	NP_620156.1	Q96C23	GALM_HUMAN	galactose mutarotase (aldose 1-epimerase)	71					galactose metabolic process (GO:0006012)|glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldose 1-epimerase activity (GO:0004034)|carbohydrate binding (GO:0030246)	p.Y71C(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	14		all_hematologic(82;0.248)				AAGCAGCCATACTTTGGAGCA	0.507																																					p.Y71C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A212G	2						.						115.0	100.0	106.0					2																	38903075		2203	4300	6503	38756579	SO:0001583	missense	130589	exon2				CCDS1797.1	2p22.3	2008-02-05			ENSG00000143891	ENSG00000143891			24063	protein-coding gene	gene with protein product	"""aldose 1 epimerase"""	608883				12753898	Standard	NM_138801		Approved		uc002rqy.3	Q96C23	OTTHUMG00000102077	ENST00000272252.5:c.212A>G	2.37:g.38903075A>G	ENSP00000272252:p.Tyr71Cys	Somatic		Capture	Illumina HiSeq	Phase_I	38756579	NM_138801	Q53RY1|Q8NIA2|V9HWA8	Missense_Mutation	SNP	ENST00000272252.5	37	CCDS1797.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.955816	0.73902	.	.	ENSG00000143891	ENST00000272252	T	0.51817	0.69	5.55	5.55	0.83447	Glycoside hydrolase-type carbohydrate-binding, subgroup (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.198970	0.44902	D	0.000413	T	0.64832	0.2634	M	0.69185	2.1	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.68315	-0.5441	10	0.87932	D	0	-18.7146	11.5025	0.50446	0.858:0.0:0.0:0.142	.	71	Q96C23	GALM_HUMAN	C	71	ENSP00000272252:Y71C	ENSP00000272252:Y71C	Y	+	2	0	GALM	38756579	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.774000	0.55341	2.108000	0.64289	0.533000	0.62120	TAC		0.507	GALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219891.2	NM_138801	
GALM	130589	broad.mit.edu	37	2	38908517	38908517	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:38908517G>A	ENST00000272252.5	+	3	693	c.441G>A	c.(439-441)tgG>tgA	p.W147*	GALM_ENST00000410063.1_Intron	NM_138801.2	NP_620156.1	Q96C23	GALM_HUMAN	galactose mutarotase (aldose 1-epimerase)	147					galactose metabolic process (GO:0006012)|glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldose 1-epimerase activity (GO:0004034)|carbohydrate binding (GO:0030246)	p.W147*(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	14		all_hematologic(82;0.248)				TAAAAGTCTGGGTGACATACA	0.547																																					p.W147X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G441A	2						.						117.0	116.0	116.0					2																	38908517		2203	4300	6503	38762021	SO:0001587	stop_gained	130589	exon3				CCDS1797.1	2p22.3	2008-02-05			ENSG00000143891	ENSG00000143891			24063	protein-coding gene	gene with protein product	"""aldose 1 epimerase"""	608883				12753898	Standard	NM_138801		Approved		uc002rqy.3	Q96C23	OTTHUMG00000102077	ENST00000272252.5:c.441G>A	2.37:g.38908517G>A	ENSP00000272252:p.Trp147*	Somatic		Capture	Illumina HiSeq	Phase_I	38762021	NM_138801	Q53RY1|Q8NIA2|V9HWA8	Nonsense_Mutation	SNP	ENST00000272252.5	37	CCDS1797.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.403909	0.83230	.	.	ENSG00000143891	ENST00000272252;ENST00000434934	.	.	.	5.4	5.4	0.78164	.	0.215679	0.46758	D	0.000275	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-9.4418	19.1893	0.93658	0.0:0.0:1.0:0.0	.	.	.	.	X	147;27	.	ENSP00000272252:W147X	W	+	3	0	GALM	38762021	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.963000	0.56773	2.527000	0.85204	0.561000	0.74099	TGG		0.547	GALM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219891.2	NM_138801	
DHX57	90957	broad.mit.edu	37	2	39081205	39081205	+	Missense_Mutation	SNP	G	G	A	rs562694324		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:39081205G>A	ENST00000295373.6	-	9	2147	c.2021C>T	c.(2020-2022)aCa>aTa	p.T674I	DHX57_ENST00000479345.2_5'Flank	NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	674	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.T674I(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)				CCTTTCTTCTGTCCTCTCATG	0.423																																					p.T674I	Melanoma(191;1090 2095 4375 23729 47341)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2021T	2						.						163.0	154.0	157.0					2																	39081205		2203	4300	6503	38934709	SO:0001583	missense	90957	exon9			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.2021C>T	2.37:g.39081205G>A	ENSP00000295373:p.Thr674Ile	Somatic		Capture	Illumina HiSeq	Phase_I	38934709	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	37	CCDS1800.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.640709	0.87859	.	.	ENSG00000163214	ENST00000295373	T	0.27104	1.69	5.93	5.05	0.67936	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.53938	D	0.000046	T	0.61261	0.2333	M	0.93197	3.39	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.997	D;D;D	0.75484	0.968;0.986;0.932	T	0.73113	-0.4085	10	0.87932	D	0	.	14.5322	0.67934	0.0703:0.0:0.9297:0.0	.	674;674;66	Q6P158;B4DKW2;Q59G60	DHX57_HUMAN;.;.	I	674	ENSP00000295373:T674I	ENSP00000295373:T674I	T	-	2	0	DHX57	38934709	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.731000	0.98807	1.521000	0.48983	0.655000	0.94253	ACA		0.423	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	
KCNG3	170850	broad.mit.edu	37	2	42671474	42671474	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:42671474C>T	ENST00000306078.1	-	2	1506	c.911G>A	c.(910-912)cGt>cAt	p.R304H	KCNG3_ENST00000394973.4_Missense_Mutation_p.R293H	NM_133329.5|NM_172344.2	NP_579875.1|NP_758847.1	Q8TAE7	KCNG3_HUMAN	potassium voltage-gated channel, subfamily G, member 3	304					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.R304H(1)		central_nervous_system(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(2)	6						AATGAAGTGACGGGCAAGCTT	0.448																																					p.R304H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G911A	2						.						106.0	99.0	101.0					2																	42671474		2203	4300	6503	42524978	SO:0001583	missense	170850	exon2			AB070604	CCDS1809.1, CCDS42674.1	2p21	2011-07-05			ENSG00000171126	ENSG00000171126		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18306	protein-coding gene	gene with protein product		606767				11852086, 16382104	Standard	NM_133329		Approved	Kv6.3	uc002rsn.3	Q8TAE7	OTTHUMG00000128604	ENST00000306078.1:c.911G>A	2.37:g.42671474C>T	ENSP00000304127:p.Arg304His	Somatic		Capture	Illumina HiSeq	Phase_I	42524978	NM_133329	Q53SC1	Missense_Mutation	SNP	ENST00000306078.1	37	CCDS1809.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.536887	0.85812	.	.	ENSG00000171126	ENST00000306078;ENST00000394973	D;D	0.98762	-5.12;-5.12	5.22	5.22	0.72569	Ion transport (1);	0.055452	0.64402	D	0.000001	D	0.99306	0.9757	M	0.90759	3.145	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.994	D	0.99113	1.0847	10	0.87932	D	0	.	18.8074	0.92043	0.0:1.0:0.0:0.0	.	304;293	Q8TAE7;Q8TAE7-2	KCNG3_HUMAN;.	H	304;293	ENSP00000304127:R304H;ENSP00000378424:R293H	ENSP00000304127:R304H	R	-	2	0	KCNG3	42524978	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.619000	0.83057	2.434000	0.82447	0.563000	0.77884	CGT		0.448	KCNG3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250464.2	NM_172344	
LRPPRC	10128	broad.mit.edu	37	2	44123819	44123819	+	Missense_Mutation	SNP	G	G	A	rs373042003	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:44123819G>A	ENST00000260665.7	-	35	3911	c.3854C>T	c.(3853-3855)cCg>cTg	p.P1285L		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	1285	RNA-binding.				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.P1285L(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)				CAACAAAATCGGGGTTTGTTC	0.363																																					p.P1285L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3854T	2						.						112.0	108.0	109.0					2																	44123819		2203	4300	6503	43977323	SO:0001583	missense	10128	exon35			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.3854C>T	2.37:g.44123819G>A	ENSP00000260665:p.Pro1285Leu	Somatic		Capture	Illumina HiSeq	Phase_I	43977323	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	37	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	G	6.267	0.417376	0.11870	.	.	ENSG00000138095	ENST00000260665;ENST00000419884	T	0.17213	2.29	5.49	4.55	0.56014	.	0.868151	0.10284	N	0.693135	T	0.13415	0.0325	L	0.34521	1.04	0.38323	D	0.943598	P	0.42584	0.784	B	0.32149	0.141	T	0.20874	-1.0262	10	0.46703	T	0.11	-11.916	14.0037	0.64449	0.0:0.0:0.8479:0.1521	.	1285	P42704	LPPRC_HUMAN	L	1285;32	ENSP00000260665:P1285L	ENSP00000260665:P1285L	P	-	2	0	LRPPRC	43977323	0.006000	0.16342	0.005000	0.12908	0.087000	0.18053	1.663000	0.37429	2.561000	0.86390	0.557000	0.71058	CCG		0.363	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
EPAS1	2034	broad.mit.edu	37	2	46602913	46602913	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:46602913C>T	ENST00000263734.3	+	8	1481	c.971C>T	c.(970-972)aCg>aTg	p.T324M		NM_001430.4	NP_001421.2	Q99814	EPAS1_HUMAN	endothelial PAS domain protein 1	324	PAC.				angiogenesis (GO:0001525)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|erythrocyte differentiation (GO:0030218)|lung development (GO:0030324)|mitochondrion organization (GO:0007005)|myoblast fate commitment (GO:0048625)|norepinephrine metabolic process (GO:0042415)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart rate (GO:0002027)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|surfactant homeostasis (GO:0043129)|transcription from RNA polymerase II promoter (GO:0006366)|visual perception (GO:0007601)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|histone acetyltransferase binding (GO:0035035)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)	p.T324M(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	LUSC - Lung squamous cell carcinoma(58;0.151)			ACCCAGGGGACGGTCATCTAC	0.597																																					p.T324M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C971T	2						.						141.0	106.0	118.0					2																	46602913		2203	4300	6503	46456417	SO:0001583	missense	2034	exon8			U81984	CCDS1825.1	2p21-p16	2013-05-21			ENSG00000116016	ENSG00000116016		"""Basic helix-loop-helix proteins"""	3374	protein-coding gene	gene with protein product	"""HIF-1 alpha-like factor"""	603349				9000051, 9079689, 18378852	Standard	NM_001430		Approved	MOP2, PASD2, HIF2A, HLF, bHLHe73	uc002ruv.3	Q99814	OTTHUMG00000128818	ENST00000263734.3:c.971C>T	2.37:g.46602913C>T	ENSP00000263734:p.Thr324Met	Somatic		Capture	Illumina HiSeq	Phase_I	46456417	NM_001430	Q86VA2|Q99630	Missense_Mutation	SNP	ENST00000263734.3	37	CCDS1825.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.899154	0.91962	.	.	ENSG00000116016	ENST00000263734	T	0.17370	2.28	5.45	5.45	0.79879	PAS fold-3 (1);PAS (1);	0.000000	0.85682	D	0.000000	T	0.55545	0.1927	M	0.93241	3.395	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67960	-0.5535	10	0.87932	D	0	.	19.2907	0.94098	0.0:1.0:0.0:0.0	.	324	Q99814	EPAS1_HUMAN	M	324	ENSP00000263734:T324M	ENSP00000263734:T324M	T	+	2	0	EPAS1	46456417	1.000000	0.71417	0.946000	0.38457	0.890000	0.51754	7.814000	0.86154	2.575000	0.86900	0.655000	0.94253	ACG		0.597	EPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250752.2	NM_001430	
FBXO11	80204	broad.mit.edu	37	2	48066030	48066030	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:48066030G>T	ENST00000403359.3	-	4	627	c.555C>A	c.(553-555)cgC>cgA	p.R185R	FBXO11_ENST00000402508.1_Silent_p.R101R|FBXO11_ENST00000378314.3_Silent_p.R67R|FBXO11_ENST00000480038.1_5'UTR|FBXO11_ENST00000316377.4_Silent_p.R101R	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	185	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				cellular protein modification process (GO:0006464)|peptidyl-arginine N-methylation (GO:0035246)|protein ubiquitination (GO:0016567)|sensory perception of sound (GO:0007605)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	protein-arginine N-methyltransferase activity (GO:0016274)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.0?(2)|p.R101R(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GTTCACTGAAGCGTTTACATA	0.358			"""Mis, F, D"""		DLBCL																																p.R185R			Rec	yes		2	2p16.3	80204	F-box protein 11		L	.	.	3	Whole gene deletion(2)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)	c.C555A	2						.						115.0	106.0	109.0					2																	48066030		2203	4300	6503	47919534	SO:0001819	synonymous_variant	80204	exon4			AF174599	CCDS1837.1, CCDS54357.1	2p16.3	2014-01-29	2008-06-23	2008-06-23	ENSG00000138081	ENSG00000138081		"""Ubiquitin protein ligase E3 component n-recognins"", ""F-boxes /  ""other"""""	13590	protein-coding gene	gene with protein product	"""ubiquitin protein ligase E3 component n-recognin 6"""	607871	"""F-box only protein 11"""			10531035, 16487488, 18162545	Standard	NM_025133		Approved	FBX11, UBR6	uc002rwe.3	Q86XK2	OTTHUMG00000129130	ENST00000403359.3:c.555C>A	2.37:g.48066030G>T		Somatic		Capture	Illumina HiSeq	Phase_I	47919534	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Silent	SNP	ENST00000403359.3	37	CCDS54357.1																																																																																				0.358	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133	
NRXN1	9378	broad.mit.edu	37	2	50282099	50282099	+	Intron	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:50282099C>T	ENST00000406316.2	-	20	5195				NRXN1_ENST00000406859.3_Intron|NRXN1_ENST00000404971.1_Missense_Mutation_p.D1308N|NRXN1_ENST00000342183.5_Intron|NRXN1_ENST00000401669.2_Missense_Mutation_p.D1268N|NRXN1_ENST00000405472.3_Missense_Mutation_p.D1260N|NRXN1_ENST00000402717.3_Missense_Mutation_p.D1260N|NRXN1_ENST00000401710.1_Intron	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1						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.D1309N(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)			TTACCTTTGTCGAGTAGCCAT	0.313																																					p.D1308N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3922A	2						.						36.0	33.0	34.0					2																	50282099		1566	3581	5147	50135603	SO:0001627	intron_variant	9378	exon21			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.3719-1371G>A	2.37:g.50282099C>T		Somatic		Capture	Illumina HiSeq	Phase_I	50135603	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.158527	0.78114	.	.	ENSG00000179915	ENST00000404971;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	5.85	5.85	0.93711	.	.	.	.	.	D	0.86678	0.5990	M	0.63843	1.955	0.80722	D	1	D;P	0.69078	0.997;0.956	D;P	0.64776	0.929;0.861	D	0.86505	0.1806	9	0.62326	D	0.03	.	20.1447	0.98073	0.0:1.0:0.0:0.0	.	1308;1260	Q9ULB1-3;A7E294	.;.	N	1308;1260;1268;1309;1260	ENSP00000385142:D1308N;ENSP00000434015:D1260N;ENSP00000385017:D1268N;ENSP00000385434:D1260N	ENSP00000385017:D1268N	D	-	1	0	NRXN1	50135603	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.756000	0.94617	0.591000	0.81541	GAC		0.313	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
NRXN1	9378	broad.mit.edu	37	2	51254932	51254932	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:51254932C>T	ENST00000406316.2	-	2	1956	c.480G>A	c.(478-480)ccG>ccA	p.P160P	NRXN1_ENST00000406859.3_Silent_p.P160P|NRXN1_ENST00000404971.1_Silent_p.P160P|NRXN1_ENST00000401669.2_Silent_p.P160P|NRXN1_ENST00000405472.3_Silent_p.P160P|NRXN1_ENST00000402717.3_Silent_p.P160P|NRXN1_ENST00000405581.1_Silent_p.P160P	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	160	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.P160P(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)			CGCGCAGTTCCGGGGGCAGCC	0.667																																					p.P160P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G480A	2						.						22.0	28.0	26.0					2																	51254932		2073	4207	6280	51108436	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.480G>A	2.37:g.51254932C>T		Somatic		Capture	Illumina HiSeq	Phase_I	51108436	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		
CLHC1	130162	broad.mit.edu	37	2	55439817	55439817	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:55439817G>T	ENST00000401408.1	-	5	836	c.491C>A	c.(490-492)cCt>cAt	p.P164H	CLHC1_ENST00000406437.2_Intron|CLHC1_ENST00000494539.1_Intron|CLHC1_ENST00000407122.1_Missense_Mutation_p.P164H|CLHC1_ENST00000406076.1_Missense_Mutation_p.P42H|AC012358.7_ENST00000366153.2_RNA	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	164								p.P164H(2)									ACCTGGAATAGGTTTTGAAGG	0.313																																					p.P164H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C491A	2						.						100.0	98.0	98.0					2																	55439817		2201	4300	6501	55293321	SO:0001583	missense	130162	exon5				CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 63"""	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.491C>A	2.37:g.55439817G>T	ENSP00000384869:p.Pro164His	Somatic		Capture	Illumina HiSeq	Phase_I	55293321	NM_152385	B2RDV1|Q53R93|Q8N403	Missense_Mutation	SNP	ENST00000401408.1	37	CCDS33201.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.293658	0.60086	.	.	ENSG00000162994	ENST00000407122;ENST00000401408;ENST00000406076	T;T;T	0.19806	2.13;2.13;2.12	4.84	3.93	0.45458	.	0.178506	0.39687	N	0.001291	T	0.36413	0.0966	M	0.68952	2.095	0.80722	D	1	D	0.65815	0.995	P	0.57371	0.819	T	0.10823	-1.0613	10	0.49607	T	0.09	-8.6558	11.2204	0.48851	0.0:0.1861:0.8139:0.0	.	164	Q8NHS4	CB063_HUMAN	H	164;164;42	ENSP00000385778:P164H;ENSP00000384869:P164H;ENSP00000385512:P42H	ENSP00000384869:P164H	P	-	2	0	C2orf63	55293321	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.091000	0.50199	1.121000	0.41925	0.650000	0.86243	CCT		0.313	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385	
BCL11A	53335	broad.mit.edu	37	2	60688624	60688624	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:60688624C>T	ENST00000335712.6	-	4	1650	c.1423G>A	c.(1423-1425)Gac>Aac	p.D475N	BCL11A_ENST00000538214.1_Missense_Mutation_p.D441N|BCL11A_ENST00000537768.1_Missense_Mutation_p.D144N|BCL11A_ENST00000358510.4_Missense_Mutation_p.D441N|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000356842.4_Missense_Mutation_p.D475N|BCL11A_ENST00000359629.5_Intron	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	475					B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|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 negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)	p.D475N(2)		NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			AGGTTGGGGTCGTTCTCGCTC	0.642			T	IGH@	B-CLL																																p.D475N			Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1423A	2						.						23.0	24.0	24.0					2																	60688624		2202	4300	6502	60542128	SO:0001583	missense	53335	exon4			AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"""Zinc fingers, C2H2-type"""	13221	protein-coding gene	gene with protein product		606557	"""ecotropic viral integration site 9"""	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.1423G>A	2.37:g.60688624C>T	ENSP00000338774:p.Asp475Asn	Somatic		Capture	Illumina HiSeq	Phase_I	60542128	NM_022893	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Missense_Mutation	SNP	ENST00000335712.6	37	CCDS1862.1	.	.	.	.	.	.	.	.	.	.	C	12.10	1.837732	0.32513	.	.	ENSG00000119866	ENST00000356842;ENST00000378117;ENST00000538214;ENST00000537768;ENST00000335712;ENST00000358510	T;T;T;T;T	0.08896	3.04;3.29;3.19;3.33;3.25	5.27	5.27	0.74061	.	0.333042	0.27730	N	0.018098	T	0.08891	0.0220	L	0.29908	0.895	0.80722	D	1	B;B;B;B;B	0.15719	0.004;0.014;0.001;0.003;0.005	B;B;B;B;B	0.09377	0.003;0.004;0.0;0.003;0.002	T	0.22871	-1.0204	10	0.33141	T	0.24	-2.7533	18.9015	0.92444	0.0:1.0:0.0:0.0	.	441;144;441;475;475	F5H2Y4;B4DT16;Q9H165-6;Q9H165;D9YZV9	.;.;.;BC11A_HUMAN;.	N	475;511;441;144;475;441	ENSP00000349300:D475N;ENSP00000438303:D441N;ENSP00000443712:D144N;ENSP00000338774:D475N;ENSP00000351307:D441N	ENSP00000338774:D475N	D	-	1	0	BCL11A	60542128	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.761000	0.62243	2.461000	0.83175	0.655000	0.94253	GAC		0.642	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893	
BCL11A	53335	broad.mit.edu	37	2	60773391	60773391	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:60773391C>T	ENST00000335712.6	-	2	327	c.100G>A	c.(100-102)Ggc>Agc	p.G34S	BCL11A_ENST00000538214.1_Missense_Mutation_p.G34S|BCL11A_ENST00000537768.1_5'UTR|BCL11A_ENST00000358510.4_Missense_Mutation_p.G34S|BCL11A_ENST00000356842.4_Missense_Mutation_p.G34S|BCL11A_ENST00000359629.5_Missense_Mutation_p.G34S	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	34	Required for nuclear body formation and for SUMO1 recruitment. {ECO:0000250}.				B cell differentiation (GO:0030183)|negative regulation of axon extension (GO:0030517)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein homooligomerization (GO:0032463)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein sumoylation (GO:0016925)|regulation of dendrite development (GO:0050773)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|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 negative regulation of transcription (GO:0001078)|transcription corepressor activity (GO:0003714)	p.G34S(2)		NS(1)|breast(6)|central_nervous_system(6)|endometrium(4)|kidney(1)|large_intestine(8)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	59			LUSC - Lung squamous cell carcinoma(5;9.29e-08)|Lung(5;1.34e-06)|Epithelial(17;0.0562)|all cancers(80;0.199)			CCCAACGGGCCGTGGTCTGGT	0.502			T	IGH@	B-CLL																																p.G34S			Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G100A	2						.						70.0	68.0	69.0					2																	60773391		2203	4300	6503	60626895	SO:0001583	missense	53335	exon2			AJ404611	CCDS1861.1, CCDS1862.1, CCDS46295.1	2p16.1	2013-01-08	2002-05-08		ENSG00000119866	ENSG00000119866		"""Zinc fingers, C2H2-type"""	13221	protein-coding gene	gene with protein product		606557	"""ecotropic viral integration site 9"""	EVI9		11719382, 18245381	Standard	NM_018014		Approved	BCL11A-XL, BCL11A-L, BCL11A-S, CTIP1, HBFQTL5, ZNF856	uc002sae.1	Q9H165	OTTHUMG00000129420	ENST00000335712.6:c.100G>A	2.37:g.60773391C>T	ENSP00000338774:p.Gly34Ser	Somatic		Capture	Illumina HiSeq	Phase_I	60626895	NM_138559	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Missense_Mutation	SNP	ENST00000335712.6	37	CCDS1862.1	.	.	.	.	.	.	.	.	.	.	C	12.43	1.935254	0.34189	.	.	ENSG00000119866	ENST00000356842;ENST00000359629;ENST00000378117;ENST00000538214;ENST00000335712;ENST00000358510	T;T;T;T	0.08102	3.13;3.4;3.39;3.34	5.68	5.68	0.88126	.	0.551480	0.19754	N	0.106837	T	0.04543	0.0124	N	0.14661	0.345	0.80722	D	1	B;B;B;B;B;B	0.20261	0.002;0.001;0.0;0.001;0.043;0.007	B;B;B;B;B;B	0.12837	0.002;0.001;0.0;0.001;0.008;0.004	T	0.18398	-1.0338	10	0.02654	T	1	-3.007	11.2203	0.48851	0.0:0.8581:0.0:0.1419	.	34;34;34;34;34;34	F5H2Y4;Q66LN6;Q9H165-6;Q9H165;Q9H165-3;D9YZV9	.;.;.;BC11A_HUMAN;.;.	S	34;34;70;34;34;34	ENSP00000349300:G34S;ENSP00000438303:G34S;ENSP00000338774:G34S;ENSP00000351307:G34S	ENSP00000338774:G34S	G	-	1	0	BCL11A	60626895	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.857000	0.48349	2.678000	0.91216	0.557000	0.71058	GGC		0.502	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893	
REL	5966	broad.mit.edu	37	2	61149071	61149071	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:61149071C>T	ENST00000295025.8	+	11	1581	c.1261C>T	c.(1261-1263)Cgc>Tgc	p.R421C	REL_ENST00000394479.3_Missense_Mutation_p.R389C	NM_002908.2	NP_002899.1	Q04864	REL_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog	421					cytokine production (GO:0001816)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of neuron death (GO:1901215)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	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 positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R421C(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(3)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	16	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			CCCCACCCCACGCTCAGGCAA	0.507			A		Hodgkin Lymphoma																																p.R421C			Dom	yes		2	2p13-p12	5966	v-rel reticuloendotheliosis viral oncogene homolog (avian)		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1261T	2						.						96.0	91.0	93.0					2																	61149071		2203	4300	6503	61002575	SO:0001583	missense	5966	exon11			M11595	CCDS1864.1, CCDS74515.1	2p13-p12	2013-07-09	2013-07-09		ENSG00000162924	ENSG00000162924			9954	protein-coding gene	gene with protein product		164910				1577270	Standard	XM_005264470		Approved	I-Rel, c-Rel	uc002sam.1	Q04864	OTTHUMG00000129418	ENST00000295025.8:c.1261C>T	2.37:g.61149071C>T	ENSP00000295025:p.Arg421Cys	Somatic		Capture	Illumina HiSeq	Phase_I	61002575	NM_002908	Q17RU2|Q2PNZ7|Q6LDY0	Missense_Mutation	SNP	ENST00000295025.8	37	CCDS1864.1	.	.	.	.	.	.	.	.	.	.	C	7.296	0.612119	0.14066	.	.	ENSG00000162924	ENST00000295025;ENST00000394479	T;T	0.45668	0.89;0.9	5.45	3.3	0.37823	.	2.338690	0.01609	N	0.022420	T	0.33059	0.0850	N	0.19112	0.55	0.21967	N	0.999449	B;B	0.13594	0.004;0.008	B;B	0.04013	0.0;0.001	T	0.22347	-1.0219	10	0.54805	T	0.06	-13.0928	8.2695	0.31836	0.1607:0.7384:0.0:0.1009	.	389;421	Q17RU2;Q04864	.;REL_HUMAN	C	421;389	ENSP00000295025:R421C;ENSP00000377989:R389C	ENSP00000295025:R421C	R	+	1	0	REL	61002575	0.007000	0.16637	0.711000	0.30485	0.292000	0.27327	0.437000	0.21543	1.174000	0.42811	0.585000	0.79938	CGC		0.507	REL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251576.3	NM_002908	
EHBP1	23301	broad.mit.edu	37	2	63206338	63206338	+	Nonsense_Mutation	SNP	C	C	T	rs564779105		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:63206338C>T	ENST00000263991.5	+	16	3063	c.2581C>T	c.(2581-2583)Cga>Tga	p.R861*	EHBP1_ENST00000405015.3_Nonsense_Mutation_p.R826*|EHBP1_ENST00000405289.1_Nonsense_Mutation_p.R826*|EHBP1_ENST00000431489.1_Nonsense_Mutation_p.R826*|EHBP1_ENST00000496857.1_3'UTR|EHBP1_ENST00000354487.3_Nonsense_Mutation_p.R826*	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	861						cytoplasm (GO:0005737)|membrane (GO:0016020)		p.R861*(1)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			AGATGAAGAGCGACGTCGGCA	0.433																																					p.R826X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2476T	2						.						78.0	81.0	80.0					2																	63206338		2203	4300	6503	63059842	SO:0001587	stop_gained	23301	exon14			AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.2581C>T	2.37:g.63206338C>T	ENSP00000263991:p.Arg861*	Somatic		Capture	Illumina HiSeq	Phase_I	63059842	NM_001142614	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Nonsense_Mutation	SNP	ENST00000263991.5	37	CCDS1872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	44|44	10.856198|10.856198	0.99478|0.99478	.|.	.|.	ENSG00000115504|ENSG00000115504	ENST00000444311;ENST00000422032|ENST00000405015;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	.|.	.|.	.|.	5.86|5.86	4.0|4.0	0.46444|0.46444	.|.	.|0.000000	.|0.64402	.|D	.|0.000002	T|.	0.35970|.	0.0950|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.33343|.	-0.9872|.	3|.	.|0.02654	.|T	.|1	.|.	14.9459|14.9459	0.71032|0.71032	0.2686:0.7314:0.0:0.0|0.2686:0.7314:0.0:0.0	.|.	.|.	.|.	.|.	V|X	85;20|826;826;861;826;826	.|.	.|ENSP00000263991:R861X	A|R	+|+	2|1	0|2	EHBP1|EHBP1	63059842|63059842	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.012000|4.012000	0.57131|0.57131	0.757000|0.757000	0.33036|0.33036	-0.182000|-0.182000	0.12963|0.12963	GCG|CGA		0.433	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252	
OTX1	5013	broad.mit.edu	37	2	63282664	63282664	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:63282664G>A	ENST00000282549.2	+	5	554	c.278G>A	c.(277-279)tGc>tAc	p.C93Y	OTX1_ENST00000366671.3_Missense_Mutation_p.C93Y	NM_014562.3	NP_055377.1	P32242	OTX1_HUMAN	orthodenticle homeobox 1	93					anterior/posterior pattern specification (GO:0009952)|diencephalon morphogenesis (GO:0048852)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	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)	p.C93Y(1)|p.C93S(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Lung NSC(7;0.121)|all_lung(7;0.211)					CGCGCCAAATGCCGCCAGCAG	0.657																																					p.C93Y												.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.G278A	2						.						20.0	24.0	23.0					2																	63282664		2202	4300	6502	63136168	SO:0001583	missense	5013	exon5				CCDS1873.1	2p15	2011-06-20	2007-02-15		ENSG00000115507	ENSG00000115507		"""Homeoboxes / PRD class"""	8521	protein-coding gene	gene with protein product		600036	"""orthodenticle (Drosophila) homolog 1"", ""orthodenticle homolog 1 (Drosophila)"""			7959790	Standard	NM_001199770		Approved		uc002scd.3	P32242	OTTHUMG00000129454	ENST00000282549.2:c.278G>A	2.37:g.63282664G>A	ENSP00000282549:p.Cys93Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	63136168	NM_001199770	A6NHA2|B3KTJ4|Q53TG6	Missense_Mutation	SNP	ENST00000282549.2	37	CCDS1873.1	.	.	.	.	.	.	.	.	.	.	g	13.05	2.120833	0.37436	.	.	ENSG00000115507	ENST00000366671;ENST00000282549	D;D	0.95885	-3.84;-3.84	3.64	2.76	0.32466	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.058969	0.64402	D	0.000001	D	0.90140	0.6919	N	0.02985	-0.445	0.53005	D	0.999968	P	0.37423	0.594	P	0.48334	0.574	D	0.88275	0.2932	10	0.39692	T	0.17	.	11.6771	0.51436	0.0:0.0:0.8206:0.1794	.	93	P32242	OTX1_HUMAN	Y	93	ENSP00000355631:C93Y;ENSP00000282549:C93Y	ENSP00000282549:C93Y	C	+	2	0	OTX1	63136168	1.000000	0.71417	1.000000	0.80357	0.402000	0.30811	7.651000	0.83577	0.884000	0.36064	-0.216000	0.12614	TGC		0.657	OTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251617.1		
BMP10	27302	broad.mit.edu	37	2	69093354	69093354	+	Silent	SNP	G	G	A	rs2231343		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:69093354G>A	ENST00000295379.1	-	2	842	c.684C>T	c.(682-684)caC>caT	p.H228H		NM_014482.1	NP_055297.1	O95393	BMP10_HUMAN	bone morphogenetic protein 10	228					activin receptor signaling pathway (GO:0032924)|adult heart development (GO:0007512)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heart trabecula formation (GO:0060347)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell migration (GO:0010596)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction (GO:0055117)|sarcomere organization (GO:0045214)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Z disc (GO:0030018)	hormone activity (GO:0005179)|receptor serine/threonine kinase binding (GO:0033612)	p.H228H(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(15)|ovary(2)	27						CAGCTTCATCGTGTTTGCTCT	0.493																																					p.H228H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C684T	2						.						118.0	104.0	109.0					2																	69093354		2203	4300	6503	68946858	SO:0001819	synonymous_variant	27302	exon2			AF101441	CCDS1890.1	2p13.2	2014-09-17			ENSG00000163217	ENSG00000163217		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	20869	protein-coding gene	gene with protein product		608748				10072785	Standard	NM_014482		Approved		uc002sez.1	O95393	OTTHUMG00000129573	ENST00000295379.1:c.684C>T	2.37:g.69093354G>A		Somatic		Capture	Illumina HiSeq	Phase_I	68946858	NM_014482	Q53R17|Q6NTE0	Silent	SNP	ENST00000295379.1	37	CCDS1890.1																																																																																				0.493	BMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251768.1	NM_014482	
ANXA4	307	broad.mit.edu	37	2	70035105	70035105	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:70035105G>A	ENST00000394295.4	+	6	622	c.374G>A	c.(373-375)cGc>cAc	p.R125H	ANXA4_ENST00000536030.1_Missense_Mutation_p.R41H|ANXA4_ENST00000409920.1_Missense_Mutation_p.R103H	NM_001153.3	NP_001144.1	P09525	ANXA4_HUMAN	annexin A4	123					epithelial cell differentiation (GO:0030855)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phospholipase inhibitor activity (GO:0004859)	p.R125H(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11						GAGATCCGGCGCATAAGCCAA	0.562																																					p.R125H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G374A	2						.						70.0	62.0	64.0					2																	70035105		2203	4300	6503	69888609	SO:0001583	missense	307	exon6			M82809	CCDS1894.1	2p13.3	2008-02-05			ENSG00000196975	ENSG00000196975		"""Annexins"""	542	protein-coding gene	gene with protein product		106491		ANX4		1346776	Standard	NM_001153		Approved		uc002sfr.4	P09525	OTTHUMG00000129649	ENST00000394295.4:c.374G>A	2.37:g.70035105G>A	ENSP00000377833:p.Arg125His	Somatic		Capture	Illumina HiSeq	Phase_I	69888609	NM_001153	B4DDF9|Q96F33|Q9BWK1	Missense_Mutation	SNP	ENST00000394295.4	37	CCDS1894.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.771000	0.49680	.	.	ENSG00000196975	ENST00000409920;ENST00000394295;ENST00000536030	T;T;T	0.03496	3.91;3.91;3.91	5.86	4.05	0.47172	Annexin repeat, conserved site (1);	0.335476	0.36303	N	0.002667	T	0.02119	0.0066	N	0.12182	0.205	0.09310	N	0.999998	B;B;B	0.10296	0.0;0.003;0.001	B;B;B	0.10450	0.001;0.005;0.001	T	0.47736	-0.9094	9	.	.	.	.	5.608	0.17391	0.1604:0.0:0.6803:0.1593	.	123;103;125	P09525;Q6P452;Q6LES2	ANXA4_HUMAN;.;.	H	103;125;41	ENSP00000386756:R103H;ENSP00000377833:R125H;ENSP00000441931:R41H	.	R	+	2	0	ANXA4	69888609	0.056000	0.20664	0.764000	0.31436	0.982000	0.71751	0.491000	0.22419	0.801000	0.34066	0.650000	0.86243	CGC		0.562	ANXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251848.2	NM_001153	
ADD2	119	broad.mit.edu	37	2	70905846	70905846	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:70905846G>T	ENST00000264436.4	-	11	1817	c.1373C>A	c.(1372-1374)cCc>cAc	p.P458H	ADD2_ENST00000430656.1_Missense_Mutation_p.P474H|ADD2_ENST00000413157.2_Missense_Mutation_p.P458H|ADD2_ENST00000355733.3_Missense_Mutation_p.P458H|ADD2_ENST00000407644.2_Missense_Mutation_p.P458H	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	458					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)	p.P458H(2)		autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						CGTGGTCTTGGGTCGGGGGCT	0.592																																					p.P458H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1373A	2						.						146.0	159.0	155.0					2																	70905846		2203	4300	6503	70759354	SO:0001583	missense	119	exon11			X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.1373C>A	2.37:g.70905846G>T	ENSP00000264436:p.Pro458His	Somatic		Capture	Illumina HiSeq	Phase_I	70759354	NM_001185054	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	37	CCDS1906.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.922538	0.52653	.	.	ENSG00000075340	ENST00000264436;ENST00000407644;ENST00000355733;ENST00000356565;ENST00000413157;ENST00000430656	T;T;T;T;T	0.19938	2.11;2.11;2.11;2.11;2.11	5.23	5.23	0.72850	.	0.378699	0.29730	N	0.011346	T	0.12008	0.0292	N	0.02539	-0.55	0.36961	D	0.893343	B;B;P;P	0.44344	0.0;0.0;0.833;0.755	B;B;P;B	0.45913	0.001;0.001;0.497;0.35	T	0.21280	-1.0250	10	0.46703	T	0.11	-23.4116	11.9349	0.52868	0.0:0.1746:0.8254:0.0	.	474;458;458;458	B4DM17;P35612-4;P35612;P35612-3	.;.;ADDB_HUMAN;.	H	458;458;458;458;458;474	ENSP00000264436:P458H;ENSP00000384677:P458H;ENSP00000347972:P458H;ENSP00000388072:P458H;ENSP00000398112:P474H	ENSP00000264436:P458H	P	-	2	0	ADD2	70759354	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.020000	0.57189	2.716000	0.92895	0.655000	0.94253	CCC		0.592	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617	
ADD2	119	broad.mit.edu	37	2	70910772	70910772	+	Missense_Mutation	SNP	C	C	T	rs370464708		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:70910772C>T	ENST00000264436.4	-	10	1520	c.1076G>A	c.(1075-1077)cGg>cAg	p.R359Q	ADD2_ENST00000430656.1_Missense_Mutation_p.R375Q|ADD2_ENST00000413157.2_Missense_Mutation_p.R359Q|ADD2_ENST00000355733.3_Missense_Mutation_p.R359Q|ADD2_ENST00000407644.2_Missense_Mutation_p.R359Q	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	359					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)	p.R359Q(2)		autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						CTCCCCCAGCCGACTCTTCTG	0.622																																					p.R359Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1076A	2						.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	50.0	44.0	46.0		1076,1124,1076,1076,1076	4.0	1.0	2		46	1,8599		0,1,4299	no	missense,missense,missense,missense,missense	ADD2	NM_001185054.1,NM_001185055.1,NM_001617.3,NM_017482.3,NM_017488.3	43,43,43,43,43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	359/727,375/576,359/727,359/560,359/644	70910772	1,13005	2203	4300	6503	70764280	SO:0001583	missense	119	exon10			X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.1076G>A	2.37:g.70910772C>T	ENSP00000264436:p.Arg359Gln	Somatic		Capture	Illumina HiSeq	Phase_I	70764280	NM_001185054	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	37	CCDS1906.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.199350	0.79015	0.0	1.16E-4	ENSG00000075340	ENST00000264436;ENST00000407644;ENST00000355733;ENST00000356565;ENST00000413157;ENST00000430656	T;T;T;T;T	0.09538	3.28;3.28;3.09;2.97;2.99	4.87	4.0	0.46444	.	0.000000	0.85682	D	0.000000	T	0.22475	0.0542	L	0.52573	1.65	0.48696	D	0.99969	D;P;P;D	0.76494	0.99;0.944;0.952;0.999	P;B;B;D	0.77557	0.709;0.301;0.372;0.99	T	0.03278	-1.1053	10	0.18276	T	0.48	-23.0016	11.0927	0.48125	0.0:0.91:0.0:0.09	.	375;359;359;359	B4DM17;P35612-4;P35612;P35612-3	.;.;ADDB_HUMAN;.	Q	359;359;359;359;359;375	ENSP00000264436:R359Q;ENSP00000384677:R359Q;ENSP00000347972:R359Q;ENSP00000388072:R359Q;ENSP00000398112:R375Q	ENSP00000264436:R359Q	R	-	2	0	ADD2	70764280	0.994000	0.37717	0.999000	0.59377	0.971000	0.66376	3.190000	0.50973	1.285000	0.44548	0.655000	0.94253	CGG		0.622	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617	
CLEC4F	165530	broad.mit.edu	37	2	71044212	71044212	+	Nonsense_Mutation	SNP	G	G	A	rs546185298	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:71044212G>A	ENST00000272367.2	-	4	377	c.301C>T	c.(301-303)Cga>Tga	p.R101*	CLEC4F_ENST00000426626.1_Nonsense_Mutation_p.R101*	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	101			R -> Q (in dbSNP:rs2075221).		endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.R101*(1)		endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						ATAAGCTCTCGCATTTCTGCC	0.488													G|||	2	0.000399361	0.0008	0.0	5008	,	,		21384	0.001		0.0	False		,,,				2504	0.0				p.R101X	Colon(107;10 2157 6841 26035)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C301T	2						.						57.0	52.0	54.0					2																	71044212		2203	4300	6503	70897720	SO:0001587	stop_gained	165530	exon4			AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"""C-type lectin domain containing"""	25357	protein-coding gene	gene with protein product			"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"""	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.301C>T	2.37:g.71044212G>A	ENSP00000272367:p.Arg101*	Somatic		Capture	Illumina HiSeq	Phase_I	70897720	NM_173535	A4QPA5	Nonsense_Mutation	SNP	ENST00000272367.2	37	CCDS1910.1	.	.	.	.	.	.	.	.	.	.	G	18.83	3.707372	0.68615	.	.	ENSG00000152672	ENST00000272367;ENST00000426626	.	.	.	5.04	2.1	0.27182	.	0.366890	0.20087	N	0.099533	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	.	8.0399	0.30515	0.0:0.1553:0.5238:0.3209	.	.	.	.	X	101	.	ENSP00000272367:R101X	R	-	1	2	CLEC4F	70897720	0.642000	0.27260	0.008000	0.14137	0.084000	0.17831	1.757000	0.38400	0.196000	0.20367	0.467000	0.42956	CGA		0.488	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
ZNF638	27332	broad.mit.edu	37	2	71661877	71661877	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:71661877C>T	ENST00000409544.1	+	28	6507	c.5877C>T	c.(5875-5877)ttC>ttT	p.F1959F	ZNF638_ENST00000409407.1_Silent_p.F899F|ZNF638_ENST00000355812.3_3'UTR|ZNF638_ENST00000264447.4_Silent_p.F1959F	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1959					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.F1959F(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						AACAGAAATTCATGGCCAAGC	0.323																																					p.F1959F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5877T	2						.						60.0	70.0	67.0					2																	71661877		2203	4300	6503	71515385	SO:0001819	synonymous_variant	27332	exon28			D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.5877C>T	2.37:g.71661877C>T		Somatic		Capture	Illumina HiSeq	Phase_I	71515385	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Silent	SNP	ENST00000409544.1	37	CCDS1917.1																																																																																				0.323	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
DYSF	8291	broad.mit.edu	37	2	71797015	71797015	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:71797015G>A	ENST00000258104.3	+	27	3153	c.2876G>A	c.(2875-2877)cGg>cAg	p.R959Q	DYSF_ENST00000429174.2_Missense_Mutation_p.R959Q|DYSF_ENST00000410020.3_Missense_Mutation_p.R977Q|DYSF_ENST00000410041.1_Missense_Mutation_p.R977Q|DYSF_ENST00000409651.1_Missense_Mutation_p.R991Q|DYSF_ENST00000409762.1_Missense_Mutation_p.R976Q|DYSF_ENST00000413539.2_Missense_Mutation_p.R990Q|DYSF_ENST00000409582.3_Missense_Mutation_p.R976Q|DYSF_ENST00000409366.1_Missense_Mutation_p.R960Q|DYSF_ENST00000409744.1_Missense_Mutation_p.R946Q|DYSF_ENST00000394120.2_Missense_Mutation_p.R960Q	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	959			R -> W (in MMD1 and LGMD2B). {ECO:0000269|PubMed:14678801, ECO:0000269|PubMed:16100712}.		plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.R959Q(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						AACCAGACCCGGCTTCCCGGA	0.577																																					p.R991Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2972A	2						.						57.0	58.0	58.0					2																	71797015		2203	4300	6503	71650523	SO:0001583	missense	8291	exon28			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.2876G>A	2.37:g.71797015G>A	ENSP00000258104:p.Arg959Gln	Somatic		Capture	Illumina HiSeq	Phase_I	71650523	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	g	36	5.684427	0.96774	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.95205	-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64	5.21	5.21	0.72293	Ferlin/Peroxisome membrane (1);	0.130714	0.49916	D	0.000129	D	0.97300	0.9117	M	0.83603	2.65	0.46044	D	0.998831	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.999;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;0.999	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.83275	0.941;0.941;0.941;0.941;0.994;0.996;0.996;0.996;0.98;0.996;0.992;0.98;0.941;0.965	D	0.97849	1.0273	10	0.87932	D	0	-33.3732	16.623	0.84934	0.0:0.0:1.0:0.0	.	991;977;960;946;977;946;976;945;990;976;959;945;960;959	O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	Q	990;976;976;959;959;991;960;946;960;977;977	ENSP00000407046:R990Q;ENSP00000387137:R976Q;ENSP00000386547:R976Q;ENSP00000398305:R959Q;ENSP00000258104:R959Q;ENSP00000386683:R991Q;ENSP00000377678:R960Q;ENSP00000386285:R946Q;ENSP00000386512:R960Q;ENSP00000386881:R977Q;ENSP00000386617:R977Q	ENSP00000258104:R959Q	R	+	2	0	DYSF	71650523	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.628000	0.98415	2.597000	0.87782	0.546000	0.68486	CGG		0.577	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
RAB11FIP5	26056	broad.mit.edu	37	2	73316062	73316062	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:73316062G>A	ENST00000258098.6	-	2	1053	c.813C>T	c.(811-813)ggC>ggT	p.G271G	RAB11FIP5_ENST00000493523.2_5'UTR	NM_015470.2	NP_056285.1	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	271					cellular response to acidic pH (GO:0071468)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|protein transport (GO:0015031)|regulated secretory pathway (GO:0045055)|regulation of protein localization to cell surface (GO:2000008)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|recycling endosome (GO:0055037)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)	p.G271G(1)		biliary_tract(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	23						GGAGTTCGGCGCCAGGTCCCT	0.682																																					p.G271G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C813T	2						.						29.0	28.0	28.0					2																	73316062		2203	4300	6503	73169570	SO:0001819	synonymous_variant	26056	exon2			AF334812	CCDS1923.1	2p13	2008-02-05			ENSG00000135631	ENSG00000135631			24845	protein-coding gene	gene with protein product		605536				10048485, 11163216	Standard	NM_015470		Approved	GAF1, KIAA0857, RIP11, pp75	uc002sis.4	Q9BXF6	OTTHUMG00000129779	ENST00000258098.6:c.813C>T	2.37:g.73316062G>A		Somatic		Capture	Illumina HiSeq	Phase_I	73169570	NM_015470	O94939|Q9P0M1	Silent	SNP	ENST00000258098.6	37	CCDS1923.1																																																																																				0.682	RAB11FIP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251995.1	NM_015470	
ALMS1	7840	broad.mit.edu	37	2	73675157	73675157	+	Silent	SNP	T	T	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:73675157T>A	ENST00000264448.6	+	8	1611	c.1500T>A	c.(1498-1500)acT>acA	p.T500T	ALMS1_ENST00000377715.1_Silent_p.T500T|ALMS1_ENST00000409009.1_Silent_p.T458T	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	500					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.T500T(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TCACTACCACTCCTGTTGATT	0.393																																					p.T500T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1500A	2						.						133.0	119.0	124.0					2																	73675157		1925	4129	6054	73528665	SO:0001819	synonymous_variant	7840	exon8			AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.1500T>A	2.37:g.73675157T>A		Somatic		Capture	Illumina HiSeq	Phase_I	73528665	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																				0.393	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
TET3	200424	broad.mit.edu	37	2	74315075	74315075	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:74315075G>A	ENST00000409262.3	+	4	2393	c.2393G>A	c.(2392-2394)cGt>cAt	p.R798H		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	798					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)	p.R798H(1)|p.R75H(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GGCATTCCCCGTAGCCTCGGA	0.627																																					p.R798H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2393A	2						.						23.0	31.0	29.0					2																	74315075		2096	4188	6284	74168583	SO:0001583	missense	200424	exon4				CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"""tet oncogene family member 3"""			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.2393G>A	2.37:g.74315075G>A	ENSP00000386869:p.Arg798His	Somatic		Capture	Illumina HiSeq	Phase_I	74168583	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Missense_Mutation	SNP	ENST00000409262.3	37	CCDS46339.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.176115	0.78564	.	.	ENSG00000187605	ENST00000409262;ENST00000233310	T	0.21734	1.99	4.9	3.96	0.45880	TET cysteine-rich domain (1);	0.181870	0.46145	D	0.000310	T	0.16557	0.0398	L	0.41710	1.295	0.58432	D	0.999992	P	0.36412	0.552	B	0.29176	0.099	T	0.05468	-1.0883	10	0.41790	T	0.15	.	14.8788	0.70516	0.0:0.1451:0.8549:0.0	.	798	O43151	TET3_HUMAN	H	798	ENSP00000386869:R798H	ENSP00000233310:R798H	R	+	2	0	TET3	74168583	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.969000	0.63735	2.698000	0.92095	0.650000	0.86243	CGT		0.627	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4		
SLC4A5	57835	broad.mit.edu	37	2	74483009	74483009	+	Silent	SNP	G	G	A	rs150389676		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:74483009G>A	ENST00000377634.4	-	13	1317	c.918C>T	c.(916-918)aaC>aaT	p.N306N	RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000377632.1_Silent_p.N306N|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000423644.1_Silent_p.N306N|SLC4A5_ENST00000346834.4_Silent_p.N306N|SLC4A5_ENST00000357822.5_Silent_p.N306N|SLC4A5_ENST00000359484.4_Silent_p.N242N|SLC4A5_ENST00000358683.4_Silent_p.N242N|SLC4A5_ENST00000394019.2_Silent_p.N306N					solute carrier family 4 (sodium bicarbonate cotransporter), member 5									p.N306N(1)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(13)|ovary(5)|pancreas(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						CCACGAGCACGTTGGACGCTT	0.582																																					p.N306N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C918T	2						.	G	,	1,4405	2.1+/-5.4	0,1,2202	164.0	118.0	133.0		918,918	-6.6	0.9	2	dbSNP_134	133	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	SLC4A5	NM_021196.3,NM_133478.2	,	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	,	306/1138,306/1122	74483009	4,13002	2203	4300	6503	74336517	SO:0001819	synonymous_variant	57835	exon8			AF243499	CCDS1936.1, CCDS1937.1	2p13.1	2013-07-19	2013-07-19		ENSG00000188687	ENSG00000188687		"""Solute carriers"""	18168	protein-coding gene	gene with protein product		606757	"""solute carrier family 4, sodium bicarbonate cotransporter, member 5"""			10978526, 11087115	Standard	NM_133478		Approved	NBC4	uc002sko.1	Q9BY07	OTTHUMG00000090263	ENST00000377634.4:c.918C>T	2.37:g.74483009G>A		Somatic		Capture	Illumina HiSeq	Phase_I	74336517	NM_021196		Silent	SNP	ENST00000377634.4	37	CCDS1936.1																																																																																				0.582	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3		
TTC31	64427	broad.mit.edu	37	2	74720217	74720217	+	Nonsense_Mutation	SNP	C	C	T	rs200567959		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:74720217C>T	ENST00000233623.5	+	13	1439	c.1432C>T	c.(1432-1434)Cga>Tga	p.R478*	TTC31_ENST00000442235.2_Silent_p.T136T|TTC31_ENST00000410003.1_3'UTR	NM_022492.4	NP_071937.4	Q49AM3	TTC31_HUMAN	tetratricopeptide repeat domain 31	478								p.R478*(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						TTCATGTCACCGAAGCCACCC	0.602																																					p.R478X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1432T	2						.						139.0	146.0	144.0					2																	74720217		1992	4147	6139	74573725	SO:0001587	stop_gained	64427	exon13			AK026819	CCDS42701.1	2p13.1	2013-01-11			ENSG00000115282	ENSG00000115282		"""Tetratricopeptide (TTC) repeat domain containing"""	25759	protein-coding gene	gene with protein product						12477932	Standard	NM_022492		Approved	FLJ12788	uc002slt.2	Q49AM3	OTTHUMG00000152887	ENST00000233623.5:c.1432C>T	2.37:g.74720217C>T	ENSP00000233623:p.Arg478*	Somatic		Capture	Illumina HiSeq	Phase_I	74573725	NM_022492	Q4KN40|Q53FD4|Q9H9F7	Nonsense_Mutation	SNP	ENST00000233623.5	37	CCDS42701.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.482|5.482	0.273923|0.273923	0.10403|0.10403	.|.	.|.	ENSG00000115282|ENSG00000115282	ENST00000435361|ENST00000233623	.|.	.|.	.|.	3.62|3.62	-0.454|-0.454	0.12197|0.12197	.|.	.|1.168260	.|0.06581	.|N	.|0.750296	T|.	0.14356|.	0.0347|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.22765|.	-1.0207|.	5|.	0.87932|0.09843	D|T	0|0.71	.|.	3.4436|3.4436	0.07473|0.07473	0.0:0.4403:0.2003:0.3594|0.0:0.4403:0.2003:0.3594	.|.	.|.	.|.	.|.	L|X	143|478	.|.	ENSP00000397652:P143L|ENSP00000233623:R478X	P|R	+|+	2|1	0|2	TTC31|TTC31	74573725|74573725	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.039000|0.039000	0.13416|0.13416	0.523000|0.523000	0.22925|0.22925	0.015000|0.015000	0.14971|0.14971	0.484000|0.484000	0.47621|0.47621	CCG|CGA		0.602	TTC31-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328422.1	NM_022492	
HTRA2	27429	broad.mit.edu	37	2	74758815	74758815	+	Missense_Mutation	SNP	G	G	A	rs201615648		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:74758815G>A	ENST00000258080.3	+	5	1661	c.1031G>A	c.(1030-1032)cGt>cAt	p.R344H	HTRA2_ENST00000352222.3_Missense_Mutation_p.R279H|HTRA2_ENST00000467961.1_3'UTR|AUP1_ENST00000377526.3_5'Flank	NM_013247.4	NP_037379.1	O43464	HTRA2_HUMAN	HtrA serine peptidase 2	344					adult walking behavior (GO:0007628)|cellular protein catabolic process (GO:0044257)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to interferon-beta (GO:0035458)|cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|ceramide metabolic process (GO:0006672)|execution phase of apoptosis (GO:0097194)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitochondrion organization (GO:0007005)|negative regulation of cell cycle (GO:0045786)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|neuron development (GO:0048666)|pentacyclic triterpenoid metabolic process (GO:0019742)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell death (GO:0010942)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001269)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of mitochondrion degradation (GO:1903146)|regulation of multicellular organism growth (GO:0040014)|response to herbicide (GO:0009635)	CD40 receptor complex (GO:0035631)|chromatin (GO:0000785)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)|unfolded protein binding (GO:0051082)	p.R344H(1)		endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12						TTTCTGCATCGTGGGGAAAAG	0.527													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21291	0.0		0.0	False		,,,				2504	0.0				p.R344H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1031A	2						.						91.0	87.0	88.0					2																	74758815		2203	4300	6503	74612323	SO:0001583	missense	27429	exon5				CCDS1951.1, CCDS1952.1	2p13.1	2011-07-21	2005-08-19	2005-08-19	ENSG00000115317	ENSG00000115317		"""Serine peptidases / Serine peptidases"", ""Parkinson disease"""	14348	protein-coding gene	gene with protein product		606441	"""protease, serine, 25"""	PRSS25		10644717, 10971580	Standard	XM_005264266		Approved	OMI, PARK13	uc002smi.1	O43464	OTTHUMG00000129957	ENST00000258080.3:c.1031G>A	2.37:g.74758815G>A	ENSP00000258080:p.Arg344His	Somatic		Capture	Illumina HiSeq	Phase_I	74612323	NM_013247	Q9HBZ4|Q9P0Y3|Q9P0Y4	Missense_Mutation	SNP	ENST00000258080.3	37	CCDS1951.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	17.80	3.477334	0.63849	.	.	ENSG00000115317	ENST00000258080;ENST00000352222;ENST00000437202	T;T;T	0.19394	2.15;2.15;2.15	4.6	4.6	0.57074	Peptidase cysteine/serine, trypsin-like (1);	0.326395	0.31031	N	0.008394	T	0.37945	0.1022	L	0.50333	1.59	0.42629	D	0.993372	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.69824	0.925;0.966;0.96;0.925	T	0.08351	-1.0726	10	0.51188	T	0.08	-5.7216	12.7765	0.57451	0.0:0.0:1.0:0.0	.	344;354;279;344	A8K7G2;O43464-3;O43464-2;O43464	.;.;.;HTRA2_HUMAN	H	344;279;341	ENSP00000258080:R344H;ENSP00000312893:R279H;ENSP00000399166:R341H	ENSP00000258080:R344H	R	+	2	0	HTRA2	74612323	1.000000	0.71417	0.999000	0.59377	0.833000	0.47200	5.265000	0.65519	2.375000	0.81037	0.455000	0.32223	CGT		0.527	HTRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252219.2	NM_013247	
SEMA4F	10505	broad.mit.edu	37	2	74907197	74907197	+	Missense_Mutation	SNP	G	G	A	rs373277680		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:74907197G>A	ENST00000357877.2	+	14	2323	c.2174G>A	c.(2173-2175)cGg>cAg	p.R725Q	SEMA4F_ENST00000339773.5_Missense_Mutation_p.R570Q	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	725					axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)	p.R725Q(1)		biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						GAAGATGAGCGGTTGCCGCTG	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17528	0.0		0.0	False		,,,				2504	0.0				p.R725Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2174A	2						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	55.0	57.0	56.0		2174	5.4	1.0	2		56	0,8600		0,0,4300	no	missense	SEMA4F	NM_004263.3	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	725/771	74907197	1,13005	2203	4300	6503	74760705	SO:0001583	missense	10505	exon14			AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"""Semaphorins"""	10734	protein-coding gene	gene with protein product	"""m-Sema M"""	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.2174G>A	2.37:g.74907197G>A	ENSP00000350547:p.Arg725Gln	Somatic		Capture	Illumina HiSeq	Phase_I	74760705	NM_004263	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	37	CCDS1955.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.800227	0.50208	2.27E-4	0.0	ENSG00000135622	ENST00000357877;ENST00000339773	T;T	0.23754	2.09;1.89	5.38	5.38	0.77491	.	0.419756	0.20028	N	0.100761	T	0.30947	0.0781	N	0.08118	0	0.34854	D	0.741976	D;D	0.71674	0.998;0.997	D;D	0.75484	0.986;0.968	T	0.47394	-0.9121	10	0.48119	T	0.1	.	14.6234	0.68602	0.0:0.0:1.0:0.0	.	570;725	O95754-2;O95754	.;SEM4F_HUMAN	Q	725;570	ENSP00000350547:R725Q;ENSP00000342675:R570Q	ENSP00000342675:R570Q	R	+	2	0	SEMA4F	74760705	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	3.773000	0.55333	2.526000	0.85167	0.467000	0.42956	CGG		0.617	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263	
HK2	3099	broad.mit.edu	37	2	75101436	75101436	+	Silent	SNP	C	C	T	rs373457354		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:75101436C>T	ENST00000290573.2	+	7	1335	c.735C>T	c.(733-735)atC>atT	p.I245I	HK2_ENST00000409174.1_Silent_p.I217I	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	245	Hexokinase type-2 1.|Regulatory.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)	p.I245I(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						TGCGCCACATCGACATGGTGG	0.607																																					p.I245I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C735T	2						.	C		0,4406		0,0,2203	62.0	60.0	61.0		735	-3.3	1.0	2		61	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	HK2	NM_000189.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		245/918	75101436	1,13005	2203	4300	6503	74954944	SO:0001819	synonymous_variant	3099	exon7				CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.735C>T	2.37:g.75101436C>T		Somatic		Capture	Illumina HiSeq	Phase_I	74954944	NM_000189	D6W5J2|Q8WU87|Q9UN82	Silent	SNP	ENST00000290573.2	37	CCDS1956.1																																																																																				0.607	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
CTNNA2	1496	broad.mit.edu	37	2	80808942	80808942	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:80808942C>T	ENST00000402739.4	+	13	2010	c.2005C>T	c.(2005-2007)Cgg>Tgg	p.R669W	CTNNA2_ENST00000541047.1_Missense_Mutation_p.R669W|CTNNA2_ENST00000361291.4_Missense_Mutation_p.R703W|CTNNA2_ENST00000343114.3_Missense_Mutation_p.R348W|CTNNA2_ENST00000496558.1_Missense_Mutation_p.R669W|AC008067.2_ENST00000596887.1_RNA|CTNNA2_ENST00000466387.1_Missense_Mutation_p.R669W|CTNNA2_ENST00000540488.1_Missense_Mutation_p.R669W|AC008067.2_ENST00000609950.1_RNA|AC008067.2_ENST00000430876.1_RNA	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	669					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)	p.R669W(1)		breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						GCAGAGCGCACGGGTGAGTGG	0.493																																					p.R670W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2008T	2						.						84.0	88.0	86.0					2																	80808942		2099	4207	6306	80662453	SO:0001583	missense	1496	exon14				CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.2005C>T	2.37:g.80808942C>T	ENSP00000384638:p.Arg669Trp	Somatic		Capture	Illumina HiSeq	Phase_I	80662453	NM_004389	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	37		.	.	.	.	.	.	.	.	.	.	C	21.6	4.173540	0.78452	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488;ENST00000343114	T;T;T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1;1.1;1.1	5.7	1.31	0.21738	.	0.000000	0.85682	D	0.000000	T	0.66237	0.2769	M	0.87097	2.86	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;1.0;0.999;0.999	D;D;D;D	0.76071	0.984;0.987;0.963;0.978	T	0.73770	-0.3878	9	.	.	.	.	14.5346	0.67950	0.6434:0.3566:0.0:0.0	.	301;669;669;669	F6KRI5;P26232;P26232-3;P26232-2	.;CTNA2_HUMAN;.;.	W	669;669;703;669;669;669;348	ENSP00000418191:R669W;ENSP00000419295:R669W;ENSP00000355398:R703W;ENSP00000384638:R669W;ENSP00000444675:R669W;ENSP00000441705:R669W;ENSP00000341500:R348W	.	R	+	1	2	CTNNA2	80662453	0.492000	0.26027	1.000000	0.80357	0.988000	0.76386	1.171000	0.31896	0.680000	0.31366	0.650000	0.86243	CGG		0.493	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
ATOH8	84913	broad.mit.edu	37	2	85991288	85991288	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:85991288C>T	ENST00000306279.3	+	2	1239	c.943C>T	c.(943-945)Cgt>Tgt	p.R315C	ATOH8_ENST00000463422.1_3'UTR	NM_032827.6	NP_116216.2	Q96SQ7	ATOH8_HUMAN	atonal homolog 8 (Drosophila)	315					cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R315C(1)		cervix(1)|endometrium(1)|large_intestine(1)|lung(2)	5						GGCCGAGGGACGTGCCAAGAA	0.657																																					p.R315C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C943T	2						.						55.0	51.0	52.0					2																	85991288		2203	4300	6503	85844799	SO:0001583	missense	84913	exon2			AK074681	CCDS1985.1	2p11.2	2013-05-21			ENSG00000168874	ENSG00000168874		"""Basic helix-loop-helix proteins"""	24126	protein-coding gene	gene with protein product	"""basic helix loop helix transcription factor 6"""					12419857	Standard	NM_032827		Approved	HATH6, FLJ14708, bHLHa21	uc002sqn.3	Q96SQ7	OTTHUMG00000130178	ENST00000306279.3:c.943C>T	2.37:g.85991288C>T	ENSP00000304676:p.Arg315Cys	Somatic		Capture	Illumina HiSeq	Phase_I	85844799	NM_032827	Q504S2|Q659B0	Missense_Mutation	SNP	ENST00000306279.3	37	CCDS1985.1	.	.	.	.	.	.	.	.	.	.	C	17.32	3.360558	0.61403	.	.	ENSG00000168874	ENST00000306279	D	0.95949	-3.86	5.02	4.02	0.46733	Helix-loop-helix DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.95956	0.8683	L	0.46157	1.445	0.49051	D	0.999741	D;D	0.89917	1.0;1.0	D;D	0.77557	0.976;0.99	D	0.95373	0.8466	10	0.87932	D	0	-2.493	10.3354	0.43847	0.3783:0.6217:0.0:0.0	.	315;315	Q96SQ7;Q96SQ7-2	ATOH8_HUMAN;.	C	315	ENSP00000304676:R315C	ENSP00000304676:R315C	R	+	1	0	ATOH8	85844799	0.920000	0.31207	0.593000	0.28771	0.981000	0.71138	1.935000	0.40173	2.510000	0.84645	0.655000	0.94253	CGT		0.657	ATOH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252496.1	NM_032827	
KDM3A	55818	broad.mit.edu	37	2	86697389	86697389	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:86697389G>A	ENST00000409556.1	+	12	1947	c.1582G>A	c.(1582-1584)Gag>Aag	p.E528K	KDM3A_ENST00000409064.1_Missense_Mutation_p.E528K|KDM3A_ENST00000312912.5_Missense_Mutation_p.E528K|KDM3A_ENST00000542128.1_Missense_Mutation_p.E476K|KDM3A_ENST00000485171.1_3'UTR			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	528					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.E528K(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						ACAGAGTGGCGAGGCCTTCGT	0.488																																					p.E528K	NSCLC(96;1150 1523 6936 46253 49736)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1582A	2						.						120.0	108.0	112.0					2																	86697389		2203	4300	6503	86550900	SO:0001583	missense	55818	exon11			AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"""Chromatin-modifying enzymes / K-demethylases"""	20815	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 2A"""	611512	"""jumonji domain containing 1"", ""jumonji domain containing 1A"""	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.1582G>A	2.37:g.86697389G>A	ENSP00000386660:p.Glu528Lys	Somatic		Capture	Illumina HiSeq	Phase_I	86550900	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	37	CCDS1990.1	.	.	.	.	.	.	.	.	.	.	G	36	5.819130	0.96982	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	5.86	5.86	0.93980	.	0.068400	0.64402	D	0.000012	T	0.68403	0.2997	M	0.75777	2.31	0.58432	D	0.999996	D;D	0.65815	0.994;0.995	P;P	0.61874	0.895;0.838	T	0.69472	-0.5136	10	0.62326	D	0.03	.	19.1654	0.93555	0.0:0.0:1.0:0.0	.	476;528	F5H070;Q9Y4C1	.;KDM3A_HUMAN	K	528;528;528;528;476	ENSP00000386660:E528K;ENSP00000323659:E528K;ENSP00000386516:E528K;ENSP00000438324:E476K	ENSP00000323659:E528K	E	+	1	0	KDM3A	86550900	1.000000	0.71417	0.970000	0.41538	0.987000	0.75469	9.845000	0.99498	2.778000	0.95560	0.655000	0.94253	GAG		0.488	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433	
PROM2	150696	broad.mit.edu	37	2	95945719	95945719	+	Silent	SNP	C	C	T	rs140258551		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:95945719C>T	ENST00000317620.9	+	11	1534	c.1401C>T	c.(1399-1401)ggC>ggT	p.G467G	PROM2_ENST00000403131.2_Silent_p.G467G|PROM2_ENST00000542147.1_Silent_p.G467G|PROM2_ENST00000317668.4_Silent_p.G467G	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	467					negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)	p.G467G(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						AAGCCAAGGGCGAGGCTGGAG	0.627													C|||	1	0.000199681	0.0	0.0	5008	,	,		18303	0.0		0.0	False		,,,				2504	0.001				p.G467G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1401T	2						.	C	,,	1,4405	2.1+/-5.4	0,1,2202	56.0	48.0	51.0		1401,1401,1401	3.5	1.0	2	dbSNP_134	51	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous	PROM2	NM_001165977.1,NM_001165978.1,NM_144707.2	,,	0,7,6496	TT,TC,CC		0.0698,0.0227,0.0538	,,	467/835,467/835,467/835	95945719	7,12999	2203	4300	6503	95309446	SO:0001819	synonymous_variant	150696	exon11			AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.1401C>T	2.37:g.95945719C>T		Somatic		Capture	Illumina HiSeq	Phase_I	95309446	NM_144707	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Silent	SNP	ENST00000317620.9	37	CCDS2012.1																																																																																				0.627	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707	
ASTL	431705	broad.mit.edu	37	2	96799194	96799194	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:96799194C>T	ENST00000342380.2	-	5	424	c.425G>A	c.(424-426)aGa>aAa	p.R142K		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)									p.R142K(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						AATGAAGTCTCTCTGGTCCTG	0.547																																					p.R142K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G425A	2						.						100.0	89.0	93.0					2																	96799194		2203	4300	6503	96162921	SO:0001583	missense	431705	exon5			AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"""sperm acrosomal SLLP1 binding"""	608860	"""astacin-like metalloendopeptidase (M12 family)"""			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.425G>A	2.37:g.96799194C>T	ENSP00000343674:p.Arg142Lys	Somatic		Capture	Illumina HiSeq	Phase_I	96162921	NM_001002036		Missense_Mutation	SNP	ENST00000342380.2	37	CCDS33249.1	.	.	.	.	.	.	.	.	.	.	C	13.80	2.343830	0.41498	.	.	ENSG00000188886	ENST00000342380	T	0.62364	0.03	5.29	0.697	0.18081	Peptidase, metallopeptidase (1);Peptidase M12A, astacin (1);Metallopeptidase, catalytic domain (1);	0.399819	0.21116	N	0.079899	T	0.38134	0.1029	N	0.16166	0.38	0.20638	N	0.999872	B	0.12013	0.005	B	0.12156	0.007	T	0.17319	-1.0373	10	0.23302	T	0.38	-5.7029	7.868	0.29549	0.0:0.5616:0.0:0.4384	.	142	Q6HA08	ASTL_HUMAN	K	142	ENSP00000343674:R142K	ENSP00000343674:R142K	R	-	2	0	ASTL	96162921	0.004000	0.15560	0.998000	0.56505	0.904000	0.53231	-0.263000	0.08670	0.207000	0.20607	-0.151000	0.13558	AGA		0.547	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1		
SNRNP200	23020	broad.mit.edu	37	2	96945252	96945252	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:96945252G>A	ENST00000323853.5	-	36	5147	c.5070C>T	c.(5068-5070)caC>caT	p.H1690H	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1690	Helicase C-terminal 2. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.H1690H(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						GGCGGTTGGCGTGGCCCACCA	0.552																																					p.H1690H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5070T	2						.						87.0	69.0	75.0					2																	96945252		2203	4300	6503	96308979	SO:0001819	synonymous_variant	23020	exon36			AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 200 KD"""	601664	"""activating signal cointegrator 1 complex subunit 3-like 1"", ""retinitis pigmentosa 33 (autosomal dominant)"""	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.5070C>T	2.37:g.96945252G>A		Somatic		Capture	Illumina HiSeq	Phase_I	96308979	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Silent	SNP	ENST00000323853.5	37	CCDS2020.1																																																																																				0.552	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014	
FER1L5	90342	broad.mit.edu	37	2	97365722	97365722	+	RNA	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:97365722G>A	ENST00000457909.1	+	0	4338							A0AVI2	FR1L5_HUMAN	fer-1-like family member 5							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R1639H(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						CTCCTAGAACGCTATGCCAAG	0.532																																					p.R1639H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4916A	2						.						56.0	59.0	58.0					2																	97365722		1943	4145	6088	96729449			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.97365722G>A		Somatic		Capture	Illumina HiSeq	Phase_I	96729449	NM_001113382	Q17RH2|Q6ZU24	Missense_Mutation	SNP	ENST00000457909.1	37		.	.	.	.	.	.	.	.	.	.	G	1.145	-0.648515	0.03506	.	.	ENSG00000214272	ENST00000414152;ENST00000436930;ENST00000397978	.	.	.	5.19	-1.83	0.07833	.	0.521868	0.15985	N	0.235085	T	0.24431	0.0592	L	0.32530	0.975	.	.	.	B;B;B	0.21309	0.032;0.014;0.054	B;B;B	0.14023	0.004;0.003;0.01	T	0.08638	-1.0712	8	0.39692	T	0.17	-11.3483	4.498	0.11848	0.5089:0.0:0.2266:0.2645	.	356;1639;357	B7ZLI3;A0AVI2;A0AVI2-2	.;FR1L5_HUMAN;.	H	1639;1652;357	.	ENSP00000442027:R357H	R	+	2	0	FER1L5	96729449	0.275000	0.24201	0.391000	0.26233	0.193000	0.23685	0.937000	0.28951	-0.355000	0.08199	-0.897000	0.02905	CGC		0.532	FER1L5-001	KNOWN	basic|exp_conf	retained_intron	pseudogene	OTTHUMT00000339030.1	NM_001077400	
REV1	51455	broad.mit.edu	37	2	100021024	100021024	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:100021024G>A	ENST00000258428.3	-	18	3156	c.2928C>T	c.(2926-2928)ggC>ggT	p.G976G	REV1_ENST00000465835.1_5'UTR|RP11-527J8.1_ENST00000608144.1_RNA|REV1_ENST00000393445.3_Silent_p.G975G	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	976					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|error-prone translesion synthesis (GO:0042276)|response to UV (GO:0009411)	nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|deoxycytidyl transferase activity (GO:0017125)|DNA-directed DNA polymerase activity (GO:0003887)|magnesium ion binding (GO:0000287)	p.G976G(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(12)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CTGTATTACAGCCATTTACTG	0.448								Direct reversal of damage																													p.G976G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2928T	2						.						200.0	186.0	191.0					2																	100021024		2203	4300	6503	99387456	SO:0001819	synonymous_variant	51455	exon18			AF206019	CCDS2045.1, CCDS42722.1	2q11.1-q11.2	2012-05-18	2012-05-18	2006-11-07	ENSG00000135945	ENSG00000135945		"""DNA polymerases"""	14060	protein-coding gene	gene with protein product		606134	"""REV1 (yeast homolog)- like"", ""REV1-like (yeast)"", ""REV1 homolog (S. cerevisiae)"""	REV1L		10536157	Standard	XM_005263968		Approved		uc002tad.3	Q9UBZ9	OTTHUMG00000130636	ENST00000258428.3:c.2928C>T	2.37:g.100021024G>A		Somatic		Capture	Illumina HiSeq	Phase_I	99387456	NM_016316	O95941|Q53SI7|Q9C0J4|Q9NUP2	Silent	SNP	ENST00000258428.3	37	CCDS2045.1																																																																																				0.448	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316	
AFF3	3899	broad.mit.edu	37	2	100185330	100185330	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:100185330T>C	ENST00000409236.2	-	17	3078	c.2966A>G	c.(2965-2967)cAt>cGt	p.H989R	AFF3_ENST00000356421.2_Missense_Mutation_p.H1014R|AFF3_ENST00000409579.1_Missense_Mutation_p.H1014R|AFF3_ENST00000317233.4_Missense_Mutation_p.H989R			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	989					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)	p.H1014R(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						ATCTGCTTTATGCTTCATTCG	0.408																																					p.H1014R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3041G	2						.						207.0	188.0	194.0					2																	100185330		2203	4300	6503	99551762	SO:0001583	missense	3899	exon18			U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"""lymphoid nuclear protein related to AF4"""	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.2966A>G	2.37:g.100185330T>C	ENSP00000387207:p.His989Arg	Somatic		Capture	Illumina HiSeq	Phase_I	99551762	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Missense_Mutation	SNP	ENST00000409236.2	37	CCDS42723.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.209723	0.79240	.	.	ENSG00000144218	ENST00000317233;ENST00000356421;ENST00000409579;ENST00000409236;ENST00000445815	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.80476	0.4630	M	0.81682	2.555	0.80722	D	1	D;D	0.89917	0.968;1.0	D;D	0.85130	0.946;0.997	T	0.82450	-0.0451	10	0.59425	D	0.04	.	16.383	0.83481	0.0:0.0:0.0:1.0	.	989;1014	P51826;P51826-2	AFF3_HUMAN;.	R	989;1014;1014;989;31	ENSP00000317421:H989R;ENSP00000348793:H1014R;ENSP00000386834:H1014R;ENSP00000387207:H989R;ENSP00000416685:H31R	ENSP00000317421:H989R	H	-	2	0	AFF3	99551762	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.741000	0.84997	2.326000	0.78906	0.533000	0.62120	CAT		0.408	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285	
AFF3	3899	broad.mit.edu	37	2	100210199	100210199	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:100210199G>A	ENST00000409236.2	-	13	2036	c.1924C>T	c.(1924-1926)Cgc>Tgc	p.R642C	AFF3_ENST00000356421.2_Missense_Mutation_p.R667C|AFF3_ENST00000409579.1_Missense_Mutation_p.R667C|AFF3_ENST00000317233.4_Missense_Mutation_p.R642C			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	642					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)	p.R667C(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						ACGGAGGAGCGCAGCTCCTTG	0.657																																					p.R667C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1999T	2						.						45.0	49.0	48.0					2																	100210199		2203	4300	6503	99576631	SO:0001583	missense	3899	exon14			U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"""lymphoid nuclear protein related to AF4"""	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.1924C>T	2.37:g.100210199G>A	ENSP00000387207:p.Arg642Cys	Somatic		Capture	Illumina HiSeq	Phase_I	99576631	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Missense_Mutation	SNP	ENST00000409236.2	37	CCDS42723.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.493608	0.64186	.	.	ENSG00000144218	ENST00000317233;ENST00000356421;ENST00000409579;ENST00000409236;ENST00000433370;ENST00000444786;ENST00000432288	T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38	4.72	4.72	0.59763	.	0.106321	0.39544	N	0.001335	T	0.81264	0.4786	M	0.76328	2.33	0.47476	D	0.999436	D;D;D	0.89917	1.0;0.998;0.999	D;P;P	0.76071	0.987;0.836;0.881	D	0.84040	0.0364	10	0.87932	D	0	.	16.2199	0.82254	0.0:0.0:1.0:0.0	.	795;642;667	B7Z4I6;P51826;P51826-2	.;AFF3_HUMAN;.	C	642;667;667;642;642;795;667	ENSP00000317421:R642C;ENSP00000348793:R667C;ENSP00000386834:R667C;ENSP00000387207:R642C	ENSP00000317421:R642C	R	-	1	0	AFF3	99576631	.	.	0.981000	0.43875	0.931000	0.56810	.	.	2.345000	0.79718	0.561000	0.74099	CGC		0.657	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285	
RBM45	129831	broad.mit.edu	37	2	178988920	178988920	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:178988920delA	ENST00000286070.5	+	8	1227	c.1135delA	c.(1135-1137)aaafs	p.K381fs		NM_152945.2	NP_694453.2	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	383					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A382fs*7(2)|p.?(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			TCCATCATGCAAAAAAAAAGC	0.353																																					p.K379fs												.	.	3	Deletion - Frameshift(2)|Unknown(1)	large_intestine(2)|skin(1)	c.1135delA	2						.			3,107,4156		0,0,3,40,27,2063	69.0	75.0	73.0			4.7	1.0	2		75	6,163,8085		0,0,6,55,53,4013	no	codingComplex	RBM45	NM_152945.2		0,0,9,95,80,6076	A1A1,A1A2,A1R,A2A2,A2R,RR		2.0475,2.5785,2.2284			178988920	9,270,12241	2203	4300	6503	178697166	SO:0001589	frameshift_variant	129831	exon8			AF526533	CCDS33335.1	2q31.2	2013-02-12			ENSG00000155636	ENSG00000155636		"""RNA binding motif (RRM) containing"""	24468	protein-coding gene	gene with protein product	"""developmentally regulated RNA binding protein 1"""	608888				12220514	Standard	XM_005246287		Approved	DRB1, FLJ44612	uc002ulv.3	Q8IUH3	OTTHUMG00000154202	ENST00000286070.5:c.1135delA	2.37:g.178988920delA	ENSP00000286070:p.Lys381fs	Somatic		Capture	Illumina HiSeq	Phase_I	178697166	NM_152945	Q6NYL0|Q8NFC9	Frame_Shift_Del	DEL	ENST00000286070.5	37	CCDS33335.1																																																																																				0.353	RBM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334375.2	NM_152945	
TTN	7273	broad.mit.edu	37	2	179417024	179417024	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:179417024delT	ENST00000591111.1	-	285	85904	c.85680delA	c.(85678-85680)aaafs	p.K28560fs	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342175.6_Frame_Shift_Del_p.K21328fs|TTN_ENST00000460472.2_Frame_Shift_Del_p.K21136fs|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586831.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.K27633fs|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Frame_Shift_Del_p.K30201fs|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.K21261fs			Q8WZ42	TITIN_HUMAN	titin	28560	Ig-like 132.				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.K21328fs*89(1)|p.K21136fs*89(1)|p.K27631fs*89(1)|p.K21261fs*89(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)			TAACAGTGTATTTTCCTCCAT	0.403																																					p.N21136fs												.	.	4	Deletion - Frameshift(4)	large_intestine(4)	c.63407delA	2						.						104.0	101.0	102.0					2																	179417024		1942	4131	6073	179125270	SO:0001589	frameshift_variant	7273	exon163			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.85680delA	2.37:g.179417024delT	ENSP00000465570:p.Lys28560fs	Somatic		Capture	Illumina HiSeq	Phase_I	179125270	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	Frame_Shift_Del	DEL	ENST00000591111.1	37																																																																																					0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
AOX1	316	broad.mit.edu	37	2	201485924	201485926	+	In_Frame_Del	DEL	CTT	CTT	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	CTT	CTT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:201485924_201485926delCTT	ENST00000374700.2	+	18	2197_2199	c.1956_1958delCTT	c.(1954-1959)tccttc>tcc	p.F653del	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	653					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)	p.F653delF(1)		breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	ACGTCAACTCCTTCTGCTTTTTT	0.409																																					p.652_653del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.1956_1958del	2						.			2,4262		0,2,2130						1.6	0.0			158	1,8253		0,1,4126	no	coding	AOX1	NM_001159.3		0,3,6256	A1A1,A1R,RR		0.0121,0.0469,0.024				3,12515				201194171	SO:0001651	inframe_deletion	316	exon18			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.1956_1958delCTT	2.37:g.201485924_201485926delCTT	ENSP00000363832:p.Phe653del	Somatic		Capture	Illumina HiSeq	Phase_I	201194169	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	In_Frame_Del	DEL	ENST00000374700.2	37	CCDS33360.1																																																																																				0.409	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	
ATG4B	23192	broad.mit.edu	37	2	242594042	242594042	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr2:242594042A>G	ENST00000404914.3	+	5	468	c.365A>G	c.(364-366)tAc>tGc	p.Y122C	ATG4B_ENST00000474739.2_Missense_Mutation_p.Y108C|ATG4B_ENST00000402096.1_Missense_Mutation_p.Y48C|ATG4B_ENST00000405546.3_Missense_Mutation_p.Y122C|ATG4B_ENST00000396411.3_Missense_Mutation_p.Y48C	NM_013325.4|NM_178326.2	NP_037457.3|NP_847896.1	Q9Y4P1	ATG4B_HUMAN	autophagy related 4B, cysteine peptidase	122					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|positive regulation of autophagy (GO:0010508)|positive regulation of protein catabolic process (GO:0045732)|protein transport (GO:0015031)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)	p.Y122C(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		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;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-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;0.0848)		AAGGACAGTTACTACTCCATT	0.527																																					p.Y122C	Melanoma(78;458 1323 6342 12171 39523)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A365G	2						.						52.0	51.0	51.0					2																	242594042		2006	4153	6159	242242715	SO:0001583	missense	23192	exon5			AB023160	CCDS46564.1, CCDS46565.1	2q37.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000168397	ENSG00000168397			20790	protein-coding gene	gene with protein product		611338	"""APG4 autophagy 4 homolog B (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog B (S. cerevisiae)"""	APG4B		12446702	Standard	NM_013325		Approved	Apg4B, KIAA0943, DKFZp586D1822, AUTL1	uc002wbv.3	Q9Y4P1	OTTHUMG00000151514	ENST00000404914.3:c.365A>G	2.37:g.242594042A>G	ENSP00000384259:p.Tyr122Cys	Somatic		Capture	Illumina HiSeq	Phase_I	242242715	NM_013325	B7WNK2|Q53NU4|Q6ZUV8|Q8WYM9|Q96K07|Q96K96|Q96SZ1|Q9Y2F2	Missense_Mutation	SNP	ENST00000404914.3	37	CCDS46564.1	.	.	.	.	.	.	.	.	.	.	A	12.73	2.026270	0.35701	.	.	ENSG00000168397	ENST00000405546;ENST00000337606;ENST00000402096;ENST00000404914;ENST00000419606;ENST00000474739;ENST00000396411;ENST00000425239;ENST00000400771;ENST00000430617;ENST00000429899;ENST00000311517	T;T;T;T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95	5.28	4.13	0.48395	.	0.057292	0.64402	N	0.000001	T	0.21509	0.0518	N	0.10782	0.045	0.58432	D	0.999999	B;B;B;B;B	0.06786	0.001;0.001;0.001;0.0;0.0	B;B;B;B;B	0.11329	0.003;0.006;0.003;0.002;0.002	T	0.04796	-1.0926	10	0.27082	T	0.32	-20.3514	7.2534	0.26162	0.8185:0.0:0.1815:0.0	.	108;239;210;122;48	F5H7P2;B4DZK0;Q9Y4P1-2;Q9Y4P1;Q9Y4P1-4	.;.;.;ATG4B_HUMAN;.	C	122;239;48;122;48;108;48;122;122;48;48;48	ENSP00000383964:Y122C;ENSP00000384661:Y48C;ENSP00000384259:Y122C;ENSP00000400050:Y48C;ENSP00000442378:Y108C;ENSP00000379692:Y48C;ENSP00000409895:Y122C;ENSP00000383582:Y122C;ENSP00000407389:Y48C;ENSP00000410526:Y48C	ENSP00000309348:Y48C	Y	+	2	0	ATG4B	242242715	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	4.041000	0.57339	0.855000	0.35359	0.379000	0.24179	TAC		0.527	ATG4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322967.3	NM_013325	
IRAK2	3656	broad.mit.edu	37	3	10251273	10251273	+	Splice_Site	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:10251273G>T	ENST00000256458.4	+	4	515	c.425G>T	c.(424-426)gGg>gTg	p.G142V		NM_001570.3	NP_001561.3	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	142					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.G142V(2)		breast(4)|large_intestine(8)|lung(11)|prostate(1)|stomach(1)	25						TCCTTTCCAGGGTCCTCTCCA	0.587																																					p.G142V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G425T	3						.						126.0	135.0	132.0					3																	10251273		2203	4300	6503	10226273	SO:0001630	splice_region_variant	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.425-1G>T	3.37:g.10251273G>T		Somatic		Capture	Illumina HiSeq	Phase_I	10226273	NM_001570	B4DQZ6|Q08AG6|Q5K546	Missense_Mutation	SNP	ENST00000256458.4	37	CCDS33697.1	.	.	.	.	.	.	.	.	.	.	G	7.347	0.622145	0.14193	.	.	ENSG00000134070	ENST00000256458	T	0.53423	0.62	4.44	2.18	0.27775	.	0.560796	0.16066	N	0.231241	T	0.22360	0.0539	N	0.08118	0	0.54753	D	0.999989	P	0.42409	0.779	B	0.39299	0.296	T	0.01982	-1.1235	9	.	.	.	.	4.9442	0.13982	0.3184:0.0:0.6816:0.0	.	142	O43187	IRAK2_HUMAN	V	142	ENSP00000256458:G142V	.	G	+	2	0	IRAK2	10226273	0.637000	0.27216	0.771000	0.31576	0.007000	0.05969	0.600000	0.24104	0.998000	0.38996	-0.253000	0.11424	GGG		0.587	IRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339623.1		Missense_Mutation
IRAK2	3656	broad.mit.edu	37	3	10264481	10264481	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:10264481T>G	ENST00000256458.4	+	9	1265	c.1175T>G	c.(1174-1176)cTg>cGg	p.L392R		NM_001570.3	NP_001561.3	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	392	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> V (in dbSNP:rs3844283). {ECO:0000269|PubMed:17344846}.		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.L392R(2)		breast(4)|large_intestine(8)|lung(11)|prostate(1)|stomach(1)	25						GTGGGGCAGCTGACAAAGCGA	0.532																																					p.L392R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1175G	3						.						107.0	105.0	106.0					3																	10264481		2203	4300	6503	10239481	SO:0001583	missense	3656	exon9			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.1175T>G	3.37:g.10264481T>G	ENSP00000256458:p.Leu392Arg	Somatic		Capture	Illumina HiSeq	Phase_I	10239481	NM_001570	B4DQZ6|Q08AG6|Q5K546	Missense_Mutation	SNP	ENST00000256458.4	37	CCDS33697.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.709395	0.68615	.	.	ENSG00000134070	ENST00000256458	T	0.36340	1.26	5.14	5.14	0.70334	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38436	N	0.001683	T	0.69278	0.3093	H	0.95712	3.71	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.78089	-0.2340	10	0.87932	D	0	-15.6131	11.3516	0.49592	0.0:0.0:0.0:1.0	.	392	O43187	IRAK2_HUMAN	R	392	ENSP00000256458:L392R	ENSP00000256458:L392R	L	+	2	0	IRAK2	10239481	1.000000	0.71417	1.000000	0.80357	0.766000	0.43426	2.936000	0.48971	1.919000	0.55581	0.533000	0.62120	CTG		0.532	IRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339623.1		
FILIP1L	11259	broad.mit.edu	37	3	99567698	99567698	+	Missense_Mutation	SNP	G	G	A	rs374858996		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:99567698G>A	ENST00000354552.3	-	5	3292	c.2822C>T	c.(2821-2823)aCg>aTg	p.T941M	FILIP1L_ENST00000476723.1_Intron|CMSS1_ENST00000421999.2_Intron|FILIP1L_ENST00000487087.1_Missense_Mutation_p.T517M|FILIP1L_ENST00000471562.1_Missense_Mutation_p.T701M|FILIP1L_ENST00000383694.2_Missense_Mutation_p.T701M|FILIP1L_ENST00000331335.5_Missense_Mutation_p.T941M|CMSS1_ENST00000496116.1_Intron	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	941						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)		p.T941M(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						TTGCTTTGGCGTGCCACAGTT	0.468													G|||	1	0.000199681	0.0	0.0014	5008	,	,		22932	0.0		0.0	False		,,,				2504	0.0				p.T941M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2822T	3						.	G	MET/THR,MET/THR,,MET/THR	1,4085		0,1,2042	277.0	265.0	269.0		2822,2102,,2822	6.2	1.0	3		269	0,8358		0,0,4179	no	missense,missense,intron,missense	FILIP1L,C3orf26	NM_001042459.1,NM_014890.2,NM_032359.3,NM_182909.2	81,81,,81	0,1,6221	AA,AG,GG		0.0,0.0245,0.0080	probably-damaging,probably-damaging,,probably-damaging	941/1134,701/894,,941/1136	99567698	1,12443	2043	4179	6222	101050388	SO:0001583	missense	11259	exon5				CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"""downregulated in ovarian cancer 1"", ""GPBP-interacting protein of 130 kDa"""	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.2822C>T	3.37:g.99567698G>A	ENSP00000346560:p.Thr941Met	Somatic		Capture	Illumina HiSeq	Phase_I	101050388	NM_182909	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Missense_Mutation	SNP	ENST00000354552.3	37	CCDS43117.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.200706	0.58126	2.45E-4	0.0	ENSG00000168386	ENST00000354552;ENST00000487087;ENST00000471562;ENST00000331335;ENST00000383694;ENST00000441620;ENST00000495625	T;T;T;T;T;T	0.23950	2.2;1.89;1.89;2.2;1.89;1.88	6.17	6.17	0.99709	.	0.000000	0.53938	D	0.000050	T	0.40743	0.1129	L	0.50333	1.59	0.46044	D	0.998838	P;P	0.52170	0.951;0.918	P;P	0.51615	0.675;0.475	T	0.04153	-1.0973	10	0.66056	D	0.02	-5.3347	20.8794	0.99867	0.0:0.0:1.0:0.0	.	941;941	Q4L180-2;Q4L180	.;FIL1L_HUMAN	M	941;517;701;941;701;687;701	ENSP00000346560:T941M;ENSP00000417774:T517M;ENSP00000419642:T701M;ENSP00000327880:T941M;ENSP00000373192:T701M;ENSP00000419874:T701M	ENSP00000327880:T941M	T	-	2	0	FILIP1L	101050388	0.999000	0.42202	1.000000	0.80357	0.977000	0.68977	4.214000	0.58527	2.941000	0.99782	0.655000	0.94253	ACG		0.468	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890	
ATP2B2	491	broad.mit.edu	37	3	10382224	10382224	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:10382224G>A	ENST00000352432.4	-	19	3151	c.3082C>T	c.(3082-3084)Cgg>Tgg	p.R1028W	ATP2B2_ENST00000360273.2_Missense_Mutation_p.R1028W|ATP2B2_ENST00000343816.4_Missense_Mutation_p.R1014W|ATP2B2_ENST00000397077.1_Missense_Mutation_p.R983W|ATP2B2_ENST00000383800.4_Missense_Mutation_p.R983W			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	1028					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)	p.R983W(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						ATGGGGTTCCGGAAGATGCCG	0.587																																					p.R983W	Ovarian(125;1619 1709 15675 19819 38835)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2947T	3						.						179.0	150.0	160.0					3																	10382224		2203	4300	6503	10357224	SO:0001583	missense	491	exon17			X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"""ATPases / P-type"""	815	protein-coding gene	gene with protein product	"""plasma membrane Ca2+ pump 2"", ""plasma membrane calcium-transporting ATPase 2"""	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.3082C>T	3.37:g.10382224G>A	ENSP00000324172:p.Arg1028Trp	Somatic		Capture	Illumina HiSeq	Phase_I	10357224	NM_001683	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	37	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.982202	0.74474	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000429937;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.89617	-2.54;-2.54;-2.54;-2.54;-2.54;-2.54	4.05	3.05	0.35203	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.93795	0.8016	M	0.86953	2.85	0.80722	D	1	D;D;D	0.89917	1.0;0.997;0.998	D;P;D	0.81914	0.995;0.849;0.918	D	0.93690	0.7006	10	0.87932	D	0	-22.9008	9.042	0.36322	0.0:0.0:0.4569:0.543	.	963;995;1028	F5H7F7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	W	1028;983;983;1028;1014;963;217;884;1028	ENSP00000324172:R1028W;ENSP00000373311:R983W;ENSP00000380267:R983W;ENSP00000353414:R1028W;ENSP00000344677:R1014W;ENSP00000414854:R884W	ENSP00000342954:R1028W	R	-	1	2	ATP2B2	10357224	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.020000	0.41010	1.814000	0.52955	0.467000	0.42956	CGG		0.587	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	
SENP7	57337	broad.mit.edu	37	3	101044881	101044881	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:101044881C>A	ENST00000394095.2	-	24	3112	c.3059G>T	c.(3058-3060)tGg>tTg	p.W1020L	SENP7_ENST00000394094.2_Missense_Mutation_p.W955L|SENP7_ENST00000394091.1_Missense_Mutation_p.W856L|SENP7_ENST00000358203.3_Missense_Mutation_p.W856L|SENP7_ENST00000348610.3_Missense_Mutation_p.W987L|SENP7_ENST00000394085.3_Missense_Mutation_p.W208L|SENP7_ENST00000314261.7_Missense_Mutation_p.W954L	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	1020	Protease.					intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.W954L(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						ACGAGGAAACCACTTCTCCAA	0.358																																					p.W1020L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3059T	3						.						108.0	97.0	101.0					3																	101044881		2203	4299	6502	102527571	SO:0001583	missense	57337	exon24				CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"""SUMO1/sentrin specific protease 7"""			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.3059G>T	3.37:g.101044881C>A	ENSP00000377655:p.Trp1020Leu	Somatic		Capture	Illumina HiSeq	Phase_I	102527571	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	.	.	.	.	.	.	.	.	.	.	C	21.8	4.208346	0.79240	.	.	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000394085;ENST00000348610	T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.58047	0.2095	M	0.72894	2.215	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;0.999;0.999;1.0;1.0	T	0.60209	-0.7308	10	0.87932	D	0	-4.8194	19.5547	0.95338	0.0:1.0:0.0:0.0	.	856;954;987;1020;208	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6;Q9BQF6-3	.;.;.;SENP7_HUMAN;.	L	1020;955;954;856;856;208;987	ENSP00000377655:W1020L;ENSP00000377654:W955L;ENSP00000313624:W954L;ENSP00000377651:W856L;ENSP00000350936:W856L;ENSP00000377647:W208L;ENSP00000342159:W987L	ENSP00000313624:W954L	W	-	2	0	SENP7	102527571	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.877000	0.75562	2.694000	0.91930	0.585000	0.79938	TGG		0.358	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
BBX	56987	broad.mit.edu	37	3	107497349	107497349	+	Missense_Mutation	SNP	C	C	T	rs150437555		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:107497349C>T	ENST00000325805.8	+	13	2473	c.2186C>T	c.(2185-2187)cCg>cTg	p.P729L	BBX_ENST00000402543.1_Missense_Mutation_p.P729L|BBX_ENST00000406780.1_Missense_Mutation_p.P729L|BBX_ENST00000473542.1_3'UTR|BBX_ENST00000416476.2_Nonsense_Mutation_p.R393*|BBX_ENST00000415149.2_Missense_Mutation_p.P729L			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	729	Lys-rich.				bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P729L(1)		breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			TCCTCAGAACCGACTAAAACC	0.443													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18410	0.0		0.0	False		,,,				2504	0.0				p.P729L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2186T	3						.	C	LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	95.0	89.0	91.0		2186,2186	1.8	0.3	3	dbSNP_134	91	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	BBX	NM_001142568.1,NM_020235.5	98,98	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign,benign	729/942,729/912	107497349	2,13004	2203	4300	6503	108980039	SO:0001583	missense	56987	exon13			AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"""x 001 protein"""					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.2186C>T	3.37:g.107497349C>T	ENSP00000319974:p.Pro729Leu	Somatic		Capture	Illumina HiSeq	Phase_I	108980039	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Nonsense_Mutation	SNP	ENST00000325805.8	37	CCDS46881.1	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	C|C	40|40	8.400016|8.400016	0.98794|0.98794	2.27E-4|2.27E-4	1.16E-4|1.16E-4	ENSG00000114439|ENSG00000114439	ENST00000415149;ENST00000402543;ENST00000325805;ENST00000406780|ENST00000416476	T;T;T;T|.	0.28666|.	1.64;1.64;1.6;1.64|.	5.92|5.92	1.8|1.8	0.24995|0.24995	.|.	0.740851|.	0.13847|.	N|.	0.358611|.	T|.	0.13628|.	0.0330|.	N|N	0.08118|0.08118	0|0	0.20196|0.20196	N|N	0.999929|0.999929	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.001;0.0|.	T|.	0.31724|.	-0.9933|.	10|.	0.46703|0.02654	T|T	0.11|1	2.4732|2.4732	5.7634|5.7634	0.18213|0.18213	0.1821:0.5139:0.0:0.304|0.1821:0.5139:0.0:0.304	.|.	729;729|.	Q8WY36;Q8WY36-2|.	BBX_HUMAN;.|.	L|X	729|393	ENSP00000408358:P729L;ENSP00000385317:P729L;ENSP00000319974:P729L;ENSP00000385530:P729L|.	ENSP00000319974:P729L|ENSP00000403860:R393X	P|R	+|+	2|1	0|2	BBX|BBX	108980039|108980039	0.971000|0.971000	0.33674|0.33674	0.295000|0.295000	0.24960|0.24960	0.832000|0.832000	0.47134|0.47134	1.807000|1.807000	0.38902|0.38902	0.417000|0.417000	0.25871|0.25871	0.650000|0.650000	0.86243|0.86243	CCG|CGA		0.443	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235	
MYH15	22989	broad.mit.edu	37	3	108178209	108178209	+	Splice_Site	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:108178209C>A	ENST00000273353.3	-	19	2136	c.2080G>T	c.(2080-2082)Ggt>Tgt	p.G694C	MYH15_ENST00000495753.2_5'UTR	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	694	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.G694C(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TAGTTCTTACCTGGTATTTTG	0.289																																					p.G694C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2080T	3						.						104.0	95.0	98.0					3																	108178209		1808	4070	5878	109660899	SO:0001630	splice_region_variant	22989	exon19			AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.2080+1G>T	3.37:g.108178209C>A		Somatic		Capture	Illumina HiSeq	Phase_I	109660899	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.558651	0.65538	.	.	ENSG00000144821	ENST00000273353	D	0.88124	-2.34	5.76	4.88	0.63580	Myosin head, motor domain (2);	.	.	.	.	D	0.96204	0.8762	H	0.98594	4.275	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97755	1.0217	8	.	.	.	.	15.256	0.73585	0.0:0.9318:0.0:0.0682	.	694	Q9Y2K3	MYH15_HUMAN	C	694	ENSP00000273353:G694C	.	G	-	1	0	MYH15	109660899	1.000000	0.71417	0.923000	0.36655	0.453000	0.32348	3.969000	0.56816	1.407000	0.46875	0.655000	0.94253	GGT		0.289	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	Missense_Mutation
ATG7	10533	broad.mit.edu	37	3	11389359	11389359	+	Silent	SNP	C	C	T	rs572456428		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:11389359C>T	ENST00000354449.3	+	12	1159	c.1134C>T	c.(1132-1134)ggC>ggT	p.G378G	ATG7_ENST00000446450.2_Silent_p.G339G|ATG7_ENST00000354956.5_Silent_p.G378G	NM_006395.2	NP_006386.1	O95352	ATG7_HUMAN	autophagy related 7	378					adult walking behavior (GO:0007628)|C-terminal protein lipidation (GO:0006501)|cardiac muscle cell development (GO:0055013)|cellular amino acid metabolic process (GO:0006520)|cellular protein modification process (GO:0006464)|cellular response to hyperoxia (GO:0071455)|cellular response to nitrogen starvation (GO:0006995)|cellular response to starvation (GO:0009267)|central nervous system neuron axonogenesis (GO:0021955)|cerebellar Purkinje cell layer development (GO:0021680)|cerebral cortex development (GO:0021987)|late nucleophagy (GO:0044805)|liver development (GO:0001889)|membrane fusion (GO:0061025)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of apoptotic process (GO:0043066)|negative stranded viral RNA replication (GO:0039689)|neurological system process (GO:0050877)|piecemeal microautophagy of nucleus (GO:0034727)|positive regulation of apoptotic process (GO:0043065)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein modification process (GO:0031401)|post-embryonic development (GO:0009791)|protein catabolic process (GO:0030163)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)|pyramidal neuron development (GO:0021860)|regulation of protein ubiquitination (GO:0031396)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)	Atg12 activating enzyme activity (GO:0019778)|Atg8 activating enzyme (GO:0019779)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)|ubiquitin activating enzyme activity (GO:0004839)	p.G378G(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(14)|prostate(1)|skin(2)|urinary_tract(1)	34						AGGGTTGGGGCGTGAGACACA	0.463													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18282	0.0		0.0	False		,,,				2504	0.0				p.G378G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1134T	3						.						95.0	84.0	88.0					3																	11389359		2203	4300	6503	11364359	SO:0001819	synonymous_variant	10533	exon12			AF094516	CCDS2605.1, CCDS46752.1, CCDS46753.1	3p25.3-p25.2	2014-02-18	2012-06-06	2005-09-11	ENSG00000197548	ENSG00000197548		"""Ubiquitin-like modifier activating enzymes"""	16935	protein-coding gene	gene with protein product	"""ubiquitin-activating enzyme E1-like protein"""	608760	"""APG7 autophagy 7-like (S. cerevisiae)"", ""ATG7 autophagy related 7 homolog (S. cerevisiae)"""	APG7L		10233149	Standard	NM_006395		Approved	GSA7, DKFZp434N0735	uc003bwc.3	O95352	OTTHUMG00000129740	ENST00000354449.3:c.1134C>T	3.37:g.11389359C>T		Somatic		Capture	Illumina HiSeq	Phase_I	11364359	NM_006395	B4E170|E9PB95|Q7L8L0|Q9BWP2|Q9UFH4	Silent	SNP	ENST00000354449.3	37	CCDS2605.1																																																																																				0.463	ATG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251951.3	NM_006395	
ABHD10	55347	broad.mit.edu	37	3	111710363	111710363	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:111710363G>A	ENST00000273359.3	+	5	743	c.716G>A	c.(715-717)tGc>tAc	p.C239Y	ABHD10_ENST00000534857.1_Missense_Mutation_p.C82Y|ABHD10_ENST00000494817.1_3'UTR	NM_018394.2	NP_060864.1	Q9NUJ1	ABHDA_HUMAN	abhydrolase domain containing 10	239					glucuronoside catabolic process (GO:0019391)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.C239Y(1)		large_intestine(2)|lung(7)|skin(1)	10						CCTGTGAACTGCCCCATAAGA	0.428																																					p.C239Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G716A	3						.						204.0	181.0	189.0					3																	111710363		2203	4300	6503	113193053	SO:0001583	missense	55347	exon5			AL713726	CCDS2963.1, CCDS63718.1	3q13.2	2012-03-26			ENSG00000144827	ENSG00000144827		"""Abhydrolase domain containing"""	25656	protein-coding gene	gene with protein product						22294686	Standard	NM_018394		Approved	FLJ11342	uc003dyk.5	Q9NUJ1	OTTHUMG00000159280	ENST00000273359.3:c.716G>A	3.37:g.111710363G>A	ENSP00000273359:p.Cys239Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	113193053	NM_018394	B7Z6A8|C9IZX5|D3DN63|Q8TCF9	Missense_Mutation	SNP	ENST00000273359.3	37	CCDS2963.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.411571	0.83340	.	.	ENSG00000144827	ENST00000534857;ENST00000273359	T;T	0.47869	0.83;0.83	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.71484	0.3345	M	0.87971	2.92	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.68191	-0.5474	10	0.12766	T	0.61	-26.6451	18.5911	0.91212	0.0:0.0:1.0:0.0	.	239	Q9NUJ1	ABHDA_HUMAN	Y	82;239	ENSP00000442932:C82Y;ENSP00000273359:C239Y	ENSP00000273359:C239Y	C	+	2	0	ABHD10	113193053	1.000000	0.71417	0.987000	0.45799	0.826000	0.46750	9.392000	0.97252	2.771000	0.95319	0.591000	0.81541	TGC		0.428	ABHD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354326.1	NM_018394	
BOC	91653	broad.mit.edu	37	3	112969450	112969450	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:112969450C>T	ENST00000495514.1	+	4	850	c.146C>T	c.(145-147)cCc>cTc	p.P49L	BOC_ENST00000485230.1_Missense_Mutation_p.P49L|BOC_ENST00000355385.3_Missense_Mutation_p.P49L|BOC_ENST00000484034.1_Missense_Mutation_p.P49L|BOC_ENST00000273395.4_Missense_Mutation_p.P49L			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	49	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.P49L(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			GTCCAGAAGCCCGGAGGCACT	0.572																																					p.P49L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C146T	3						.						120.0	114.0	116.0					3																	112969450		2203	4300	6503	114452140	SO:0001583	missense	91653	exon4			AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.146C>T	3.37:g.112969450C>T	ENSP00000418663:p.Pro49Leu	Somatic		Capture	Illumina HiSeq	Phase_I	114452140	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	37	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	c	10.23	1.293253	0.23564	.	.	ENSG00000144857	ENST00000464546;ENST00000495514;ENST00000485230;ENST00000273395;ENST00000355385;ENST00000484034	T;T;T;T;T;T	0.75589	-0.95;2.74;2.74;2.74;2.74;2.74	5.78	3.32	0.38043	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.347112	0.26828	N	0.022293	T	0.42562	0.1208	N	0.04669	-0.19	0.28638	N	0.907302	B;B;B;B	0.10296	0.0;0.0;0.0;0.003	B;B;B;B	0.14023	0.0;0.001;0.002;0.01	T	0.37842	-0.9688	10	0.02654	T	1	.	4.6933	0.12791	0.2478:0.1731:0.0:0.5791	.	49;49;49;49	C9J2L7;Q9BWV1-3;Q9BWV1;Q96DN7	.;.;BOC_HUMAN;.	L	49	ENSP00000417362:P49L;ENSP00000418663:P49L;ENSP00000420154:P49L;ENSP00000273395:P49L;ENSP00000347546:P49L;ENSP00000417337:P49L	ENSP00000273395:P49L	P	+	2	0	BOC	114452140	0.066000	0.20996	0.843000	0.33291	0.958000	0.62258	0.441000	0.21611	1.026000	0.39733	-0.310000	0.09108	CCC		0.572	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
BOC	91653	broad.mit.edu	37	3	112991542	112991542	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:112991542A>G	ENST00000495514.1	+	7	1657	c.953A>G	c.(952-954)cAg>cGg	p.Q318R	BOC_ENST00000355385.3_Missense_Mutation_p.Q318R|BOC_ENST00000273395.4_Missense_Mutation_p.Q318R			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	318					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.Q318R(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TACAATGTCCAGGTGTTTGGT	0.572																																					p.Q318R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A953G	3						.						126.0	108.0	114.0					3																	112991542		2203	4300	6503	114474232	SO:0001583	missense	91653	exon7			AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.953A>G	3.37:g.112991542A>G	ENSP00000418663:p.Gln318Arg	Somatic		Capture	Illumina HiSeq	Phase_I	114474232	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	37	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	A	14.35	2.510054	0.44660	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	T;T;T	0.28666	1.6;1.6;1.6	5.92	5.92	0.95590	.	0.056942	0.64402	D	0.000001	T	0.28797	0.0714	L	0.41906	1.305	0.50632	D	0.999887	B;B	0.28783	0.108;0.222	B;B	0.32805	0.153;0.117	T	0.06006	-1.0851	10	0.16420	T	0.52	.	16.3636	0.83296	1.0:0.0:0.0:0.0	.	318;318	Q9BWV1-3;Q9BWV1	.;BOC_HUMAN	R	318	ENSP00000418663:Q318R;ENSP00000273395:Q318R;ENSP00000347546:Q318R	ENSP00000273395:Q318R	Q	+	2	0	BOC	114474232	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	8.829000	0.92055	2.267000	0.75376	0.528000	0.53228	CAG		0.572	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
SIDT1	54847	broad.mit.edu	37	3	113342523	113342523	+	Silent	SNP	C	C	T	rs142301843	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:113342523C>T	ENST00000264852.4	+	23	2976	c.2250C>T	c.(2248-2250)acC>acT	p.T750T	SIDT1_ENST00000393830.3_Silent_p.T755T|SIDT1_ENST00000463226.1_3'UTR	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	750					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)	p.T750T(2)		breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						TCGTGGCCACCGCTGTGATGT	0.572																																					p.T750T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2250T	3						.	C		0,4406		0,0,2203	102.0	104.0	103.0		2250	-9.4	0.7	3	dbSNP_134	103	3,8597	3.7+/-12.6	0,3,4297	no	coding-synonymous	SIDT1	NM_017699.2		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		750/828	113342523	3,13003	2203	4300	6503	114825213	SO:0001819	synonymous_variant	54847	exon23			AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.2250C>T	3.37:g.113342523C>T		Somatic		Capture	Illumina HiSeq	Phase_I	114825213	NM_017699	Q17RR4	Silent	SNP	ENST00000264852.4	37	CCDS2974.1																																																																																				0.572	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699	
KIAA2018	205717	broad.mit.edu	37	3	113374414	113374414	+	Missense_Mutation	SNP	G	G	A	rs369738835		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:113374414G>A	ENST00000478658.1	-	5	6132	c.6115C>T	c.(6115-6117)Cgt>Tgt	p.R2039C	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Missense_Mutation_p.R2039C			Q68DE3	K2018_HUMAN	KIAA2018	2039						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.R2039C(1)		NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						GGCATGAAACGAACAATACTT	0.433																																					p.R2039C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6115T	3						.	G	CYS/ARG	1,3867		0,1,1933	91.0	90.0	90.0		6115	5.8	1.0	3		90	1,8267		0,1,4133	no	missense	KIAA2018	NM_001009899.2	180	0,2,6066	AA,AG,GG		0.0121,0.0259,0.0165	probably-damaging	2039/2246	113374414	2,12134	1934	4134	6068	114857104	SO:0001583	missense	205717	exon7			AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.6115C>T	3.37:g.113374414G>A	ENSP00000420721:p.Arg2039Cys	Somatic		Capture	Illumina HiSeq	Phase_I	114857104	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	37	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.249862	0.59212	2.59E-4	1.21E-4	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.35236	1.32;1.32	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.51295	0.1666	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.50381	-0.8835	10	0.87932	D	0	-11.1053	15.6492	0.77078	0.0:0.0:0.8623:0.1377	.	2039	Q68DE3	K2018_HUMAN	C	2039	ENSP00000320794:R2039C;ENSP00000420721:R2039C	ENSP00000320794:R2039C	R	-	1	0	KIAA2018	114857104	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.208000	0.77907	2.758000	0.94735	0.563000	0.77884	CGT		0.433	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
KIAA2018	205717	broad.mit.edu	37	3	113375294	113375294	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:113375294C>A	ENST00000478658.1	-	5	5252	c.5235G>T	c.(5233-5235)caG>caT	p.Q1745H	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Missense_Mutation_p.Q1745H			Q68DE3	K2018_HUMAN	KIAA2018	1745						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.Q1745H(1)		NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						TACTCTGGGGCTGTTGACTAG	0.433																																					p.Q1745H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5235T	3						.						107.0	102.0	103.0					3																	113375294		1856	4112	5968	114857984	SO:0001583	missense	205717	exon7			AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.5235G>T	3.37:g.113375294C>A	ENSP00000420721:p.Gln1745His	Somatic		Capture	Illumina HiSeq	Phase_I	114857984	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	37	CCDS43133.1	.	.	.	.	.	.	.	.	.	.	C	6.190	0.403169	0.11754	.	.	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.16073	2.37;2.37	5.49	3.69	0.42338	.	0.194131	0.45606	D	0.000349	T	0.09468	0.0233	N	0.12746	0.255	0.50313	D	0.999863	B	0.17465	0.022	B	0.11329	0.006	T	0.16482	-1.0401	10	0.33940	T	0.23	-1.9502	9.9143	0.41425	0.0:0.7627:0.0:0.2373	.	1745	Q68DE3	K2018_HUMAN	H	1745	ENSP00000320794:Q1745H;ENSP00000420721:Q1745H	ENSP00000320794:Q1745H	Q	-	3	2	KIAA2018	114857984	0.998000	0.40836	0.996000	0.52242	0.983000	0.72400	0.520000	0.22878	0.681000	0.31386	0.655000	0.94253	CAG		0.433	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
ZNF80	7634	broad.mit.edu	37	3	113955601	113955601	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:113955601G>A	ENST00000482457.2	-	1	824	c.321C>T	c.(319-321)tgC>tgT	p.C107C	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	107					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.C107C(1)		NS(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				CGCACTCCACGCACTTACAGG	0.542																																					p.C107C	GBM(23;986 1114 21716)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C321T	3						.						59.0	52.0	55.0					3																	113955601		2203	4300	6503	115438291	SO:0001819	synonymous_variant	7634	exon1			X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"""Zinc fingers, C2H2-type"""	13155	protein-coding gene	gene with protein product		194553	"""zinc finger protein 80 (pT17)"""			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.321C>T	3.37:g.113955601G>A		Somatic		Capture	Illumina HiSeq	Phase_I	115438291	NM_007136	Q6NSW4|Q6NT14	Silent	SNP	ENST00000482457.2	37	CCDS2979.1																																																																																				0.542	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136	
LSAMP	4045	broad.mit.edu	37	3	115560703	115560703	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:115560703A>G	ENST00000490035.2	-	6	1407	c.908T>C	c.(907-909)cTa>cCa	p.L303P	LSAMP_ENST00000539563.1_Missense_Mutation_p.L300P|LSAMP_ENST00000498645.1_5'Flank	NM_002338.3	NP_002329.2	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein	303	Ig-like C2-type 3.				cell adhesion (GO:0007155)|locomotory exploration behavior (GO:0035641)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.L303P(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(1)|large_intestine(4)|lung(14)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	31		all_cancers(1;0.00189)|all_epithelial(1;0.0366)|Myeloproliferative disorder(1037;0.17)|all_neural(597;0.208)|Lung NSC(201;0.215)		GBM - Glioblastoma multiforme(114;0.00117)|LUSC - Lung squamous cell carcinoma(41;0.0407)|Lung(219;0.152)		GAAAAGGACTAGGCTGGCATT	0.483																																					p.L303P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T908C	3						.						95.0	82.0	86.0					3																	115560703		2203	4300	6503	117043393	SO:0001583	missense	4045	exon6			U41901	CCDS2982.1	3q13.2-q21	2013-01-11			ENSG00000185565	ENSG00000185565		"""Immunoglobulin superfamily / I-set domain containing"""	6705	protein-coding gene	gene with protein product	"""IgLON family member 3"""	603241				9615236	Standard	NM_002338		Approved	LAMP, IGLON3	uc003ebs.3	Q13449	OTTHUMG00000159308	ENST00000490035.2:c.908T>C	3.37:g.115560703A>G	ENSP00000419000:p.Leu303Pro	Somatic		Capture	Illumina HiSeq	Phase_I	117043393	NM_002338	Q8IV49	Missense_Mutation	SNP	ENST00000490035.2	37	CCDS2982.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.505952	0.85282	.	.	ENSG00000185565	ENST00000333617;ENST00000490035;ENST00000539563	T;T;T	0.70164	-0.46;-0.46;-0.46	6.08	6.08	0.98989	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.133817	0.51477	D	0.000093	D	0.82747	0.5104	M	0.81112	2.525	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.75020	0.985;0.979	D	0.85005	0.0902	10	0.87932	D	0	-4.8311	16.6438	0.85155	1.0:0.0:0.0:0.0	.	303;303	B2RCU8;Q13449	.;LSAMP_HUMAN	P	287;303;300	ENSP00000328455:L287P;ENSP00000419000:L303P;ENSP00000443429:L300P	ENSP00000328455:L287P	L	-	2	0	LSAMP	117043393	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.962000	0.93254	2.333000	0.79357	0.533000	0.62120	CTA		0.483	LSAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354495.4	NM_002338	
PLA1A	51365	broad.mit.edu	37	3	119347667	119347667	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:119347667C>T	ENST00000273371.4	+	10	1313	c.1241C>T	c.(1240-1242)aCc>aTc	p.T414I	PLA1A_ENST00000495992.1_Missense_Mutation_p.T398I|PLA1A_ENST00000488919.1_Missense_Mutation_p.T241I|PLA1A_ENST00000494440.1_Missense_Mutation_p.T398I	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	414	Involved in the recognition of diacyl- phospholipids.				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.T414I(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						GACCGGACTACCATTATTGGG	0.473																																					p.T414I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1241T	3						.						129.0	126.0	127.0					3																	119347667		2203	4300	6503	120830357	SO:0001583	missense	51365	exon10			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.1241C>T	3.37:g.119347667C>T	ENSP00000273371:p.Thr414Ile	Somatic		Capture	Illumina HiSeq	Phase_I	120830357	NM_015900	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Missense_Mutation	SNP	ENST00000273371.4	37	CCDS2991.1	.	.	.	.	.	.	.	.	.	.	C	1.977	-0.435175	0.04669	.	.	ENSG00000144837	ENST00000273371;ENST00000488919;ENST00000495992;ENST00000494440	D;D;D;D	0.93189	-2.59;-3.18;-2.58;-2.69	5.39	2.66	0.31614	.	0.540522	0.20812	N	0.085238	D	0.84893	0.5573	N	0.17082	0.46	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.71052	-0.4704	10	0.27785	T	0.31	-5.1826	8.71	0.34378	0.0:0.7588:0.0:0.2412	.	398;414	Q53H76-3;Q53H76	.;PLA1A_HUMAN	I	414;241;398;398	ENSP00000273371:T414I;ENSP00000420625:T241I;ENSP00000417326:T398I;ENSP00000418793:T398I	ENSP00000273371:T414I	T	+	2	0	PLA1A	120830357	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.255000	0.08769	0.275000	0.22094	-0.258000	0.10820	ACC		0.473	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2		
GOLGB1	2804	broad.mit.edu	37	3	121412993	121412993	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:121412993T>C	ENST00000340645.5	-	13	6487	c.6362A>G	c.(6361-6363)gAa>gGa	p.E2121G	GOLGB1_ENST00000393667.3_Missense_Mutation_p.E2126G	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2121					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.E2121G(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CTCAAGATCTTCATCCTTTTG	0.413																																					p.E2121G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A6362G	3						.						201.0	205.0	204.0					3																	121412993		2203	4300	6503	122895683	SO:0001583	missense	2804	exon13			X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.6362A>G	3.37:g.121412993T>C	ENSP00000341848:p.Glu2121Gly	Somatic		Capture	Illumina HiSeq	Phase_I	122895683	NM_004487	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.287801	0.40494	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.16743	2.32;2.33	5.75	5.75	0.90469	.	0.333714	0.25765	N	0.028456	T	0.31420	0.0796	M	0.69823	2.125	0.58432	D	0.999994	D;D;D;D	0.59357	0.985;0.985;0.985;0.967	P;P;P;P	0.51657	0.676;0.676;0.676;0.642	T	0.03086	-1.1074	10	0.44086	T	0.13	.	14.0228	0.64568	0.0:0.0:0.0:1.0	.	2046;2126;2126;2121	F1T0J2;E7EP74;B2ZZ91;Q14789	.;.;.;GOGB1_HUMAN	G	2121;2126	ENSP00000341848:E2121G;ENSP00000377275:E2126G	ENSP00000341848:E2121G	E	-	2	0	GOLGB1	122895683	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.176000	0.50863	2.194000	0.70268	0.533000	0.62120	GAA		0.413	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
PARP14	54625	broad.mit.edu	37	3	122399735	122399735	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:122399735C>T	ENST00000474629.2	+	1	271	c.5C>T	c.(4-6)gCt>gTt	p.A2V		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	2					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.A2V(1)		NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		CTGAGGATGGCTGTGCCCGGC	0.637																																					p.A2V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5T	3						.						11.0	13.0	12.0					3																	122399735		1915	4095	6010	123882425	SO:0001583	missense	54625	exon1			AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.5C>T	3.37:g.122399735C>T	ENSP00000418194:p.Ala2Val	Somatic		Capture	Illumina HiSeq	Phase_I	123882425	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.594268	0.66219	.	.	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.11930	2.73	4.4	3.44	0.39384	.	.	.	.	.	T	0.22627	0.0546	M	0.74881	2.28	0.27082	N	0.963073	D	0.58268	0.982	P	0.49477	0.612	T	0.06320	-1.0833	9	0.40728	T	0.16	.	8.6037	0.33760	0.2471:0.7529:0.0:0.0	.	2	Q460N5	PAR14_HUMAN	V	2	ENSP00000418194:A2V	ENSP00000381228:A2V	A	+	2	0	PARP14	123882425	0.803000	0.28956	0.920000	0.36463	0.257000	0.26127	0.764000	0.26532	2.277000	0.76020	0.643000	0.83706	GCT		0.637	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
PARP14	54625	broad.mit.edu	37	3	122418599	122418599	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:122418599G>T	ENST00000474629.2	+	6	1464	c.1198G>T	c.(1198-1200)Gtc>Ttc	p.V400F		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	400					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.V400F(1)|p.V237F(1)		NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		TAAATATAAAGTCAACCCAAT	0.413																																					p.V400F												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1198T	3						.						133.0	127.0	129.0					3																	122418599		1899	4126	6025	123901289	SO:0001583	missense	54625	exon6			AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1198G>T	3.37:g.122418599G>T	ENSP00000418194:p.Val400Phe	Somatic		Capture	Illumina HiSeq	Phase_I	123901289	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	G	12.35	1.910515	0.33721	.	.	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.10860	2.83	5.19	3.36	0.38483	.	0.337495	0.24520	N	0.037807	T	0.25975	0.0633	M	0.71581	2.175	0.23260	N	0.99803	B;D	0.76494	0.102;0.999	B;D	0.64042	0.051;0.921	T	0.03566	-1.1024	10	0.72032	D	0.01	.	8.597	0.33721	0.0799:0.0:0.7586:0.1615	.	400;400	Q460N5-4;Q460N5	.;PAR14_HUMAN	F	400;319	ENSP00000418194:V400F	ENSP00000381228:V319F	V	+	1	0	PARP14	123901289	0.002000	0.14202	0.026000	0.17262	0.333000	0.28666	1.101000	0.31037	0.729000	0.32403	0.563000	0.77884	GTC		0.413	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
MYLK	4638	broad.mit.edu	37	3	123359173	123359173	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:123359173T>C	ENST00000475616.1	-	25	4797	c.4798A>G	c.(4798-4800)Agg>Ggg	p.R1600G	MYLK_ENST00000346322.5_Missense_Mutation_p.R1531G|MYLK_ENST00000359169.1_Missense_Mutation_p.R1600G|MYLK-AS1_ENST00000485162.1_RNA|MYLK_ENST00000360304.3_Missense_Mutation_p.R1600G|MYLK_ENST00000354792.5_Missense_Mutation_p.R400G|MYLK_ENST00000360772.3_Missense_Mutation_p.R1600G			Q15746	MYLK_HUMAN	myosin light chain kinase	1600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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.R1600G(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)		AGCTTGATCCTGGTGCCCGTC	0.572																																					p.R1600G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4798G	3						.						250.0	192.0	211.0					3																	123359173		2203	4300	6503	124841863	SO:0001583	missense	4638	exon28			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.4798A>G	3.37:g.123359173T>C	ENSP00000418335:p.Arg1600Gly	Somatic		Capture	Illumina HiSeq	Phase_I	124841863	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	.	.	.	.	.	.	.	.	.	.	T	17.23	3.337687	0.60963	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000354792;ENST00000475616	T;T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03;1.03	5.55	4.37	0.52481	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.45955	0.1368	L	0.50847	1.595	0.29341	N	0.865999	P;P;P;P;B	0.52692	0.481;0.955;0.787;0.914;0.367	B;P;B;B;B	0.48454	0.228;0.578;0.228;0.341;0.253	T	0.42498	-0.9448	9	0.51188	T	0.08	.	12.7986	0.57573	0.0:0.0:0.1368:0.8632	.	1600;1531;1600;1531;1600	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	G	1600;1600;1600;1531;400;1600	ENSP00000354004:R1600G;ENSP00000353452:R1600G;ENSP00000352088:R1600G;ENSP00000320622:R1531G;ENSP00000346846:R400G;ENSP00000418335:R1600G	ENSP00000320622:R1531G	R	-	1	2	MYLK	124841863	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.365000	0.52335	0.913000	0.36797	0.455000	0.32223	AGG		0.572	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
MYLK	4638	broad.mit.edu	37	3	123452565	123452565	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:123452565C>A	ENST00000475616.1	-	7	1277	c.1278G>T	c.(1276-1278)aaG>aaT	p.K426N	MYLK_ENST00000346322.5_Missense_Mutation_p.K426N|MYLK_ENST00000359169.1_Missense_Mutation_p.K426N|MYLK_ENST00000360304.3_Missense_Mutation_p.K426N|MYLK_ENST00000360772.3_Missense_Mutation_p.K426N			Q15746	MYLK_HUMAN	myosin light chain kinase	426	Ig-like C2-type 3.				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.K426N(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)		TTTGATTTTCCTTGACCTCCT	0.502																																					p.K426N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1278T	3						.						170.0	172.0	171.0					3																	123452565		2203	4300	6503	124935255	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.1278G>T	3.37:g.123452565C>A	ENSP00000418335:p.Lys426Asn	Somatic		Capture	Illumina HiSeq	Phase_I	124935255	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	9.876	1.200240	0.22121	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.16;-0.29	5.43	-0.916	0.10489	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.38585	0.1046	N	0.10629	0.01	0.49915	D	0.999835	B;B;B;B;B	0.18968	0.026;0.0;0.026;0.0;0.032	B;B;B;B;B	0.23852	0.029;0.0;0.047;0.0;0.049	T	0.09975	-1.0650	9	0.42905	T	0.14	.	2.1752	0.03860	0.2906:0.4145:0.178:0.1169	.	426;426;426;426;426	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	N	426	ENSP00000354004:K426N;ENSP00000353452:K426N;ENSP00000352088:K426N;ENSP00000320622:K426N;ENSP00000418335:K426N	ENSP00000320622:K426N	K	-	3	2	MYLK	124935255	0.005000	0.15991	0.575000	0.28536	0.961000	0.63080	-0.155000	0.10115	-0.028000	0.13850	-0.140000	0.14226	AAG		0.502	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
MKRN2	23609	broad.mit.edu	37	3	12610439	12610439	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:12610439G>T	ENST00000170447.7	+	2	229	c.92G>T	c.(91-93)aGc>aTc	p.S31I	MKRN2_ENST00000448482.1_Missense_Mutation_p.S31I|MKRN2_ENST00000411987.1_Intron	NM_001271707.1|NM_014160.3	NP_001258636.1|NP_054879.3	Q9H000	MKRN2_HUMAN	makorin ring finger protein 2	31					protein ubiquitination (GO:0016567)	intracellular (GO:0005622)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.S31I(1)		breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)	16						TTGGCAAACAGCAAACCGTCC	0.488																																					p.S31I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G92T	3						.						184.0	155.0	165.0					3																	12610439		2203	4300	6503	12585439	SO:0001583	missense	23609	exon2				CCDS33702.1, CCDS63545.1	3p25	2008-08-13	2008-08-13		ENSG00000075975	ENSG00000075975		"""RING-type (C3HC4) zinc fingers"""	7113	protein-coding gene	gene with protein product		608426				11597136	Standard	NM_014160		Approved	RNF62, HSPC070	uc003bxd.4	Q9H000	OTTHUMG00000155371	ENST00000170447.7:c.92G>T	3.37:g.12610439G>T	ENSP00000170447:p.Ser31Ile	Somatic		Capture	Illumina HiSeq	Phase_I	12585439	NM_014160	A6NIA2|B3KRC5|B4DPR4|Q8N391|Q96BD4|Q9BUY2|Q9NRY1	Missense_Mutation	SNP	ENST00000170447.7	37	CCDS33702.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.925886	0.92319	.	.	ENSG00000075975	ENST00000170447;ENST00000448482	T;T	0.25912	2.61;1.77	5.78	4.91	0.64330	Zinc finger, CCCH-type (1);	0.000000	0.85682	D	0.000000	T	0.53270	0.1786	M	0.79693	2.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.57774	-0.7753	10	0.48119	T	0.1	.	15.2672	0.73672	0.0675:0.0:0.9325:0.0	.	31;31	C9J494;Q9H000	.;MKRN2_HUMAN	I	31	ENSP00000170447:S31I;ENSP00000397983:S31I	ENSP00000170447:S31I	S	+	2	0	MKRN2	12585439	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.342000	0.97044	1.589000	0.49982	0.591000	0.81541	AGC		0.488	MKRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339679.1	NM_014160	
KALRN	8997	broad.mit.edu	37	3	123983352	123983352	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:123983352G>A	ENST00000240874.3	+	4	422	c.265G>A	c.(265-267)Gtg>Atg	p.V89M	KALRN_ENST00000360013.3_Missense_Mutation_p.V89M|KALRN_ENST00000460856.1_Missense_Mutation_p.V89M	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	89	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V89M(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						CAGTGAGGACGTGTGCAAACG	0.557																																					p.V89M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G265A	3						.						62.0	51.0	55.0					3																	123983352		2203	4300	6503	125466042	SO:0001583	missense	8997	exon4			U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.265G>A	3.37:g.123983352G>A	ENSP00000240874:p.Val89Met	Somatic		Capture	Illumina HiSeq	Phase_I	125466042	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	37	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200965	0.79015	.	.	ENSG00000160145	ENST00000460856;ENST00000240874;ENST00000360013	T;T;T	0.66638	-0.22;-0.22;-0.22	4.69	4.69	0.59074	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.000000	0.64402	D	0.000001	T	0.80813	0.4695	M	0.69823	2.125	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.969;0.996	T	0.79262	-0.1876	10	0.35671	T	0.21	.	18.1663	0.89729	0.0:0.0:1.0:0.0	.	89;89;89	C9IZQ6;O60229;O60229-2	.;KALRN_HUMAN;.	M	89	ENSP00000418611:V89M;ENSP00000240874:V89M;ENSP00000353109:V89M	ENSP00000240874:V89M	V	+	1	0	KALRN	125466042	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.860000	0.86993	2.600000	0.87896	0.655000	0.94253	GTG		0.557	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
ALDH1L1	10840	broad.mit.edu	37	3	125850317	125850317	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:125850317C>T	ENST00000393434.2	-	13	1882	c.1533G>A	c.(1531-1533)gcG>gcA	p.A511A	ALDH1L1_ENST00000393431.2_Intron|ALDH1L1_ENST00000452905.2_Silent_p.A410A|ALDH1L1_ENST00000472186.1_Silent_p.A511A|ALDH1L1_ENST00000273450.3_Silent_p.A521A	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	511	Aldehyde dehydrogenase.		A -> V (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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.A511A(1)		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)	AGACGGCACCCGCATCCAGGG	0.637																																					p.A511A												ALDH1L1,large_intestine,colon,Substitution - Missense,-1 	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1533A	3						.						90.0	79.0	83.0					3																	125850317		2203	4300	6503	127333007	SO:0001819	synonymous_variant	10840	exon13			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.1533G>A	3.37:g.125850317C>T		Somatic		Capture	Illumina HiSeq	Phase_I	127333007	NM_012190	B4DG36|E9PBX3|Q68CS1	Silent	SNP	ENST00000393434.2	37	CCDS3034.1																																																																																				0.637	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
ALDH1L1	10840	broad.mit.edu	37	3	125876304	125876304	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:125876304G>A	ENST00000393434.2	-	4	759	c.410C>T	c.(409-411)gCg>gTg	p.A137V	ALDH1L1_ENST00000455064.2_5'UTR|ALDH1L1_ENST00000393431.2_Missense_Mutation_p.A137V|ALDH1L1_ENST00000452905.2_Intron|U1_ENST00000606575.1_RNA|ALDH1L1_ENST00000413612.1_5'Flank|ALDH1L1_ENST00000472186.1_Missense_Mutation_p.A137V|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.A147V	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	137	GART.				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.A137V(1)		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)	ACCATCATCCGCCCAGAAGAT	0.572																																					p.A137V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C410T	3						.						100.0	101.0	101.0					3																	125876304		2203	4300	6503	127358994	SO:0001583	missense	10840	exon4			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.410C>T	3.37:g.125876304G>A	ENSP00000377083:p.Ala137Val	Somatic		Capture	Illumina HiSeq	Phase_I	127358994	NM_012190	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.627045	0.66901	.	.	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000393434;ENST00000393431;ENST00000490367;ENST00000460368;ENST00000488356	T;T;T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62;-0.62;-0.62	4.39	4.39	0.52855	Formyl transferase, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.72614	0.3482	N	0.16233	0.39	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.99;0.995;0.99	T	0.77638	-0.2513	10	0.87932	D	0	.	14.4889	0.67637	0.0:0.0:1.0:0.0	.	189;44;137	Q59G10;Q9UFA9;O75891	.;.;AL1L1_HUMAN	V	147;137;137;137;137;137;137	ENSP00000273450:A147V;ENSP00000420293:A137V;ENSP00000377083:A137V;ENSP00000377081:A137V;ENSP00000418711:A137V;ENSP00000419826:A137V;ENSP00000419955:A137V	ENSP00000273450:A147V	A	-	2	0	ALDH1L1	127358994	1.000000	0.71417	0.935000	0.37517	0.036000	0.12997	9.327000	0.96396	2.277000	0.76020	0.467000	0.42956	GCG		0.572	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
UROC1	131669	broad.mit.edu	37	3	126219597	126219597	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:126219597C>T	ENST00000290868.2	-	11	1139	c.1086G>A	c.(1084-1086)acG>acA	p.T362T	UROC1_ENST00000383579.3_Silent_p.T422T	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	362					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)	p.T362T(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		TCTGGGCCTCCGTGAAGCTGA	0.602																																					p.T362T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1086A	3						.						127.0	119.0	122.0					3																	126219597		2203	4300	6503	127702287	SO:0001819	synonymous_variant	131669	exon11			AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"""urocanase 1"""	613012	"""urocanase domain containing 1"""			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.1086G>A	3.37:g.126219597C>T		Somatic		Capture	Illumina HiSeq	Phase_I	127702287	NM_144639	E9PE13|Q14C64|Q68CJ7	Silent	SNP	ENST00000290868.2	37	CCDS3038.1																																																																																				0.602	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639	
IQSEC1	9922	broad.mit.edu	37	3	12950003	12950003	+	Silent	SNP	G	G	A	rs200644277		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:12950003G>A	ENST00000273221.4	-	12	2859	c.2643C>T	c.(2641-2643)ggC>ggT	p.G881G		NM_014869.5	NP_055684.3	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1	881					actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.G881G(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GCCGCACGACGCCTTTCTGCT	0.632													G|||	1	0.000199681	0.0	0.0	5008	,	,		18019	0.001		0.0	False		,,,				2504	0.0				p.G881G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2643T	3						.						68.0	76.0	73.0					3																	12950003		2203	4300	6503	12925003	SO:0001819	synonymous_variant	9922	exon12			BC010267	CCDS33703.1, CCDS74902.1	3p25.2	2011-09-23			ENSG00000144711	ENSG00000144711			29112	protein-coding gene	gene with protein product	"""brefeldin A-resistant ARF-GEF2"""	610166				9872452, 8619474	Standard	NM_001134382		Approved	KIAA0763, GEP100, BRAG2, ARF-GEP100	uc011auw.2	Q6DN90	OTTHUMG00000155398	ENST00000273221.4:c.2643C>T	3.37:g.12950003G>A		Somatic		Capture	Illumina HiSeq	Phase_I	12925003	NM_014869	O94863|Q96D85	Silent	SNP	ENST00000273221.4	37	CCDS33703.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	0.933	-0.712207	0.03206	.	.	ENSG00000144711	ENST00000450726	.	.	.	4.99	-9.98	0.00438	.	.	.	.	.	T	0.35770	0.0943	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44314	-0.9336	4	.	.	.	.	4.5027	0.11872	0.5453:0.2411:0.0857:0.1278	.	.	.	.	C	882	.	.	R	-	1	0	IQSEC1	12925003	0.000000	0.05858	0.414000	0.26521	0.134000	0.20937	-2.838000	0.00739	-1.714000	0.01390	-0.982000	0.02568	CGT		0.632	IQSEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339865.2	NM_014869	
PLXNA1	5361	broad.mit.edu	37	3	126710379	126710379	+	Silent	SNP	C	C	T	rs373383019		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:126710379C>T	ENST00000393409.2	+	2	1347	c.1347C>T	c.(1345-1347)ttC>ttT	p.F449F	PLXNA1_ENST00000251772.4_Silent_p.F426F	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	449	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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.F426F(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)		CTGTGGTATTCGCCGGCACGC	0.667																																					p.F449F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1347T	3						.	C		0,4406		0,0,2203	42.0	36.0	38.0		1347	-2.8	0.2	3		38	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous	PLXNA1	NM_032242.3		0,1,6498	TT,TC,CC		0.0116,0.0,0.0077		449/1897	126710379	1,12997	2203	4296	6499	128193069	SO:0001819	synonymous_variant	5361	exon2			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.1347C>T	3.37:g.126710379C>T		Somatic		Capture	Illumina HiSeq	Phase_I	128193069	NM_032242		Silent	SNP	ENST00000393409.2	37	CCDS33847.2																																																																																				0.667	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
RUVBL1	8607	broad.mit.edu	37	3	127831743	127831743	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:127831743G>A	ENST00000322623.5	-	3	448	c.349C>T	c.(349-351)Cgc>Tgc	p.R117C	RUVBL1_ENST00000464873.1_Missense_Mutation_p.R57C|RUVBL1_ENST00000417360.1_Missense_Mutation_p.R117C	NM_003707.2	NP_003698.1	Q9Y265	RUVB1_HUMAN	RuvB-like AAA ATPase 1	117					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Ino80 complex (GO:0031011)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)	p.R117C(2)		endometrium(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26				GBM - Glioblastoma multiforme(114;0.181)		ATGGCCCTGCGGAAGTTCTCC	0.512																																					p.R117C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C349T	3						.						145.0	133.0	137.0					3																	127831743		2203	4300	6503	129314433	SO:0001583	missense	8607	exon3			AF070735	CCDS3047.1	3q21	2013-09-12	2013-09-12		ENSG00000175792	ENSG00000175792		"""INO80 complex subunits"", ""ATPases / AAA-type"""	10474	protein-coding gene	gene with protein product	"""pontin"", ""INO80 complex subunit H"""	603449	"""RuvB (E coli homolog)-like 1"", ""RuvB-like 1 (E. coli)"", ""RuvB-like AAA ATPase"""			9774387, 9588198	Standard	NM_003707		Approved	TIP49, NMP238, RVB1, TIP49a, Pontin52, ECP54, TIH1, Rvb1, INO80H	uc003ekh.3	Q9Y265	OTTHUMG00000159658	ENST00000322623.5:c.349C>T	3.37:g.127831743G>A	ENSP00000318297:p.Arg117Cys	Somatic		Capture	Illumina HiSeq	Phase_I	129314433	NM_003707	B2R5S0|P82276|Q1KMR0|Q53HK5|Q53HL7|Q53Y27|Q9BSX9	Missense_Mutation	SNP	ENST00000322623.5	37	CCDS3047.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.111641	0.77210	.	.	ENSG00000175792	ENST00000464873;ENST00000322623;ENST00000417360	T;T;T	0.71341	-0.43;-0.56;-0.13	5.79	4.84	0.62591	TIP49, C-terminal (1);ATPase, AAA+ type, core (1);	0.045924	0.85682	D	0.000000	D	0.90256	0.6953	H	0.98407	4.225	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.998	D	0.93586	0.6917	10	0.87932	D	0	-29.8555	16.0471	0.80727	0.0:0.0:0.8099:0.1901	.	117;117;57	Q9Y265-2;Q9Y265;E7ETR0	.;RUVB1_HUMAN;.	C	57;117;117	ENSP00000420738:R57C;ENSP00000318297:R117C;ENSP00000393755:R117C	ENSP00000318297:R117C	R	-	1	0	RUVBL1	129314433	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.321000	0.51999	2.735000	0.93741	0.591000	0.81541	CGC		0.512	RUVBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356728.2		
EFCAB12	90288	broad.mit.edu	37	3	129127570	129127570	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:129127570C>T	ENST00000505956.1	-	6	1329	c.1167G>A	c.(1165-1167)agG>agA	p.R389R	EFCAB12_ENST00000326085.3_Silent_p.R389R	NM_207307.1	NP_997190.1	Q6NXP0	EFC12_HUMAN	EF-hand calcium binding domain 12	389							calcium ion binding (GO:0005509)	p.R389R(1)									GAAAGTTGTGCCTGCGGGCCG	0.567																																					p.R389R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1167A	3						.						42.0	44.0	44.0					3																	129127570		2048	4189	6237	130610260	SO:0001819	synonymous_variant	90288	exon6			AK096099	CCDS54638.1	3q21.3	2013-01-10	2012-07-20	2012-07-20	ENSG00000172771	ENSG00000172771		"""EF-hand domain containing"""	28061	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 25"""	C3orf25			Standard	NM_207307		Approved		uc003emg.3	Q6NXP0	OTTHUMG00000159464	ENST00000505956.1:c.1167G>A	3.37:g.129127570C>T		Somatic		Capture	Illumina HiSeq	Phase_I	130610260	NM_207307	Q69YX4	Silent	SNP	ENST00000505956.1	37	CCDS54638.1																																																																																				0.567	EFCAB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355530.1	NM_207307	
EFCAB12	90288	broad.mit.edu	37	3	129137111	129137111	+	Missense_Mutation	SNP	C	C	T	rs149643945		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:129137111C>T	ENST00000505956.1	-	3	829	c.667G>A	c.(667-669)Gcg>Acg	p.A223T	EFCAB12_ENST00000326085.3_Missense_Mutation_p.A223T	NM_207307.1	NP_997190.1	Q6NXP0	EFC12_HUMAN	EF-hand calcium binding domain 12	223	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)	p.A223T(1)									TTTACAGCCGCGATGAACTCC	0.562													C|||	1	0.000199681	0.0	0.0	5008	,	,		17049	0.0		0.001	False		,,,				2504	0.0				p.A223T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G667A	3						.						49.0	46.0	47.0					3																	129137111		2004	4161	6165	130619801	SO:0001583	missense	90288	exon3			AK096099	CCDS54638.1	3q21.3	2013-01-10	2012-07-20	2012-07-20	ENSG00000172771	ENSG00000172771		"""EF-hand domain containing"""	28061	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 25"""	C3orf25			Standard	NM_207307		Approved		uc003emg.3	Q6NXP0	OTTHUMG00000159464	ENST00000505956.1:c.667G>A	3.37:g.129137111C>T	ENSP00000420854:p.Ala223Thr	Somatic		Capture	Illumina HiSeq	Phase_I	130619801	NM_207307	Q69YX4	Missense_Mutation	SNP	ENST00000505956.1	37	CCDS54638.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	2.834	-0.241900	0.05906	.	.	ENSG00000172771	ENST00000505956;ENST00000326085;ENST00000503957	T;T;T	0.43294	0.95;0.95;0.95	4.73	-9.46	0.00597	EF-hand-like domain (1);	3.055330	0.00786	N	0.001319	T	0.19327	0.0464	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17561	-1.0365	10	0.09843	T	0.71	0.0877	11.2669	0.49116	0.0:0.5911:0.2571:0.1518	.	223	Q6NXP0	CC025_HUMAN	T	223;223;73	ENSP00000420854:A223T;ENSP00000324241:A223T;ENSP00000421462:A73T	ENSP00000324241:A223T	A	-	1	0	C3orf25	130619801	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.974000	0.00666	-2.404000	0.00576	-1.300000	0.01332	GCG		0.562	EFCAB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355530.1	NM_207307	
IFT122	55764	broad.mit.edu	37	3	129185838	129185838	+	Silent	SNP	C	C	T	rs139008392	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:129185838C>T	ENST00000348417.2	+	8	746	c.669C>T	c.(667-669)taC>taT	p.Y223Y	IFT122_ENST00000347300.2_Intron|IFT122_ENST00000296266.3_Silent_p.Y274Y|IFT122_ENST00000349441.2_Intron|IFT122_ENST00000431818.2_Silent_p.Y73Y|IFT122_ENST00000507564.1_Intron|IFT122_ENST00000440957.2_Intron|IFT122_ENST00000504021.1_Intron	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	223					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)		p.Y274Y(1)		breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						CAGCAGTGTACAGTAGTCAGG	0.507																																					p.Y223Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C669T	3						.	C	,,,	0,4406		0,0,2203	154.0	155.0	155.0		,822,669,	3.9	1.0	3	dbSNP_134	155	1,8599	1.2+/-3.3	0,1,4299	no	intron,coding-synonymous,coding-synonymous,intron	IFT122	NM_018262.2,NM_052985.2,NM_052989.1,NM_052990.1	,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,	,274/1293,223/1242,	129185838	1,13005	2203	4300	6503	130668528	SO:0001819	synonymous_variant	55764	exon8			AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	13556	protein-coding gene	gene with protein product		606045	"""WD repeat domain 10"", ""intraflagellar transport 122 homolog (Chlamydomonas)"""	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.669C>T	3.37:g.129185838C>T		Somatic		Capture	Illumina HiSeq	Phase_I	130668528	NM_052989	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Silent	SNP	ENST00000348417.2	37	CCDS3061.1																																																																																				0.507	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262	
COL6A6	131873	broad.mit.edu	37	3	130285693	130285693	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:130285693C>T	ENST00000358511.6	+	4	1461	c.1430C>T	c.(1429-1431)gCc>gTc	p.A477V	COL6A6_ENST00000453409.2_Missense_Mutation_p.A477V	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	477	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.A477V(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						CGGGTTGGGGCCGTTCAGTAT	0.493																																					p.A477V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1430T	3						.						132.0	133.0	133.0					3																	130285693		1923	4111	6034	131768383	SO:0001583	missense	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.1430C>T	3.37:g.130285693C>T	ENSP00000351310:p.Ala477Val	Somatic		Capture	Illumina HiSeq	Phase_I	131768383	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	C	14.93	2.682222	0.47991	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.74002	-0.8;-0.8	5.24	5.24	0.73138	von Willebrand factor, type A (3);	0.000000	0.64402	D	0.000013	T	0.39759	0.1090	N	0.02420	-0.555	0.40613	D	0.981699	P	0.37370	0.592	B	0.33454	0.164	T	0.56986	-0.7888	10	0.02654	T	1	.	7.1941	0.25843	0.0:0.7883:0.0:0.2117	.	477	A6NMZ7	CO6A6_HUMAN	V	477	ENSP00000351310:A477V;ENSP00000399236:A477V	ENSP00000351310:A477V	A	+	2	0	COL6A6	131768383	0.962000	0.33011	0.823000	0.32752	0.979000	0.70002	2.340000	0.43974	2.448000	0.82819	0.561000	0.74099	GCC		0.493	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
CPNE4	131034	broad.mit.edu	37	3	131624258	131624258	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:131624258G>A	ENST00000512055.1	-	6	2156	c.30C>T	c.(28-30)tcC>tcT	p.S10S	CPNE4_ENST00000512332.1_Silent_p.S28S|CPNE4_ENST00000511604.1_Silent_p.S10S|CPNE4_ENST00000502818.1_Silent_p.S28S|CPNE4_ENST00000429747.1_Silent_p.S10S			Q96A23	CPNE4_HUMAN	copine IV	10						extracellular vesicular exosome (GO:0070062)		p.S10S(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						TGTTGGCAGCGGACTCATAAA	0.438																																					p.S10S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C30T	3						.						58.0	56.0	57.0					3																	131624258		2203	4300	6503	133106948	SO:0001819	synonymous_variant	131034	exon2			H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"""copine 8"""	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.30C>T	3.37:g.131624258G>A		Somatic		Capture	Illumina HiSeq	Phase_I	133106948	NM_130808	D3DNC5|Q8TEX1	Silent	SNP	ENST00000512055.1	37	CCDS3072.1																																																																																				0.438	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808	
DNAJC13	23317	broad.mit.edu	37	3	132172491	132172491	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:132172491C>T	ENST00000260818.6	+	8	1041	c.793C>T	c.(793-795)Cgt>Tgt	p.R265C	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	265					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)		p.R265C(1)		breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						TTTAGTAGAACGTGATCCGGC	0.303																																					p.R265C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C793T	3						.						99.0	110.0	106.0					3																	132172491		2203	4299	6502	133655181	SO:0001583	missense	23317	exon8			AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.793C>T	3.37:g.132172491C>T	ENSP00000260818:p.Arg265Cys	Somatic		Capture	Illumina HiSeq	Phase_I	133655181	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.544105	0.65198	.	.	ENSG00000138246	ENST00000260818	T	0.50277	0.75	5.64	2.57	0.30868	.	0.000000	0.85682	D	0.000000	T	0.68659	0.3025	M	0.88979	2.995	0.80722	D	1	D;P	0.60575	0.988;0.885	P;B	0.58970	0.849;0.299	T	0.77400	-0.2602	10	0.87932	D	0	.	14.9624	0.71166	0.5876:0.4124:0.0:0.0	.	265;265	A7E2Y5;O75165	.;DJC13_HUMAN	C	265	ENSP00000260818:R265C	ENSP00000260818:R265C	R	+	1	0	DNAJC13	133655181	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.093000	0.30939	0.648000	0.30732	0.650000	0.86243	CGT		0.303	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
CNTN6	27255	broad.mit.edu	37	3	1367510	1367510	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:1367510T>A	ENST00000446702.2	+	9	1585	c.958T>A	c.(958-960)Tgg>Agg	p.W320R	CNTN6_ENST00000350110.2_Missense_Mutation_p.W320R|CNTN6_ENST00000539053.1_Missense_Mutation_p.W248R			Q9UQ52	CNTN6_HUMAN	contactin 6	320	Ig-like C2-type 4.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.W320R(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TCCTCCAGAATGGGAACAGAA	0.413																																					p.W320R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T958A	3						.						108.0	100.0	103.0					3																	1367510		2203	4300	6503	1342510	SO:0001583	missense	27255	exon9			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.958T>A	3.37:g.1367510T>A	ENSP00000407822:p.Trp320Arg	Somatic		Capture	Illumina HiSeq	Phase_I	1342510	NM_014461	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	37	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	T	17.89	3.499096	0.64298	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.66460	-0.21;-0.21;-0.21	5.27	5.27	0.74061	Immunoglobulin I-set (1);Immunoglobulin-like (1);	0.000000	0.51477	D	0.000081	D	0.85279	0.5660	M	0.93062	3.375	0.35580	D	0.806185	D	0.89917	1.0	D	0.91635	0.999	D	0.91849	0.5490	10	0.87932	D	0	.	13.7897	0.63133	0.0:0.0:0.0:1.0	.	320	Q9UQ52	CNTN6_HUMAN	R	320;248;320	ENSP00000407822:W320R;ENSP00000442791:W248R;ENSP00000341882:W320R	ENSP00000341882:W320R	W	+	1	0	CNTN6	1342510	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.154000	0.58125	1.997000	0.58415	0.533000	0.62120	TGG		0.413	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
DNAJC13	23317	broad.mit.edu	37	3	132179153	132179153	+	Silent	SNP	G	G	A	rs190052100		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:132179153G>A	ENST00000260818.6	+	14	1757	c.1509G>A	c.(1507-1509)tcG>tcA	p.S503S	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	503					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)		p.S503S(1)		breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						CTCTTCTCTCGTCAAAGAAGT	0.318													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16661	0.0		0.0	False		,,,				2504	0.0				p.S503S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1509A	3						.						61.0	65.0	63.0					3																	132179153		2203	4299	6502	133661843	SO:0001819	synonymous_variant	23317	exon14			AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.1509G>A	3.37:g.132179153G>A		Somatic		Capture	Illumina HiSeq	Phase_I	133661843	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Silent	SNP	ENST00000260818.6	37	CCDS33857.1																																																																																				0.318	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
AMOTL2	51421	broad.mit.edu	37	3	134086428	134086428	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:134086428G>A	ENST00000422605.2	-	3	1118	c.952C>T	c.(952-954)Ctg>Ttg	p.L318L	AMOTL2_ENST00000511759.1_5'Flank|AMOTL2_ENST00000249883.5_Silent_p.L318L|AMOTL2_ENST00000513145.1_Silent_p.L318L|AMOTL2_ENST00000514516.1_Silent_p.L376L			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	318					hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)		p.L318L(1)		endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						TTCTCCCTCAGCACGGCCTCC	0.662																																					p.L318L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C952T	3						.						49.0	53.0	51.0					3																	134086428		2203	4300	6503	135569118	SO:0001819	synonymous_variant	51421	exon3			AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"""Leman coiled-coil protein"", ""angiomotin-like protein 2"""	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.952C>T	3.37:g.134086428G>A		Somatic		Capture	Illumina HiSeq	Phase_I	135569118	NM_016201	A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Silent	SNP	ENST00000422605.2	37																																																																																					0.662	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201	
CHCHD4	131474	broad.mit.edu	37	3	14163467	14163467	+	Intron	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:14163467G>A	ENST00000396914.3	-	1	204				CHCHD4_ENST00000295767.5_Missense_Mutation_p.S4L|TMEM43_ENST00000306077.4_5'Flank	NM_001098502.1	NP_001091972.1	Q8N4Q1	MIA40_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 4						'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein import into mitochondrial intermembrane space (GO:0045041)|protein maturation by protein folding (GO:0022417)|protein targeting to mitochondrion (GO:0006626)	mitochondrial intermembrane space (GO:0005758)	protein disulfide oxidoreductase activity (GO:0015035)	p.S4L(1)		kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5						AGATGAATACGACACAGGCAT	0.493																																					p.S4L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C11T	3						.						106.0	89.0	95.0					3																	14163467		2203	4300	6503	14138468	SO:0001627	intron_variant	131474	exon2			BC017082	CCDS2617.1, CCDS43054.1	3p25.1	2012-10-15			ENSG00000163528	ENSG00000163528		"""Coiled-coil-helix-coiled-coil-helix domain containing"""	26467	protein-coding gene	gene with protein product	"""translocase of inner mitochondrial membrane 40 homolog (S. cerevisiae)"", ""mitochondrial intermembrane space import and assembly 40 homolog (S. cerevisiae)"""	611077				22214851	Standard	NM_001098502		Approved	FLJ31709, TIMM40, MIA40	uc003byj.4	Q8N4Q1	OTTHUMG00000129805	ENST00000396914.3:c.22+2687C>T	3.37:g.14163467G>A		Somatic		Capture	Illumina HiSeq	Phase_I	14138468	NM_144636	A8K3Z9|Q96AI2|Q96MY6	Missense_Mutation	SNP	ENST00000396914.3	37	CCDS43054.1	.	.	.	.	.	.	.	.	.	.	G	9.759	1.169488	0.21621	.	.	ENSG00000163528	ENST00000295767	.	.	.	0.813	-0.802	0.10889	.	.	.	.	.	T	0.26919	0.0659	.	.	.	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.26467	-1.0102	7	0.87932	D	0	.	3.1008	0.06325	0.5789:0.0:0.4211:0.0	.	4	Q8N4Q1-2	.	L	4	.	ENSP00000295767:S4L	S	-	2	0	CHCHD4	14138468	0.003000	0.15002	0.045000	0.18777	0.144000	0.21451	0.100000	0.15231	-0.331000	0.08501	0.313000	0.20887	TCG		0.493	CHCHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340423.1	NM_144636	
EPHB1	2047	broad.mit.edu	37	3	134670483	134670483	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:134670483G>A	ENST00000398015.3	+	3	764	c.394G>A	c.(394-396)Gcc>Acc	p.A132T	EPHB1_ENST00000488154.1_3'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	132	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				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.A132T(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						CTGGTCTGAGGCCCCCTACCT	0.507																																					p.A132T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G394A	3						.						114.0	114.0	114.0					3																	134670483		2009	4225	6234	136153173	SO:0001583	missense	2047	exon3			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.394G>A	3.37:g.134670483G>A	ENSP00000381097:p.Ala132Thr	Somatic		Capture	Illumina HiSeq	Phase_I	136153173	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.292916	0.60086	.	.	ENSG00000154928	ENST00000460895;ENST00000398015;ENST00000474732	T;T;T	0.09630	2.96;2.96;2.96	5.49	5.49	0.81192	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.056036	0.64402	D	0.000001	T	0.15349	0.0370	L	0.28274	0.84	0.80722	D	1	P;P	0.46578	0.88;0.762	P;P	0.52031	0.688;0.569	T	0.00761	-1.1577	10	0.59425	D	0.04	.	14.2376	0.65937	0.0:0.0:0.8509:0.1491	.	132;132	B5A969;P54762	.;EPHB1_HUMAN	T	110;132;110	ENSP00000417435:A110T;ENSP00000381097:A132T;ENSP00000418352:A110T	ENSP00000381097:A132T	A	+	1	0	EPHB1	136153173	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.084000	0.57650	2.574000	0.86865	0.650000	0.86243	GCC		0.507	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441	
TRIM42	287015	broad.mit.edu	37	3	140401947	140401947	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:140401947G>A	ENST00000286349.3	+	2	1176	c.985G>A	c.(985-987)Gcc>Acc	p.A329T		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	329						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.A329T(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						CCTCATCGACGCCTGCTCCGA	0.542																																					p.A329T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G985A	3						.						164.0	148.0	153.0					3																	140401947		2203	4300	6503	141884637	SO:0001583	missense	287015	exon2			AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"""Tripartite motif containing / Tripartite motif containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	19014	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 40"""		"""tripartite motif-containing 42"""				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.985G>A	3.37:g.140401947G>A	ENSP00000286349:p.Ala329Thr	Somatic		Capture	Illumina HiSeq	Phase_I	141884637	NM_152616	A1L4B4|Q8N832|Q8NDL3	Missense_Mutation	SNP	ENST00000286349.3	37	CCDS3113.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.468459	0.84533	.	.	ENSG00000155890	ENST00000286349	T	0.60672	0.17	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000011	T	0.62962	0.2471	N	0.19112	0.55	0.37637	D	0.921912	D	0.89917	1.0	D	0.76071	0.987	T	0.70324	-0.4903	10	0.72032	D	0.01	-39.3178	14.805	0.69945	0.0:0.0:1.0:0.0	.	329	Q8IWZ5	TRI42_HUMAN	T	329	ENSP00000286349:A329T	ENSP00000286349:A329T	A	+	1	0	TRIM42	141884637	1.000000	0.71417	0.993000	0.49108	0.944000	0.59088	4.880000	0.63107	2.567000	0.86603	0.561000	0.74099	GCC		0.542	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616	
RASA2	5922	broad.mit.edu	37	3	141272711	141272711	+	Silent	SNP	C	C	T	rs148503095	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:141272711C>T	ENST00000452898.1	+	6	575	c.540C>T	c.(538-540)tgC>tgT	p.C180C	RASA2_ENST00000286364.3_Silent_p.C180C	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	180	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)	p.C180C(2)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						TCAAGGCATGCCATGGGTTGC	0.328																																					p.C180C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C540T	3						.	C		0,4406		0,0,2203	116.0	117.0	117.0		540	5.4	1.0	3	dbSNP_134	117	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	RASA2	NM_006506.2		0,8,6495	TT,TC,CC		0.093,0.0,0.0615		180/850	141272711	8,12998	2203	4300	6503	142755401	SO:0001819	synonymous_variant	5922	exon6			AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"""Pleckstrin homology (PH) domain containing"""	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.540C>T	3.37:g.141272711C>T		Somatic		Capture	Illumina HiSeq	Phase_I	142755401	NM_006506	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Silent	SNP	ENST00000452898.1	37																																																																																					0.328	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506	
SLC6A6	6533	broad.mit.edu	37	3	14508142	14508142	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:14508142G>A	ENST00000454876.2	+	7	1180	c.851G>A	c.(850-852)cGc>cAc	p.R284H	SLC6A6_ENST00000360861.3_Missense_Mutation_p.R284H			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	284					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|taurine transport (GO:0015734)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|taurine binding (GO:0030977)|taurine:sodium symporter activity (GO:0005369)	p.R284H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)	28						GACATCACCCGCCTTGAGGAC	0.637																																					p.R284H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G851A	3						.						64.0	59.0	61.0					3																	14508142		2203	4300	6503	14483146	SO:0001583	missense	6533	exon7				CCDS33705.1, CCDS46765.1	3p25.1	2013-07-19	2013-07-19		ENSG00000131389	ENSG00000131389		"""Solute carriers"""	11052	protein-coding gene	gene with protein product	"""taurine transporter"""	186854	"""solute carrier family 6 (neurotransmitter transporter, taurine), member 6"""			8010975, 8382624	Standard	XM_006713307		Approved	TAUT	uc010heg.4	P31641	OTTHUMG00000155525	ENST00000454876.2:c.851G>A	3.37:g.14508142G>A	ENSP00000398063:p.Arg284His	Somatic		Capture	Illumina HiSeq	Phase_I	14483146	NM_003043	B2RNU7|Q9BRI2|Q9BXB0	Missense_Mutation	SNP	ENST00000454876.2	37	CCDS33705.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.823856	0.90873	.	.	ENSG00000131389	ENST00000454876;ENST00000360861	T;T	0.75821	-0.97;-0.97	4.55	4.55	0.56014	.	0.092585	0.64402	D	0.000003	D	0.86070	0.5845	M	0.87682	2.9	0.80722	D	1	D	0.67145	0.996	P	0.58391	0.838	D	0.89321	0.3640	10	0.72032	D	0.01	.	17.6676	0.88207	0.0:0.0:1.0:0.0	.	284	P31641	SC6A6_HUMAN	H	284	ENSP00000398063:R284H;ENSP00000354107:R284H	ENSP00000354107:R284H	R	+	2	0	SLC6A6	14483146	1.000000	0.71417	0.975000	0.42487	0.923000	0.55619	6.638000	0.74309	2.241000	0.73720	0.491000	0.48974	CGC		0.637	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043	
ATR	545	broad.mit.edu	37	3	142281238	142281238	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:142281238G>A	ENST00000350721.4	-	4	1127	c.1006C>T	c.(1006-1008)Cgg>Tgg	p.R336W	ATR_ENST00000383101.3_Missense_Mutation_p.R336W	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	336					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R336W(2)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						GACTTAAGCCGCATGAGCACA	0.388								Other conserved DNA damage response genes																													p.R336W												.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.C1006T	3						.						76.0	78.0	78.0					3																	142281238		2203	4300	6503	143763928	SO:0001583	missense	545	exon4			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.1006C>T	3.37:g.142281238G>A	ENSP00000343741:p.Arg336Trp	Somatic		Capture	Illumina HiSeq	Phase_I	143763928	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	G	10.58	1.391280	0.25118	.	.	ENSG00000175054	ENST00000350721;ENST00000383101;ENST00000515149	T;T	0.68479	-0.33;-0.33	5.46	3.47	0.39725	Armadillo-like helical (1);Armadillo-type fold (1);	0.811573	0.10726	N	0.641204	T	0.50446	0.1616	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43294	-0.9400	10	0.56958	D	0.05	0.0107	8.1248	0.30992	0.1544:0.0:0.6422:0.2033	.	336	Q13535	ATR_HUMAN	W	336;336;17	ENSP00000343741:R336W;ENSP00000372581:R336W	ENSP00000343741:R336W	R	-	1	2	ATR	143763928	0.002000	0.14202	0.992000	0.48379	0.950000	0.60333	0.634000	0.24614	1.304000	0.44892	0.591000	0.81541	CGG		0.388	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
FGD5	152273	broad.mit.edu	37	3	14939159	14939159	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:14939159G>T	ENST00000285046.5	+	5	3002	c.2892G>T	c.(2890-2892)gaG>gaT	p.E964D	FGD5_ENST00000543601.1_Missense_Mutation_p.E723D|FGD5_ENST00000476851.1_3'UTR	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	964	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.E723D(1)		NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						AGGAGCTGGAGGAAAGGCTGT	0.552																																					p.E964D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2892T	3						.						48.0	51.0	50.0					3																	14939159		1962	4150	6112	14914163	SO:0001583	missense	152273	exon5			AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.2892G>T	3.37:g.14939159G>T	ENSP00000285046:p.Glu964Asp	Somatic		Capture	Illumina HiSeq	Phase_I	14914163	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	37	CCDS46767.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.53|17.53	3.412401|3.412401	0.62511|0.62511	.|.	.|.	ENSG00000154783|ENSG00000154783	ENST00000285046;ENST00000543601|ENST00000457774	T;T|.	0.68181|.	-0.31;-0.31|.	5.05|5.05	1.77|1.77	0.24775|0.24775	Dbl homology (DH) domain (5);|.	0.486714|.	0.18440|.	N|.	0.141180|.	T|.	0.64778|.	0.2629|.	M|M	0.80422|0.80422	2.495|2.495	0.42755|0.42755	D|D	0.993785|0.993785	P;P|.	0.52692|.	0.922;0.955|.	P;P|.	0.47673|.	0.467;0.554|.	T|.	0.62062|.	-0.6933|.	10|.	0.56958|.	D|.	0.05|.	-9.1514|-9.1514	5.5399|5.5399	0.17031|0.17031	0.2117:0.1832:0.6051:0.0|0.2117:0.1832:0.6051:0.0	.|.	723;964|.	B7ZM68;Q6ZNL6|.	.;FGD5_HUMAN|.	D|X	964;723|148	ENSP00000285046:E964D;ENSP00000445949:E723D|.	ENSP00000285046:E964D|.	E|G	+|+	3|1	2|0	FGD5|FGD5	14914163|14914163	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.974000|0.974000	0.67602|0.67602	0.637000|0.637000	0.24659|0.24659	0.523000|0.523000	0.28482|0.28482	0.591000|0.591000	0.81541|0.81541	GAG|GGA		0.552	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536	
ZIC1	7545	broad.mit.edu	37	3	147128190	147128190	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:147128190G>A	ENST00000282928.4	+	1	1020	c.291G>A	c.(289-291)acG>acA	p.T97T		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	97					adult walking behavior (GO:0007628)|brain development (GO:0007420)|cell differentiation (GO:0030154)|inner ear morphogenesis (GO:0042472)|pattern specification process (GO:0007389)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord development (GO:0021510)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T97T(1)		central_nervous_system(4)|cervix(1)|endometrium(2)|large_intestine(8)|lung(38)|ovary(1)|prostate(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	63						TCAACTCCACGCGGGACTTTC	0.701																																					p.T97T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G291A	3						.						14.0	17.0	16.0					3																	147128190		2072	4236	6308	148610880	SO:0001819	synonymous_variant	7545	exon1			D76435	CCDS3136.1	3q24	2013-01-08	2011-05-19		ENSG00000152977	ENSG00000152977		"""Zinc fingers, C2H2-type"""	12872	protein-coding gene	gene with protein product		600470	"""Zic family member 1 (odd-paired Drosophila homolog)"", ""Zic family member 1 (odd-paired homolog, Drosophila)"""			8542595	Standard	NM_003412		Approved	ZIC, ZNF201	uc003ewe.3	Q15915	OTTHUMG00000159456	ENST00000282928.4:c.291G>A	3.37:g.147128190G>A		Somatic		Capture	Illumina HiSeq	Phase_I	148610880	NM_003412	Q2M3N1	Silent	SNP	ENST00000282928.4	37	CCDS3136.1																																																																																				0.701	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412	
PFN2	5217	broad.mit.edu	37	3	149686283	149686283	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:149686283C>T	ENST00000239940.7	-	2	439	c.187G>A	c.(187-189)Ggt>Agt	p.G63S	PFN2_ENST00000461868.1_Missense_Mutation_p.G63S|PFN2_ENST00000423691.2_Missense_Mutation_p.G63S|PFN2_ENST00000461930.1_3'UTR|AC117395.1_ENST00000593416.1_5'Flank|PFN2_ENST00000481275.1_Missense_Mutation_p.G14S|PFN2_ENST00000481767.1_Missense_Mutation_p.G14S|PFN2_ENST00000452853.2_Missense_Mutation_p.G63S|PFN2_ENST00000475518.1_Missense_Mutation_p.G14S|PFN2_ENST00000494827.1_Missense_Mutation_p.G14S|PFN2_ENST00000497148.1_Missense_Mutation_p.G14S|PFN2_ENST00000489155.1_Missense_Mutation_p.G14S|PFN2_ENST00000498307.1_Missense_Mutation_p.G14S|PFN2_ENST00000490975.1_Missense_Mutation_p.G63S			P35080	PROF2_HUMAN	profilin 2	63					actin cytoskeleton organization (GO:0030036)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of ATPase activity (GO:0032781)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|regulation of synaptic vesicle exocytosis (GO:2000300)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|terminal bouton (GO:0043195)	actin monomer binding (GO:0003785)|adenyl-nucleotide exchange factor activity (GO:0000774)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.G63S(1)		large_intestine(1)|lung(4)|ovary(1)|prostate(1)	7			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			AGAGTCAAACCGTTGGTAAAG	0.433																																					p.G63S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G187A	3						.						179.0	192.0	188.0					3																	149686283		2203	4300	6503	151168973	SO:0001583	missense	5217	exon2			L10678	CCDS3148.1, CCDS46934.1	3q25.1	2006-10-16			ENSG00000070087	ENSG00000070087			8882	protein-coding gene	gene with protein product		176590				8975700, 8365484	Standard	NM_002628		Approved		uc003ext.1	P35080	OTTHUMG00000159683	ENST00000239940.7:c.187G>A	3.37:g.149686283C>T	ENSP00000239940:p.Gly63Ser	Somatic		Capture	Illumina HiSeq	Phase_I	151168973	NM_002628	B2R4C8|D3DNI4|Q4VBQ4|Q8WVF9|Q9HBK2	Missense_Mutation	SNP	ENST00000239940.7	37	CCDS3148.1	.	.	.	.	.	.	.	.	.	.	.	37	6.020911	0.97211	.	.	ENSG00000070087	ENST00000452853;ENST00000239940;ENST00000423691;ENST00000481767;ENST00000494827;ENST00000490975;ENST00000497148;ENST00000475518;ENST00000481275;ENST00000498307;ENST00000489155;ENST00000461868	D;D;D;D;D;D;D;D;D;D;D;D	0.97850	-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-3.64;-4.57	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	D	0.98896	0.9626	M	0.87827	2.91	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.994;0.998;0.99;1.0	D	0.99797	1.1034	10	0.87932	D	0	.	19.2173	0.93783	0.0:1.0:0.0:0.0	.	63;257;63;14	G5E9Q6;D3DNI2;P35080;C9J0J7	.;.;PROF2_HUMAN;.	S	63;63;63;14;14;63;14;14;14;14;14;63	ENSP00000410464:G63S;ENSP00000239940:G63S;ENSP00000408283:G63S;ENSP00000420417:G14S;ENSP00000418523:G14S;ENSP00000417351:G63S;ENSP00000417817:G14S;ENSP00000418142:G14S;ENSP00000418216:G14S;ENSP00000420202:G14S;ENSP00000420504:G14S;ENSP00000420244:G63S	ENSP00000239940:G63S	G	-	1	0	PFN2	151168973	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.485000	0.81204	2.532000	0.85374	0.655000	0.94253	GGT		0.433	PFN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356873.2	NM_002628	
CAPN7	23473	broad.mit.edu	37	3	15288252	15288252	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:15288252G>A	ENST00000253693.2	+	18	2277	c.2024G>A	c.(2023-2025)tGc>tAc	p.C675Y		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	675	Domain III.				positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)	p.C675Y(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						TATTCAGCATGCAGCTTTACT	0.279																																					p.C675Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2024A	3						.						80.0	80.0	80.0					3																	15288252		2201	4300	6501	15263256	SO:0001583	missense	23473	exon18			AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"""calpain like protease"", ""homolog of Aspergillus Nidulans PALB"""	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.2024G>A	3.37:g.15288252G>A	ENSP00000253693:p.Cys675Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	15263256	NM_014296		Missense_Mutation	SNP	ENST00000253693.2	37	CCDS2624.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.295972	0.81025	.	.	ENSG00000131375	ENST00000253693	T	0.41758	0.99	5.48	5.48	0.80851	Peptidase C2, calpain, large subunit, domain III (1);	0.046744	0.85682	D	0.000000	T	0.47248	0.1435	L	0.47716	1.5	0.80722	D	1	D	0.54964	0.969	P	0.49683	0.619	T	0.22103	-1.0226	10	0.22706	T	0.39	-12.5133	18.9472	0.92626	0.0:0.0:1.0:0.0	.	675	Q9Y6W3	CAN7_HUMAN	Y	675	ENSP00000253693:C675Y	ENSP00000253693:C675Y	C	+	2	0	CAPN7	15263256	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.244000	0.89823	2.588000	0.87417	0.655000	0.94253	TGC		0.279	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296	
ERICH6	131831	broad.mit.edu	37	3	150384575	150384575	+	Splice_Site	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:150384575T>G	ENST00000295910.6	-	13	1779	c.1727A>C	c.(1726-1728)aAg>aCg	p.K576T	FAM194A_ENST00000491361.1_Splice_Site_p.K430T	NM_152394.3	NP_689607.2												p.K576T(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						TGTACCTACCTTCACTTTGGT	0.318																																					p.K576T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1727C	3						.						85.0	81.0	82.0					3																	150384575		2203	4300	6503	151867265	SO:0001630	splice_region_variant	131831	exon13																														ENST00000295910.6:c.1728+1A>C	3.37:g.150384575T>G		Somatic		Capture	Illumina HiSeq	Phase_I	151867265	NM_152394		Missense_Mutation	SNP	ENST00000295910.6	37	CCDS3151.2	.	.	.	.	.	.	.	.	.	.	T	12.77	2.036652	0.35893	.	.	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.13538	2.58;2.58	5.41	2.85	0.33270	.	0.492438	0.20362	N	0.093839	T	0.13072	0.0317	M	0.61703	1.905	0.26717	N	0.970854	P	0.38250	0.624	B	0.34452	0.183	T	0.13764	-1.0497	10	0.59425	D	0.04	-10.8038	6.6158	0.22776	0.1573:0.0:0.1536:0.6891	.	576	Q7L0X2	F194A_HUMAN	T	576;430;534	ENSP00000295910:K576T;ENSP00000419366:K430T	ENSP00000295910:K576T	K	-	2	0	FAM194A	151867265	0.988000	0.35896	1.000000	0.80357	0.995000	0.86356	1.265000	0.33027	0.854000	0.35336	0.533000	0.62120	AAG		0.318	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1		Missense_Mutation
MBNL1	4154	broad.mit.edu	37	3	152018023	152018023	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:152018023T>C	ENST00000463374.1	+	1	552	c.41T>C	c.(40-42)cTa>cCa	p.L14P	MBNL1_ENST00000357472.3_Missense_Mutation_p.L14P|MBNL1_ENST00000282488.7_Missense_Mutation_p.L14P|MBNL1_ENST00000324210.5_Missense_Mutation_p.L14P|MBNL1_ENST00000492948.1_Missense_Mutation_p.L14P|MBNL1_ENST00000485910.1_Missense_Mutation_p.L14P|MBNL1_ENST00000545754.1_Missense_Mutation_p.L14P|MBNL1_ENST00000324196.5_Missense_Mutation_p.L14P|MBNL1_ENST00000355460.2_Missense_Mutation_p.L14P|MBNL1_ENST00000282486.6_Missense_Mutation_p.L14P|MBNL1_ENST00000461436.1_3'UTR|MBNL1_ENST00000485509.1_Missense_Mutation_p.L14P|MBNL1_ENST00000493459.1_Intron|MBNL1_ENST00000498502.1_Missense_Mutation_p.L14P	NM_207293.1	NP_997176.1	Q9NR56	MBNL1_HUMAN	muscleblind-like splicing regulator 1	14					alternative mRNA splicing, via spliceosome (GO:0000380)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|mRNA splice site selection (GO:0006376)|myoblast differentiation (GO:0045445)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|skeletal muscle tissue development (GO:0007519)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.L14P(2)		endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			ACAAAATGGCTAACACTGGAA	0.438																																					p.L14P												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T41C	3						.						96.0	90.0	92.0					3																	152018023		2203	4300	6503	153500713	SO:0001583	missense	4154	exon1			Y13829	CCDS3163.1, CCDS3164.1, CCDS3165.1, CCDS3166.1, CCDS3167.1, CCDS3168.1, CCDS54656.1	3q25	2013-01-18	2012-02-23	2003-03-14	ENSG00000152601	ENSG00000152601		"""Zinc fingers, CCCH-type domain containing"""	6923	protein-coding gene	gene with protein product		606516	"""muscleblind (Drosophila)-like"", ""muscleblind-like (Drosophila)"""	MBNL			Standard	NM_021038		Approved	KIAA0428, EXP42, EXP40, EXP35, EXP	uc003ezm.3	Q9NR56	OTTHUMG00000159163	ENST00000463374.1:c.41T>C	3.37:g.152018023T>C	ENSP00000418108:p.Leu14Pro	Somatic		Capture	Illumina HiSeq	Phase_I	153500713	NM_207293	E9PBW7|O43311|O43797|Q86UV8|Q86UV9|Q96P92|Q96RE3	Missense_Mutation	SNP	ENST00000463374.1	37	CCDS3165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.63|12.63	1.996943|1.996943	0.35226|0.35226	.|.	.|.	ENSG00000152601|ENSG00000152601	ENST00000282486;ENST00000282488;ENST00000355460;ENST00000324210;ENST00000498502;ENST00000324196;ENST00000545754;ENST00000357472;ENST00000485910;ENST00000463374;ENST00000465907;ENST00000492948;ENST00000485509|ENST00000464596	T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.62498|.	0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02;0.02|.	5.43|5.43	5.43|5.43	0.79202|0.79202	Zinc finger, CCCH-type (2);|.	0.143278|.	0.47852|.	D|.	0.000206|.	T|.	0.72574|.	0.3477|.	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	B;B;B;B;B;P;B|.	0.34892|.	0.416;0.058;0.282;0.301;0.109;0.474;0.071|.	B;B;B;B;B;B;B|.	0.42386|.	0.26;0.065;0.159;0.315;0.077;0.386;0.105|.	T|.	0.72316|.	-0.4330|.	10|.	0.87932|.	D|.	0|.	.|.	15.5235|15.5235	0.75885|0.75885	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	14;14;14;14;14;14;14|.	E9PBW7;Q9NR56-3;Q96RE3;Q9NR56;Q86UV8;Q9NR56-2;Q96P92|.	.;.;.;MBNL1_HUMAN;.;.;.|.	P|Q	14|13	ENSP00000282486:L14P;ENSP00000282488:L14P;ENSP00000347637:L14P;ENSP00000319429:L14P;ENSP00000420327:L14P;ENSP00000319374:L14P;ENSP00000437491:L14P;ENSP00000350064:L14P;ENSP00000418427:L14P;ENSP00000418108:L14P;ENSP00000417630:L14P;ENSP00000420103:L14P;ENSP00000418876:L14P|.	ENSP00000282486:L14P|.	L|X	+|+	2|1	0|0	MBNL1|MBNL1	153500713|153500713	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.927000|7.927000	0.87577|0.87577	2.071000|2.071000	0.62044|0.62044	0.477000|0.477000	0.44152|0.44152	CTA|TAA		0.438	MBNL1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353604.1	NM_021038	
METTL6	131965	broad.mit.edu	37	3	15467989	15467989	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:15467989C>A	ENST00000443029.1	-	2	270	c.30G>T	c.(28-30)caG>caT	p.Q10H	EAF1_ENST00000396842.2_5'Flank|METTL6_ENST00000383790.3_Missense_Mutation_p.Q10H|EAF1_ENST00000432764.2_5'Flank|METTL6_ENST00000383789.5_Missense_Mutation_p.Q10H|METTL6_ENST00000450816.2_Missense_Mutation_p.Q10H			Q8TCB7	METL6_HUMAN	methyltransferase like 6	10							methyltransferase activity (GO:0008168)	p.Q10H(1)		endometrium(1)|kidney(1)|large_intestine(9)|lung(3)|prostate(1)	15						GAATCCTTGCCTGCAGCCCTT	0.413																																					p.Q10H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G30T	3						.						114.0	104.0	107.0					3																	15467989		1856	4112	5968	15442993	SO:0001583	missense	131965	exon2			AK057791	CCDS43056.1	3p25.1	2005-11-02			ENSG00000206562	ENSG00000206562			28343	protein-coding gene	gene with protein product						12477932	Standard	NM_152396		Approved	MGC24132	uc003bzs.1	Q8TCB7	OTTHUMG00000156431	ENST00000443029.1:c.30G>T	3.37:g.15467989C>A	ENSP00000407613:p.Gln10His	Somatic		Capture	Illumina HiSeq	Phase_I	15442993	NM_152396	Q96LU4	Missense_Mutation	SNP	ENST00000443029.1	37	CCDS43056.1	.	.	.	.	.	.	.	.	.	.	C	3.972	-0.008169	0.07773	.	.	ENSG00000206562	ENST00000383790;ENST00000450816;ENST00000383789	T;T;T	0.30981	1.93;1.51;1.91	4.96	-2.13	0.07144	.	0.426202	0.23750	N	0.044925	T	0.16981	0.0408	L	0.38175	1.15	0.09310	N	1	B;B;B	0.22080	0.008;0.064;0.001	B;B;B	0.23852	0.003;0.049;0.002	T	0.10132	-1.0643	10	0.46703	T	0.11	-13.7138	1.7272	0.02924	0.1126:0.2655:0.223:0.3989	.	10;10;10	B4DDX3;Q8TCB7-2;Q8TCB7	.;.;METL6_HUMAN	H	10	ENSP00000373300:Q10H;ENSP00000410726:Q10H;ENSP00000373299:Q10H	ENSP00000373299:Q10H	Q	-	3	2	METTL6	15442993	0.000000	0.05858	0.009000	0.14445	0.192000	0.23643	-0.743000	0.04845	-0.134000	0.11516	0.555000	0.69702	CAG		0.413	METTL6-007	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346373.1	NM_152396	
EAF1	85403	broad.mit.edu	37	3	15473633	15473633	+	Missense_Mutation	SNP	C	C	T	rs145558221		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:15473633C>T	ENST00000396842.2	+	3	663	c.238C>T	c.(238-240)Cgg>Tgg	p.R80W	EAF1_ENST00000432764.2_Intron|RNU6-1024P_ENST00000384199.1_RNA	NM_033083.6	NP_149074.3	Q96JC9	EAF1_HUMAN	ELL associated factor 1	80					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ELL-EAF complex (GO:0032783)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.R80W(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	7						GGGGAACAAACGGCCTTACCA	0.393																																					p.R80W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C238T	3						.	C	TRP/ARG	0,4406		0,0,2203	150.0	137.0	141.0		238	4.2	1.0	3	dbSNP_134	141	1,8599	1.2+/-3.3	0,1,4299	no	missense	EAF1	NM_033083.6	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	80/269	15473633	1,13005	2203	4300	6503	15448637	SO:0001583	missense	85403	exon3			AF272973	CCDS2626.1	3p25.1	2011-06-10			ENSG00000144597	ENSG00000144597			20907	protein-coding gene	gene with protein product		608315				11418481	Standard	NM_033083		Approved		uc003bzu.3	Q96JC9	OTTHUMG00000162544	ENST00000396842.2:c.238C>T	3.37:g.15473633C>T	ENSP00000380054:p.Arg80Trp	Somatic		Capture	Illumina HiSeq	Phase_I	15448637	NM_033083	B4E3F5|Q8IW10	Missense_Mutation	SNP	ENST00000396842.2	37	CCDS2626.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.274122	0.59649	0.0	1.16E-4	ENSG00000144597	ENST00000396842	.	.	.	6.17	4.19	0.49359	Transcription elognation factor  Eaf, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.75087	0.3802	M	0.73217	2.22	0.80722	D	1	D	0.76494	0.999	D	0.63033	0.91	T	0.79070	-0.1954	9	0.87932	D	0	-16.2768	13.7007	0.62606	0.3768:0.6232:0.0:0.0	.	80	Q96JC9	EAF1_HUMAN	W	80	.	ENSP00000380054:R80W	R	+	1	2	EAF1	15448637	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	2.727000	0.47311	1.561000	0.49584	0.655000	0.94253	CGG		0.393	EAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252100.4	NM_033083	
COLQ	8292	broad.mit.edu	37	3	15529767	15529767	+	Silent	SNP	C	C	T	rs144897863		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:15529767C>T	ENST00000383788.5	-	3	392	c.267G>A	c.(265-267)tcG>tcA	p.S89S	COLQ_ENST00000383786.5_Intron|COLQ_ENST00000383781.4_Silent_p.S79S|COLQ_ENST00000383787.2_Silent_p.S89S|COLQ_ENST00000383785.2_Silent_p.S89S|COLQ_ENST00000603808.1_Silent_p.S89S|COLQ_ENST00000435459.2_Silent_p.S79S	NM_005677.3	NP_005668.2	Q9Y215	COLQ_HUMAN	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	89					acetylcholine catabolic process in synaptic cleft (GO:0001507)|asymmetric protein localization (GO:0008105)	basal lamina (GO:0005605)|cell junction (GO:0030054)|collagen trimer (GO:0005581)|extracellular space (GO:0005615)|synapse (GO:0045202)		p.S89S(1)		endometrium(2)|large_intestine(4)|lung(10)|skin(3)	19						ACGGGGACTGCGAGGTCTCCA	0.587																																					p.S89S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G267A	3						.	C	,,	0,4406		0,0,2203	63.0	60.0	61.0		267,237,	-9.9	0.0	3	dbSNP_134	61	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,intron	COLQ	NM_005677.3,NM_080538.2,NM_080539.3	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	89/456,79/446,	15529767	1,13005	2203	4300	6503	15504771	SO:0001819	synonymous_variant	8292	exon3			AF057036	CCDS33709.1, CCDS43057.1, CCDS46768.1	3p	2008-07-18			ENSG00000206561	ENSG00000206561			2226	protein-coding gene	gene with protein product	"""single strand of homotrimeric collagen-like tail subunit of asymmetric acetylcholinesterase"", ""collagenic tail of endplate acetylcholinesterase"", ""AChE Q subunit"", ""acetylcholinesterase-associated collagen"""	603033				9689136	Standard	NM_005677		Approved	EAD	uc003bzx.3	Q9Y215	OTTHUMG00000156233	ENST00000383788.5:c.267G>A	3.37:g.15529767C>T		Somatic		Capture	Illumina HiSeq	Phase_I	15504771	NM_005677	B3KY09|Q6DK18|Q6YH18|Q6YH19|Q6YH20|Q6YH21|Q9NP18|Q9NP19|Q9NP20|Q9NP21|Q9NP22|Q9NP23|Q9NP24|Q9UP88	Silent	SNP	ENST00000383788.5	37	CCDS33709.1																																																																																				0.587	COLQ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343575.1	NM_005677	
HACL1	26061	broad.mit.edu	37	3	15628073	15628073	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:15628073G>A	ENST00000321169.5	-	6	785	c.418C>T	c.(418-420)Cgc>Tgc	p.R140C	HACL1_ENST00000457447.2_Intron|HACL1_ENST00000435217.2_Intron|HACL1_ENST00000451445.2_Intron|HACL1_ENST00000456194.2_Missense_Mutation_p.R113C	NM_012260.2	NP_036392.2	Q9UJ83	HACL1_HUMAN	2-hydroxyacyl-CoA lyase 1	140					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carbon-carbon lyase activity (GO:0016830)|cofactor binding (GO:0048037)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|receptor binding (GO:0005102)|thiamine pyrophosphate binding (GO:0030976)	p.R140C(1)		NS(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	16						CTGCTTGGGCGGGCAGAGAAC	0.358																																					p.R140C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C418T	3						.						78.0	81.0	80.0					3																	15628073		2203	4300	6503	15603077	SO:0001583	missense	26061	exon6			AJ131753	CCDS2627.1, CCDS68360.1, CCDS68361.1, CCDS68362.1	3p24.3	2009-01-14	2006-05-16	2006-05-16	ENSG00000131373	ENSG00000131373	4.1.-.-		17856	protein-coding gene	gene with protein product		604300	"""2-hydroxyphytanoyl-CoA lyase"""	HPCL		10468558, 15644336	Standard	NM_001284416		Approved	2-HPCL, PHYH2	uc003caf.3	Q9UJ83	OTTHUMG00000129862	ENST00000321169.5:c.418C>T	3.37:g.15628073G>A	ENSP00000323811:p.Arg140Cys	Somatic		Capture	Illumina HiSeq	Phase_I	15603077	NM_012260	B4DWI1|B4DXI5|E9PEN4|Q9BV42|Q9P0A2	Missense_Mutation	SNP	ENST00000321169.5	37	CCDS2627.1	.	.	.	.	.	.	.	.	.	.	G	17.25	3.342683	0.61073	.	.	ENSG00000131373	ENST00000321169;ENST00000456194;ENST00000421993;ENST00000414979	T;T	0.35421	1.31;1.36	5.83	4.88	0.63580	Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.68668	0.3026	H	0.95437	3.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.76162	-0.3060	10	0.72032	D	0.01	.	11.1039	0.48190	0.0:0.0:0.6525:0.3475	.	113;140	B4DWI1;Q9UJ83	.;HACL1_HUMAN	C	140;113;113;75	ENSP00000323811:R140C;ENSP00000390699:R113C	ENSP00000323811:R140C	R	-	1	0	HACL1	15603077	1.000000	0.71417	0.992000	0.48379	0.498000	0.33706	2.625000	0.46452	2.757000	0.94681	0.563000	0.77884	CGC		0.358	HACL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252104.3	NM_012260	
P2RY1	5028	broad.mit.edu	37	3	152554233	152554233	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:152554233C>T	ENST00000305097.3	+	1	1498	c.662C>T	c.(661-663)aCg>aTg	p.T221M	RP11-38P22.2_ENST00000460407.1_lincRNA	NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	221					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)	p.T221M(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			AGCATGTGCACGACCGTGGCC	0.483																																					p.T221M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C662T	3						.						161.0	145.0	150.0					3																	152554233		2203	4300	6503	154036923	SO:0001583	missense	5028	exon1			U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.662C>T	3.37:g.152554233C>T	ENSP00000304767:p.Thr221Met	Somatic		Capture	Illumina HiSeq	Phase_I	154036923	NM_002563		Missense_Mutation	SNP	ENST00000305097.3	37	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	C	13.16	2.155606	0.38021	.	.	ENSG00000169860	ENST00000305097	T	0.12672	2.66	5.44	5.44	0.79542	GPCR, rhodopsin-like superfamily (1);	0.137149	0.50627	D	0.000111	T	0.11922	0.0290	N	0.12527	0.23	0.48975	D	0.999732	D	0.54964	0.969	P	0.47915	0.561	T	0.28299	-1.0048	10	0.15952	T	0.53	.	18.2487	0.89996	0.0:1.0:0.0:0.0	.	221	P47900	P2RY1_HUMAN	M	221	ENSP00000304767:T221M	ENSP00000304767:T221M	T	+	2	0	P2RY1	154036923	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	5.854000	0.69503	2.531000	0.85337	0.563000	0.77884	ACG		0.483	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563	
PLCH1	23007	broad.mit.edu	37	3	155212268	155212268	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:155212268C>A	ENST00000340059.7	-	15	1896	c.1897G>T	c.(1897-1899)Gca>Tca	p.A633S	PLCH1_ENST00000494598.1_Missense_Mutation_p.A633S|PLCH1_ENST00000460012.1_Missense_Mutation_p.A615S|PLCH1_ENST00000414191.1_Missense_Mutation_p.A615S|PLCH1_ENST00000447496.2_Missense_Mutation_p.A633S|PLCH1_ENST00000334686.6_Missense_Mutation_p.A615S	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	633	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				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.A615S(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)			ACCTGATGTGCTCTTGTTTCA	0.403																																					p.A633S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1897T	3						.						164.0	157.0	159.0					3																	155212268		2203	4300	6503	156694962	SO:0001583	missense	23007	exon15			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.1897G>T	3.37:g.155212268C>A	ENSP00000345988:p.Ala633Ser	Somatic		Capture	Illumina HiSeq	Phase_I	156694962	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	C	33	5.256810	0.95336	.	.	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42;-0.42;-0.42	5.63	5.63	0.86233	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific, Y domain (3);	0.000000	0.85682	D	0.000000	D	0.83899	0.5354	M	0.83223	2.63	0.80722	D	1	D;D;D	0.69078	0.997;0.997;0.994	D;D;D	0.74348	0.971;0.983;0.945	D	0.85529	0.1208	10	0.72032	D	0.01	.	19.7096	0.96089	0.0:1.0:0.0:0.0	.	615;633;633	Q4KWH8-2;Q4KWH8;Q4KWH8-3	.;PLCH1_HUMAN;.	S	633;615;633;633;615;615	ENSP00000419100:A633S;ENSP00000417502:A615S;ENSP00000402759:A633S;ENSP00000345988:A633S;ENSP00000335469:A615S;ENSP00000412977:A615S	ENSP00000335469:A615S	A	-	1	0	PLCH1	156694962	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.657000	0.67996	2.652000	0.90054	0.655000	0.94253	GCA		0.403	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996	
MECOM	2122	broad.mit.edu	37	3	168840423	168840423	+	Missense_Mutation	SNP	C	C	T	rs147788700		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:168840423C>T	ENST00000464456.1	-	5	1559	c.359G>A	c.(358-360)cGc>cAc	p.R120H	MECOM_ENST00000494292.1_Missense_Mutation_p.R308H|MECOM_ENST00000433243.2_Missense_Mutation_p.R120H|MECOM_ENST00000264674.3_Missense_Mutation_p.R184H|MECOM_ENST00000468789.1_Missense_Mutation_p.R120H|MECOM_ENST00000460814.1_Missense_Mutation_p.R120H|MECOM_ENST00000472280.1_Missense_Mutation_p.R120H|MECOM_ENST00000392736.3_Missense_Mutation_p.R120H	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0			P -> S (in dbSNP:rs7622799).		regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R120H(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						CATCTGGTGGCGAATTAAATT	0.443																																					p.R184H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G551A	3						.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	237.0	197.0	211.0		551,359,359,359,359,923,359	4.8	1.0	3	dbSNP_134	211	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense,missense	MECOM	NM_001105077.3,NM_001105078.3,NM_001163999.1,NM_001164000.1,NM_001205194.1,NM_004991.3,NM_005241.3	29,29,29,29,29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	184/1117,120/1052,120/1044,120/1043,120/1052,308/1240,120/1052	168840423	1,13005	2203	4300	6503	170323117	SO:0001583	missense	2122	exon6			S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.359G>A	3.37:g.168840423C>T	ENSP00000419770:p.Arg120His	Somatic		Capture	Illumina HiSeq	Phase_I	170323117	NM_001105077	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	37	CCDS54669.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.705850	0.89018	0.0	1.16E-4	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243;ENST00000492586;ENST00000484519	T;T;T;T;T;T;T;T;T;T	0.30981	2.32;2.34;2.34;2.32;2.94;2.34;2.34;2.32;2.34;1.51	5.68	4.81	0.61882	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.206207	0.34603	N	0.003829	T	0.51024	0.1650	L	0.60957	1.885	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;0.977;1.0;0.999;0.999	D;B;D;D;D	0.69824	0.966;0.336;0.926;0.942;0.966	T	0.54186	-0.8331	10	0.72032	D	0.01	-9.6786	14.6945	0.69110	0.0:0.9305:0.0:0.0695	.	308;120;308;184;120	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	H	184;120;120;120;308;120;120;120;95;120	ENSP00000264674:R184H;ENSP00000376493:R120H;ENSP00000419770:R120H;ENSP00000420048:R120H;ENSP00000417899:R308H;ENSP00000419995:R120H;ENSP00000420466:R120H;ENSP00000394302:R120H;ENSP00000417506:R95H;ENSP00000417299:R120H	ENSP00000264674:R184H	R	-	2	0	MECOM	170323117	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	1.412000	0.46977	0.655000	0.94253	CGC		0.443	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	
LRRIQ4	344657	broad.mit.edu	37	3	169540029	169540029	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:169540029T>C	ENST00000340806.6	+	1	320	c.320T>C	c.(319-321)tTc>tCc	p.F107S		NM_001080460.1	NP_001073929.1	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	107								p.F107S(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30						AACCCCATCTTCTCCTCCTCC	0.592																																					p.F107S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T320C	3						.						64.0	71.0	69.0					3																	169540029		2051	4202	6253	171022723	SO:0001583	missense	344657	exon1				CCDS46951.1	3q26.2	2008-08-08	2008-06-12	2008-06-12	ENSG00000188306	ENSG00000188306			34298	protein-coding gene	gene with protein product	"""leucine rich repeat containing 64"""						Standard	NM_001080460		Approved	LRRC64	uc003fgb.3	A6NIV6	OTTHUMG00000164420	ENST00000340806.6:c.320T>C	3.37:g.169540029T>C	ENSP00000342188:p.Phe107Ser	Somatic		Capture	Illumina HiSeq	Phase_I	171022723	NM_001080460		Missense_Mutation	SNP	ENST00000340806.6	37	CCDS46951.1	.	.	.	.	.	.	.	.	.	.	T	9.173	1.021551	0.19433	.	.	ENSG00000188306	ENST00000340806	T	0.02121	4.44	5.56	-1.75	0.08031	.	1.626640	0.03208	N	0.175724	T	0.00815	0.0027	N	0.00754	-1.215	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44832	-0.9302	10	0.07813	T	0.8	.	4.2883	0.10865	0.4962:0.2545:0.0:0.2493	.	107	A6NIV6	LRIQ4_HUMAN	S	107	ENSP00000342188:F107S	ENSP00000342188:F107S	F	+	2	0	LRRIQ4	171022723	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-0.443000	0.06862	-0.181000	0.10619	0.379000	0.24179	TTC		0.592	LRRIQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378698.1	NM_001080460	
FNDC3B	64778	broad.mit.edu	37	3	172025161	172025161	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:172025161C>T	ENST00000336824.4	+	10	1169	c.1070C>T	c.(1069-1071)gCc>gTc	p.A357V	FNDC3B_ENST00000415807.2_Missense_Mutation_p.A357V|FNDC3B_ENST00000416957.1_Missense_Mutation_p.A357V	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	357	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)	p.A357V(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		AGGGTGTATGCCATGTACAAT	0.493																																					p.A357V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1070T	3						.						152.0	131.0	138.0					3																	172025161		2203	4300	6503	173507855	SO:0001583	missense	64778	exon10			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"""Fibronectin type III domain containing"""	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.1070C>T	3.37:g.172025161C>T	ENSP00000338523:p.Ala357Val	Somatic		Capture	Illumina HiSeq	Phase_I	173507855	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	37	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.567672	0.86439	.	.	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957	T;T;T	0.69806	-0.43;-0.43;-0.43	5.93	5.93	0.95920	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.093928	0.64402	D	0.000001	T	0.64494	0.2603	L	0.42245	1.32	0.80722	D	1	P;B	0.37914	0.611;0.231	B;B	0.39185	0.265;0.293	T	0.62044	-0.6937	10	0.38643	T	0.18	-23.9131	19.949	0.97192	0.0:1.0:0.0:0.0	.	357;357	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	V	357	ENSP00000411242:A357V;ENSP00000338523:A357V;ENSP00000389094:A357V	ENSP00000338523:A357V	A	+	2	0	FNDC3B	173507855	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.914000	0.75764	2.826000	0.97356	0.655000	0.94253	GCC		0.493	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763	
NAALADL2	254827	broad.mit.edu	37	3	175345104	175345104	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:175345104G>A	ENST00000454872.1	+	11	1954	c.1826G>A	c.(1825-1827)cGt>cAt	p.R609H		NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	609						integral component of membrane (GO:0016021)		p.R609H(1)		central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		TCCGAGGCCCGTTTTTCTACA	0.363																																					p.R609H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1826A	3						.						61.0	53.0	55.0					3																	175345104		1797	4056	5853	176827798	SO:0001583	missense	254827	exon11				CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase II-type non-peptidase homologue"""	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.1826G>A	3.37:g.175345104G>A	ENSP00000404705:p.Arg609His	Somatic		Capture	Illumina HiSeq	Phase_I	176827798	NM_207015	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Missense_Mutation	SNP	ENST00000454872.1	37	CCDS46960.1	.	.	.	.	.	.	.	.	.	.	T	16.34	3.095321	0.56075	.	.	ENSG00000177694	ENST00000454872	T	0.39592	1.07	5.35	5.35	0.76521	.	0.265240	0.26460	N	0.024247	T	0.16471	0.0396	N	0.02011	-0.69	0.19945	N	0.999943	B	0.25351	0.124	B	0.09377	0.004	T	0.18085	-1.0348	10	0.15499	T	0.54	-0.3979	11.0669	0.47980	0.0:0.0:0.1556:0.8444	.	609	Q58DX5	NADL2_HUMAN	H	609	ENSP00000404705:R609H	ENSP00000404705:R609H	R	+	2	0	NAALADL2	176827798	0.960000	0.32886	0.816000	0.32577	0.403000	0.30841	1.577000	0.36515	0.862000	0.35528	-0.346000	0.07831	CGT		0.363	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015	
KCNMB2	10242	broad.mit.edu	37	3	178546004	178546004	+	Missense_Mutation	SNP	C	C	T	rs573122943		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:178546004C>T	ENST00000432997.1	+	4	618	c.266C>T	c.(265-267)gCg>gTg	p.A89V	KCNMB2_ENST00000420517.2_Missense_Mutation_p.A89V|KCNMB2_ENST00000358316.3_Missense_Mutation_p.A89V|RP11-385J1.2_ENST00000437488.1_RNA|KCNMB2_ENST00000452583.1_Missense_Mutation_p.A89V|RP11-385J1.2_ENST00000432385.1_RNA|RP11-385J1.2_ENST00000451742.1_RNA|RP11-385J1.2_ENST00000425330.1_RNA	NM_001278911.1	NP_001265840.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 2	100					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)|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)|potassium channel regulator activity (GO:0015459)	p.A89V(1)		NS(2)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)		Miconazole(DB01110)|Procaine(DB00721)	TTGCTGAATGCGTCCATCACG	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		20589	0.0		0.0	False		,,,				2504	0.001				p.A89V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C266T	3						.						147.0	122.0	131.0					3																	178546004		2203	4300	6503	180028698	SO:0001583	missense	10242	exon5			AF099137	CCDS3223.1	3q26.32	2005-10-13			ENSG00000197584	ENSG00000197584		"""Potassium channels"""	6286	protein-coding gene	gene with protein product		605214				10097176	Standard	NM_181361		Approved		uc003fjd.3	Q9Y691	OTTHUMG00000157264	ENST00000432997.1:c.266C>T	3.37:g.178546004C>T	ENSP00000407592:p.Ala89Val	Somatic		Capture	Illumina HiSeq	Phase_I	180028698	NM_005832	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Missense_Mutation	SNP	ENST00000432997.1	37	CCDS3223.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.768408	0.49680	.	.	ENSG00000197584	ENST00000437510;ENST00000420517;ENST00000452583;ENST00000432997;ENST00000455865;ENST00000358316;ENST00000457763	T;T;T;T;T;T	0.09163	3.01;3.01;3.01;3.01;3.01;3.01	5.87	1.53	0.23141	.	0.260581	0.43919	N	0.000517	T	0.11239	0.0274	N	0.11427	0.14	0.32759	N	0.505378	D	0.69078	0.997	D	0.64506	0.926	T	0.20940	-1.0260	10	0.22109	T	0.4	-3.6689	9.4789	0.38889	0.0:0.6036:0.0:0.3964	.	89	Q9Y691	KCMB2_HUMAN	V	89;89;89;89;89;89;70	ENSP00000395807:A89V;ENSP00000408252:A89V;ENSP00000397483:A89V;ENSP00000407592:A89V;ENSP00000399100:A89V;ENSP00000351068:A89V	ENSP00000351068:A89V	A	+	2	0	KCNMB2	180028698	0.913000	0.31002	0.091000	0.20842	0.904000	0.53231	2.998000	0.49465	-0.014000	0.14175	0.650000	0.86243	GCG		0.493	KCNMB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348251.1	NM_181361	
PIK3CA	5290	broad.mit.edu	37	3	178916876	178916876	+	Missense_Mutation	SNP	G	G	A	rs121913287		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:178916876G>A	ENST00000263967.3	+	2	420	c.263G>A	c.(262-264)cGa>cAa	p.R88Q		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	88	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.		R -> Q (in MCAP; also found in a glioblastoma multiforme sample; may disrupt the interaction between the PI3K- ABD domain and the N-terminal lobe of PI3K/PI4K kinase domain possibly affecting the conformation of the kinase domain). {ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|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)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|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)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.R88Q(53)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	GAAACAAGACGACTTTGTGAC	0.363	R88Q(JHUEM1_ENDOMETRIUM)|R88Q(SKUT1_SOFT_TISSUE)|R88Q(SNGM_ENDOMETRIUM)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.R88Q	Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	PIK3CA,central_nervous_system,brain,Substitution - Missense,0 	.	53	Substitution - Missense(53)	endometrium(27)|large_intestine(13)|central_nervous_system(8)|cervix(3)|soft_tissue(1)|breast(1)	c.G263A	3						.						107.0	102.0	104.0					3																	178916876		1821	4078	5899	180399570	SO:0001583	missense	5290	exon2				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.263G>A	3.37:g.178916876G>A	ENSP00000263967:p.Arg88Gln	Somatic		Capture	Illumina HiSeq	Phase_I	180399570	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.971870	0.92919	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	T;T	0.80033	-1.33;-1.33	5.44	5.44	0.79542	Phosphatidylinositol 3-kinase, p85-binding (2);	0.000000	0.85682	D	0.000000	D	0.89079	0.6613	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	D	0.88404	0.3017	9	.	.	.	-14.8194	19.2635	0.93977	0.0:0.0:1.0:0.0	.	88	P42336	PK3CA_HUMAN	Q	88	ENSP00000263967:R88Q;ENSP00000417479:R88Q	.	R	+	2	0	PIK3CA	180399570	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.571000	0.82399	2.547000	0.85894	0.555000	0.69702	CGA		0.363	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
ZNF639	51193	broad.mit.edu	37	3	179051264	179051264	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:179051264C>T	ENST00000326361.3	+	7	957	c.512C>T	c.(511-513)cCg>cTg	p.P171L	ZNF639_ENST00000496856.1_Missense_Mutation_p.P171L|ZNF639_ENST00000484866.1_Missense_Mutation_p.P171L|ZNF639_ENST00000466663.1_3'UTR	NM_016331.1	NP_057415.1	Q9UID6	ZN639_HUMAN	zinc finger protein 639	171					negative regulation by host of viral transcription (GO:0043922)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|transcription, DNA-templated (GO:0006351)|viral entry into host cell (GO:0046718)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein self-association (GO:0043621)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.P171L(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(10)|urinary_tract(1)	16	all_cancers(143;7.9e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			GATGAAGAACCGCCAGCTAAA	0.423																																					p.P171L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C512T	3						.						68.0	72.0	71.0					3																	179051264		2203	4300	6503	180533958	SO:0001583	missense	51193	exon7			BC020500	CCDS3227.1	3q27.1	2010-03-26			ENSG00000121864	ENSG00000121864		"""Zinc fingers, C2H2-type"""	30950	protein-coding gene	gene with protein product	"""zinc finger amplified in esophageal squamous cell carcinomas 1"""					14522885	Standard	NM_016331		Approved	ANC-2H01, ZASC1	uc003fjr.1	Q9UID6	OTTHUMG00000157439	ENST00000326361.3:c.512C>T	3.37:g.179051264C>T	ENSP00000325634:p.Pro171Leu	Somatic		Capture	Illumina HiSeq	Phase_I	180533958	NM_016331	A9X3Z9|D3DNR3	Missense_Mutation	SNP	ENST00000326361.3	37	CCDS3227.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.064584	0.55432	.	.	ENSG00000121864	ENST00000496856;ENST00000491818;ENST00000326361;ENST00000466264;ENST00000484866	T;T;T;T	0.03801	3.8;3.8;4.41;3.8	5.87	5.87	0.94306	.	0.273852	0.32134	N	0.006523	T	0.10895	0.0266	L	0.27053	0.805	0.48511	D	0.999664	D	0.89917	1.0	D	0.85130	0.997	T	0.02075	-1.1218	10	0.62326	D	0.03	.	9.4846	0.38922	0.0:0.8823:0.0:0.1177	.	171	Q9UID6	ZN639_HUMAN	L	171	ENSP00000417740:P171L;ENSP00000325634:P171L;ENSP00000419650:P171L;ENSP00000418766:P171L	ENSP00000325634:P171L	P	+	2	0	ZNF639	180533958	0.995000	0.38212	1.000000	0.80357	0.973000	0.67179	3.179000	0.50887	2.941000	0.99782	0.655000	0.94253	CCG		0.423	ZNF639-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348855.1	NM_016331	
ABCC5	10057	broad.mit.edu	37	3	183696434	183696434	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:183696434G>A	ENST00000334444.6	-	9	1393	c.1153C>T	c.(1153-1155)Cgc>Tgc	p.R385C	ABCC5_ENST00000492216.1_5'UTR|ABCC5_ENST00000265586.6_Missense_Mutation_p.R385C	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	385	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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.I384>?(1)|p.R385C(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)	TCCTCCTCGCGGATTTCTATG	0.488																																					p.R385C												.	.	2	Substitution - Missense(1)|Complex(1)	large_intestine(1)|skin(1)	c.C1153T	3						.						56.0	63.0	61.0					3																	183696434		1912	4137	6049	185179128	SO:0001583	missense	10057	exon9			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.1153C>T	3.37:g.183696434G>A	ENSP00000333926:p.Arg385Cys	Somatic		Capture	Illumina HiSeq	Phase_I	185179128	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Missense_Mutation	SNP	ENST00000334444.6	37	CCDS43176.1	.	.	.	.	.	.	.	.	.	.	G	19.74	3.883240	0.72410	.	.	ENSG00000114770	ENST00000334444;ENST00000382495;ENST00000265586	D;D	0.90197	-2.63;-2.63	5.7	4.82	0.62117	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	0.95701	0.8602	M	0.88512	2.96	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96154	0.9110	10	0.87932	D	0	-6.7836	13.3183	0.60419	0.0:0.0:0.5919:0.408	.	385;385	Q86UX3;O15440	.;MRP5_HUMAN	C	385;321;385	ENSP00000333926:R385C;ENSP00000265586:R385C	ENSP00000265586:R385C	R	-	1	0	ABCC5	185179128	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	4.499000	0.60380	1.371000	0.46172	0.650000	0.86243	CGC		0.488	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	
HTR3E	285242	broad.mit.edu	37	3	183823620	183823620	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:183823620C>T	ENST00000415389.2	+	7	1254	c.788C>T	c.(787-789)gCc>gTc	p.A263V	HTR3E_ENST00000436361.2_Missense_Mutation_p.A263V|HTR3E_ENST00000440596.2_Missense_Mutation_p.A289V|HTR3E_ENST00000425359.2_Missense_Mutation_p.A248V|HTR3E_ENST00000335304.2_Missense_Mutation_p.A278V|HTR3E-AS1_ENST00000431427.1_RNA	NM_001256613.1|NM_198313.2	NP_001243542.1|NP_938055.1	A5X5Y0	5HT3E_HUMAN	5-hydroxytryptamine (serotonin) receptor 3E, ionotropic	263					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.A278V(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)	TTTCTGGTTGCCATCGATGCC	0.537																																					p.A278V	Melanoma(7;227 727 6634 44770)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C833T	3						.						160.0	137.0	145.0					3																	183823620		2203	4300	6503	185306314	SO:0001583	missense	285242	exon6			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.788C>T	3.37:g.183823620C>T	ENSP00000401444:p.Ala263Val	Somatic		Capture	Illumina HiSeq	Phase_I	185306314	NM_182589	A8IKD7|E9PGF1|Q495G1|Q495G3|Q6V706|Q6V707|Q7Z6B2	Missense_Mutation	SNP	ENST00000415389.2	37	CCDS58868.1	.	.	.	.	.	.	.	.	.	.	c	1.665	-0.510577	0.04231	.	.	ENSG00000186038	ENST00000415389;ENST00000425359;ENST00000335304;ENST00000436361;ENST00000440596	D;D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89;-1.89	3.79	2.9	0.33743	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.277635	0.28671	U	0.014538	T	0.81683	0.4874	N	0.25992	0.78	0.09310	N	1	B;D;D;D;D	0.67145	0.002;0.99;0.996;0.968;0.996	B;D;D;P;D	0.65874	0.02;0.917;0.939;0.792;0.939	T	0.69910	-0.5017	10	0.09084	T	0.74	.	6.3963	0.21614	0.0:0.7722:0.0:0.2278	.	289;263;263;278;248	E9PGF1;A5X5Y0;A5X5Y0-4;A5X5Y0-3;A5X5Y0-2	.;5HT3E_HUMAN;.;.;.	V	263;248;278;263;289	ENSP00000401444:A263V;ENSP00000401900:A248V;ENSP00000335511:A278V;ENSP00000395833:A263V;ENSP00000406050:A289V	ENSP00000335511:A278V	A	+	2	0	HTR3E	185306314	0.972000	0.33761	0.078000	0.20375	0.011000	0.07611	1.803000	0.38863	0.913000	0.36797	0.655000	0.94253	GCC		0.537	HTR3E-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346284.1	NM_182589	
HTR3E	285242	broad.mit.edu	37	3	183824102	183824102	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:183824102G>A	ENST00000415389.2	+	8	1578	c.1112G>A	c.(1111-1113)gGc>gAc	p.G371D	HTR3E_ENST00000436361.2_Missense_Mutation_p.G371D|HTR3E_ENST00000440596.2_Missense_Mutation_p.G397D|HTR3E_ENST00000425359.2_Missense_Mutation_p.G356D|HTR3E_ENST00000335304.2_Missense_Mutation_p.G386D|HTR3E-AS1_ENST00000431427.1_RNA	NM_001256613.1|NM_198313.2	NP_001243542.1|NP_938055.1	A5X5Y0	5HT3E_HUMAN	5-hydroxytryptamine (serotonin) receptor 3E, ionotropic	371					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.G386D(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)	GAAAATAAGGGCCCGGGTCTC	0.662																																					p.G386D	Melanoma(7;227 727 6634 44770)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1157A	3						.						21.0	25.0	24.0					3																	183824102		2201	4300	6501	185306796	SO:0001583	missense	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.1112G>A	3.37:g.183824102G>A	ENSP00000401444:p.Gly371Asp	Somatic		Capture	Illumina HiSeq	Phase_I	185306796	NM_182589	A8IKD7|E9PGF1|Q495G1|Q495G3|Q6V706|Q6V707|Q7Z6B2	Missense_Mutation	SNP	ENST00000415389.2	37	CCDS58868.1	.	.	.	.	.	.	.	.	.	.	g	8.318	0.823577	0.16678	.	.	ENSG00000186038	ENST00000415389;ENST00000425359;ENST00000335304;ENST00000436361;ENST00000440596	D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53	4.28	2.46	0.29980	Neurotransmitter-gated ion-channel transmembrane domain (2);	1.381910	0.05474	N	0.553551	T	0.73853	0.3640	L	0.41236	1.265	0.09310	N	1	B;B;B;B;B	0.25272	0.0;0.05;0.033;0.004;0.122	B;B;B;B;B	0.30572	0.005;0.086;0.056;0.014;0.117	T	0.55860	-0.8074	10	0.21014	T	0.42	.	6.9152	0.24355	0.221:0.0:0.779:0.0	.	397;371;371;386;356	E9PGF1;A5X5Y0;A5X5Y0-4;A5X5Y0-3;A5X5Y0-2	.;5HT3E_HUMAN;.;.;.	D	371;356;386;371;397	ENSP00000401444:G371D;ENSP00000401900:G356D;ENSP00000335511:G386D;ENSP00000395833:G371D;ENSP00000406050:G397D	ENSP00000335511:G386D	G	+	2	0	HTR3E	185306796	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.471000	0.22100	0.357000	0.24183	0.561000	0.74099	GGC		0.662	HTR3E-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346284.1	NM_182589	
ECE2	9718	broad.mit.edu	37	3	183995204	183995204	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:183995204C>T	ENST00000402825.3	+	4	782	c.782C>T	c.(781-783)aCc>aTc	p.T261I	ECE2_ENST00000359140.4_Missense_Mutation_p.T114I|ECE2_ENST00000404464.3_Missense_Mutation_p.T143I|EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000357474.5_Missense_Mutation_p.T189I	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	261	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.T114I(1)|p.T261I(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)			CGCTGGAACACCTTCAACAGC	0.612																																					p.T261I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C782T	3						.						48.0	46.0	47.0					3																	183995204		2203	4300	6503	185477898	SO:0001583	missense	9718	exon4			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.782C>T	3.37:g.183995204C>T	ENSP00000384223:p.Thr261Ile	Somatic		Capture	Illumina HiSeq	Phase_I	185477898	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	ENST00000402825.3	37	CCDS3256.2	.	.	.	.	.	.	.	.	.	.	C	18.42	3.619507	0.66787	.	.	ENSG00000145194	ENST00000402825;ENST00000359140;ENST00000404464;ENST00000357474;ENST00000430587	T;T;T;T;T	0.75704	-0.96;-0.96;-0.96;-0.96;-0.96	5.91	5.04	0.67666	Peptidase M13 (1);	0.145976	0.64402	D	0.000010	T	0.81240	0.4781	L	0.53249	1.67	0.58432	D	0.999999	P;D;B;P;D;P	0.69078	0.895;0.987;0.081;0.872;0.997;0.702	P;P;B;P;P;B	0.62813	0.659;0.907;0.03;0.528;0.827;0.431	T	0.81618	-0.0851	10	0.48119	T	0.1	-23.6084	13.7834	0.63094	0.0:0.9258:0.0:0.0742	.	114;189;143;189;114;261	B4DKF3;B7Z1P1;O60344-2;O60344-5;O60344-3;O60344	.;.;.;.;.;ECE2_HUMAN	I	261;114;143;189;135	ENSP00000384223:T261I;ENSP00000352052:T114I;ENSP00000385846:T143I;ENSP00000350066:T189I;ENSP00000398444:T135I	ENSP00000350066:T189I	T	+	2	0	ECE2	185477898	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	7.786000	0.85741	1.515000	0.48885	-0.136000	0.14681	ACC		0.612	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
THPO	7066	broad.mit.edu	37	3	184093749	184093749	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:184093749G>A	ENST00000204615.7	-	3	282	c.68C>T	c.(67-69)cCg>cTg	p.P23L	THPO_ENST00000421442.2_Missense_Mutation_p.P23L|THPO_ENST00000445696.2_Missense_Mutation_p.P23L|EIF2B5_ENST00000444495.1_Intron|THPO_ENST00000477594.1_5'Flank	NM_000460.2|NM_001177597.1|NM_001177598.1	NP_000451.1|NP_001171068.1|NP_001171069.1	P40225	TPO_HUMAN	thrombopoietin	23					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|thrombopoietin-mediated signaling pathway (GO:0038163)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)	p.P23L(1)		NS(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AGGAGGAGCCGGGCTGGACAG	0.512																																					p.P23L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C68T	3						.						113.0	102.0	106.0					3																	184093749		2203	4300	6503	185576443	SO:0001583	missense	7066	exon3				CCDS3265.1, CCDS54693.1	3q27	2014-01-30	2008-07-31		ENSG00000090534	ENSG00000090534		"""Endogenous ligands"""	11795	protein-coding gene	gene with protein product	"""prepro-thrombopoietin"", ""megakaryocyte stimulating factor"", ""myeloproliferative leukemia virus oncogene ligand"", ""megakaryocyte growth and development factor"", ""MPL ligand"", ""megakaryocyte colony-stimulating factor"", ""c-mpl ligand"", ""thrombopoietin nirs variant 1"""	600044		MGDF		8202154	Standard	XM_006713738		Approved	TPO, MPLLG	uc003fol.1	P40225	OTTHUMG00000156745	ENST00000204615.7:c.68C>T	3.37:g.184093749G>A	ENSP00000204615:p.Pro23Leu	Somatic		Capture	Illumina HiSeq	Phase_I	185576443	NM_001177597	A1L3Y0|B7ZLR8|B9EGA8|Q13020|Q15790|Q15791|Q15792	Missense_Mutation	SNP	ENST00000204615.7	37	CCDS3265.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.956419	0.73902	.	.	ENSG00000090534	ENST00000204615;ENST00000445696;ENST00000421442;ENST00000353488	T;T;T	0.78595	-1.19;-1.07;-0.54	4.19	4.19	0.49359	Erythropoietin/thrombopoeitin, conserved site (1);Four-helical cytokine, core (1);	0.327214	0.22355	N	0.061153	T	0.80116	0.4564	L	0.27053	0.805	0.48135	D	0.999596	D;D;D;D;D;D	0.89917	0.993;0.981;0.967;1.0;1.0;1.0	P;P;B;D;D;D	0.87578	0.476;0.467;0.276;0.992;0.998;0.995	T	0.81931	-0.0707	10	0.87932	D	0	-4.3415	11.8723	0.52527	0.0:0.0:1.0:0.0	.	23;23;23;23;23;23	Q5FBX4;P40225-3;Q5FBX8;F8W6L1;P40225-2;P40225	.;.;.;.;.;TPO_HUMAN	L	23	ENSP00000204615:P23L;ENSP00000410763:P23L;ENSP00000411704:P23L	ENSP00000204615:P23L	P	-	2	0	THPO	185576443	0.998000	0.40836	0.996000	0.52242	0.983000	0.72400	4.415000	0.59809	2.157000	0.67596	0.467000	0.42956	CCG		0.512	THPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345554.1	NM_000460	
MAP3K13	9175	broad.mit.edu	37	3	185146619	185146619	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:185146619G>A	ENST00000265026.3	+	2	584	c.250G>A	c.(250-252)Gtt>Att	p.V84I	MAP3K13_ENST00000424227.1_Missense_Mutation_p.V84I|MAP3K13_ENST00000535426.1_Intron|MAP3K13_ENST00000446828.1_Intron|MAP3K13_ENST00000443863.1_Intron	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13									p.V84I(1)		NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			TGAGAACAGCGTTCTTCAGCT	0.532																																					p.V84I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G250A	3						.						106.0	80.0	89.0					3																	185146619		2203	4300	6503	186629313	SO:0001583	missense	9175	exon2			BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6852	protein-coding gene	gene with protein product	"""leucine zipper-bearing kinase"""	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.250G>A	3.37:g.185146619G>A	ENSP00000265026:p.Val84Ile	Somatic		Capture	Illumina HiSeq	Phase_I	186629313	NM_004721		Missense_Mutation	SNP	ENST00000265026.3	37	CCDS3270.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.461115	0.84317	.	.	ENSG00000073803	ENST00000447637;ENST00000424227;ENST00000428617;ENST00000265026	T;T;T;T	0.78816	0.45;-1.21;0.18;-1.21	5.61	3.83	0.44106	.	0.076735	0.52532	N	0.000076	T	0.56731	0.2005	N	0.08118	0	0.80722	D	1	D	0.56287	0.975	B	0.39152	0.292	T	0.60530	-0.7245	10	0.48119	T	0.1	.	12.0077	0.53270	0.1395:0.0:0.8605:0.0	.	84	O43283	M3K13_HUMAN	I	84	ENSP00000389495:V84I;ENSP00000399910:V84I;ENSP00000405163:V84I;ENSP00000265026:V84I	ENSP00000265026:V84I	V	+	1	0	MAP3K13	186629313	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	6.429000	0.73387	0.733000	0.32492	0.655000	0.94253	GTT		0.532	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721	
MAP3K13	9175	broad.mit.edu	37	3	185183578	185183578	+	Silent	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:185183578C>A	ENST00000265026.3	+	9	1766	c.1432C>A	c.(1432-1434)Cgg>Agg	p.R478R	MAP3K13_ENST00000424227.1_Silent_p.R478R|MAP3K13_ENST00000535426.1_Silent_p.R334R|MAP3K13_ENST00000446828.1_Silent_p.R271R|MAP3K13_ENST00000443863.1_Silent_p.R334R	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13									p.R478W(2)|p.R478R(1)		NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			GAAGCTTGAGCGGGCGAATAA	0.478																																					p.R478R												.	.	3	Substitution - Missense(2)|Substitution - coding silent(1)	large_intestine(3)	c.C1432A	3						.						139.0	143.0	142.0					3																	185183578		2203	4300	6503	186666272	SO:0001819	synonymous_variant	9175	exon9			BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6852	protein-coding gene	gene with protein product	"""leucine zipper-bearing kinase"""	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.1432C>A	3.37:g.185183578C>A		Somatic		Capture	Illumina HiSeq	Phase_I	186666272	NM_004721		Silent	SNP	ENST00000265026.3	37	CCDS3270.1																																																																																				0.478	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721	
TBCCD1	55171	broad.mit.edu	37	3	186272719	186272719	+	Silent	SNP	G	G	A	rs192772134		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:186272719G>A	ENST00000424280.1	-	5	1493	c.1014C>T	c.(1012-1014)aaC>aaT	p.N338N	TBCCD1_ENST00000338733.5_Silent_p.N338N|TBCCD1_ENST00000446782.1_Silent_p.N242N|TBCCD1_ENST00000479590.1_5'Flank	NM_001134415.1	NP_001127887.1	Q9NVR7	TBCC1_HUMAN	TBCC domain containing 1	338	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				cell morphogenesis (GO:0000902)|cytoskeleton organization (GO:0007010)|maintenance of centrosome location (GO:0051661)|maintenance of Golgi location (GO:0051684)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|spindle pole centrosome (GO:0031616)		p.N338N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|skin(1)	17	all_cancers(143;3.75e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;4.3e-21)	GBM - Glioblastoma multiforme(93;0.0474)		TAAAAGATTCGTTGCAACGAT	0.443													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17935	0.0		0.0	False		,,,				2504	0.0				p.N338N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1014T	3						.	G	,	1,4405	2.1+/-5.4	0,1,2202	101.0	93.0	96.0		1014,1014	-1.4	1.0	3		96	0,8600		0,0,4300	yes	coding-synonymous,coding-synonymous	TBCCD1	NM_001134415.1,NM_018138.3	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	338/558,338/558	186272719	1,13005	2203	4300	6503	187755413	SO:0001819	synonymous_variant	55171	exon5			BC025748	CCDS3276.1, CCDS75061.1	3q27.3	2006-03-09			ENSG00000113838	ENSG00000113838			25546	protein-coding gene	gene with protein product						12477932	Standard	NM_001134415		Approved	FLJ10560	uc003fqg.3	Q9NVR7	OTTHUMG00000156613	ENST00000424280.1:c.1014C>T	3.37:g.186272719G>A		Somatic		Capture	Illumina HiSeq	Phase_I	187755413	NM_001134415	B3KW69|D3DNU6|G5E9J4	Silent	SNP	ENST00000424280.1	37	CCDS3276.1																																																																																				0.443	TBCCD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344774.1	NM_018138	
AHSG	197	broad.mit.edu	37	3	186338468	186338468	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:186338468G>A	ENST00000273784.5	+	7	932	c.856G>A	c.(856-858)Gca>Aca	p.A286T	AHSG_ENST00000411641.2_Missense_Mutation_p.A285T	NM_001622.2	NP_001613.2	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	285					acute-phase response (GO:0006953)|negative regulation of bone mineralization (GO:0030502)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|ossification (GO:0001503)|pinocytosis (GO:0006907)|positive regulation of phagocytosis (GO:0050766)|regulation of bone mineralization (GO:0030500)|regulation of inflammatory response (GO:0050727)|skeletal system development (GO:0001501)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|kinase inhibitor activity (GO:0019210)	p.A285T(2)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(2)|stomach(1)	22	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)		TCCACTTGGCGCACCTGGACT	0.642																																					p.A285T												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.G853A	3						.						110.0	114.0	113.0					3																	186338468		2203	4300	6503	187821162	SO:0001583	missense	197	exon7			D67013, M16961	CCDS3278.1	3q27.3	2006-02-22			ENSG00000145192	ENSG00000145192			349	protein-coding gene	gene with protein product		138680				9322749, 7736783	Standard	NM_001622		Approved	FETUA, A2HS, HSGA	uc003fqk.4	P02765	OTTHUMG00000156605	ENST00000273784.5:c.856G>A	3.37:g.186338468G>A	ENSP00000273784:p.Ala286Thr	Somatic		Capture	Illumina HiSeq	Phase_I	187821162	NM_001622	A8K9N6|B2R7G1|O14961|O14962|Q9P152	Missense_Mutation	SNP	ENST00000273784.5	37		.	.	.	.	.	.	.	.	.	.	g	8.418	0.845807	0.16963	.	.	ENSG00000145192	ENST00000411641;ENST00000541510;ENST00000273784	T;T	0.05199	3.48;3.48	5.32	-4.37	0.03633	.	0.939020	0.08935	N	0.872506	T	0.03095	0.0091	N	0.08118	0	0.09310	N	1	B;B;B	0.18166	0.026;0.0;0.001	B;B;B	0.10450	0.005;0.0;0.0	T	0.47674	-0.9099	10	0.21014	T	0.42	-0.2865	11.5864	0.50920	0.2477:0.1865:0.5658:0.0	.	351;285;286	F5H0Q5;P02765;C9JV77	.;FETUA_HUMAN;.	T	285;351;286	ENSP00000393887:A285T;ENSP00000273784:A286T	ENSP00000273784:A286T	A	+	1	0	AHSG	187821162	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.463000	0.02361	-0.270000	0.09285	-1.467000	0.01014	GCA		0.642	AHSG-002	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000344762.1	NM_001622	
FETUB	26998	broad.mit.edu	37	3	186358445	186358445	+	Nonsense_Mutation	SNP	C	C	T	rs367977932		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:186358445C>T	ENST00000265029.3	+	1	297	c.196C>T	c.(196-198)Cga>Tga	p.R66*	FETUB_ENST00000450521.1_Nonsense_Mutation_p.R66*|RP11-134F2.2_ENST00000428501.1_RNA|FETUB_ENST00000382134.3_Nonsense_Mutation_p.R66*|FETUB_ENST00000382136.3_Nonsense_Mutation_p.R66*|RP11-134F2.2_ENST00000455926.1_RNA|FETUB_ENST00000488561.1_3'UTR|FETUB_ENST00000539949.1_Intron	NM_014375.2	NP_055190.2	Q9UGM5	FETUB_HUMAN	fetuin B	66	Cystatin fetuin-B-type 1. {ECO:0000255|PROSITE-ProRule:PRU00862}.				binding of sperm to zona pellucida (GO:0007339)|negative regulation of endopeptidase activity (GO:0010951)|single fertilization (GO:0007338)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)	p.R66*(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)	20	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0479)		GAGACTCAACCGAGTGAACGA	0.572																																					p.R66X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C196T	3						.	C	stop/ARG	0,4406		0,0,2203	132.0	140.0	137.0		196	3.3	1.0	3		137	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	FETUB	NM_014375.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		66/383	186358445	1,13005	2203	4300	6503	187841139	SO:0001587	stop_gained	26998	exon1			AJ242928	CCDS3279.1	3q27.3	2008-05-15			ENSG00000090512	ENSG00000090512			3658	protein-coding gene	gene with protein product		605954				10947975	Standard	XM_005247350		Approved		uc003fqn.3	Q9UGM5	OTTHUMG00000156586	ENST00000265029.3:c.196C>T	3.37:g.186358445C>T	ENSP00000265029:p.Arg66*	Somatic		Capture	Illumina HiSeq	Phase_I	187841139	NM_014375	B2RCW6|E9PG06|Q1RMZ0|Q5J876|Q6DK58|Q6GRB6|Q9Y6Z0	Nonsense_Mutation	SNP	ENST00000265029.3	37	CCDS3279.1	.	.	.	.	.	.	.	.	.	.	C	36	5.713496	0.96830	0.0	1.16E-4	ENSG00000090512	ENST00000450521;ENST00000265029;ENST00000382134;ENST00000382136	.	.	.	5.17	3.32	0.38043	.	0.137251	0.33916	N	0.004427	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.1746	6.7457	0.23460	0.1819:0.7253:0.0:0.0928	.	.	.	.	X	66	.	ENSP00000265029:R66X	R	+	1	2	FETUB	187841139	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.472000	0.45136	0.790000	0.33803	0.591000	0.81541	CGA		0.572	FETUB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344679.1	NM_014375	
KCNH8	131096	broad.mit.edu	37	3	19384132	19384132	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:19384132C>T	ENST00000328405.2	+	4	762	c.496C>T	c.(496-498)Cgg>Tgg	p.R166W		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	166					potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)	p.R166G(1)|p.R166W(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(3)|lung(37)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	77						AGCCCGGAGACGGAGTCGAGC	0.433																																					p.R166W	NSCLC(124;1625 1765 8018 24930 42026)											.	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.C496T	3						.						88.0	86.0	86.0					3																	19384132		2203	4300	6503	19359136	SO:0001583	missense	131096	exon4			AY053503	CCDS2632.1	3p24.3	2012-07-05			ENSG00000183960	ENSG00000183960		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18864	protein-coding gene	gene with protein product		608260				16382104	Standard	NM_144633		Approved	Kv12.1, elk3	uc003cbk.1	Q96L42	OTTHUMG00000129891	ENST00000328405.2:c.496C>T	3.37:g.19384132C>T	ENSP00000328813:p.Arg166Trp	Somatic		Capture	Illumina HiSeq	Phase_I	19359136	NM_144633	B7Z2I7|Q59GQ6	Missense_Mutation	SNP	ENST00000328405.2	37	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.312917	0.81358	.	.	ENSG00000183960	ENST00000328405	D	0.99014	-5.33	5.76	4.87	0.63330	.	0.000000	0.29466	U	0.012070	D	0.99187	0.9718	M	0.79011	2.435	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.931;0.997	D	0.99285	1.0897	9	.	.	.	.	16.0147	0.80427	0.1356:0.8644:0.0:0.0	.	166;166	B7Z398;Q96L42	.;KCNH8_HUMAN	W	166	ENSP00000328813:R166W	.	R	+	1	2	KCNH8	19359136	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.562000	0.45914	1.388000	0.46506	0.585000	0.79938	CGG		0.433	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633	
MASP1	5648	broad.mit.edu	37	3	186953583	186953583	+	Intron	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:186953583G>A	ENST00000337774.5	-	10	1693				MASP1_ENST00000392472.2_Silent_p.C579C|MASP1_ENST00000296280.6_Silent_p.C692C|MASP1_ENST00000495249.1_5'Flank	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)						complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)	p.C692C(1)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		GCTTGCTGCCGCATTCTTCAG	0.577																																					p.C692C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2076T	3						.						88.0	84.0	85.0					3																	186953583		2203	4300	6503	188436277	SO:0001627	intron_variant	5648	exon11			D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"""Serine peptidases / Serine peptidases"""	6901	protein-coding gene	gene with protein product		600521	"""mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"""	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.1303+5685C>T	3.37:g.186953583G>A		Somatic		Capture	Illumina HiSeq	Phase_I	188436277	NM_139125	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Silent	SNP	ENST00000337774.5	37	CCDS33907.1																																																																																				0.577	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879	
GP5	2814	broad.mit.edu	37	3	194118411	194118411	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:194118411G>T	ENST00000401815.1	-	1	672	c.601C>A	c.(601-603)Ctc>Atc	p.L201I	GP5_ENST00000323007.3_Missense_Mutation_p.L201I			P40197	GPV_HUMAN	glycoprotein V (platelet)	201					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|negative regulation of platelet activation (GO:0010544)|platelet activation (GO:0030168)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.L201I(1)		breast(3)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(14)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	35	all_cancers(143;6.64e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;7.38e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.06e-05)		TTCGAGTGGAGCAGAAGTCTC	0.562																																					p.L201I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C601A	3						.						77.0	83.0	81.0					3																	194118411		2203	4300	6503	195599700	SO:0001583	missense	2814	exon2			L11238	CCDS3307.1	3q29	2008-02-01			ENSG00000178732	ENSG00000178732		"""CD molecules"""	4443	protein-coding gene	gene with protein product		173511				7690959	Standard	NM_004488		Approved	CD42d	uc003ftv.1	P40197	OTTHUMG00000150345	ENST00000401815.1:c.601C>A	3.37:g.194118411G>T	ENSP00000383931:p.Leu201Ile	Somatic		Capture	Illumina HiSeq	Phase_I	195599700	NM_004488	D1MER9	Missense_Mutation	SNP	ENST00000401815.1	37	CCDS3307.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.536495	0.27475	.	.	ENSG00000178732	ENST00000401815;ENST00000323007	T;T	0.72505	-0.66;-0.66	4.66	3.77	0.43336	.	0.236599	0.21990	N	0.066179	T	0.79986	0.4541	M	0.62154	1.92	0.19300	N	0.999972	D	0.89917	1.0	D	0.87578	0.998	T	0.69661	-0.5085	10	0.66056	D	0.02	.	10.0906	0.42445	0.0798:0.1401:0.7801:0.0	.	201	P40197	GPV_HUMAN	I	201	ENSP00000383931:L201I;ENSP00000319286:L201I	ENSP00000319286:L201I	L	-	1	0	GP5	195599700	0.575000	0.26692	0.043000	0.18650	0.026000	0.11368	0.799000	0.27028	1.248000	0.43934	-0.315000	0.08773	CTC		0.562	GP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317710.1	NM_004488	
GP5	2814	broad.mit.edu	37	3	194118558	194118558	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:194118558C>T	ENST00000401815.1	-	1	525	c.454G>A	c.(454-456)Gct>Act	p.A152T	GP5_ENST00000323007.3_Missense_Mutation_p.A152T			P40197	GPV_HUMAN	glycoprotein V (platelet)	152					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|negative regulation of platelet activation (GO:0010544)|platelet activation (GO:0030168)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.A152T(1)		breast(3)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(14)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	35	all_cancers(143;6.64e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;7.38e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.06e-05)		TGGTTCAGAGCGAGCTCCTGC	0.483																																					p.A152T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G454A	3						.						77.0	78.0	78.0					3																	194118558		2203	4300	6503	195599847	SO:0001583	missense	2814	exon2			L11238	CCDS3307.1	3q29	2008-02-01			ENSG00000178732	ENSG00000178732		"""CD molecules"""	4443	protein-coding gene	gene with protein product		173511				7690959	Standard	NM_004488		Approved	CD42d	uc003ftv.1	P40197	OTTHUMG00000150345	ENST00000401815.1:c.454G>A	3.37:g.194118558C>T	ENSP00000383931:p.Ala152Thr	Somatic		Capture	Illumina HiSeq	Phase_I	195599847	NM_004488	D1MER9	Missense_Mutation	SNP	ENST00000401815.1	37	CCDS3307.1	.	.	.	.	.	.	.	.	.	.	C	5.440	0.266329	0.10294	.	.	ENSG00000178732	ENST00000401815;ENST00000323007	T;T	0.56275	0.47;0.47	4.82	-0.725	0.11174	.	1.007950	0.07987	N	0.986494	T	0.25457	0.0619	N	0.11201	0.11	0.09310	N	1	B	0.25667	0.131	B	0.19391	0.025	T	0.14504	-1.0470	10	0.22109	T	0.4	.	1.4417	0.02356	0.4179:0.2693:0.1372:0.1756	.	152	P40197	GPV_HUMAN	T	152	ENSP00000383931:A152T;ENSP00000319286:A152T	ENSP00000319286:A152T	A	-	1	0	GP5	195599847	0.000000	0.05858	0.008000	0.14137	0.653000	0.38743	-1.076000	0.03420	-0.209000	0.10156	-0.410000	0.06199	GCT		0.483	GP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317710.1	NM_004488	
ACAP2	23527	broad.mit.edu	37	3	195027310	195027310	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:195027310C>T	ENST00000326793.6	-	13	1276	c.1046G>A	c.(1045-1047)cGc>cAc	p.R349H		NM_012287.5	NP_036419.3	Q15057	ACAP2_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 2	349	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular response to nerve growth factor stimulus (GO:1990090)|protein localization to endosome (GO:0036010)|regulation of ARF GTPase activity (GO:0032312)	endosome membrane (GO:0010008)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.R349H(1)		cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	27						CCATGCCTGGCGCAGCTTTTC	0.403																																					p.R349H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1046A	3						.						151.0	151.0	151.0					3																	195027310		2203	4300	6503	196508599	SO:0001583	missense	23527	exon13				CCDS33924.1	3q29	2013-01-10	2008-09-22	2008-09-22	ENSG00000114331	ENSG00000114331		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16469	protein-coding gene	gene with protein product		607766	"""centaurin, beta 2"""	CENTB2		11050434, 11062263	Standard	NM_012287		Approved	KIAA0041, CNT-B2	uc003fun.4	Q15057	OTTHUMG00000155885	ENST00000326793.6:c.1046G>A	3.37:g.195027310C>T	ENSP00000324287:p.Arg349His	Somatic		Capture	Illumina HiSeq	Phase_I	196508599	NM_012287	A8K2V4|Q8N5Z8|Q9UQR3	Missense_Mutation	SNP	ENST00000326793.6	37	CCDS33924.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.835956	0.91117	.	.	ENSG00000114331	ENST00000326793	T	0.78126	-1.15	5.55	5.55	0.83447	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.105878	0.64402	D	0.000003	D	0.89079	0.6613	M	0.84846	2.72	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87353	0.2339	10	0.29301	T	0.29	.	18.484	0.90821	0.0:1.0:0.0:0.0	.	349	Q15057	ACAP2_HUMAN	H	349	ENSP00000324287:R349H	ENSP00000324287:R349H	R	-	2	0	ACAP2	196508599	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.593000	0.87608	0.511000	0.50034	CGC		0.403	ACAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342126.2	NM_012287	
CRBN	51185	broad.mit.edu	37	3	3192604	3192604	+	Missense_Mutation	SNP	G	G	A	rs566932471	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:3192604G>A	ENST00000231948.4	-	11	1296	c.1274C>T	c.(1273-1275)aCg>aTg	p.T425M	CRBN_ENST00000432408.2_Missense_Mutation_p.T424M|RP11-97C16.1_ENST00000607052.1_RNA	NM_016302.3	NP_057386.2	Q96SW2	CRBN_HUMAN	cereblon	425	Thalidomide-binding.				negative regulation of ion transmembrane transport (GO:0034766)|negative regulation of protein homooligomerization (GO:0032463)|positive regulation of protein homodimerization activity (GO:0090073)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP-dependent peptidase activity (GO:0004176)	p.T425M(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	11				Epithelial(13;0.00244)|OV - Ovarian serous cystadenocarcinoma(96;0.00617)|all cancers(10;0.0079)	Lenalidomide(DB00480)|Pomalidomide(DB08910)|Thalidomide(DB01041)	GTCTGGGATCGTGGGCAACAG	0.388													G|||	6	0.00119808	0.0	0.0	5008	,	,		19239	0.0		0.0	False		,,,				2504	0.0061				p.T424M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1271T	3						.						122.0	100.0	107.0					3																	3192604		2203	4300	6503	3167604	SO:0001583	missense	51185	exon11			BC017419	CCDS2562.1, CCDS54547.1	3p26.3	2014-05-27			ENSG00000113851	ENSG00000113851			30185	protein-coding gene	gene with protein product		609262	"""mental retardation, non-syndromic, autosomal recessive, 2A"""	MRT2A		15557513	Standard	NM_016302		Approved	MRT2	uc003bpq.3	Q96SW2	OTTHUMG00000090261	ENST00000231948.4:c.1274C>T	3.37:g.3192604G>A	ENSP00000231948:p.Thr425Met	Somatic		Capture	Illumina HiSeq	Phase_I	3167604	NM_001173482	B2R6H4|C9IZA9|C9JAH6|Q6AI62|Q6NVZ0|Q9UHW4	Missense_Mutation	SNP	ENST00000231948.4	37	CCDS2562.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.65|17.65	3.441988|3.441988	0.63067|0.63067	.|.	.|.	ENSG00000113851|ENSG00000113851	ENST00000424814|ENST00000231948;ENST00000432408;ENST00000546075	.|.	.|.	.|.	5.62|5.62	3.79|3.79	0.43588|0.43588	.|.	.|0.109699	.|0.64402	.|D	.|0.000011	.|T	.|0.32585	.|0.0834	L|L	0.29908|0.29908	0.895|0.895	0.35483|0.35483	D|D	0.79829|0.79829	.|P;B;B	.|0.52577	.|0.954;0.028;0.016	.|B;B;B	.|0.40782	.|0.34;0.01;0.004	.|T	.|0.45512	.|-0.9256	.|9	.|0.48119	.|T	.|0.1	-20.9665|-20.9665	8.4297|8.4297	0.32750|0.32750	0.0957:0.3766:0.5278:0.0|0.0957:0.3766:0.5278:0.0	.|.	.|359;424;425	.|F5H3U1;Q96SW2-2;Q96SW2	.|.;.;CRBN_HUMAN	X|M	377|425;424;359	.|.	.|ENSP00000231948:T425M	R|T	-|-	1|2	2|0	CRBN|CRBN	3167604|3167604	1.000000|1.000000	0.71417|0.71417	0.977000|0.977000	0.42913|0.42913	0.978000|0.978000	0.69477|0.69477	4.955000|4.955000	0.63638|0.63638	1.394000|1.394000	0.46624|0.46624	0.655000|0.655000	0.94253|0.94253	CGA|ACG		0.388	CRBN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206579.3	NM_016302	
ITPR1	3708	broad.mit.edu	37	3	4712444	4712444	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:4712444G>A	ENST00000443694.2	+	17	1993	c.1993G>A	c.(1993-1995)Gtc>Atc	p.V665I	ITPR1_ENST00000357086.4_Missense_Mutation_p.V680I|ITPR1_ENST00000456211.2_Missense_Mutation_p.V665I|ITPR1_ENST00000423119.2_Missense_Mutation_p.V680I|ITPR1_ENST00000354582.6_Missense_Mutation_p.V680I|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000302640.8_Missense_Mutation_p.V665I			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	680					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|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)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.V665I(1)		NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	ATTTGAAGGTGTCTCTTCCAC	0.423																																					p.V680I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2038A	3						.						74.0	65.0	68.0					3																	4712444		1881	4124	6005	4687444	SO:0001583	missense	3708	exon20			D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.1993G>A	3.37:g.4712444G>A	ENSP00000401671:p.Val665Ile	Somatic		Capture	Illumina HiSeq	Phase_I	4687444	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	7.276	0.608187	0.14002	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.90788	-2.73;-2.73;-2.73;-2.73;-2.73;-2.73	5.1	5.1	0.69264	.	0.253941	0.39475	N	0.001348	T	0.80042	0.4551	N	0.08118	0	0.80722	D	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.09377	0.0;0.001;0.004	T	0.74788	-0.3546	10	0.17369	T	0.5	.	14.2934	0.66295	0.0:0.0:0.8509:0.1491	.	665;680;680	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	I	680;665;680;680;680;665;665	ENSP00000306253:V665I;ENSP00000346595:V680I;ENSP00000405934:V680I;ENSP00000349597:V680I;ENSP00000397885:V665I;ENSP00000401671:V665I	ENSP00000306253:V665I	V	+	1	0	ITPR1	4687444	0.787000	0.28750	0.441000	0.26858	0.099000	0.18886	3.024000	0.49674	2.368000	0.80403	0.655000	0.94253	GTC		0.423	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
EDEM1	9695	broad.mit.edu	37	3	5243542	5243542	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:5243542C>G	ENST00000256497.4	+	4	924	c.791C>G	c.(790-792)gCc>gGc	p.A264G	EDEM1_ENST00000445686.1_Missense_Mutation_p.A69G	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like 1	264					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)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	calcium ion binding (GO:0005509)|misfolded protein binding (GO:0051787)	p.A264G(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)		TTATACATGGCCCATGACCTG	0.483																																					p.A264G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C791G	3						.						114.0	107.0	110.0					3																	5243542		2203	4300	6503	5218542	SO:0001583	missense	9695	exon4			D86967	CCDS33686.1	3p26.1	2008-02-05			ENSG00000134109	ENSG00000134109			18967	protein-coding gene	gene with protein product		607673				12610306	Standard	NM_014674		Approved	KIAA0212, EDEM	uc003bqi.3	Q92611	OTTHUMG00000154896	ENST00000256497.4:c.791C>G	3.37:g.5243542C>G	ENSP00000256497:p.Ala264Gly	Somatic		Capture	Illumina HiSeq	Phase_I	5218542	NM_014674	A8K9C8|B4DXP3	Missense_Mutation	SNP	ENST00000256497.4	37	CCDS33686.1	.	.	.	.	.	.	.	.	.	.	C	34	5.380682	0.95945	.	.	ENSG00000134109	ENST00000419550;ENST00000256497;ENST00000445686	D;D	0.87334	-2.24;-2.24	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.95806	0.8635	H	0.95645	3.7	0.80722	D	1	P;D;D	0.71674	0.865;0.998;0.998	P;D;D	0.79108	0.716;0.992;0.992	D	0.96656	0.9485	10	0.72032	D	0.01	-13.8072	19.5182	0.95174	0.0:1.0:0.0:0.0	.	69;264;42	B4DXP3;Q92611;B4DPV5	.;EDEM1_HUMAN;.	G	42;264;69	ENSP00000256497:A264G;ENSP00000394099:A69G	ENSP00000256497:A264G	A	+	2	0	EDEM1	5218542	1.000000	0.71417	0.994000	0.49952	0.983000	0.72400	7.490000	0.81461	2.603000	0.88011	0.655000	0.94253	GCC		0.483	EDEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337566.2	NM_014674	
LMCD1	29995	broad.mit.edu	37	3	8590555	8590555	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:8590555G>A	ENST00000157600.3	+	4	921	c.689G>A	c.(688-690)gGc>gAc	p.G230D	LMCD1_ENST00000535732.1_Missense_Mutation_p.G230D|LMCD1_ENST00000397386.3_Missense_Mutation_p.G118D|LMCD1_ENST00000454244.1_Missense_Mutation_p.G157D|LMCD1-AS1_ENST00000439407.1_RNA	NM_014583.2	NP_055398.1	Q9NZU5	LMCD1_HUMAN	LIM and cysteine-rich domains 1	230					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|regulation of cardiac muscle hypertrophy (GO:0010611)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.G230D(1)		breast(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)	16				OV - Ovarian serous cystadenocarcinoma(96;0.124)		ACCACCAACGGCAGTCTCAGT	0.617																																					p.G230D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G689A	3						.						35.0	26.0	29.0					3																	8590555		2203	4300	6503	8565555	SO:0001583	missense	29995	exon4			AF169284	CCDS33688.1, CCDS63533.1, CCDS63534.1	3p26-p24	2008-07-18			ENSG00000071282	ENSG00000071282			6633	protein-coding gene	gene with protein product	"""dyxin"""	604859				10662546	Standard	NM_001278233		Approved		uc003bqq.4	Q9NZU5	OTTHUMG00000154971	ENST00000157600.3:c.689G>A	3.37:g.8590555G>A	ENSP00000157600:p.Gly230Asp	Somatic		Capture	Illumina HiSeq	Phase_I	8565555	NM_014583	B4DG80	Missense_Mutation	SNP	ENST00000157600.3	37	CCDS33688.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.154059	0.57259	.	.	ENSG00000071282	ENST00000157600;ENST00000535732;ENST00000454244;ENST00000397386;ENST00000426878	T;D;T;T;T	0.81579	0.76;-1.51;0.75;0.77;-1.46	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000002	D	0.84338	0.5450	L	0.32530	0.975	0.80722	D	1	D;P;D	0.89917	0.999;0.928;1.0	D;P;D	0.91635	0.982;0.533;0.999	T	0.82265	-0.0543	10	0.31617	T	0.26	-34.7744	16.4205	0.83757	0.0:0.0:1.0:0.0	.	230;118;230	F5GX84;B4DEY6;Q9NZU5	.;.;LMCD1_HUMAN	D	230;230;157;118;187	ENSP00000157600:G230D;ENSP00000441100:G230D;ENSP00000396515:G157D;ENSP00000380542:G118D;ENSP00000411222:G187D	ENSP00000157600:G230D	G	+	2	0	LMCD1	8565555	1.000000	0.71417	1.000000	0.80357	0.034000	0.12701	7.224000	0.78042	2.657000	0.90304	0.655000	0.94253	GGC		0.617	LMCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337854.1	NM_014583	
SSUH2	51066	broad.mit.edu	37	3	8675622	8675622	+	Start_Codon_SNP	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:8675622C>T	ENST00000317371.4	-	11	1228	c.3G>A	c.(1-3)atG>atA	p.M1I	SSUH2_ENST00000544814.1_Intron|SSUH2_ENST00000341795.3_Start_Codon_SNP_p.M1I|SSUH2_ENST00000415132.1_Start_Codon_SNP_p.M1I			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	1						cytoplasm (GO:0005737)		p.M1I(1)									CTGGGGAGGGCATCTCCTGCA	0.582																																					p.M1I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3A	3						.						31.0	30.0	31.0					3																	8675622		2203	4300	6503	8650622	SO:0001582	initiator_codon_variant	51066	exon4			AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 32"""	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.3G>A	3.37:g.8675622C>T	ENSP00000324551:p.Met1Ile	Somatic		Capture	Illumina HiSeq	Phase_I	8650622	NM_015931	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Missense_Mutation	SNP	ENST00000317371.4	37	CCDS2568.1	.	.	.	.	.	.	.	.	.	.	C	9.487	1.099560	0.20552	.	.	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000415132	T;T;T	0.41400	1.03;1.03;1.0	3.36	-3.26	0.05064	.	3.160820	0.01086	U	0.005083	T	0.26666	0.0652	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.09751	-1.0660	9	0.52906	T	0.07	-0.0075	0.8006	0.01074	0.1502:0.33:0.2132:0.3066	.	1	Q9Y2M2	CC032_HUMAN	I	1	ENSP00000339150:M1I;ENSP00000324551:M1I;ENSP00000410757:M1I	ENSP00000324551:M1I	M	-	3	0	C3orf32	8650622	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-3.546000	0.00435	-0.900000	0.03896	-0.235000	0.12190	ATG		0.582	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931	Missense_Mutation
BRPF1	7862	broad.mit.edu	37	3	9776020	9776020	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:9776020C>T	ENST00000457855.1	+	1	207	c.196C>T	c.(196-198)Cgc>Tgc	p.R66C	BRPF1_ENST00000424362.1_Missense_Mutation_p.R66C|BRPF1_ENST00000433861.2_Missense_Mutation_p.R66C|BRPF1_ENST00000302054.3_Missense_Mutation_p.R66C|BRPF1_ENST00000383829.2_Missense_Mutation_p.R66C			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	66	Interaction with KAT6A and KAT6B.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R66C(2)		central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					GAAAAAGGGGCGCCAGTCACG	0.572																																					p.R66C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C196T	3						.						178.0	205.0	196.0					3																	9776020		2203	4300	6503	9751020	SO:0001583	missense	7862	exon2			M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"""peregrin"", ""bromodomain-containing protein, 140kD"""	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.196C>T	3.37:g.9776020C>T	ENSP00000410210:p.Arg66Cys	Somatic		Capture	Illumina HiSeq	Phase_I	9751020	NM_004634	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	ENST00000457855.1	37	CCDS2575.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.434743	0.83885	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000420291;ENST00000426583;ENST00000457855	T;T;T;T;T;T	0.52983	2.13;2.12;3.51;2.12;0.64;2.12	5.73	5.73	0.89815	.	0.051626	0.85682	D	0.000000	T	0.64735	0.2625	L	0.58101	1.795	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;P	0.76071	0.987;0.966;0.931;0.854	T	0.66172	-0.5990	10	0.87932	D	0	.	14.2034	0.65719	0.1502:0.8498:0.0:0.0	.	66;66;66;66	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	C	66	ENSP00000402485:R66C;ENSP00000398863:R66C;ENSP00000373340:R66C;ENSP00000306297:R66C;ENSP00000404235:R66C;ENSP00000410210:R66C	ENSP00000306297:R66C	R	+	1	0	BRPF1	9751020	0.996000	0.38824	1.000000	0.80357	0.980000	0.70556	3.602000	0.54066	2.709000	0.92574	0.563000	0.77884	CGC		0.572	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694	
TTLL3	26140	broad.mit.edu	37	3	9871013	9871013	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:9871013C>T	ENST00000547186.1	+	10	1704	c.1488C>T	c.(1486-1488)cgC>cgT	p.R496R	ARPC4-TTLL3_ENST00000397256.1_Silent_p.R557R|TTLL3_ENST00000455274.1_Silent_p.R284R|TTLL3_ENST00000397241.1_Silent_p.R284R|TTLL3_ENST00000427853.3_Silent_p.R284R|TTLL3_ENST00000466245.1_3'UTR|TTLL3_ENST00000426895.4_Silent_p.R639R|TTLL3_ENST00000383827.1_Silent_p.R284R|TTLL3_ENST00000430793.1_Silent_p.R284R	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	496	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.R496R(2)		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)					ACACCCTGCGCGTGGTCATTG	0.617																																					p.R639R												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C1917T	3						.						68.0	68.0	68.0					3																	9871013		2203	4300	6503	9846013	SO:0001819	synonymous_variant	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.1488C>T	3.37:g.9871013C>T		Somatic		Capture	Illumina HiSeq	Phase_I	9846013	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Silent	SNP	ENST00000547186.1	37		.	.	.	.	.	.	.	.	.	.	C	8.216	0.801441	0.16397	.	.	ENSG00000214021	ENST00000310252	T	0.19806	2.12	5.03	-10.1	0.00402	.	0.070909	0.53938	U	0.000044	T	0.27313	0.0670	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63791	-0.6557	7	0.56958	D	0.05	.	12.6263	0.56632	0.0771:0.1524:0.0:0.7705	.	.	.	.	C	452	ENSP00000312148:R452C	ENSP00000312148:R452C	R	+	1	0	TTLL3	9846013	0.000000	0.05858	0.440000	0.26846	0.776000	0.43924	-3.582000	0.00424	-2.490000	0.00517	-1.138000	0.01928	CGT		0.617	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2	
EFHB	151651	broad.mit.edu	37	3	19924163	19924163	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:19924163C>T	ENST00000295824.9	-	12	2368	c.2207G>A	c.(2206-2208)cGc>cAc	p.R736H	EFHB_ENST00000344838.4_Missense_Mutation_p.R606H	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	736							calcium ion binding (GO:0005509)	p.R736H(1)		breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						GTCACTGATGCGACGAATTCG	0.423																																					p.R736H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2207A	3						.						97.0	81.0	86.0					3																	19924163		2203	4300	6503	19899167	SO:0001583	missense	151651	exon12			AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"""EF-hand domain containing"""	26330	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 21"""					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.2207G>A	3.37:g.19924163C>T	ENSP00000295824:p.Arg736His	Somatic		Capture	Illumina HiSeq	Phase_I	19899167	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Missense_Mutation	SNP	ENST00000295824.9	37	CCDS33715.2	.	.	.	.	.	.	.	.	.	.	C	24.6	4.551641	0.86127	.	.	ENSG00000163576	ENST00000295824;ENST00000344838	T;T	0.29142	1.58;1.61	5.55	4.68	0.58851	.	0.128703	0.56097	N	0.000032	T	0.57125	0.2032	M	0.80847	2.515	0.37776	D	0.926858	P;D	0.89917	0.897;1.0	B;D	0.76071	0.196;0.987	T	0.66288	-0.5961	9	.	.	.	-6.7366	14.6957	0.69121	0.0:0.9302:0.0:0.0698	.	606;736	Q8N7U6-3;Q8N7U6	.;EFHB_HUMAN	H	736;606	ENSP00000295824:R736H;ENSP00000342263:R606H	.	R	-	2	0	EFHB	19899167	0.997000	0.39634	0.876000	0.34364	0.987000	0.75469	4.184000	0.58323	1.489000	0.48450	0.655000	0.94253	CGC		0.423	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	
TOP2B	7155	broad.mit.edu	37	3	25665149	25665149	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:25665149A>G	ENST00000264331.4	-	21	2583	c.2584T>C	c.(2584-2586)Tat>Cat	p.Y862H	TOP2B_ENST00000435706.2_Missense_Mutation_p.Y857H	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	862					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.Y857H(1)		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)	ATAGGAATATACCACTCAGGC	0.398																																					p.Y857H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2569C	3						.						92.0	85.0	87.0					3																	25665149		1874	4101	5975	25640153	SO:0001583	missense	7155	exon21			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.2584T>C	3.37:g.25665149A>G	ENSP00000264331:p.Tyr862His	Somatic		Capture	Illumina HiSeq	Phase_I	25640153	NM_001068	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	37		.	.	.	.	.	.	.	.	.	.	A	27.4	4.824691	0.90955	.	.	ENSG00000077097	ENST00000435706;ENST00000264331;ENST00000424225	T;T	0.53206	0.64;0.63	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.79064	0.4383	H	0.95884	3.735	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86061	0.1532	10	0.87932	D	0	-11.7676	16.1472	0.81578	1.0:0.0:0.0:0.0	.	857	Q02880-2	.	H	857;862;857	ENSP00000396704:Y857H;ENSP00000264331:Y862H	ENSP00000264331:Y862H	Y	-	1	0	TOP2B	25640153	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.243000	0.95416	2.272000	0.75746	0.455000	0.32223	TAT		0.398	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			
SLC4A7	9497	broad.mit.edu	37	3	27462220	27462220	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:27462220G>A	ENST00000295736.5	-	10	1526	c.1456C>T	c.(1456-1458)Cga>Tga	p.R486*	SLC4A7_ENST00000425128.2_Nonsense_Mutation_p.R478*|SLC4A7_ENST00000428386.1_Nonsense_Mutation_p.R362*|SLC4A7_ENST00000455077.1_Nonsense_Mutation_p.R367*|SLC4A7_ENST00000388777.4_Nonsense_Mutation_p.R36*|SLC4A7_ENST00000445684.1_Nonsense_Mutation_p.R482*|RN7SL859P_ENST00000578725.1_RNA|SLC4A7_ENST00000446700.1_Nonsense_Mutation_p.R478*|SLC4A7_ENST00000437179.1_Nonsense_Mutation_p.R367*|SLC4A7_ENST00000440156.1_Nonsense_Mutation_p.R482*|SLC4A7_ENST00000454389.1_Nonsense_Mutation_p.R495*|SLC4A7_ENST00000435667.2_Nonsense_Mutation_p.R371*	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	486					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)	p.R486*(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	GCTATTGATCGTCCAATTTCA	0.343																																					p.R486X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1456T	3						.						139.0	112.0	121.0					3																	27462220		2203	4300	6503	27437224	SO:0001587	stop_gained	9497	exon10			AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.1456C>T	3.37:g.27462220G>A	ENSP00000295736:p.Arg486*	Somatic		Capture	Illumina HiSeq	Phase_I	27437224	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Nonsense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	T	42	9.251588	0.99115	.	.	ENSG00000033867	ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777;ENST00000425128;ENST00000428179	.	.	.	5.63	5.63	0.86233	.	0.069653	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.475	0.61303	0.0:0.0:0.3319:0.6681	.	.	.	.	X	37;486;362;495;482;367;478;367;482;371;36;478;382	.	ENSP00000295736:R486X	R	-	1	2	SLC4A7	27437224	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.618000	0.36954	1.063000	0.40649	-0.256000	0.11100	CGA		0.343	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
TRIM71	131405	broad.mit.edu	37	3	32859658	32859658	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:32859658C>T	ENST00000383763.5	+	1	149	c.86C>T	c.(85-87)tCg>tTg	p.S29L		NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase	29	Ser-rich.				fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S29L(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TCCTCCAACTCGTCCGCGTCG	0.711																																					p.S29L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C86T	3						.						31.0	31.0	31.0					3																	32859658		1902	4108	6010	32834662	SO:0001583	missense	131405	exon1				CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	32669	protein-coding gene	gene with protein product			"""tripartite motif-containing 71"", ""tripartite motif containing 71"""				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	ENST00000383763.5:c.86C>T	3.37:g.32859658C>T	ENSP00000373272:p.Ser29Leu	Somatic		Capture	Illumina HiSeq	Phase_I	32834662	NM_001039111		Missense_Mutation	SNP	ENST00000383763.5	37	CCDS43060.1	.	.	.	.	.	.	.	.	.	.	C	18.85	3.710591	0.68730	.	.	ENSG00000206557	ENST00000383763	D	0.85088	-1.94	4.43	3.48	0.39840	Zinc finger, RING-type (2);	0.454594	0.17087	U	0.187546	D	0.85013	0.5600	N	0.19112	0.55	0.48975	D	0.999737	D	0.69078	0.997	D	0.67725	0.953	D	0.86116	0.1565	10	0.87932	D	0	.	12.0084	0.53272	0.1728:0.8272:0.0:0.0	.	29	Q2Q1W2	LIN41_HUMAN	L	29	ENSP00000373272:S29L	ENSP00000373272:S29L	S	+	2	0	TRIM71	32834662	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	5.192000	0.65115	2.171000	0.68590	0.462000	0.41574	TCG		0.711	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111	
MLH1	4292	broad.mit.edu	37	3	37053562	37053562	+	Missense_Mutation	SNP	C	C	T	rs63750380|rs4986984	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:37053562C>T	ENST00000231790.2	+	8	865	c.649C>T	c.(649-651)Cgc>Tgc	p.R217C	MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000435176.1_Missense_Mutation_p.R119C|MLH1_ENST00000458205.2_5'UTR|MLH1_ENST00000455445.2_5'UTR	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	217			R -> C (in HNPCC2; unknown pathological significance; proficient in a mismatch repair assay; dbSNP:rs4986984). {ECO:0000269|PubMed:15365995, ECO:0000269|PubMed:8797773, ECO:0000269|PubMed:9559627}.|R -> G.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.R217C(1)|p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						GGACAATATTCGCTCCATCTT	0.358		1	"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian, CNS"""	"""colorectal, endometrial, ovarian, CNS"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				C|||	3	0.000599042	0.0	0.0	5008	,	,		18079	0.002		0.0	False		,,,				2504	0.001				p.R217C		yes	Rec	yes	"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	3	3p21.3	4292	E.coli MutL homolog gene		"""E, O"""	.	.	2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|large_intestine(1)	c.C649T	3	GRCh37	CM950803	MLH1	M	rs4986984	.						156.0	140.0	146.0					3																	37053562		2203	4300	6503	37028566	SO:0001583	missense	4292	exon8	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	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"""mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)"", ""mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"""	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.649C>T	3.37:g.37053562C>T	ENSP00000231790:p.Arg217Cys	Somatic		Capture	Illumina HiSeq	Phase_I	37028566	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	25.1	4.602096	0.87055	.	.	ENSG00000076242	ENST00000231790;ENST00000436867;ENST00000537937;ENST00000383761;ENST00000435176	D;D	0.84873	-1.91;-1.91	5.76	5.76	0.90799	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94345	0.8182	H	0.95539	3.685	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.996	D	0.95235	0.8346	10	0.87932	D	0	-13.3583	12.9503	0.58397	0.2686:0.7314:0.0:0.0	rs4986984	119;217;217	E9PCU2;Q53GX1;P40692	.;.;MLH1_HUMAN	C	217;183;183;81;119	ENSP00000231790:R217C;ENSP00000402564:R119C	ENSP00000231790:R217C	R	+	1	0	MLH1	37028566	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.638000	0.54332	2.736000	0.93811	0.655000	0.94253	CGC		0.358	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	
LRRFIP2	9209	broad.mit.edu	37	3	37170588	37170588	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:37170588A>G	ENST00000336686.4	-	3	223	c.143T>C	c.(142-144)aTa>aCa	p.I48T	LRRFIP2_ENST00000421307.1_Missense_Mutation_p.I48T|LRRFIP2_ENST00000440230.1_Missense_Mutation_p.I48T|LRRFIP2_ENST00000421276.2_Missense_Mutation_p.I48T|LRRFIP2_ENST00000396428.2_Missense_Mutation_p.I48T|LRRFIP2_ENST00000354379.4_Missense_Mutation_p.I48T			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	48	DVL3-binding.				Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)|p.I48T(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						TCTCATGCGTATATCTCTTGC	0.403																																					p.I48T												.	.	2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|large_intestine(1)	c.T143C	3						.						164.0	165.0	164.0					3																	37170588		2203	4300	6503	37145592	SO:0001583	missense	9209	exon4			AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.143T>C	3.37:g.37170588A>G	ENSP00000338727:p.Ile48Thr	Somatic		Capture	Illumina HiSeq	Phase_I	37145592	NM_017724	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	37	CCDS2664.1	.	.	.	.	.	.	.	.	.	.	A	29.6	5.021175	0.93462	.	.	ENSG00000093167	ENST00000421307;ENST00000354379;ENST00000336686;ENST00000421276;ENST00000396428;ENST00000440230;ENST00000416425;ENST00000438374;ENST00000434749;ENST00000436858;ENST00000452742	T;T;T;T;T;T;T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34	5.47	5.47	0.80525	.	0.043564	0.85682	D	0.000000	T	0.70902	0.3277	M	0.67397	2.05	0.58432	D	0.999991	D;D;D;D	0.89917	0.997;1.0;0.999;1.0	D;D;D;D	0.87578	0.994;0.996;0.998;0.998	T	0.73830	-0.3859	10	0.66056	D	0.02	-16.1665	15.5144	0.75812	1.0:0.0:0.0:0.0	.	48;48;48;48	A8MXR0;Q9Y608-2;Q9Y608-4;Q9Y608	.;.;.;LRRF2_HUMAN	T	48	ENSP00000392217:I48T;ENSP00000346349:I48T;ENSP00000338727:I48T;ENSP00000416364:I48T;ENSP00000379705:I48T;ENSP00000405480:I48T;ENSP00000409574:I48T;ENSP00000412206:I48T;ENSP00000416907:I48T;ENSP00000416013:I48T;ENSP00000391360:I48T	ENSP00000338727:I48T	I	-	2	0	LRRFIP2	37145592	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.878000	0.92393	2.203000	0.70933	0.533000	0.62120	ATA		0.403	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309	
GOLGA4	2803	broad.mit.edu	37	3	37363342	37363342	+	Missense_Mutation	SNP	C	C	T	rs113898889		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:37363342C>T	ENST00000361924.2	+	13	2040	c.1666C>T	c.(1666-1668)Cgg>Tgg	p.R556W	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.R578W	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	556	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)	p.R556W(1)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						AAATAAACTTCGGGACCTTCA	0.348																																					p.R578W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1732T	3						.	C	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	63.0	68.0	66.0		1732,1666	2.0	0.0	3	dbSNP_132	66	0,8600		0,0,4300	no	missense,missense	GOLGA4	NM_001172713.1,NM_002078.4	101,101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	578/2244,556/2231	37363342	1,13005	2203	4300	6503	37338346	SO:0001583	missense	2803	exon14			U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.1666C>T	3.37:g.37363342C>T	ENSP00000354486:p.Arg556Trp	Somatic		Capture	Illumina HiSeq	Phase_I	37338346	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.552818	0.65425	2.27E-4	0.0	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000429018;ENST00000437131	T;T;T	0.24151	1.88;1.88;1.87	5.98	1.98	0.26296	.	0.827528	0.09891	N	0.742401	T	0.25568	0.0622	L	0.47716	1.5	0.09310	N	1	B;B;B;D	0.63880	0.083;0.017;0.017;0.993	B;B;B;P	0.46825	0.018;0.007;0.007;0.528	T	0.15723	-1.0427	10	0.72032	D	0.01	.	4.5577	0.12145	0.4262:0.3507:0.1528:0.0702	.	556;556;578;556	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	W	556;578;117;427	ENSP00000354486:R556W;ENSP00000349305:R578W;ENSP00000405842:R427W	ENSP00000349305:R578W	R	+	1	2	GOLGA4	37338346	0.110000	0.22057	0.020000	0.16555	0.985000	0.73830	0.356000	0.20181	0.074000	0.16767	0.591000	0.81541	CGG		0.348	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	
SLC22A13	9390	broad.mit.edu	37	3	38315860	38315860	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:38315860G>A	ENST00000311856.4	+	2	525	c.476G>A	c.(475-477)tGc>tAc	p.C159Y	SLC22A13_ENST00000450935.2_Missense_Mutation_p.C118Y	NM_004256.3	NP_004247.2	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 13	159					nicotinate transport (GO:2001142)|organic cation transport (GO:0015695)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	nicotinate transporter activity (GO:0090416)|organic cation transmembrane transporter activity (GO:0015101)	p.C159Y(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)		GGGCCCCTCTGCGACCGGTAA	0.582																																					p.C159Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G476A	3						.						156.0	136.0	143.0					3																	38315860		2203	4300	6503	38290864	SO:0001583	missense	9390	exon2			AB010438	CCDS2676.1	3p22.2	2013-07-18	2013-07-18	2003-10-15	ENSG00000172940	ENSG00000172940		"""Solute carriers"""	8494	protein-coding gene	gene with protein product		604047	"""organic cationic transporter-like 3"", ""solute carrier family 22 (organic anion transporter), member 13"""	ORCTL3		10072596, 18411268	Standard	NM_004256		Approved	OCTL1, OCTL3, OAT10	uc003chz.3	Q9Y226	OTTHUMG00000131086	ENST00000311856.4:c.476G>A	3.37:g.38315860G>A	ENSP00000310241:p.Cys159Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	38290864	NM_004256	B2RCV9|Q8IYG1	Missense_Mutation	SNP	ENST00000311856.4	37	CCDS2676.1	.	.	.	.	.	.	.	.	.	.	G	13.85	2.360401	0.41801	.	.	ENSG00000172940	ENST00000311856;ENST00000450935	T;T	0.58506	0.33;0.79	5.07	5.07	0.68467	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.302689	0.37530	N	0.002046	T	0.73164	0.3552	M	0.76574	2.34	0.31008	N	0.719587	D;D	0.58970	0.98;0.984	P;P	0.59115	0.77;0.852	T	0.76708	-0.2860	10	0.72032	D	0.01	.	17.4309	0.87539	0.0:0.0:1.0:0.0	.	159;159	Q9Y226-2;Q9Y226	.;S22AD_HUMAN	Y	159;118	ENSP00000310241:C159Y;ENSP00000406929:C118Y	ENSP00000310241:C159Y	C	+	2	0	SLC22A13	38290864	0.998000	0.40836	0.837000	0.33122	0.017000	0.09413	3.552000	0.53705	2.525000	0.85131	0.650000	0.86243	TGC		0.582	SLC22A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253746.2	NM_004256	
MYRIP	25924	broad.mit.edu	37	3	40231827	40231827	+	Missense_Mutation	SNP	C	C	T	rs199860359		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:40231827C>T	ENST00000302541.6	+	10	1880	c.1538C>T	c.(1537-1539)cCg>cTg	p.P513L	MYRIP_ENST00000444716.1_Missense_Mutation_p.P513L|MYRIP_ENST00000459828.1_3'UTR|MYRIP_ENST00000539167.1_Missense_Mutation_p.P326L|MYRIP_ENST00000396217.3_Missense_Mutation_p.P424L|MYRIP_ENST00000425621.1_Missense_Mutation_p.P513L	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	513	Actin-binding.|Myosin-binding.				intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)	p.P513L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		AGCAGCGAGCCGGAGGAGGCC	0.647													C|||	1	0.000199681	0.0	0.0	5008	,	,		16341	0.001		0.0	False		,,,				2504	0.0				p.P513L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1538T	3						.						47.0	54.0	51.0					3																	40231827		2203	4300	6503	40206831	SO:0001583	missense	25924	exon10			AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"""A-kinase anchor proteins"""	19156	protein-coding gene	gene with protein product	"""synaptotagmin-like protein homologue lacking C2 domains-c"", ""rab effector MYRIP"", ""Slp homologue lacking C2 domains"""	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.1538C>T	3.37:g.40231827C>T	ENSP00000301972:p.Pro513Leu	Somatic		Capture	Illumina HiSeq	Phase_I	40206831	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	37	CCDS2689.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	15.88	2.964888	0.53507	.	.	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000425621;ENST00000396217;ENST00000539167	T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81	5.94	4.09	0.47781	Myelin-associated oligodendrocytic basic protein (MOBP) (1);	0.377320	0.27826	N	0.017694	T	0.36082	0.0954	L	0.47716	1.5	0.44570	D	0.997536	D;D;D	0.69078	0.994;0.986;0.997	P;P;P	0.56398	0.797;0.552;0.778	T	0.02909	-1.1095	9	.	.	.	.	13.1852	0.59677	0.2909:0.7091:0.0:0.0	.	424;513;513	Q32M42;G3XAI8;Q8NFW9	.;.;MYRIP_HUMAN	L	513;513;513;424;326	ENSP00000398665:P513L;ENSP00000301972:P513L;ENSP00000389323:P513L;ENSP00000379519:P424L;ENSP00000438297:P326L	.	P	+	2	0	MYRIP	40206831	0.291000	0.24352	0.676000	0.29932	0.118000	0.20060	2.020000	0.41010	0.792000	0.33850	0.655000	0.94253	CCG		0.647	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460	
ENTPD3	956	broad.mit.edu	37	3	40468836	40468836	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:40468836C>A	ENST00000301825.3	+	11	1545	c.1427C>A	c.(1426-1428)cCt>cAt	p.P476H	ENTPD3_ENST00000456402.1_Missense_Mutation_p.P476H|ENTPD3-AS1_ENST00000425156.1_RNA|ENTPD3-AS1_ENST00000439293.1_RNA|ENTPD3-AS1_ENST00000452768.1_RNA	NM_001248.2	NP_001239.2	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase 3	476					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.P476H(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)		GCTGAAAGCCCTCTGATCCGT	0.557																																					p.P476H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1427A	3						.						127.0	106.0	113.0					3																	40468836		2203	4300	6503	40443840	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.1427C>A	3.37:g.40468836C>A	ENSP00000301825:p.Pro476His	Somatic		Capture	Illumina HiSeq	Phase_I	40443840	NM_001248	B2R8D0|G5E9N0|O60495|Q8N6K2	Missense_Mutation	SNP	ENST00000301825.3	37	CCDS2691.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.223583	0.58668	.	.	ENSG00000168032	ENST00000301825;ENST00000456402	T;T	0.11277	2.79;2.79	5.18	4.3	0.51218	.	0.589034	0.19091	N	0.122974	T	0.29749	0.0743	M	0.87038	2.855	0.29170	N	0.87723	P	0.44281	0.831	P	0.51657	0.676	T	0.19943	-1.0290	10	0.72032	D	0.01	-8.1592	12.806	0.57614	0.0:0.6847:0.3153:0.0	.	476	O75355	ENTP3_HUMAN	H	476	ENSP00000301825:P476H;ENSP00000401565:P476H	ENSP00000301825:P476H	P	+	2	0	ENTPD3	40443840	0.002000	0.14202	0.397000	0.26308	0.982000	0.71751	1.407000	0.34657	1.495000	0.48549	0.655000	0.94253	CCT		0.557	ENTPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254179.2	NM_001248	
NKTR	4820	broad.mit.edu	37	3	42678670	42678670	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:42678670T>C	ENST00000232978.8	+	13	1662	c.1474T>C	c.(1474-1476)Tct>Cct	p.S492P	RP4-613B23.1_ENST00000434363.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	492	Arg/Ser-rich.				protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.S492P(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		CTCATTGTCATCTCATCACTC	0.403																																					p.S492P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1474C	3						.						69.0	69.0	69.0					3																	42678670		2203	4300	6503	42653674	SO:0001583	missense	4820	exon13				CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"""NK-tumor recognition protein"", ""natural-killer cells cyclophilin-related protein"", ""NK-TR protein"""	161565	"""natural killer-tumor recognition sequence"""			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.1474T>C	3.37:g.42678670T>C	ENSP00000232978:p.Ser492Pro	Somatic		Capture	Illumina HiSeq	Phase_I	42653674	NM_005385		Missense_Mutation	SNP	ENST00000232978.8	37	CCDS2702.1	.	.	.	.	.	.	.	.	.	.	T	11.81	1.748366	0.30955	.	.	ENSG00000114857	ENST00000232978	T	0.14022	2.54	5.71	5.71	0.89125	.	0.233048	0.44483	D	0.000449	T	0.27967	0.0689	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.963	T	0.01692	-1.1294	10	0.87932	D	0	-10.6404	15.9738	0.80044	0.0:0.0:0.0:1.0	.	192;492	Q6M1B8;P30414	.;NKTR_HUMAN	P	492	ENSP00000232978:S492P	ENSP00000232978:S492P	S	+	1	0	NKTR	42653674	0.990000	0.36364	0.943000	0.38184	0.419000	0.31324	2.188000	0.42612	2.179000	0.69175	0.528000	0.53228	TCT		0.403	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385	
NKTR	4820	broad.mit.edu	37	3	42679712	42679712	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:42679712delA	ENST00000232978.8	+	13	2704	c.2516delA	c.(2515-2517)gaafs	p.E839fs	RP4-613B23.1_ENST00000434363.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	839					protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.N841fs*21(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		AATAAACAAGAAAAAAACAGA	0.398																																					p.E839fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2516delA	3						.						53.0	59.0	57.0					3																	42679712		2180	4294	6474	42654716	SO:0001589	frameshift_variant	4820	exon13				CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"""NK-tumor recognition protein"", ""natural-killer cells cyclophilin-related protein"", ""NK-TR protein"""	161565	"""natural killer-tumor recognition sequence"""			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.2516delA	3.37:g.42679712delA	ENSP00000232978:p.Glu839fs	Somatic		Capture	Illumina HiSeq	Phase_I	42654716	NM_005385		Frame_Shift_Del	DEL	ENST00000232978.8	37	CCDS2702.1																																																																																				0.398	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385	
POMGNT2	84892	broad.mit.edu	37	3	43121927	43121927	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:43121927G>A	ENST00000344697.2	-	2	1342	c.997C>T	c.(997-999)Cgg>Tgg	p.R333W	POMGNT2_ENST00000441964.1_Missense_Mutation_p.R333W	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	333					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)	p.R333W(2)									CTGACCAGCCGCACGACATCA	0.602																																					p.R333W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C997T	3						.						70.0	64.0	66.0					3																	43121927		2203	4300	6503	43096931	SO:0001583	missense	84892	exon2			AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"""chromosome 3 open reading frame 39"", ""glycosyltransferase-like domain containing 2"""	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.997C>T	3.37:g.43121927G>A	ENSP00000344125:p.Arg333Trp	Somatic		Capture	Illumina HiSeq	Phase_I	43096931	NM_032806	B3KWC3|Q96SY3	Missense_Mutation	SNP	ENST00000344697.2	37	CCDS2709.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816164	0.50527	.	.	ENSG00000144647	ENST00000441964;ENST00000344697	T;T	0.79653	-1.29;-1.29	5.56	4.67	0.58626	.	0.060639	0.64402	D	0.000002	D	0.87010	0.6071	M	0.61703	1.905	0.54753	D	0.999986	D	0.76494	0.999	D	0.63033	0.91	D	0.88462	0.3056	10	0.87932	D	0	-23.1393	15.5053	0.75735	0.0:0.1388:0.8612:0.0	.	333	Q8NAT1	AGO61_HUMAN	W	333	ENSP00000408992:R333W;ENSP00000344125:R333W	ENSP00000344125:R333W	R	-	1	2	C3orf39	43096931	1.000000	0.71417	0.996000	0.52242	0.561000	0.35649	5.434000	0.66526	1.317000	0.45149	0.650000	0.86243	CGG		0.602	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806	
ZNF35	7584	broad.mit.edu	37	3	44700822	44700822	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:44700822C>T	ENST00000396056.2	+	4	1202	c.967C>T	c.(967-969)Cgg>Tgg	p.R323W	ZNF35_ENST00000542250.1_Missense_Mutation_p.R163W|RP11-944L7.4_ENST00000457331.1_RNA|ZNF35_ENST00000296092.3_3'UTR	NM_003420.3	NP_003411.3	P13682	ZNF35_HUMAN	zinc finger protein 35	323					cellular response to retinoic acid (GO:0071300)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cell (GO:0005623)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R323W(1)		large_intestine(3)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	12		Ovarian(412;0.0228)		OV - Ovarian serous cystadenocarcinoma(275;2.49e-27)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)		ACAACTTGCTCGGCACCAGAA	0.388																																					p.R323W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C967T	3						.						57.0	60.0	59.0					3																	44700822		2203	4300	6503	44675826	SO:0001583	missense	7584	exon4			X07289	CCDS2718.2	3p21.32	2013-01-08	2006-05-11		ENSG00000169981	ENSG00000169981		"""Zinc fingers, C2H2-type"""	13099	protein-coding gene	gene with protein product		194533	"""zinc finger protein 35 (clone HF.10)"""			2108922, 1572646	Standard	NM_003420		Approved	HF.10, HF10, Zfp105	uc003cnq.3	P13682	OTTHUMG00000133091	ENST00000396056.2:c.967C>T	3.37:g.44700822C>T	ENSP00000379368:p.Arg323Trp	Somatic		Capture	Illumina HiSeq	Phase_I	44675826	NM_003420	B2RBU6|Q53Y54|Q96D01	Missense_Mutation	SNP	ENST00000396056.2	37	CCDS2718.2	.	.	.	.	.	.	.	.	.	.	C	16.03	3.008224	0.54361	.	.	ENSG00000169981	ENST00000396056;ENST00000542250	T;T	0.36878	1.23;1.23	5.1	4.22	0.49857	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42548	D	0.000691	T	0.60508	0.2274	M	0.91872	3.25	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	T	0.58907	-0.7553	10	0.66056	D	0.02	-24.5525	4.3158	0.10993	0.1965:0.6403:0.0:0.1632	.	323	P13682	ZNF35_HUMAN	W	323;163	ENSP00000379368:R323W;ENSP00000443714:R163W	ENSP00000379368:R323W	R	+	1	2	ZNF35	44675826	0.000000	0.05858	0.997000	0.53966	0.999000	0.98932	-0.922000	0.04004	2.824000	0.97209	0.655000	0.94253	CGG		0.388	ZNF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256749.4	NM_003420	
LARS2	23395	broad.mit.edu	37	3	45557631	45557631	+	Missense_Mutation	SNP	C	C	T	rs575606480	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:45557631C>T	ENST00000415258.1	+	16	2048	c.1907C>T	c.(1906-1908)aCg>aTg	p.T636M	LARS2_ENST00000467936.1_3'UTR|LARS2_ENST00000265537.3_Missense_Mutation_p.T636M|LARS2_ENST00000414984.1_Missense_Mutation_p.T593M			Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial	636					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)	p.T636M(2)		endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)	TTAGAGGTGACGTGGGAGAAG	0.448													C|||	5	0.000998403	0.0	0.0	5008	,	,		20413	0.0		0.0	False		,,,				2504	0.0051				p.T636M												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C1907T	3						.						167.0	138.0	148.0					3																	45557631		2203	4300	6503	45532635	SO:0001583	missense	23395	exon17			AJ312685	CCDS2728.1	3p21.3	2012-10-26			ENSG00000011376	ENSG00000011376	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	17095	protein-coding gene	gene with protein product	"""leucine tRNA ligase 2, mitochondrial"""	604544				20194621, 15123417	Standard	NM_015340		Approved	KIAA0028, LEURS, MGC26121	uc003cop.1	Q15031	OTTHUMG00000133177	ENST00000415258.1:c.1907C>T	3.37:g.45557631C>T	ENSP00000408576:p.Thr636Met	Somatic		Capture	Illumina HiSeq	Phase_I	45532635	NM_015340		Missense_Mutation	SNP	ENST00000415258.1	37	CCDS2728.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.677612	0.47886	.	.	ENSG00000011376	ENST00000265537;ENST00000415258;ENST00000414984	T;T;T	0.76968	-1.06;-1.06;-1.06	5.39	4.5	0.54988	.	0.234311	0.42821	D	0.000656	T	0.58864	0.2152	N	0.19112	0.55	0.53688	D	0.999979	P;B	0.37176	0.586;0.357	B;B	0.25140	0.058;0.058	T	0.62572	-0.6826	10	0.59425	D	0.04	-14.3513	10.4617	0.44583	0.0:0.7922:0.1355:0.0722	.	593;636	E9PHM2;Q15031	.;SYLM_HUMAN	M	636;636;593	ENSP00000265537:T636M;ENSP00000408576:T636M;ENSP00000412893:T593M	ENSP00000265537:T636M	T	+	2	0	LARS2	45532635	1.000000	0.71417	0.992000	0.48379	0.959000	0.62525	4.690000	0.61731	1.261000	0.44149	0.655000	0.94253	ACG		0.448	LARS2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345001.1	NM_015340	
SLC6A20	54716	broad.mit.edu	37	3	45812818	45812818	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:45812818C>T	ENST00000358525.4	-	6	941	c.826G>A	c.(826-828)Gcc>Acc	p.A276T	SLC6A20_ENST00000456124.2_Missense_Mutation_p.A276T|SLC6A20_ENST00000353278.4_Missense_Mutation_p.A239T	NM_020208.3	NP_064593.1	Q9NP91	S6A20_HUMAN	solute carrier family 6 (proline IMINO transporter), member 20	276					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|glycine transport (GO:0015816)|ion transport (GO:0006811)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)	p.A239T(1)|p.A276T(1)		breast(1)|endometrium(1)|large_intestine(6)|ovary(2)|skin(2)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(193;0.01)|KIRC - Kidney renal clear cell carcinoma(197;0.0225)|Kidney(197;0.0267)		ACGATGATGGCGTGCTTCTGG	0.517																																					p.A239T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G715A	3						.						215.0	172.0	186.0					3																	45812818		2203	4300	6503	45787822	SO:0001583	missense	54716	exon5			AF075260	CCDS2730.1, CCDS43077.1	3p21.6	2013-05-22			ENSG00000163817	ENSG00000163817		"""Solute carriers"""	30927	protein-coding gene	gene with protein product		605616				9932288, 11352561	Standard	NM_022405		Approved	XT3, Xtrp3	uc011bai.2	Q9NP91	OTTHUMG00000133446	ENST00000358525.4:c.826G>A	3.37:g.45812818C>T	ENSP00000346298:p.Ala276Thr	Somatic		Capture	Illumina HiSeq	Phase_I	45787822	NM_022405	A1A4F2|O75590|Q8TF10|Q9NPQ2|Q9NQ77	Missense_Mutation	SNP	ENST00000358525.4	37	CCDS43077.1	.	.	.	.	.	.	.	.	.	.	C	18.46	3.629099	0.67015	.	.	ENSG00000163817	ENST00000353278;ENST00000358525;ENST00000456124;ENST00000413781	T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44	5.2	4.33	0.51752	.	0.056297	0.64402	N	0.000001	T	0.76047	0.3933	L	0.56280	1.765	0.52099	D	0.99994	B;B	0.26120	0.117;0.142	B;B	0.23018	0.025;0.043	T	0.73225	-0.4050	10	0.46703	T	0.11	.	13.5036	0.61471	0.0:0.9243:0.0:0.0757	.	239;276	Q9NP91-2;Q9NP91	.;S6A20_HUMAN	T	239;276;276;229	ENSP00000296133:A239T;ENSP00000346298:A276T;ENSP00000404310:A276T;ENSP00000395506:A229T	ENSP00000296133:A239T	A	-	1	0	SLC6A20	45787822	1.000000	0.71417	0.999000	0.59377	0.859000	0.49053	5.730000	0.68546	1.190000	0.43042	0.467000	0.42956	GCC		0.517	SLC6A20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257318.3	NM_020208	
CCR1	1230	broad.mit.edu	37	3	46244961	46244961	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:46244961C>T	ENST00000296140.3	-	2	969	c.844G>A	c.(844-846)Gct>Act	p.A282T	CCR3_ENST00000357422.2_Intron	NM_001295.2	NP_001286.1	P32246	CCR1_HUMAN	chemokine (C-C motif) receptor 1	282					calcium ion transport (GO:0006816)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell chemotaxis (GO:0002407)|exocytosis (GO:0006887)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of bone mineralization (GO:0030502)|negative regulation of gene expression (GO:0010629)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of osteoclast differentiation (GO:0045672)|response to wounding (GO:0009611)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine (C-C motif) ligand 7 binding (GO:0035717)|chemokine receptor activity (GO:0004950)|phosphatidylinositol phospholipase C activity (GO:0004435)	p.A282T(1)		autonomic_ganglia(1)|large_intestine(6)|lung(6)|pancreas(1)|skin(3)	17				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		ACTTGCACAGCCAGGTCCAAA	0.498																																					p.A282T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G844A	3						.						66.0	59.0	62.0					3																	46244961		2203	4300	6503	46219965	SO:0001583	missense	1230	exon2				CCDS2737.1	3p21	2012-08-08			ENSG00000163823	ENSG00000163823		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1602	protein-coding gene	gene with protein product		601159		SCYAR1, CMKBR1		7679328	Standard	NM_001295		Approved	CKR-1, MIP1aR, CD191	uc003cph.1	P32246	OTTHUMG00000133451	ENST00000296140.3:c.844G>A	3.37:g.46244961C>T	ENSP00000296140:p.Ala282Thr	Somatic		Capture	Illumina HiSeq	Phase_I	46219965	NM_001295	Q86VA9	Missense_Mutation	SNP	ENST00000296140.3	37	CCDS2737.1	.	.	.	.	.	.	.	.	.	.	C	16.78	3.217869	0.58560	.	.	ENSG00000163823	ENST00000296140	T	0.38401	1.14	5.33	5.33	0.75918	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	T	0.58878	0.2153	M	0.77616	2.38	0.46654	D	0.999145	P	0.52692	0.955	P	0.57283	0.817	T	0.59752	-0.7395	10	0.48119	T	0.1	.	19.3805	0.94530	0.0:1.0:0.0:0.0	.	282	P32246	CCR1_HUMAN	T	282	ENSP00000296140:A282T	ENSP00000296140:A282T	A	-	1	0	CCR1	46219965	1.000000	0.71417	0.994000	0.49952	0.020000	0.10135	3.201000	0.51059	2.656000	0.90262	0.655000	0.94253	GCT		0.498	CCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257325.2	NM_001295	
NBEAL2	23218	broad.mit.edu	37	3	47049804	47049804	+	Missense_Mutation	SNP	G	G	A	rs528281960		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:47049804G>A	ENST00000450053.3	+	51	7930	c.7751G>A	c.(7750-7752)cGc>cAc	p.R2584H	NBEAL2_ENST00000383740.2_Missense_Mutation_p.R833H|NBEAL2_ENST00000292309.5_Missense_Mutation_p.R2400H	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2584					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.R1961H(1)|p.R2584H(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)		ACTGTACGCCGCGGACAGTTT	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		21901	0.001		0.0	False		,,,				2504	0.0				p.R2584H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G7751A	3						.						56.0	53.0	54.0					3																	47049804		2009	4174	6183	47024808	SO:0001583	missense	23218	exon51			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.7751G>A	3.37:g.47049804G>A	ENSP00000415034:p.Arg2584His	Somatic		Capture	Illumina HiSeq	Phase_I	47024808	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	37	CCDS46817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.02|14.02	2.411671|2.411671	0.42817|0.42817	.|.	.|.	ENSG00000160796|ENSG00000160796	ENST00000416683|ENST00000292309;ENST00000383740;ENST00000450053;ENST00000445550	.|T;T;T	.|0.17691	.|2.26;2.26;2.26	5.16|5.16	3.38|3.38	0.38709|0.38709	.|WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.|0.060599	.|0.64402	.|N	.|0.000003	T|T	0.19846|0.19846	0.0477|0.0477	M|M	0.71581|0.71581	2.175|2.175	0.47037|0.47037	D|D	0.99929|0.99929	.|B;B	.|0.13145	.|0.007;0.004	.|B;B	.|0.08055	.|0.002;0.003	T|T	0.03608|0.03608	-1.1020|-1.1020	5|10	.|0.66056	.|D	.|0.02	.|.	9.4658|9.4658	0.38811|0.38811	0.1714:0.0:0.8286:0.0|0.1714:0.0:0.8286:0.0	.|.	.|2400;2584	.|Q6ZNJ1-2;Q6ZNJ1	.|.;NBEL2_HUMAN	T|H	1872|2400;833;2584;527	.|ENSP00000292309:R2400H;ENSP00000373246:R833H;ENSP00000415034:R2584H	.|ENSP00000292309:R2400H	A|R	+|+	1|2	0|0	NBEAL2|NBEAL2	47024808|47024808	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.921000|0.921000	0.55340|0.55340	3.338000|3.338000	0.52128|0.52128	0.756000|0.756000	0.33013|0.33013	0.561000|0.561000	0.74099|0.74099	GCG|CGC		0.582	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
PTPN23	25930	broad.mit.edu	37	3	47450515	47450515	+	Missense_Mutation	SNP	G	G	A	rs200808850		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:47450515G>A	ENST00000265562.4	+	16	1657	c.1580G>A	c.(1579-1581)cGc>cAc	p.R527H	PTPN23_ENST00000431726.1_Missense_Mutation_p.R401H	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	527					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.R527H(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)		GGCAACCTGCGCCTGCTCAGC	0.652																																					p.R527H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1580A	3						.	G	HIS/ARG	0,4406		0,0,2203	87.0	85.0	86.0		1580	4.3	1.0	3		86	2,8598	2.2+/-6.3	0,2,4298	yes	missense	PTPN23	NM_015466.2	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	527/1637	47450515	2,13004	2203	4300	6503	47425519	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.1580G>A	3.37:g.47450515G>A	ENSP00000265562:p.Arg527His	Somatic		Capture	Illumina HiSeq	Phase_I	47425519	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	37	CCDS2754.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.017400	0.93404	0.0	2.33E-4	ENSG00000076201	ENST00000456408;ENST00000265562	T	0.30714	1.52	4.29	4.29	0.51040	.	0.000000	0.85682	D	0.000000	T	0.52517	0.1739	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.80764	0.978;0.994	T	0.57271	-0.7840	10	0.72032	D	0.01	-21.4084	15.6718	0.77283	0.0:0.0:1.0:0.0	.	401;527	B4DST5;Q9H3S7	.;PTN23_HUMAN	H	492;527	ENSP00000265562:R527H	ENSP00000265562:R527H	R	+	2	0	PTPN23	47425519	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	9.215000	0.95146	2.220000	0.72140	0.557000	0.71058	CGC		0.652	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466	
CSPG5	10675	broad.mit.edu	37	3	47614362	47614362	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:47614362C>T	ENST00000383738.2	-	3	3294	c.1196G>A	c.(1195-1197)tGc>tAc	p.C399Y	CSPG5_ENST00000264723.4_Missense_Mutation_p.C399Y|CSPG5_ENST00000456150.1_Missense_Mutation_p.C261Y	NM_001206943.1|NM_001206945.1	NP_001193872.1|NP_001193874.1	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan C)	399	EGF-like.				axon regeneration (GO:0031103)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)|regulation of growth (GO:0040008)|regulation of synaptic transmission (GO:0050804)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	growth factor activity (GO:0008083)	p.C399Y(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	22				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		CTGCGTGTTGCACCTGCAGCA	0.632																																					p.C399Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1196A	3						.						68.0	60.0	62.0					3																	47614362		2203	4300	6503	47589366	SO:0001583	missense	10675	exon3			AF059274	CCDS2757.1, CCDS56252.1, CCDS56253.1, CCDS74930.1	3p21.3	2008-07-18			ENSG00000114646	ENSG00000114646			2467	protein-coding gene	gene with protein product		606775				9950058	Standard	NM_006574		Approved	NGC	uc003crp.4	O95196	OTTHUMG00000133518	ENST00000383738.2:c.1196G>A	3.37:g.47614362C>T	ENSP00000373244:p.Cys399Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	47589366	NM_006574	Q71M39|Q71M40	Missense_Mutation	SNP	ENST00000383738.2	37	CCDS56253.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.726591	0.89298	.	.	ENSG00000114646	ENST00000456150;ENST00000383738;ENST00000264723	T;T;T	0.56611	0.45;0.53;0.6	4.81	4.81	0.61882	Epidermal growth factor-like (1);	0.000000	0.85682	D	0.000000	T	0.71953	0.3401	M	0.75085	2.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.75258	-0.3381	10	0.66056	D	0.02	-13.6925	15.4314	0.75102	0.0:1.0:0.0:0.0	.	399;399	O95196;O95196-2	CSPG5_HUMAN;.	Y	261;399;399	ENSP00000392096:C261Y;ENSP00000373244:C399Y;ENSP00000264723:C399Y	ENSP00000264723:C399Y	C	-	2	0	CSPG5	47589366	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.029000	0.76477	2.501000	0.84356	0.561000	0.74099	TGC		0.632	CSPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257489.1	NM_006574	
DHX30	22907	broad.mit.edu	37	3	47889427	47889427	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:47889427G>A	ENST00000445061.1	+	14	2674	c.2267G>A	c.(2266-2268)cGc>cAc	p.R756H	DHX30_ENST00000446256.2_Missense_Mutation_p.R717H|MIR1226_ENST00000408658.1_RNA|DHX30_ENST00000457607.1_Missense_Mutation_p.R784H|DHX30_ENST00000348968.4_Missense_Mutation_p.R728H	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	756	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)	p.R756H(1)		endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		AAGGAAGAACGCTATGACCTG	0.567																																					p.R756H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2267A	3						.						142.0	121.0	128.0					3																	47889427		2203	4300	6503	47864431	SO:0001583	missense	22907	exon14			AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"""DEAH-boxes"""	16716	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 30"""	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.2267G>A	3.37:g.47889427G>A	ENSP00000405620:p.Arg756His	Somatic		Capture	Illumina HiSeq	Phase_I	47864431	NM_138615	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Missense_Mutation	SNP	ENST00000445061.1	37	CCDS2759.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.399638	0.42512	.	.	ENSG00000132153	ENST00000446256;ENST00000445061;ENST00000348968;ENST00000457607	T;T;T;T	0.02763	4.17;4.17;4.17;4.17	5.73	4.86	0.63082	Helicase, C-terminal (3);	0.167002	0.53938	N	0.000045	T	0.06600	0.0169	L	0.52573	1.65	0.50467	D	0.999879	D;P	0.58620	0.983;0.763	P;B	0.50231	0.635;0.254	T	0.40496	-0.9560	10	0.38643	T	0.18	.	13.936	0.64026	0.0728:0.0:0.9272:0.0	.	756;717	Q7L2E3;Q7L2E3-3	DHX30_HUMAN;.	H	717;756;728;784	ENSP00000392601:R717H;ENSP00000405620:R756H;ENSP00000343442:R728H;ENSP00000394682:R784H	ENSP00000343442:R728H	R	+	2	0	DHX30	47864431	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.761000	0.62243	1.429000	0.47314	0.563000	0.77884	CGC		0.567	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615	
NME6	10201	broad.mit.edu	37	3	48336203	48336203	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:48336203C>T	ENST00000452211.1	-	7	722	c.485G>A	c.(484-486)cGc>cAc	p.R162H	NME6_ENST00000415644.1_Missense_Mutation_p.R95H|NME6_ENST00000435684.1_Missense_Mutation_p.A149T|NME6_ENST00000450160.1_Missense_Mutation_p.A149T|NME6_ENST00000442597.1_Missense_Mutation_p.R162H|NME6_ENST00000415053.1_Missense_Mutation_p.R162H|NME6_ENST00000451657.1_Missense_Mutation_p.A149T|NME6_ENST00000426723.1_Missense_Mutation_p.R95H|NME6_ENST00000426689.2_Missense_Mutation_p.R162H|NME6_ENST00000421967.1_Missense_Mutation_p.R170H|NME6_ENST00000447314.1_Missense_Mutation_p.R117H|ZNF589_ENST00000412564.1_Intron|NME6_ENST00000444069.1_5'UTR			O75414	NDK6_HUMAN	NME/NM23 nucleoside diphosphate kinase 6	162					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.R170H(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)		AGGGCCACAGCGCAACTGGGG	0.562																																					p.R170H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G509A	3						.						100.0	92.0	95.0					3																	48336203		2203	4300	6503	48311207	SO:0001583	missense	10201	exon6			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.485G>A	3.37:g.48336203C>T	ENSP00000392352:p.Arg162His	Somatic		Capture	Illumina HiSeq	Phase_I	48311207	NM_005793	B4DGW7|B4DM99|Q53HM5|Q96E73|Q9BQ63	Missense_Mutation	SNP	ENST00000452211.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.298969|5.298969	0.95574|0.95574	.|.	.|.	ENSG00000172113|ENSG00000172113	ENST00000450160;ENST00000451657;ENST00000435684|ENST00000421967;ENST00000426689;ENST00000452211;ENST00000426723;ENST00000415644;ENST00000415053;ENST00000442597;ENST00000447314;ENST00000425930	.|T;T;T;T;T;T;T	.|0.66638	.|0.35;0.36;0.36;0.36;0.36;-0.22;0.38	4.48|4.48	4.48|4.48	0.54585|0.54585	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.72566|0.72566	0.3476|0.3476	L|L	0.29908|0.29908	0.895|0.895	0.30258|0.30258	N|N	0.793406|0.793406	P|D;D;D	0.46327|0.89917	0.876|1.0;1.0;0.998	B|D;P;P	0.39738|0.87578	0.308|0.998;0.894;0.799	T|T	0.71839|0.71839	-0.4471|-0.4471	8|10	0.87932|0.62326	D|D	0|0.03	-3.3845|-3.3845	15.0702|15.0702	0.72030|0.72030	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	149|95;162;162	O75414-3|O75414-2;O75414;C9J9V6	.|.;NDK6_HUMAN;.	T|H	149|170;162;162;95;95;162;162;117;162	.|ENSP00000416658:R170H;ENSP00000440286:R162H;ENSP00000392352:R162H;ENSP00000399582:R162H;ENSP00000406642:R162H;ENSP00000414842:R117H;ENSP00000411116:R162H	ENSP00000393261:A149T|ENSP00000399582:R162H	A|R	-|-	1|2	0|0	NME6|NME6	48311207|48311207	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.916000|0.916000	0.54674|0.54674	4.866000|4.866000	0.63005|0.63005	2.494000|2.494000	0.84150|0.84150	0.561000|0.561000	0.74099|0.74099	GCT|CGC		0.562	NME6-005	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000346107.1	NM_005793	
PFKFB4	5210	broad.mit.edu	37	3	48573795	48573795	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:48573795A>G	ENST00000232375.3	-	8	846	c.734T>C	c.(733-735)aTc>aCc	p.I245T	PFKFB4_ENST00000541519.1_Missense_Mutation_p.I211T|PFKFB4_ENST00000545984.1_3'UTR|PFKFB4_ENST00000383734.2_Missense_Mutation_p.I245T|PFKFB4_ENST00000416568.1_Missense_Mutation_p.I245T|PFKFB4_ENST00000536104.1_Missense_Mutation_p.I234T|PFKFB4_ENST00000490115.1_5'UTR	NM_004567.2	NP_004558.1	Q16877	F264_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	245	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)	p.I245T(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(193;0.0003)|KIRC - Kidney renal clear cell carcinoma(197;0.00596)|Kidney(197;0.00684)		GGTCACGTGGATGTTCATGAG	0.607																																					p.I245T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T734C	3						.						150.0	147.0	148.0					3																	48573795		2203	4300	6503	48548799	SO:0001583	missense	5210	exon8			BC010269	CCDS2771.1	3p22-p21	2004-03-02			ENSG00000114268	ENSG00000114268			8875	protein-coding gene	gene with protein product		605320				8830046, 10095107	Standard	NM_004567		Approved		uc003ctv.3	Q16877	OTTHUMG00000133528	ENST00000232375.3:c.734T>C	3.37:g.48573795A>G	ENSP00000232375:p.Ile245Thr	Somatic		Capture	Illumina HiSeq	Phase_I	48548799	NM_004567	Q5S3G5|Q5XLC2|Q64EX5	Missense_Mutation	SNP	ENST00000232375.3	37	CCDS2771.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.172863	0.78452	.	.	ENSG00000114268	ENST00000232375;ENST00000536104;ENST00000416568;ENST00000383734;ENST00000541519;ENST00000452531	.	.	.	4.43	4.43	0.53597	6-phosphofructo-2-kinase (1);	0.000000	0.85682	D	0.000000	T	0.76941	0.4058	M	0.74467	2.265	0.80722	D	1	P;D;D;P	0.89917	0.494;0.997;1.0;0.876	D;D;D;D	0.97110	0.911;0.996;1.0;0.969	T	0.79524	-0.1768	9	0.66056	D	0.02	-23.957	11.9766	0.53096	1.0:0.0:0.0:0.0	.	234;245;245;245	B7Z5C3;Q5XLC2;Q66S35;Q16877	.;.;.;F264_HUMAN	T	245;234;245;245;211;234	.	ENSP00000232375:I245T	I	-	2	0	PFKFB4	48548799	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.079000	0.94032	1.999000	0.58509	0.459000	0.35465	ATC		0.607	PFKFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257503.2	NM_004567	
QARS	5859	broad.mit.edu	37	3	49137837	49137837	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:49137837G>A	ENST00000306125.6	-	12	1368	c.1031C>T	c.(1030-1032)gCg>gTg	p.A344V	QARS_ENST00000414533.1_Missense_Mutation_p.A333V|QARS_ENST00000470225.1_5'UTR			P47897	SYQ_HUMAN	glutaminyl-tRNA synthetase	344					brain development (GO:0007420)|gene expression (GO:0010467)|glutaminyl-tRNA aminoacylation (GO:0006425)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|glutamine-tRNA ligase activity (GO:0004819)	p.A344V(1)		breast(1)|endometrium(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)	L-Glutamine(DB00130)	CACAGCCCACGCATATAGCTG	0.542																																					p.A344V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1031T	3						.						65.0	58.0	61.0					3																	49137837		2203	4300	6503	49112841	SO:0001583	missense	5859	exon12			X76013	CCDS2788.1, CCDS63633.1	3p21.31	2011-07-01			ENSG00000172053	ENSG00000172053	6.1.1.18	"""Aminoacyl tRNA synthetases / Class I"""	9751	protein-coding gene	gene with protein product	"""glutamine tRNA ligase"""	603727				8078941, 10393422	Standard	NM_005051		Approved		uc003cvx.4	P47897	OTTHUMG00000156774	ENST00000306125.6:c.1031C>T	3.37:g.49137837G>A	ENSP00000307567:p.Ala344Val	Somatic		Capture	Illumina HiSeq	Phase_I	49112841	NM_005051	B4DWJ2	Missense_Mutation	SNP	ENST00000306125.6	37	CCDS2788.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.457749	0.43634	.	.	ENSG00000172053	ENST00000306125;ENST00000414533	T;T	0.24723	1.84;1.84	5.93	4.13	0.48395	Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain (1);	0.195780	0.53938	D	0.000057	T	0.23249	0.0562	M	0.69358	2.11	0.80722	D	1	P;P	0.35107	0.484;0.484	B;B	0.27608	0.081;0.081	T	0.08411	-1.0723	10	0.66056	D	0.02	-7.8141	7.6911	0.28569	0.1389:0.0:0.7303:0.1308	.	333;344	B4DWJ2;P47897	.;SYQ_HUMAN	V	344;333	ENSP00000307567:A344V;ENSP00000390015:A333V	ENSP00000307567:A344V	A	-	2	0	QARS	49112841	1.000000	0.71417	0.984000	0.44739	0.729000	0.41735	3.833000	0.55790	1.526000	0.49068	-0.136000	0.14681	GCG		0.542	QARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345689.2	NM_005051	
KLHDC8B	200942	broad.mit.edu	37	3	49210331	49210331	+	Silent	SNP	A	A	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:49210331A>T	ENST00000332780.2	+	2	338	c.129A>T	c.(127-129)ggA>ggT	p.G43G	KLHDC8B_ENST00000476495.2_3'UTR	NM_173546.2	NP_775817.1	Q8IXV7	KLD8B_HUMAN	kelch domain containing 8B	43						cytoplasm (GO:0005737)		p.G43G(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|stomach(1)	7				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GCCGGGCTGGACTGCCCCTGG	0.657																																					p.G43G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A129T	3						.						71.0	64.0	67.0					3																	49210331		2203	4300	6503	49185335	SO:0001819	synonymous_variant	200942	exon2				CCDS2791.1	3p21.31	2008-02-05			ENSG00000185909	ENSG00000185909			28557	protein-coding gene	gene with protein product		613169					Standard	NM_173546		Approved	MGC35097	uc003cwh.3	Q8IXV7	OTTHUMG00000156814	ENST00000332780.2:c.129A>T	3.37:g.49210331A>T		Somatic		Capture	Illumina HiSeq	Phase_I	49185335	NM_173546		Silent	SNP	ENST00000332780.2	37	CCDS2791.1																																																																																				0.657	KLHDC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345974.1	NM_173546	
BSN	8927	broad.mit.edu	37	3	49690354	49690354	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:49690354C>T	ENST00000296452.4	+	5	3479	c.3365C>T	c.(3364-3366)tCc>tTc	p.S1122F		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1122					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.S1122F(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)		CACCGCTCCTCCTGCTCTGAG	0.612																																					p.S1122F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3365T	3						.						71.0	71.0	71.0					3																	49690354		2203	4300	6503	49665358	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.3365C>T	3.37:g.49690354C>T	ENSP00000296452:p.Ser1122Phe	Somatic		Capture	Illumina HiSeq	Phase_I	49665358	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.101952	0.56183	.	.	ENSG00000164061	ENST00000296452	T	0.34275	1.37	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.63803	0.2542	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.68322	-0.5439	10	0.87932	D	0	.	18.8333	0.92150	0.0:1.0:0.0:0.0	.	1122	Q9UPA5	BSN_HUMAN	F	1122	ENSP00000296452:S1122F	ENSP00000296452:S1122F	S	+	2	0	BSN	49665358	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.792000	0.85828	2.468000	0.83385	0.561000	0.74099	TCC		0.612	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
SEMA3B	7869	broad.mit.edu	37	3	50312302	50312302	+	RNA	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:50312302G>A	ENST00000418948.1	+	0	1620							Q13214	SEM3B_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B						axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.S461S(1)		central_nervous_system(2)|kidney(1)|lung(2)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		AGGTGATCTCGGTCCCCAAGG	0.647											OREG0015583	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R462Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1385A	3						.						27.0	31.0	29.0					3																	50312302		2056	4201	6257	50287306			7869	exon13			U28369	CCDS74941.1	3p21.3	2013-01-11			ENSG00000012171	ENSG00000012171		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10724	protein-coding gene	gene with protein product		601281		SEMAA		7748561, 8633026	Standard	NM_004636		Approved	SemA, semaV, LUCA-1, sema5	uc003cyu.3	Q13214	OTTHUMG00000156970		3.37:g.50312302G>A		Somatic	968	Capture	Illumina HiSeq	Phase_I	50287306	NM_004636	Q6GU46|Q8TB71|Q8TDV7|Q93018|Q96GX0	Silent	SNP	ENST00000418948.1	37																																																																																					0.647	SEMA3B-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000346890.2	NM_001005914	
RBM15B	29890	broad.mit.edu	37	3	51430910	51430910	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:51430910G>A	ENST00000323686.4	+	1	2180	c.2080G>A	c.(2080-2082)Gag>Aag	p.E694K		NM_013286.4	NP_037418.3	Q8NDT2	RB15B_HUMAN	RNA binding motif protein 15B	694					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.E694K(1)		endometrium(4)|large_intestine(5)|lung(3)	12				BRCA - Breast invasive adenocarcinoma(193;0.000224)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CACAGAGGCCGAGCCCAAGCC	0.572																																					p.E694K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2080A	3						.						86.0	87.0	86.0					3																	51430910		2203	4300	6503	51405950	SO:0001583	missense	29890	exon1			AL831838	CCDS33764.1	3p21.1	2013-02-12			ENSG00000179837	ENSG00000259956		"""RNA binding motif (RRM) containing"""	24303	protein-coding gene	gene with protein product		612602				16129689	Standard	NM_013286		Approved	HUMAGCGB, OTT3	uc003dbd.3	Q8NDT2	OTTHUMG00000156896	ENST00000323686.4:c.2080G>A	3.37:g.51430910G>A	ENSP00000313890:p.Glu694Lys	Somatic		Capture	Illumina HiSeq	Phase_I	51405950	NM_013286	A4QPG7|Q6QE19|Q9BV96	Missense_Mutation	SNP	ENST00000323686.4	37	CCDS33764.1	.	.	.	.	.	.	.	.	.	.	G	1.924	-0.447588	0.04572	.	.	ENSG00000179837	ENST00000323686;ENST00000540284;ENST00000541145;ENST00000536338	T	0.14766	2.48	5.54	5.54	0.83059	.	.	.	.	.	T	0.12220	0.0297	N	0.24115	0.695	0.41759	D	0.989709	D	0.65815	0.995	P	0.49192	0.602	T	0.06023	-1.0850	9	0.06757	T	0.87	-13.2875	14.3237	0.66505	0.0:0.0:0.8516:0.1484	.	694	Q8NDT2	RB15B_HUMAN	K	694;15;367;113	ENSP00000313890:E694K	ENSP00000313890:E694K	E	+	1	0	RBM15B	51405950	1.000000	0.71417	0.533000	0.28001	0.157000	0.22087	4.670000	0.61583	2.590000	0.87494	0.655000	0.94253	GAG		0.572	RBM15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346489.1	NM_013286	
RAD54L2	23132	broad.mit.edu	37	3	51696554	51696554	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:51696554G>T	ENST00000409535.2	+	22	3647	c.3522G>T	c.(3520-3522)gaG>gaT	p.E1174D	RAD54L2_ENST00000296477.3_Missense_Mutation_p.E868D	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	1174						nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)	p.E1174D(1)		NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		ACAGCCCAGAGATCATCAGTG	0.647																																					p.E1174D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3522T	3						.						57.0	60.0	59.0					3																	51696554		2203	4300	6503	51671594	SO:0001583	missense	23132	exon22			AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.3522G>T	3.37:g.51696554G>T	ENSP00000386520:p.Glu1174Asp	Somatic		Capture	Illumina HiSeq	Phase_I	51671594	NM_015106	Q8TB57|Q9BV54	Missense_Mutation	SNP	ENST00000409535.2	37	CCDS33765.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.05|16.05	3.012496|3.012496	0.54468|0.54468	.|.	.|.	ENSG00000164080|ENSG00000164080	ENST00000432863|ENST00000409535;ENST00000296477	.|D;D	.|0.94232	.|-3.3;-3.38	5.4|5.4	3.58|3.58	0.41010|0.41010	.|.	.|0.112431	.|0.64402	.|D	.|0.000010	D|D	0.90417|0.90417	0.7000|0.7000	N|N	0.24115|0.24115	0.695|0.695	0.32418|0.32418	N|N	0.549803|0.549803	.|D;D	.|0.61080	.|0.989;0.989	.|P;P	.|0.55391	.|0.775;0.696	D|D	0.88885|0.88885	0.3342|0.3342	5|10	.|0.33940	.|T	.|0.23	-18.5438|-18.5438	8.0748|8.0748	0.30710|0.30710	0.3296:0.0:0.6704:0.0|0.3296:0.0:0.6704:0.0	.|.	.|1174;763	.|Q9Y4B4;B3KV54	.|ARIP4_HUMAN;.	Y|D	1003|1174;868	.|ENSP00000386520:E1174D;ENSP00000296477:E868D	.|ENSP00000296477:E868D	D|E	+|+	1|3	0|2	RAD54L2|RAD54L2	51671594|51671594	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	1.513000|1.513000	0.35823|0.35823	0.621000|0.621000	0.30232|0.30232	0.563000|0.563000	0.77884|0.77884	GAT|GAG		0.647	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328700.2	NM_015106	
RRP9	9136	broad.mit.edu	37	3	51969469	51969469	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:51969469G>T	ENST00000232888.6	-	10	933	c.860C>A	c.(859-861)gCt>gAt	p.A287D		NM_004704.3	NP_004695.1	O43818	U3IP2_HUMAN	ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)	287					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.A287D(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)		ATCCAGTGCAGCCACAGCGTC	0.627																																					p.A287D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C860A	3						.						67.0	56.0	60.0					3																	51969469		2203	4300	6503	51944509	SO:0001583	missense	9136	exon10			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.860C>A	3.37:g.51969469G>T	ENSP00000232888:p.Ala287Asp	Somatic		Capture	Illumina HiSeq	Phase_I	51944509	NM_004704	B2R996|Q8IZ30	Missense_Mutation	SNP	ENST00000232888.6	37	CCDS2837.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.758266	0.49468	.	.	ENSG00000114767	ENST00000232888	T	0.60040	0.22	4.36	3.46	0.39613	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.107337	0.64402	D	0.000005	T	0.49983	0.1589	L	0.38175	1.15	0.43841	D	0.996427	P	0.38195	0.622	B	0.42245	0.381	T	0.50693	-0.8798	10	0.37606	T	0.19	-10.8253	12.446	0.55651	0.0848:0.0:0.9152:0.0	.	287	O43818	U3IP2_HUMAN	D	287	ENSP00000232888:A287D	ENSP00000232888:A287D	A	-	2	0	RRP9	51944509	1.000000	0.71417	0.992000	0.48379	0.050000	0.14768	5.913000	0.69957	2.278000	0.76064	0.561000	0.74099	GCT		0.627	RRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346637.1	NM_004704	
NISCH	11188	broad.mit.edu	37	3	52512553	52512553	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:52512553G>A	ENST00000479054.1	+	12	1334	c.1262G>A	c.(1261-1263)cGg>cAg	p.R421Q	NISCH_ENST00000464280.1_3'UTR|NISCH_ENST00000488380.1_Missense_Mutation_p.R421Q|NISCH_ENST00000345716.4_Missense_Mutation_p.R421Q|NISCH_ENST00000420808.2_Missense_Mutation_p.R421Q			Q9Y2I1	NISCH_HUMAN	nischarin	421	Interaction with PAK1. {ECO:0000250}.|Necessary for homooligomerization and targeting to endosomes.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)	p.R421Q(1)		NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	CCCGACTACCGGACCAAGGTG	0.602																																					p.R421Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1262A	3						.						79.0	71.0	73.0					3																	52512553		2203	4300	6503	52487593	SO:0001583	missense	11188	exon11			AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"""imidazoline receptor candidate"", ""I-1 receptor candidate protein"", ""imidazoline receptor antisera selected"""	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.1262G>A	3.37:g.52512553G>A	ENSP00000418232:p.Arg421Gln	Somatic		Capture	Illumina HiSeq	Phase_I	52487593	NM_007184	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Missense_Mutation	SNP	ENST00000479054.1	37	CCDS33767.1	.	.	.	.	.	.	.	.	.	.	G	36	5.624201	0.96660	.	.	ENSG00000010322	ENST00000479054;ENST00000345716;ENST00000488380;ENST00000420808	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	5.85	4.98	0.66077	.	0.057183	0.85682	D	0.000000	T	0.57829	0.2080	M	0.88512	2.96	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	T	0.67569	-0.5637	10	0.87932	D	0	-33.0055	14.9211	0.70838	0.0685:0.0:0.9315:0.0	.	421;421	Q9Y2I1;C9J715	NISCH_HUMAN;.	Q	421	ENSP00000418232:R421Q;ENSP00000339958:R421Q;ENSP00000417812:R421Q;ENSP00000392484:R421Q	ENSP00000339958:R421Q	R	+	2	0	NISCH	52487593	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.060000	0.93907	1.492000	0.48499	0.655000	0.94253	CGG		0.602	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184	
NEK4	6787	broad.mit.edu	37	3	52773516	52773516	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:52773516C>T	ENST00000233027.5	-	14	2430	c.2228G>A	c.(2227-2229)cGg>cAg	p.R743Q	NEK4_ENST00000535191.1_Missense_Mutation_p.R654Q|NEK4_ENST00000383721.4_Missense_Mutation_p.R697Q	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	743					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.R743Q(1)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(10)	26				BRCA - Breast invasive adenocarcinoma(193;7.44e-05)|Kidney(197;0.000711)|KIRC - Kidney renal clear cell carcinoma(197;0.00086)|OV - Ovarian serous cystadenocarcinoma(275;0.0513)		CAGTGTGTCCCGATATTTCCG	0.408																																					p.R654Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1961A	3						.						200.0	198.0	199.0					3																	52773516		2203	4300	6503	52748556	SO:0001583	missense	6787	exon13			L20321	CCDS2863.1, CCDS54593.1	3p21.1	2012-11-15	2012-11-15	2002-05-10	ENSG00000114904	ENSG00000114904	2.7.11.1		11399	protein-coding gene	gene with protein product	"""serine/threonine protein kinase-2"""	601959	"""serine/threonine kinase 2"", ""NIMA (never in mitosis gene a)-related kinase 4"""	STK2		8208544	Standard	NM_001193533		Approved	NRK2, pp12301	uc003dfq.4	P51957	OTTHUMG00000158836	ENST00000233027.5:c.2228G>A	3.37:g.52773516C>T	ENSP00000233027:p.Arg743Gln	Somatic		Capture	Illumina HiSeq	Phase_I	52748556	NM_001193533	A5YM70|B2R633|B7Z200|Q6P576	Missense_Mutation	SNP	ENST00000233027.5	37	CCDS2863.1	.	.	.	.	.	.	.	.	.	.	C	35	5.596683	0.96602	.	.	ENSG00000114904	ENST00000233027;ENST00000535191;ENST00000383721;ENST00000461689	T;T;D;D	0.82803	-1.21;-1.33;-1.5;-1.65	5.95	5.95	0.96441	.	0.000000	0.64402	D	0.000015	D	0.90865	0.7130	M	0.75264	2.295	0.49798	D	0.999822	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.75484	0.986;0.96;0.94	D	0.90869	0.4744	10	0.62326	D	0.03	.	17.3748	0.87389	0.0:1.0:0.0:0.0	.	654;697;743	B7Z200;P51957-2;P51957	.;.;NEK4_HUMAN	Q	743;654;697;654	ENSP00000233027:R743Q;ENSP00000437703:R654Q;ENSP00000373227:R697Q;ENSP00000419666:R654Q	ENSP00000233027:R743Q	R	-	2	0	NEK4	52748556	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.787000	0.62432	2.835000	0.97688	0.650000	0.86243	CGG		0.408	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157	
ITIH1	3697	broad.mit.edu	37	3	52824919	52824919	+	Missense_Mutation	SNP	C	C	T	rs201776145		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:52824919C>T	ENST00000273283.2	+	20	2500	c.2476C>T	c.(2476-2478)Cgg>Tgg	p.R826W	ITIH1_ENST00000540715.1_Missense_Mutation_p.R684W|ITIH1_ENST00000405128.3_Missense_Mutation_p.R192W|ITIH1_ENST00000537050.1_Missense_Mutation_p.R538W|ITIH1_ENST00000542827.1_3'UTR	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	826	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.R826W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		GATGTCAGCCCGGACGCACGG	0.627													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19487	0.0		0.0	False		,,,				2504	0.0				p.R684W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2050T	3						.						97.0	91.0	93.0					3																	52824919		2203	4300	6503	52799959	SO:0001583	missense	3697	exon18				CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"""inter-alpha (globulin) inhibitor, H1 polypeptide"""			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.2476C>T	3.37:g.52824919C>T	ENSP00000273283:p.Arg826Trp	Somatic		Capture	Illumina HiSeq	Phase_I	52799959	NM_001166434	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	16.60	3.169095	0.57584	.	.	ENSG00000055957	ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133;ENST00000405128	T;T;T;T;T	0.12465	2.68;2.68;2.68;2.68;2.68	5.75	4.85	0.62838	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.529435	0.20649	N	0.088241	T	0.18215	0.0437	M	0.62723	1.935	0.41933	D	0.990577	B;B;B;B	0.22746	0.036;0.026;0.068;0.074	B;B;B;B	0.21708	0.021;0.014;0.019;0.036	T	0.01966	-1.1238	10	0.52906	T	0.07	-26.9622	14.9028	0.70692	0.1438:0.8562:0.0:0.0	.	684;192;427;826	F5H165;B5MCP1;Q9P1C5;P19827	.;.;.;ITIH1_HUMAN	W	826;684;538;379;192	ENSP00000273283:R826W;ENSP00000443973:R684W;ENSP00000443847:R538W;ENSP00000395836:R379W;ENSP00000384589:R192W	ENSP00000273283:R826W	R	+	1	2	ITIH1	52799959	0.000000	0.05858	0.957000	0.39632	0.885000	0.51271	0.087000	0.14958	2.719000	0.93026	0.655000	0.94253	CGG		0.627	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
TKT	7086	broad.mit.edu	37	3	53275237	53275237	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:53275237C>T	ENST00000462138.1	-	3	338	c.250G>A	c.(250-252)Gcg>Acg	p.A84T	TKT_ENST00000423525.2_Missense_Mutation_p.A84T|TKT_ENST00000423516.1_Missense_Mutation_p.A84T|TKT_ENST00000296289.6_Missense_Mutation_p.A37T			P29401	TKT_HUMAN	transketolase	84					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.A84T(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)		GCCCAGACCGCGTAGAGGATG	0.637																																					p.A84T	Colon(133;1506 2347 35238 42177)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G250A	3						.						50.0	42.0	45.0					3																	53275237		2203	4300	6503	53250277	SO:0001583	missense	7086	exon3				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.250G>A	3.37:g.53275237C>T	ENSP00000417773:p.Ala84Thr	Somatic		Capture	Illumina HiSeq	Phase_I	53250277	NM_001135055	A8K089|B4DE31|E7EPA7|Q8TBA3|Q96HH3	Missense_Mutation	SNP	ENST00000462138.1	37	CCDS2871.1	.	.	.	.	.	.	.	.	.	.	C	19.79	3.892883	0.72524	.	.	ENSG00000163931	ENST00000462138;ENST00000423525;ENST00000423516;ENST00000296289	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	5.9	5.9	0.94986	Transketolase, N-terminal (1);	0.102880	0.64402	D	0.000003	T	0.49541	0.1563	M	0.77616	2.38	0.80722	D	1	D;P	0.56035	0.974;0.933	P;P	0.53006	0.685;0.715	T	0.51965	-0.8638	10	0.66056	D	0.02	-0.3828	15.918	0.79539	0.1432:0.8568:0.0:0.0	.	84;84	E7EPA7;P29401	.;TKT_HUMAN	T	84;84;84;37	ENSP00000417773:A84T;ENSP00000405455:A84T;ENSP00000391481:A84T;ENSP00000296289:A37T	ENSP00000296289:A37T	A	-	1	0	TKT	53250277	0.681000	0.27614	0.354000	0.25760	0.256000	0.26092	1.377000	0.34317	2.792000	0.96026	0.655000	0.94253	GCG		0.637	TKT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350356.1		
CACNA2D3	55799	broad.mit.edu	37	3	54661844	54661844	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:54661844G>A	ENST00000474759.1	+	10	1042	c.994G>A	c.(994-996)Gcc>Acc	p.A332T	CACNA2D3_ENST00000288197.5_Missense_Mutation_p.A332T|CACNA2D3_ENST00000490478.1_Missense_Mutation_p.A238T|CACNA2D3_ENST00000415676.2_Missense_Mutation_p.A332T	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	332	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.A332T(2)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	CAAACTTTTCGCCAAAGGAAT	0.408																																					p.A332T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G994A	3						.						105.0	96.0	99.0					3																	54661844		1934	4125	6059	54636884	SO:0001583	missense	55799	exon10			AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"""Calcium channel subunits"""	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.994G>A	3.37:g.54661844G>A	ENSP00000419101:p.Ala332Thr	Somatic		Capture	Illumina HiSeq	Phase_I	54636884	NM_018398	B2RPL6|Q9NY16|Q9NY18	Missense_Mutation	SNP	ENST00000474759.1	37	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	G	18.01	3.528621	0.64860	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624;ENST00000438476	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	5.37	5.37	0.77165	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	T	0.30978	0.0782	M	0.68317	2.08	0.47949	D	0.999553	D	0.61697	0.99	P	0.59012	0.85	T	0.01480	-1.1344	10	0.22706	T	0.39	.	17.2805	0.87127	0.0:0.0:1.0:0.0	.	332	Q8IZS8	CA2D3_HUMAN	T	332;332;332;238;238;237	ENSP00000389506:A332T;ENSP00000419101:A332T;ENSP00000288197:A332T;ENSP00000417279:A238T	ENSP00000288197:A332T	A	+	1	0	CACNA2D3	54636884	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	9.167000	0.94773	2.524000	0.85096	0.561000	0.74099	GCC		0.408	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1		
SPATA12	353324	broad.mit.edu	37	3	57107723	57107723	+	Start_Codon_SNP	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:57107723A>G	ENST00000334325.1	+	2	676	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	ARHGEF3_ENST00000338458.4_Intron	NM_181727.1	NP_859078.1	Q7Z6I5	SPT12_HUMAN	spermatogenesis associated 12	1								p.M1V(1)		large_intestine(2)|lung(1)	3				KIRC - Kidney renal clear cell carcinoma(284;0.0111)|Kidney(284;0.0129)		CTTGGGCCCCATGTCCAGTTC	0.542																																					p.M1V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1G	3						.						32.0	32.0	32.0					3																	57107723		2203	4300	6503	57082763	SO:0001582	initiator_codon_variant	353324	exon2			AY221117	CCDS2879.1	3p21.2	2012-09-19			ENSG00000186451	ENSG00000186451			23221	protein-coding gene	gene with protein product		609869				22981541, 17251597	Standard	NM_181727		Approved		uc003dij.1	Q7Z6I5	OTTHUMG00000158862	ENST00000334325.1:c.1A>G	3.37:g.57107723A>G	ENSP00000335392:p.Met1Val	Somatic		Capture	Illumina HiSeq	Phase_I	57082763	NM_181727	A0AVA8|B2RMW1	Missense_Mutation	SNP	ENST00000334325.1	37	CCDS2879.1	.	.	.	.	.	.	.	.	.	.	A	6.840	0.524133	0.13066	.	.	ENSG00000186451	ENST00000334325	.	.	.	3.02	0.372	0.16173	.	.	.	.	.	T	0.27205	0.0667	.	.	.	0.21184	N	0.999769	B	0.14012	0.009	B	0.16289	0.015	T	0.30119	-0.9989	7	0.87932	D	0	.	2.2953	0.04149	0.6071:0.0:0.1539:0.239	.	1	Q7Z6I5	SPT12_HUMAN	V	1	.	ENSP00000335392:M1V	M	+	1	0	SPATA12	57082763	0.001000	0.12720	0.001000	0.08648	0.502000	0.33828	0.288000	0.18939	0.071000	0.16664	0.460000	0.39030	ATG		0.542	SPATA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352457.2	NM_181727	Missense_Mutation
APPL1	26060	broad.mit.edu	37	3	57293902	57293902	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:57293902C>T	ENST00000288266.3	+	17	1660	c.1513C>T	c.(1513-1515)Cga>Tga	p.R505*		NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	505	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)	p.R505*(1)		breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		ATTTATTGTCCGATTCCTTGG	0.328																																					p.R505X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1513T	3						.						71.0	71.0	71.0					3																	57293902		2203	4300	6503	57268942	SO:0001587	stop_gained	26060	exon17			AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"""Pleckstrin homology (PH) domain containing"""	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.1513C>T	3.37:g.57293902C>T	ENSP00000288266:p.Arg505*	Somatic		Capture	Illumina HiSeq	Phase_I	57268942	NM_012096	Q9P2B9	Nonsense_Mutation	SNP	ENST00000288266.3	37	CCDS2882.1	.	.	.	.	.	.	.	.	.	.	C	39	7.357119	0.98235	.	.	ENSG00000157500	ENST00000288266	.	.	.	5.43	4.5	0.54988	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7576	0.69579	0.2157:0.7843:0.0:0.0	.	.	.	.	X	505	.	ENSP00000288266:R505X	R	+	1	2	APPL1	57268942	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.987000	0.56944	2.712000	0.92718	0.557000	0.71058	CGA		0.328	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096	
ARF4	378	broad.mit.edu	37	3	57561285	57561285	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:57561285C>T	ENST00000303436.6	-	5	713	c.446G>A	c.(445-447)cGt>cAt	p.R149H	ARF4_ENST00000489843.1_Missense_Mutation_p.R40H|ARF4_ENST00000496292.1_Missense_Mutation_p.R122H	NM_001660.3	NP_001651.1	P18085	ARF4_HUMAN	ADP-ribosylation factor 4	149					activation of phospholipase D activity (GO:0031584)|brain development (GO:0007420)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein transport (GO:0015031)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to axon injury (GO:0048678)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	epidermal growth factor receptor binding (GO:0005154)|GTP binding (GO:0005525)	p.R149H(2)		large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.0449)|Kidney(284;0.0561)		TGTTCTGTTACGAAGAGACTG	0.353																																					p.R149H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G446A	3						.						107.0	96.0	100.0					3																	57561285		2203	4300	6503	57536325	SO:0001583	missense	378	exon5			M36341	CCDS2884.1	3p21.2-p21.1	2007-03-19			ENSG00000168374	ENSG00000168374		"""ADP-ribosylation factors"""	655	protein-coding gene	gene with protein product		601177	"""ADP-ribosylation factor 2"""	ARF2		2107548	Standard	NM_001660		Approved		uc003dix.4	P18085	OTTHUMG00000158601	ENST00000303436.6:c.446G>A	3.37:g.57561285C>T	ENSP00000306010:p.Arg149His	Somatic		Capture	Illumina HiSeq	Phase_I	57536325	NM_001660	B2R7J7|P21371	Missense_Mutation	SNP	ENST00000303436.6	37	CCDS2884.1	.	.	.	.	.	.	.	.	.	.	C	19.47	3.833214	0.71258	.	.	ENSG00000168374	ENST00000303436;ENST00000496292	D;D	0.82984	-1.67;-1.67	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.84768	0.5545	M	0.81341	2.54	0.80722	D	1	B;B	0.28208	0.203;0.037	B;B	0.19666	0.026;0.019	T	0.83074	-0.0141	10	0.62326	D	0.03	-1.2058	19.946	0.97183	0.0:1.0:0.0:0.0	.	122;149	C9JAK5;P18085	.;ARF4_HUMAN	H	149;122	ENSP00000306010:R149H;ENSP00000417501:R122H	ENSP00000306010:R149H	R	-	2	0	ARF4	57536325	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.781000	0.68964	2.711000	0.92665	0.591000	0.81541	CGT		0.353	ARF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351443.1	NM_001660	
DENND6A	201627	broad.mit.edu	37	3	57619065	57619065	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:57619065C>T	ENST00000311128.5	-	15	1350	c.1280G>A	c.(1279-1281)cGt>cAt	p.R427H	RP11-755B10.2_ENST00000470427.1_RNA	NM_152678.2	NP_689891.1	Q8IWF6	DEN6A_HUMAN	DENN/MADD domain containing 6A	427					positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)|recycling endosome (GO:0055037)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R427H(1)									CTCAGAAGGACGTTTCTGTTG	0.308																																					p.R427H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1280A	3						.						72.0	75.0	74.0					3																	57619065		2203	4298	6501	57594105	SO:0001583	missense	201627	exon15			AK074156	CCDS33773.1	3p14.3	2013-10-11	2012-10-03	2012-10-03	ENSG00000174839	ENSG00000174839		"""DENN/MADD domain containing"""	26635	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member A"""	FAM116A		21330364	Standard	NM_152678		Approved	FLJ34969, AFI1A	uc003dja.3	Q8IWF6	OTTHUMG00000158639	ENST00000311128.5:c.1280G>A	3.37:g.57619065C>T	ENSP00000311401:p.Arg427His	Somatic		Capture	Illumina HiSeq	Phase_I	57594105	NM_152678	Q7Z5T4|Q8N235|Q8TEG8	Missense_Mutation	SNP	ENST00000311128.5	37	CCDS33773.1	.	.	.	.	.	.	.	.	.	.	C	31	5.082807	0.94050	.	.	ENSG00000174839	ENST00000311128	.	.	.	5.39	5.39	0.77823	.	0.114877	0.64402	D	0.000009	D	0.84556	0.5498	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.70935	0.971	D	0.86729	0.1947	9	0.72032	D	0.01	-9.1811	19.5103	0.95139	0.0:1.0:0.0:0.0	.	427	Q8IWF6	F116A_HUMAN	H	427	.	ENSP00000311401:R427H	R	-	2	0	FAM116A	57594105	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.363000	0.79516	2.668000	0.90789	0.557000	0.71058	CGT		0.308	DENND6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351594.1	NM_152678	
FLNB	2317	broad.mit.edu	37	3	58087993	58087993	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:58087993G>A	ENST00000295956.4	+	9	1574	c.1409G>A	c.(1408-1410)cGg>cAg	p.R470Q	FLNB_ENST00000358537.3_Missense_Mutation_p.R470Q|FLNB_ENST00000429972.2_Missense_Mutation_p.R470Q|FLNB_ENST00000419752.2_Missense_Mutation_p.R301Q|FLNB_ENST00000493452.1_Missense_Mutation_p.R301Q|FLNB_ENST00000348383.5_Missense_Mutation_p.R470Q|FLNB_ENST00000357272.4_Missense_Mutation_p.R470Q|FLNB_ENST00000490882.1_Missense_Mutation_p.R470Q	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	470					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.R470Q(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)		GTCCGTATCCGGGAGACCACA	0.507																																					p.R470Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1409A	3						.						110.0	114.0	113.0					3																	58087993		2203	4300	6503	58063033	SO:0001583	missense	2317	exon9			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.1409G>A	3.37:g.58087993G>A	ENSP00000295956:p.Arg470Gln	Somatic		Capture	Illumina HiSeq	Phase_I	58063033	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	.	.	.	.	.	.	.	.	.	.	G	23.5	4.418357	0.83559	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91	5.43	5.43	0.79202	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.168245	0.48767	D	0.000171	D	0.90055	0.6894	N	0.25647	0.755	0.49915	D	0.999837	P;P;P;B;P;P	0.44260	0.796;0.827;0.83;0.243;0.723;0.723	B;B;B;B;P;P	0.46253	0.284;0.41;0.41;0.199;0.509;0.509	D	0.90169	0.4234	10	0.48119	T	0.1	.	19.5914	0.95514	0.0:0.0:1.0:0.0	.	470;470;301;301;470;470	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	Q	470;470;470;470;470;470;301;301	ENSP00000295956:R470Q;ENSP00000420213:R470Q;ENSP00000351339:R470Q;ENSP00000415599:R470Q;ENSP00000232447:R470Q;ENSP00000349819:R470Q;ENSP00000418510:R301Q;ENSP00000414532:R301Q	ENSP00000295956:R470Q	R	+	2	0	FLNB	58063033	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	7.558000	0.82253	2.720000	0.93068	0.591000	0.81541	CGG		0.507	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
FLNB	2317	broad.mit.edu	37	3	58107100	58107100	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:58107100G>A	ENST00000295956.4	+	20	3161	c.2996G>A	c.(2995-2997)cGg>cAg	p.R999Q	FLNB_ENST00000358537.3_Missense_Mutation_p.R999Q|FLNB_ENST00000429972.2_Missense_Mutation_p.R999Q|FLNB_ENST00000419752.2_Missense_Mutation_p.R830Q|FLNB_ENST00000493452.1_Missense_Mutation_p.R830Q|FLNB_ENST00000348383.5_Missense_Mutation_p.R999Q|FLNB_ENST00000357272.4_Missense_Mutation_p.R999Q|FLNB_ENST00000490882.1_Missense_Mutation_p.R999Q	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	999					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.R999Q(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)		GTGACAGGCCGGGAGAACAGC	0.627																																					p.R999Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2996A	3						.						119.0	103.0	108.0					3																	58107100		2203	4300	6503	58082140	SO:0001583	missense	2317	exon20			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.2996G>A	3.37:g.58107100G>A	ENSP00000295956:p.Arg999Gln	Somatic		Capture	Illumina HiSeq	Phase_I	58082140	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	.	.	.	.	.	.	.	.	.	.	G	14.79	2.640499	0.47153	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89	5.99	5.02	0.67125	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.204099	0.49916	D	0.000131	T	0.69575	0.3126	N	0.20685	0.6	0.33952	D	0.644608	B;B;P;B;P;P	0.40250	0.434;0.429;0.489;0.177;0.709;0.709	B;B;B;B;B;B	0.39840	0.207;0.108;0.311;0.096;0.311;0.311	T	0.70099	-0.4965	10	0.13470	T	0.59	.	3.9802	0.09492	0.3106:0.0:0.6894:0.0	.	999;999;830;830;999;999	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	Q	999;999;999;999;999;999;830;830	ENSP00000295956:R999Q;ENSP00000420213:R999Q;ENSP00000351339:R999Q;ENSP00000415599:R999Q;ENSP00000232447:R999Q;ENSP00000349819:R999Q;ENSP00000418510:R830Q;ENSP00000414532:R830Q	ENSP00000295956:R999Q	R	+	2	0	FLNB	58082140	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	3.451000	0.52964	2.840000	0.97914	0.655000	0.94253	CGG		0.627	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
PTPRG	5793	broad.mit.edu	37	3	62254810	62254810	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:62254810G>A	ENST00000474889.1	+	20	3352	c.2975G>A	c.(2974-2976)cGt>cAt	p.R992H	PTPRG-AS1_ENST00000479018.1_RNA|PTPRG-AS1_ENST00000495542.1_RNA|PTPRG_ENST00000295874.10_Missense_Mutation_p.R963H|PTPRG-AS1_ENST00000475371.1_RNA|PTPRG-AS1_ENST00000462497.1_RNA|PTPRG-AS1_ENST00000474795.1_RNA	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	992	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R992H(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TACACTGTTCGTCGTTTTTCA	0.393																																					p.R992H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2975A	3						.						100.0	93.0	95.0					3																	62254810		2203	4300	6503	62229850	SO:0001583	missense	5793	exon20			L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.2975G>A	3.37:g.62254810G>A	ENSP00000418112:p.Arg992His	Somatic		Capture	Illumina HiSeq	Phase_I	62229850	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	37	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.968731	0.92855	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.15834	2.39;2.39	5.82	5.82	0.92795	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.050957	0.85682	D	0.000000	T	0.54208	0.1844	M	0.91818	3.245	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.62886	-0.6759	10	0.87932	D	0	.	20.1142	0.97922	0.0:0.0:1.0:0.0	.	238;963;992	B7Z3T1;P23470-2;P23470	.;.;PTPRG_HUMAN	H	992;963	ENSP00000418112:R992H;ENSP00000295874:R963H	ENSP00000295874:R963H	R	+	2	0	PTPRG	62229850	1.000000	0.71417	1.000000	0.80357	0.576000	0.36127	9.710000	0.98732	2.765000	0.95021	0.650000	0.86243	CGT		0.393	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	
ATXN7	6314	broad.mit.edu	37	3	63965619	63965619	+	Silent	SNP	G	G	A	rs528008421		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:63965619G>A	ENST00000295900.6	+	6	1078	c.528G>A	c.(526-528)ccG>ccA	p.P176P	ATXN7_ENST00000538065.1_Silent_p.P176P|ATXN7_ENST00000398590.3_Silent_p.P176P|ATXN7_ENST00000487717.1_Silent_p.P176P|ATXN7_ENST00000488239.1_3'UTR|ATXN7_ENST00000484332.1_Silent_p.P31P	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	176	Ser-rich.				cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.P176P(1)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		CCAGCAAGCCGCCTTTGGCCG	0.443																																					p.P176P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G528A	3						.						86.0	82.0	84.0					3																	63965619		1920	4144	6064	63940659	SO:0001819	synonymous_variant	6314	exon5			AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"""Ataxins"""	10560	protein-coding gene	gene with protein product		607640	"""spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"""	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.528G>A	3.37:g.63965619G>A		Somatic		Capture	Illumina HiSeq	Phase_I	63940659	NM_001177387	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Silent	SNP	ENST00000295900.6	37	CCDS43102.1																																																																																				0.443	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333	
MAGI1	9223	broad.mit.edu	37	3	65342508	65342508	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:65342508C>T	ENST00000402939.2	-	23	3933	c.3934G>A	c.(3934-3936)Gcg>Acg	p.A1312T	RP11-88H12.2_ENST00000602316.1_RNA|MAGI1_ENST00000330909.8_3'UTR	NM_001033057.1	NP_001028229.1	Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	1341					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.A1312T(1)		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)		GCGGCTGCCGCGCGCTCGGCC	0.697																																					p.A1312T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3934A	3						.						36.0	40.0	38.0					3																	65342508		2201	4296	6497	65317548	SO:0001583	missense	9223	exon23			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	ENST00000402939.2:c.3934G>A	3.37:g.65342508C>T	ENSP00000385450:p.Ala1312Thr	Somatic		Capture	Illumina HiSeq	Phase_I	65317548	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000402939.2	37	CCDS33780.1	.	.	.	.	.	.	.	.	.	.	C	1.227	-0.625325	0.03610	.	.	ENSG00000151276	ENST00000402939	T	0.11277	2.79	5.04	-10.1	0.00402	.	1.561710	0.03535	N	0.222932	T	0.03651	0.0104	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32508	-0.9904	10	0.14656	T	0.56	0.1522	4.1999	0.10460	0.0863:0.3638:0.2779:0.2719	.	1312	Q96QZ7-2	.	T	1312	ENSP00000385450:A1312T	ENSP00000385450:A1312T	A	-	1	0	MAGI1	65317548	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.484000	0.06528	-1.676000	0.01457	-2.214000	0.00298	GCG		0.697	MAGI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349126.1	NM_004742	
MAGI1	9223	broad.mit.edu	37	3	65464413	65464413	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:65464413G>A	ENST00000497477.2	-	4	610	c.611C>T	c.(610-612)aCg>aTg	p.T204M	MAGI1_ENST00000402939.2_Missense_Mutation_p.T204M|MAGI1_ENST00000483466.1_Missense_Mutation_p.T204M|MAGI1_ENST00000330909.8_Missense_Mutation_p.T204M|MAGI1_ENST00000470990.1_5'UTR			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	204	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				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.T204M(2)		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)		CAAGGCATCCGTCGTGATCAC	0.507																																					p.T204M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C611T	3						.						145.0	131.0	136.0					3																	65464413		2203	4300	6503	65439453	SO:0001583	missense	9223	exon4			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.611C>T	3.37:g.65464413G>A	ENSP00000424369:p.Thr204Met	Somatic		Capture	Illumina HiSeq	Phase_I	65439453	NM_015520	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000497477.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.5|22.5	4.297132|4.297132	0.81025|0.81025	.|.	.|.	ENSG00000151276|ENSG00000151276	ENST00000460329|ENST00000402939;ENST00000330909;ENST00000422949;ENST00000463103;ENST00000483466;ENST00000497477	.|T;T;T;T;T	.|0.19532	.|2.69;2.27;2.26;2.27;2.14	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Guanylate kinase/L-type calcium channel (1);	.|0.191343	.|0.53938	.|D	.|0.000050	T|T	0.31575|0.31575	0.0801|0.0801	L|L	0.28400|0.28400	0.85|0.85	0.34130|0.34130	D|D	0.665193|0.665193	.|D;D;D;D;D;D	.|0.76494	.|0.998;0.996;0.999;0.998;0.996;0.998	.|P;P;P;P;P;P	.|0.62885	.|0.813;0.54;0.908;0.747;0.854;0.729	T|T	0.25467|0.25467	-1.0131|-1.0131	5|10	.|0.36615	.|T	.|0.2	-18.1394|-18.1394	15.2391|15.2391	0.73455|0.73455	0.0:0.1399:0.8601:0.0|0.0:0.1399:0.8601:0.0	.|.	.|204;204;204;204;204;204	.|Q96QZ7-6;Q96QZ7;Q96QZ7-4;Q96QZ7-3;Q96QZ7-2;Q96QZ7-5	.|.;MAGI1_HUMAN;.;.;.;.	W|M	85|204;204;100;79;204;204	.|ENSP00000385450:T204M;ENSP00000331157:T204M;ENSP00000418177:T79M;ENSP00000420323:T204M;ENSP00000424369:T204M	.|ENSP00000331157:T204M	R|T	-|-	1|2	2|0	MAGI1|MAGI1	65439453|65439453	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.995000|0.995000	0.86356|0.86356	4.647000|4.647000	0.61418|0.61418	2.668000|2.668000	0.90789|0.90789	0.655000|0.655000	0.94253|0.94253	CGG|ACG		0.507	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742	
KBTBD8	84541	broad.mit.edu	37	3	67054330	67054330	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:67054330G>A	ENST00000417314.2	+	3	988	c.939G>A	c.(937-939)agG>agA	p.R313R	KBTBD8_ENST00000460576.1_Intron|KBTBD8_ENST00000295568.4_Silent_p.R287R			Q8NFY9	KBTB8_HUMAN	kelch repeat and BTB (POZ) domain containing 8	313						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)		p.R287R(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)		TCACAGGAAGGGTGTTTAAAC	0.418																																					p.R313R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G939A	3						.						136.0	132.0	134.0					3																	67054330		2203	4300	6503	67137020	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.939G>A	3.37:g.67054330G>A		Somatic		Capture	Illumina HiSeq	Phase_I	67137020	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	
LMOD3	56203	broad.mit.edu	37	3	69171273	69171273	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:69171273G>A	ENST00000420581.2	-	1	444	c.265C>T	c.(265-267)Cga>Tga	p.R89*	LMOD3_ENST00000489031.1_Nonsense_Mutation_p.R89*|LMOD3_ENST00000475434.1_Nonsense_Mutation_p.R89*	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	89	Glu-rich.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R89*(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)	13		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		ACAGGAACTCGTTCCTCTTCC	0.453																																					p.R89X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C265T	3						.						75.0	71.0	72.0					3																	69171273		1897	4116	6013	69253963	SO:0001587	stop_gained	56203	exon1			AK096900	CCDS46862.1	3p14.1	2003-03-07			ENSG00000163380	ENSG00000163380			6649	protein-coding gene	gene with protein product							Standard	NM_198271		Approved		uc003dns.2	Q0VAK6	OTTHUMG00000158774	ENST00000420581.2:c.265C>T	3.37:g.69171273G>A	ENSP00000414670:p.Arg89*	Somatic		Capture	Illumina HiSeq	Phase_I	69253963	NM_198271	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	Nonsense_Mutation	SNP	ENST00000420581.2	37	CCDS46862.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.577621	0.86645	.	.	ENSG00000163380	ENST00000420581;ENST00000489031;ENST00000475434	.	.	.	5.69	4.74	0.60224	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.6536	11.2973	0.49286	0.0:0.0:0.6019:0.3981	.	.	.	.	X	89	.	ENSP00000414670:R89X	R	-	1	2	LMOD3	69253963	1.000000	0.71417	0.721000	0.30653	0.305000	0.27757	2.016000	0.40971	2.702000	0.92279	0.591000	0.81541	CGA		0.453	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529	
GXYLT2	727936	broad.mit.edu	37	3	73016753	73016753	+	Silent	SNP	C	C	T	rs370320248		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:73016753C>T	ENST00000389617.4	+	6	1193	c.1032C>T	c.(1030-1032)taC>taT	p.Y344Y		NM_001080393.1	NP_001073862.1	A0PJZ3	GXLT2_HUMAN	glucoside xylosyltransferase 2	344					O-glycan processing (GO:0016266)	integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)	p.Y344Y(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	18						ACTGCATGTACGGAAGCAACT	0.498																																					p.Y344Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1032T	3						.	C		0,4108		0,0,2054	100.0	97.0	98.0		1032	-11.0	0.2	3		98	1,8403		0,1,4201	no	coding-synonymous	GXYLT2	NM_001080393.1		0,1,6255	TT,TC,CC		0.0119,0.0,0.0080		344/444	73016753	1,12511	2054	4202	6256	73099443	SO:0001819	synonymous_variant	727936	exon6			AC098481	CCDS46870.1	3p13	2013-02-22	2009-11-17	2009-11-17	ENSG00000172986	ENSG00000172986		"""Glycosyltransferase family 8 domain containing"""	33383	protein-coding gene	gene with protein product		613322	"""glycosyltransferase 8 domain containing 4"""	GLT8D4		19940119	Standard	NM_001080393		Approved		uc003dpg.3	A0PJZ3	OTTHUMG00000158815	ENST00000389617.4:c.1032C>T	3.37:g.73016753C>T		Somatic		Capture	Illumina HiSeq	Phase_I	73099443	NM_001080393		Silent	SNP	ENST00000389617.4	37	CCDS46870.1																																																																																				0.498	GXYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352318.1	NM_001080393	
PDZRN3	23024	broad.mit.edu	37	3	73433788	73433788	+	Silent	SNP	G	G	A	rs368693865		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:73433788G>A	ENST00000263666.4	-	10	2043	c.1929C>T	c.(1927-1929)tgC>tgT	p.C643C	PDZRN3_ENST00000462146.2_Silent_p.C300C|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000479530.1_Silent_p.C360C|PDZRN3_ENST00000466780.1_Silent_p.C300C|PDZRN3_ENST00000535920.1_Silent_p.C365C	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	643					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.C643C(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GGAAGCGCTCGCACTCGTCCA	0.657																																					p.C643C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1929T	3						.	G		1,4405	2.1+/-5.4	0,1,2202	60.0	65.0	63.0		1929	1.2	1.0	3		63	0,8600		0,0,4300	no	coding-synonymous	PDZRN3	NM_015009.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		643/1067	73433788	1,13005	2203	4300	6503	73516478	SO:0001819	synonymous_variant	23024	exon10			AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"""RING-type (C3HC4) zinc fingers"""	17704	protein-coding gene	gene with protein product	"""likely ortholog of mouse semaF cytoplasmic domain associated protein 3"""	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.1929C>T	3.37:g.73433788G>A		Somatic		Capture	Illumina HiSeq	Phase_I	73516478	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	37	CCDS33789.1																																																																																				0.657	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363	
POU1F1	5449	broad.mit.edu	37	3	87322563	87322563	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:87322563C>A	ENST00000350375.2	-	2	272	c.148G>T	c.(148-150)Gga>Tga	p.G50*	POU1F1_ENST00000344265.3_Nonsense_Mutation_p.G76*|POU1F1_ENST00000560656.1_Nonsense_Mutation_p.G50*	NM_000306.2	NP_000297.1	P28069	PIT1_HUMAN	POU class 1 homeobox 1	50					B cell differentiation (GO:0030183)|cell fate specification (GO:0001708)|determination of adult lifespan (GO:0008340)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear transport (GO:0051169)|positive regulation of cell proliferation (GO:0008284)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of insulin-like growth factor receptor signaling pathway (GO:0043567)|somatotropin secreting cell development (GO:0060133)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II activating transcription factor binding (GO:0001102)|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 coactivator activity (GO:0001105)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.G50*(1)		central_nervous_system(1)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(2)	18	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00229)|Lung(72;0.00677)		TAATGAAGTCCTGTTGCTGTG	0.383																																					p.G76X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G226T	3						.						112.0	98.0	103.0					3																	87322563		2203	4300	6503	87405253	SO:0001587	stop_gained	5449	exon2			D10216	CCDS2919.1, CCDS46873.1	3p11.2	2011-06-20	2007-07-13		ENSG00000064835	ENSG00000064835		"""Homeoboxes / POU class"""	9210	protein-coding gene	gene with protein product	"""growth hormone factor 1"""	173110	"""POU domain class 1, transcription factor 1"""	PIT1		1956794	Standard	NM_001122757		Approved	GHF-1, POU1F1a	uc010hoj.1	P28069	OTTHUMG00000158992	ENST00000350375.2:c.148G>T	3.37:g.87322563C>A	ENSP00000263781:p.Gly50*	Somatic		Capture	Illumina HiSeq	Phase_I	87405253	NM_001122757	O75757|Q15132|Q15133|Q9UD34|Q9UEL3	Nonsense_Mutation	SNP	ENST00000350375.2	37	CCDS2919.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.913676	0.92178	.	.	ENSG00000064835	ENST00000350375;ENST00000344265	.	.	.	5.78	4.72	0.59763	.	0.708586	0.13971	N	0.350162	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	15.71	0.77620	0.0:0.9239:0.0:0.0761	.	.	.	.	X	50;76	.	ENSP00000342931:G76X	G	-	1	0	POU1F1	87405253	0.997000	0.39634	0.998000	0.56505	0.934000	0.57294	3.327000	0.52045	2.717000	0.92951	0.585000	0.79938	GGA		0.383	POU1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352827.1	NM_000306	
OR5K4	403278	broad.mit.edu	37	3	98073096	98073096	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:98073096C>T	ENST00000354924.2	+	1	399	c.399C>T	c.(397-399)caC>caT	p.H133H	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005517.1	NP_001005517.1	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K, member 4	133						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H133H(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	21						TGCAGTACCACACCATGATGT	0.468																																					p.H133H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C399T	3						.						145.0	141.0	142.0					3																	98073096		2203	4300	6503	99555786	SO:0001819	synonymous_variant	403278	exon1				CCDS33802.1	3q11.2	2013-09-23			ENSG00000196098	ENSG00000196098		"""GPCR / Class A : Olfactory receptors"""	31291	protein-coding gene	gene with protein product							Standard	NM_001005517		Approved		uc011bgv.2	A6NMS3	OTTHUMG00000160081	ENST00000354924.2:c.399C>T	3.37:g.98073096C>T		Somatic		Capture	Illumina HiSeq	Phase_I	99555786	NM_001005517		Silent	SNP	ENST00000354924.2	37	CCDS33802.1																																																																																				0.468	OR5K4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359114.1		
ALCAM	214	broad.mit.edu	37	3	105266101	105266102	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	AG	AG	AG	-	AG	AG	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:105266101_105266102delAG	ENST00000306107.5	+	10	1713_1714	c.1213_1214delAG	c.(1213-1215)agafs	p.R405fs	ALCAM_ENST00000486979.2_Frame_Shift_Del_p.R354fs|ALCAM_ENST00000472644.2_Frame_Shift_Del_p.R405fs|ALCAM_ENST00000389927.4_Frame_Shift_Del_p.R127fs	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	405	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)	p.E406fs*19(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						ACTAAAGAAAAGAGAGTCATTG	0.381																																					p.405_405del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1213_1214del	3						.																																			106748792	SO:0001589	frameshift_variant	214	exon10			AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	400	protein-coding gene	gene with protein product		601662	"""activated leucocyte cell adhesion molecule"""			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.1213_1214delAG	3.37:g.105266105_105266106delAG	ENSP00000305988:p.Arg405fs	Somatic		Capture	Illumina HiSeq	Phase_I	106748791	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Frame_Shift_Del	DEL	ENST00000306107.5	37	CCDS33810.1																																																																																				0.381	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627	
NCBP2	22916	broad.mit.edu	37	3	196664498	196664498	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr3:196664498C>T	ENST00000321256.5	-	3	375	c.282G>A	c.(280-282)gcG>gcA	p.A94A	NCBP2-AS1_ENST00000447775.1_RNA|NCBP2_ENST00000422610.1_Silent_p.A24A|NCBP2_ENST00000447325.1_Silent_p.A24A|NCBP2_ENST00000467803.1_5'UTR|NCBP2_ENST00000427641.2_Silent_p.A41A|NCBP2_ENST00000452404.2_Silent_p.A76A	NM_007362.3	NP_031388.2	P52298	NCBP2_HUMAN	nuclear cap binding protein subunit 2, 20kDa	94	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of RNA export from nucleus (GO:0046833)|positive regulation of viral transcription (GO:0050434)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|snRNA export from nucleus (GO:0006408)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mRNA cap binding complex (GO:0005845)|nuclear cap binding complex (GO:0005846)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|RNA cap binding (GO:0000339)	p.A94A(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.42e-24)|all cancers(36;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(49;4.13e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00551)		TGGCGTTTTCCGCATCTGCGC	0.468																																					p.A94A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G282A	3						.						111.0	102.0	105.0					3																	196664498		2203	4300	6503	198148895	SO:0001819	synonymous_variant	22916	exon3			D59253	CCDS3323.1, CCDS46986.1	3q29	2013-02-12	2002-08-29		ENSG00000114503	ENSG00000114503		"""RNA binding motif (RRM) containing"""	7659	protein-coding gene	gene with protein product		605133	"""nuclear cap binding protein subunit 2, 20kD"""			7478990, 7651522, 8682299	Standard	NM_001042540		Approved	NIP1, CBP20, Cbc2	uc003fxd.1	P52298	OTTHUMG00000155520	ENST00000321256.5:c.282G>A	3.37:g.196664498C>T		Somatic		Capture	Illumina HiSeq	Phase_I	198148895	NM_007362	B2RE91|B4DMK7|E9PAR5|Q14924|Q2TS50	Silent	SNP	ENST00000321256.5	37	CCDS3323.1																																																																																				0.468	NCBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340470.2	NM_007362	
FRYL	285527	broad.mit.edu	37	4	48604082	48604083	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:48604082_48604083insA	ENST00000503238.1	-	10	988_989	c.989_990insT	c.(988-990)ttafs	p.L330fs	FRYL_ENST00000506685.1_Frame_Shift_Ins_p.L36fs|FRYL_ENST00000537810.1_Frame_Shift_Ins_p.L330fs|FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000358350.4_Frame_Shift_Ins_p.L330fs|FRYL_ENST00000507711.1_Frame_Shift_Ins_p.L330fs			O94915	FRYL_HUMAN	FRY-like	330					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)			p.L330fs*3(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						GCCAGTTATTTAAAAAAAATTG	0.307																																					p.L330fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.990_991insT	4						.																																			48298840	SO:0001589	frameshift_variant	285527	exon13			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.990dupT	4.37:g.48604090_48604090dupA	ENSP00000426064:p.Leu330fs	Somatic		Capture	Illumina HiSeq	Phase_I	48298839	NM_015030	O95640|Q8WTZ5|Q9NT40	Frame_Shift_Ins	INS	ENST00000503238.1	37	CCDS43227.1																																																																																				0.307	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2		
TACR3	6870	broad.mit.edu	37	4	104577388	104577388	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:104577388C>A	ENST00000304883.2	-	3	991	c.851G>T	c.(850-852)tGt>tTt	p.C284F		NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	284					aging (GO:0007568)|hyperosmotic salinity response (GO:0042538)|positive regulation of blood pressure (GO:0045777)|positive regulation of heart rate (GO:0010460)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of dopamine metabolic process (GO:0042053)|regulation of feeding behavior (GO:0060259)|response to cocaine (GO:0042220)|response to estradiol (GO:0032355)|response to morphine (GO:0043278)|tachykinin receptor signaling pathway (GO:0007217)	cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	tachykinin receptor activity (GO:0004995)	p.C284F(1)		breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51		Hepatocellular(203;0.217)		UCEC - Uterine corpus endometrioid carcinoma (10;0.22)|OV - Ovarian serous cystadenocarcinoma(123;3.4e-08)		ATACTTGTCACAGGTATCTCC	0.403																																					p.C284F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G851T	4						.						148.0	146.0	146.0					4																	104577388		2203	4300	6503	104796837	SO:0001583	missense	6870	exon3			M89473	CCDS3664.1	4q25	2012-08-08			ENSG00000169836	ENSG00000169836		"""GPCR / Class A : Tachykinin receptors"""	11528	protein-coding gene	gene with protein product	"""neurokinin beta receptor"""	162332				1374246	Standard	NM_001059		Approved	NK3R	uc003hxe.1	P29371	OTTHUMG00000131124	ENST00000304883.2:c.851G>T	4.37:g.104577388C>A	ENSP00000303325:p.Cys284Phe	Somatic		Capture	Illumina HiSeq	Phase_I	104796837	NM_001059	Q0P510	Missense_Mutation	SNP	ENST00000304883.2	37	CCDS3664.1	.	.	.	.	.	.	.	.	.	.	C	17.56	3.421194	0.62622	.	.	ENSG00000169836	ENST00000304883	T	0.36878	1.23	5.72	3.85	0.44370	GPCR, rhodopsin-like superfamily (1);	0.156238	0.64402	D	0.000014	T	0.36468	0.0968	L	0.29908	0.895	0.39110	D	0.961467	B	0.33073	0.396	B	0.43623	0.425	T	0.45804	-0.9236	10	0.66056	D	0.02	.	14.1057	0.65088	0.0:0.4826:0.5174:0.0	.	284	P29371	NK3R_HUMAN	F	284	ENSP00000303325:C284F	ENSP00000303325:C284F	C	-	2	0	TACR3	104796837	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.039000	0.64185	1.514000	0.48869	0.650000	0.86243	TGT		0.403	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059	
TBCK	93627	broad.mit.edu	37	4	107114776	107114776	+	Silent	SNP	G	G	A	rs557016175	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:107114776G>A	ENST00000273980.5	-	23	2496	c.2049C>T	c.(2047-2049)tcC>tcT	p.S683S	TBCK_ENST00000394706.3_Silent_p.S644S|TBCK_ENST00000514689.1_5'UTR|TBCK_ENST00000361687.4_Silent_p.S620S|TBCK_ENST00000394708.2_Silent_p.S683S|TBCK_ENST00000432496.2_Silent_p.S683S					TBC1 domain containing kinase									p.S683S(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						CTGGTAAATCGGAGAAGAGAA	0.383													G|||	3	0.000599042	0.0	0.0029	5008	,	,		16106	0.001		0.0	False		,,,				2504	0.0				p.S644S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1932T	4						.						59.0	64.0	62.0					4																	107114776		2203	4300	6503	107334225	SO:0001819	synonymous_variant	93627	exon22				CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.2049C>T	4.37:g.107114776G>A		Somatic		Capture	Illumina HiSeq	Phase_I	107334225	NM_001163437		Silent	SNP	ENST00000273980.5	37	CCDS54788.1																																																																																				0.383	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115	
SGMS2	166929	broad.mit.edu	37	4	108820787	108820787	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:108820787G>A	ENST00000394684.4	+	4	1069	c.512G>A	c.(511-513)tGc>tAc	p.C171Y	SGMS2_ENST00000359079.4_Missense_Mutation_p.C171Y|SGMS2_ENST00000394686.3_Missense_Mutation_p.C171Y|RP11-286E11.1_ENST00000499098.1_RNA|RP11-286E11.1_ENST00000513071.1_RNA	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	171					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.C171Y(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)		CTGTATCGCTGCATTACAATG	0.403																																					p.C171Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G512A	4						.						189.0	177.0	181.0					4																	108820787		2203	4300	6503	109040236	SO:0001583	missense	166929	exon3			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.512G>A	4.37:g.108820787G>A	ENSP00000378176:p.Cys171Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	109040236	NM_001136257	A8K2S9|B2RA61	Missense_Mutation	SNP	ENST00000394684.4	37	CCDS3677.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.336249	0.81801	.	.	ENSG00000164023	ENST00000394684;ENST00000359079;ENST00000394686	T;T;T	0.51071	0.72;0.72;0.72	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.69611	0.3130	M	0.77616	2.38	0.80722	D	1	D	0.71674	0.998	P	0.61940	0.896	T	0.70648	-0.4814	10	0.59425	D	0.04	-2.35	20.2181	0.98305	0.0:0.0:1.0:0.0	.	171	Q8NHU3	SMS2_HUMAN	Y	171	ENSP00000378176:C171Y;ENSP00000351981:C171Y;ENSP00000378178:C171Y	ENSP00000351981:C171Y	C	+	2	0	SGMS2	109040236	1.000000	0.71417	0.967000	0.41034	0.588000	0.36517	9.869000	0.99810	2.785000	0.95823	0.655000	0.94253	TGC		0.403	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254752.1	NM_152621	
ANK2	287	broad.mit.edu	37	4	114274329	114274329	+	Missense_Mutation	SNP	G	G	A	rs200920714		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:114274329G>A	ENST00000357077.4	+	38	4608	c.4555G>A	c.(4555-4557)Gcc>Acc	p.A1519T	ANK2_ENST00000394537.3_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.A1486T|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1519	Death 1. {ECO:0000255|PROSITE- ProRule:PRU00064}.				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.A1519T(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)		CAAAATGACCGCCATCTTGAC	0.453																																					p.A1519T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4555A	4						.						73.0	74.0	74.0					4																	114274329		2203	4300	6503	114493778	SO:0001583	missense	287	exon38			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.4555G>A	4.37:g.114274329G>A	ENSP00000349588:p.Ala1519Thr	Somatic		Capture	Illumina HiSeq	Phase_I	114493778	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.810005	0.90707	.	.	ENSG00000145362	ENST00000503423;ENST00000504454;ENST00000357077;ENST00000264366	T;T;T;T	0.73575	1.87;1.87;-0.76;-0.67	5.83	5.83	0.93111	.	0.000000	0.53938	D	0.000045	D	0.86251	0.5888	M	0.74647	2.275	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.71656	0.92;0.974	D	0.84583	0.0662	10	0.41790	T	0.15	.	20.1195	0.97955	0.0:0.0:1.0:0.0	.	1486;1519	Q01484;Q01484-4	ANK2_HUMAN;.	T	1432;1534;1519;1486	ENSP00000421011:A1432T;ENSP00000424722:A1534T;ENSP00000349588:A1519T;ENSP00000264366:A1486T	ENSP00000264366:A1486T	A	+	1	0	ANK2	114493778	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	6.662000	0.74426	2.759000	0.94783	0.650000	0.86243	GCC		0.453	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
ANK2	287	broad.mit.edu	37	4	114275362	114275362	+	Missense_Mutation	SNP	C	C	T	rs536962908		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:114275362C>T	ENST00000357077.4	+	38	5641	c.5588C>T	c.(5587-5589)aCg>aTg	p.T1863M	ANK2_ENST00000394537.3_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.T1830M|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1863	Repeat-rich region.				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.T1863M(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)		TCTGCAAAAACGGAAAGACAT	0.453													C|||	1	0.000199681	0.0	0.0	5008	,	,		21258	0.001		0.0	False		,,,				2504	0.0				p.T1863M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5588T	4						.						198.0	188.0	191.0					4																	114275362		2203	4300	6503	114494811	SO:0001583	missense	287	exon38			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.5588C>T	4.37:g.114275362C>T	ENSP00000349588:p.Thr1863Met	Somatic		Capture	Illumina HiSeq	Phase_I	114494811	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	2.296	-0.361198	0.05103	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.68479	-0.32;-0.33	5.85	3.25	0.37280	.	0.511218	0.17606	N	0.168254	T	0.51024	0.1650	L	0.48642	1.525	0.09310	N	1	P;B	0.43662	0.814;0.004	B;B	0.35727	0.209;0.003	T	0.43523	-0.9386	9	.	.	.	.	4.8253	0.13412	0.1381:0.57:0.0:0.2919	.	1830;1863	Q01484;Q01484-4	ANK2_HUMAN;.	M	1863;1830	ENSP00000349588:T1863M;ENSP00000264366:T1830M	.	T	+	2	0	ANK2	114494811	0.021000	0.18746	0.001000	0.08648	0.131000	0.20780	0.064000	0.14437	0.402000	0.25451	-0.751000	0.03497	ACG		0.453	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
ANK2	287	broad.mit.edu	37	4	114275691	114275691	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:114275691C>T	ENST00000357077.4	+	38	5970	c.5917C>T	c.(5917-5919)Cca>Tca	p.P1973S	ANK2_ENST00000394537.3_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.P1940S|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000510275.2_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1973	Repeat-rich region.				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.P1973S(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)		AGAAAAGCAACCACCTGTATC	0.498																																					p.P1973S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5917T	4						.						97.0	103.0	101.0					4																	114275691		2203	4300	6503	114495140	SO:0001583	missense	287	exon38			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.5917C>T	4.37:g.114275691C>T	ENSP00000349588:p.Pro1973Ser	Somatic		Capture	Illumina HiSeq	Phase_I	114495140	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	C	9.746	1.166111	0.21621	.	.	ENSG00000145362	ENST00000357077;ENST00000264366	T;T	0.69040	-0.36;-0.37	6.06	5.21	0.72293	.	0.222118	0.31438	N	0.007655	T	0.53270	0.1786	N	0.20685	0.6	0.80722	D	1	B;P	0.38078	0.264;0.617	B;B	0.37144	0.044;0.242	T	0.51020	-0.8758	9	.	.	.	.	17.3144	0.87218	0.0:0.8746:0.1254:0.0	.	1940;1973	Q01484;Q01484-4	ANK2_HUMAN;.	S	1973;1940	ENSP00000349588:P1973S;ENSP00000264366:P1940S	.	P	+	1	0	ANK2	114495140	0.529000	0.26322	0.352000	0.25734	0.853000	0.48598	5.089000	0.64492	1.529000	0.49120	0.655000	0.94253	CCA		0.498	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
UGT8	7368	broad.mit.edu	37	4	115544601	115544601	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:115544601A>G	ENST00000310836.6	+	2	1087	c.565A>G	c.(565-567)Aac>Gac	p.N189D	UGT8_ENST00000394511.3_Missense_Mutation_p.N189D	NM_001128174.1	NP_001121646	Q16880	CGT_HUMAN	UDP glycosyltransferase 8	189					axon cargo transport (GO:0008088)|central nervous system development (GO:0007417)|cytoskeleton organization (GO:0007010)|galactosylceramide biosynthetic process (GO:0006682)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to paranode region of axon (GO:0002175)	integral component of membrane (GO:0016021)	2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity (GO:0003851)|UDP-galactose:glucosylceramide beta-1,4-galactosyltransferase activity (GO:0008489)	p.N189D(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000632)		AGACCGCATGAACTTGCTGCA	0.448																																					p.N189D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A565G	4						.						113.0	108.0	110.0					4																	115544601		2203	4300	6503	115764050	SO:0001583	missense	7368	exon2			AK127970	CCDS3705.1	4q26	2013-02-21	2008-07-31	2005-07-20	ENSG00000174607	ENSG00000174607	2.4.1.45	"""UDP glucuronosyltransferases"""	12555	protein-coding gene	gene with protein product	"""2-hydroxyacylsphingosine 1-beta-galactosyltransferase"""	601291	"""UDP-galactose ceramide galactosyltransferase"""	CGT		8661025	Standard	NM_003360		Approved		uc003ibs.2	Q16880	OTTHUMG00000132915	ENST00000310836.6:c.565A>G	4.37:g.115544601A>G	ENSP00000311648:p.Asn189Asp	Somatic		Capture	Illumina HiSeq	Phase_I	115764050	NM_001128174	B3KXU7|O00196	Missense_Mutation	SNP	ENST00000310836.6	37	CCDS3705.1	.	.	.	.	.	.	.	.	.	.	A	14.88	2.667047	0.47677	.	.	ENSG00000174607	ENST00000310836;ENST00000394511	T;T	0.59364	0.27;0.27	5.34	5.34	0.76211	.	0.350989	0.36101	N	0.002783	T	0.38612	0.1047	N	0.04063	-0.285	0.51233	D	0.999912	B	0.09022	0.002	B	0.17722	0.019	T	0.29941	-0.9995	10	0.59425	D	0.04	.	15.6121	0.76733	1.0:0.0:0.0:0.0	.	189	Q16880	CGT_HUMAN	D	189	ENSP00000311648:N189D;ENSP00000378019:N189D	ENSP00000311648:N189D	N	+	1	0	UGT8	115764050	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.054000	0.57434	2.151000	0.67156	0.528000	0.53228	AAC		0.448	UGT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256426.2	NM_003360	
NDST4	64579	broad.mit.edu	37	4	115773977	115773977	+	Splice_Site	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:115773977T>G	ENST00000264363.2	-	8	2398	c.1720A>C	c.(1720-1722)Aat>Cat	p.N574H		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	574	Heparan sulfate N-deacetylase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)	p.N574H(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		TCACATGGATTCTGCAAGAAG	0.373																																					p.N574H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1720C	4						.						111.0	107.0	108.0					4																	115773977		2203	4300	6503	115993426	SO:0001630	splice_region_variant	64579	exon8			AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"""Sulfotransferases, membrane-bound"""	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.1720-1A>C	4.37:g.115773977T>G		Somatic		Capture	Illumina HiSeq	Phase_I	115993426	NM_022569	Q2KHM8	Missense_Mutation	SNP	ENST00000264363.2	37	CCDS3706.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.054088	0.75960	.	.	ENSG00000138653	ENST00000264363	T	0.55760	0.5	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.74650	0.3744	M	0.85630	2.765	0.58432	D	0.999999	D	0.76494	0.999	D	0.67900	0.954	T	0.79754	-0.1670	10	0.87932	D	0	.	15.7449	0.77932	0.0:0.0:0.0:1.0	.	574	Q9H3R1	NDST4_HUMAN	H	574	ENSP00000264363:N574H	ENSP00000264363:N574H	N	-	1	0	NDST4	115993426	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.546000	0.60705	2.114000	0.64651	0.533000	0.62120	AAT		0.373	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569	Missense_Mutation
C4orf3	401152	broad.mit.edu	37	4	120221586	120221586	+	Silent	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:120221586C>A	ENST00000504110.1	-	1	490	c.105G>T	c.(103-105)ggG>ggT	p.G35G	C4orf3_ENST00000399075.4_Silent_p.G168G	NM_001001701.3	NP_001001701.2	Q8WVX3	CD003_HUMAN	chromosome 4 open reading frame 3	35						integral component of membrane (GO:0016021)		p.G168G(1)		breast(1)|large_intestine(1)|lung(4)	6						GCCCATTTGCCCCAGACTGAG	0.547																																					p.G168G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G504T	4						.						157.0	166.0	163.0					4																	120221586		1985	4160	6145	120441034	SO:0001819	synonymous_variant	401152	exon2				CCDS43266.1, CCDS54798.1	4q26	2012-02-24			ENSG00000164096	ENSG00000164096			19225	protein-coding gene	gene with protein product	"""HCV F-transactivated protein 1"""						Standard	NM_001001701		Approved		uc021xrf.1	Q8WVX3	OTTHUMG00000161333	ENST00000504110.1:c.105G>T	4.37:g.120221586C>A		Somatic		Capture	Illumina HiSeq	Phase_I	120441034	NM_001170330	Q6J203	Silent	SNP	ENST00000504110.1	37	CCDS43266.1																																																																																				0.547	C4orf3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364576.3	NM_001001701	
ANXA5	308	broad.mit.edu	37	4	122605872	122605872	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:122605872C>T	ENST00000296511.5	-	4	434	c.149G>A	c.(148-150)cGc>cAc	p.R50H	ANXA5_ENST00000501272.2_Intron|ANXA5_ENST00000515017.1_Intron|ANXA5_ENST00000509016.1_5'UTR	NM_001154.3	NP_001145.1	P08758	ANXA5_HUMAN	annexin A5	50					blood coagulation (GO:0007596)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of coagulation (GO:0050819)|response to organic substance (GO:0010033)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipase inhibitor activity (GO:0004859)|phospholipid binding (GO:0005543)	p.R50H(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)	15						GATTTCCTGGCGCTGAGCATT	0.443																																					p.R50H	Pancreas(191;1279 2147 16046 17806 52646)|GBM(88;628 1285 16585 32846 50188)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G149A	4						.						163.0	145.0	151.0					4																	122605872		2203	4300	6503	122825322	SO:0001583	missense	308	exon4			U05770	CCDS3720.1	4q27	2008-02-05			ENSG00000164111	ENSG00000164111		"""Annexins"""	543	protein-coding gene	gene with protein product		131230		ENX2, ANX5		2960376	Standard	NM_001154		Approved		uc003idv.4	P08758	OTTHUMG00000133034	ENST00000296511.5:c.149G>A	4.37:g.122605872C>T	ENSP00000296511:p.Arg50His	Somatic		Capture	Illumina HiSeq	Phase_I	122825322	NM_001154	D3DNW7|Q6FHB3|Q6FI16|Q8WV69|Q9UDH9	Missense_Mutation	SNP	ENST00000296511.5	37	CCDS3720.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.935265	0.92458	.	.	ENSG00000164111	ENST00000296511;ENST00000512232	T	0.03951	3.75	6.06	6.06	0.98353	Annexin repeat, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.39655	0.1086	H	0.98256	4.185	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.59241	-0.7491	10	0.72032	D	0.01	.	19.3997	0.94623	0.0:1.0:0.0:0.0	.	50;50	E7ENQ5;P08758	.;ANXA5_HUMAN	H	50	ENSP00000296511:R50H	ENSP00000296511:R50H	R	-	2	0	ANXA5	122825322	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	5.947000	0.70242	2.871000	0.98454	0.655000	0.94253	CGC		0.443	ANXA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256636.2	NM_001154	
KIAA1109	84162	broad.mit.edu	37	4	123207740	123207740	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:123207740C>T	ENST00000264501.4	+	53	9455	c.9082C>T	c.(9082-9084)Cgt>Tgt	p.R3028C	KIAA1109_ENST00000388738.3_Missense_Mutation_p.R3028C|KIAA1109_ENST00000455637.1_Missense_Mutation_p.R3028C			Q2LD37	K1109_HUMAN	KIAA1109	3028					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.R3028C(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						TCACAGATTGCGTTTTACTTC	0.388																																					p.R3028C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C9082T	4						.						131.0	122.0	125.0					4																	123207740		1896	4119	6015	123427190	SO:0001583	missense	84162	exon51			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.9082C>T	4.37:g.123207740C>T	ENSP00000264501:p.Arg3028Cys	Somatic		Capture	Illumina HiSeq	Phase_I	123427190	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.40|15.40	2.822830|2.822830	0.50739|0.50739	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000419325|ENST00000264501;ENST00000388738;ENST00000455637	.|T;T;T	.|0.23147	.|2.51;2.51;1.92	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	.|0.068600	.|0.64402	.|D	.|0.000012	T|T	0.13457|0.13457	0.0326|0.0326	N|N	0.01705|0.01705	-0.755|-0.755	0.54753|0.54753	D|D	0.999986|0.999986	.|B;B	.|0.15141	.|0.012;0.005	.|B;B	.|0.08055	.|0.003;0.001	T|T	0.15752|0.15752	-1.0426|-1.0426	5|10	.|0.44086	.|T	.|0.13	.|.	19.6736|19.6736	0.95921|0.95921	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|3028;3028	.|Q2LD37-6;Q2LD37	.|.;K1109_HUMAN	V|C	985|3028	.|ENSP00000264501:R3028C;ENSP00000373390:R3028C;ENSP00000389925:R3028C	.|ENSP00000264501:R3028C	A|R	+|+	2|1	0|0	KIAA1109|KIAA1109	123427190|123427190	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.998000|0.998000	0.95712|0.95712	4.252000|4.252000	0.58785|0.58785	2.660000|2.660000	0.90430|0.90430	0.650000|0.650000	0.86243|0.86243	GCG|CGT		0.388	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
KIAA1109	84162	broad.mit.edu	37	4	123265623	123265623	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:123265623C>T	ENST00000264501.4	+	74	13013	c.12640C>T	c.(12640-12642)Cgg>Tgg	p.R4214W	KIAA1109_ENST00000388738.3_Missense_Mutation_p.R4214W			Q2LD37	K1109_HUMAN	KIAA1109	4214					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.R4214W(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						GAGTTTGTCACGGATCAGGCG	0.398																																					p.R4214W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C12640T	4						.						137.0	133.0	134.0					4																	123265623		1894	4121	6015	123485073	SO:0001583	missense	84162	exon72			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.12640C>T	4.37:g.123265623C>T	ENSP00000264501:p.Arg4214Trp	Somatic		Capture	Illumina HiSeq	Phase_I	123485073	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.8|21.8	4.205321|4.205321	0.79127|0.79127	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707|ENST00000442707	T;T;T|.	0.51325|.	1.89;1.89;0.71|.	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72518|0.72518	0.3470|0.3470	M|M	0.70595|0.70595	2.14|2.14	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.83275|.	0.996;0.993|.	T|T	0.71656|0.71656	-0.4527|-0.4527	10|5	0.87932|.	D|.	0|.	.|.	13.336|13.336	0.60518|0.60518	0.2758:0.7241:0.0:0.0|0.2758:0.7241:0.0:0.0	.|.	4213;4214|.	Q2LD37-4;Q2LD37|.	.;K1109_HUMAN|.	W|M	4214;4214;883|159	ENSP00000264501:R4214W;ENSP00000373390:R4214W;ENSP00000410874:R883W|.	ENSP00000264501:R4214W|.	R|T	+|+	1|2	2|0	KIAA1109|KIAA1109	123485073|123485073	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	4.156000|4.156000	0.58138|0.58138	2.692000|2.692000	0.91855|0.91855	0.655000|0.655000	0.94253|0.94253	CGG|ACG		0.398	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
ADAD1	132612	broad.mit.edu	37	4	123329126	123329126	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:123329126C>T	ENST00000296513.2	+	8	973	c.788C>T	c.(787-789)cCa>cTa	p.P263L	ADAD1_ENST00000388724.2_Missense_Mutation_p.P263L|ADAD1_ENST00000388725.2_Missense_Mutation_p.P245L	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	263	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)	p.P263L(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						GACATTAAGCCAGATGGAAGA	0.368																																					p.P263L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C788T	4						.						119.0	109.0	113.0					4																	123329126		2203	4300	6503	123548576	SO:0001583	missense	132612	exon8			AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.788C>T	4.37:g.123329126C>T	ENSP00000296513:p.Pro263Leu	Somatic		Capture	Illumina HiSeq	Phase_I	123548576	NM_139243	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Missense_Mutation	SNP	ENST00000296513.2	37	CCDS34058.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.924085	0.52653	.	.	ENSG00000164113	ENST00000296513;ENST00000388724;ENST00000388725	D;D;D	0.93547	-3.24;-3.24;-3.24	5.83	5.83	0.93111	Adenosine deaminase/editase (3);	0.245478	0.42682	D	0.000680	D	0.88005	0.6321	N	0.25380	0.74	0.58432	D	0.999991	B;B	0.17038	0.0;0.02	B;B	0.23716	0.003;0.048	T	0.82621	-0.0367	10	0.09590	T	0.72	-8.8709	15.5867	0.76489	0.0:0.863:0.137:0.0	.	263;263	Q96M93-2;Q96M93	.;ADAD1_HUMAN	L	263;263;245	ENSP00000296513:P263L;ENSP00000373376:P263L;ENSP00000373377:P245L	ENSP00000296513:P263L	P	+	2	0	ADAD1	123548576	0.023000	0.18921	1.000000	0.80357	0.973000	0.67179	1.893000	0.39758	2.763000	0.94921	0.655000	0.94253	CCA		0.368	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243	
FAT4	79633	broad.mit.edu	37	4	126238928	126238928	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:126238928G>A	ENST00000394329.3	+	1	1375	c.1362G>A	c.(1360-1362)gcG>gcA	p.A454A		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	454	Cadherin 4. {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.A454A(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						CAGTCCAGGCGCGCTCTTCTG	0.567											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A454A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1362A	4						.						42.0	45.0	44.0					4																	126238928		2039	4174	6213	126458378	SO:0001819	synonymous_variant	79633	exon1			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.1362G>A	4.37:g.126238928G>A		Somatic	1548	Capture	Illumina HiSeq	Phase_I	126458378	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.567	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FAT4	79633	broad.mit.edu	37	4	126367515	126367515	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:126367515G>A	ENST00000394329.3	+	8	7274	c.7261G>A	c.(7261-7263)Gca>Aca	p.A2421T	FAT4_ENST00000335110.5_Missense_Mutation_p.A719T	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2421	Cadherin 23. {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.A2421T(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						CATCACCAGCGCATTGTTAGA	0.443																																					p.A2421T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G7261A	4						.						122.0	121.0	121.0					4																	126367515		2203	4300	6503	126586965	SO:0001583	missense	79633	exon8			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.7261G>A	4.37:g.126367515G>A	ENSP00000377862:p.Ala2421Thr	Somatic		Capture	Illumina HiSeq	Phase_I	126586965	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	13.10	2.135541	0.37728	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.52526	0.66;0.66	5.69	5.69	0.88448	Cadherin (4);Cadherin-like (1);	0.000000	0.34110	U	0.004257	T	0.46464	0.1394	L	0.48218	1.51	0.42535	D	0.993055	P;D	0.59357	0.827;0.985	B;P	0.48795	0.182;0.59	T	0.29212	-1.0019	10	0.10902	T	0.67	.	14.637	0.68696	0.0:0.0:0.8545:0.1455	.	719;2421	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	T	2421;719	ENSP00000377862:A2421T;ENSP00000335169:A719T	ENSP00000335169:A719T	A	+	1	0	FAT4	126586965	1.000000	0.71417	0.845000	0.33349	0.191000	0.23601	4.077000	0.57598	2.677000	0.91161	0.655000	0.94253	GCA		0.443	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FAT4	79633	broad.mit.edu	37	4	126389700	126389700	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:126389700A>G	ENST00000394329.3	+	11	11946	c.11933A>G	c.(11932-11934)tAt>tGt	p.Y3978C	FAT4_ENST00000335110.5_Missense_Mutation_p.Y2241C	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3978	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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.Y3978C(1)|p.Y3943C(1)		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						TTGAACAGTTATGGATTTGAG	0.323																																					p.Y3978C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A11933G	4						.						59.0	60.0	60.0					4																	126389700		2203	4300	6503	126609150	SO:0001583	missense	79633	exon11			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.11933A>G	4.37:g.126389700A>G	ENSP00000377862:p.Tyr3978Cys	Somatic		Capture	Illumina HiSeq	Phase_I	126609150	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	21.2	4.107363	0.77096	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.79845	-1.31;-1.31	5.17	5.17	0.71159	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.000000	0.31834	U	0.006992	D	0.86847	0.6031	L	0.54323	1.7	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.998;0.994;0.998	D	0.86353	0.1712	10	0.40728	T	0.16	.	15.0242	0.71656	1.0:0.0:0.0:0.0	.	2241;3978;3978	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	C	3978;2241	ENSP00000377862:Y3978C;ENSP00000335169:Y2241C	ENSP00000335169:Y2241C	Y	+	2	0	FAT4	126609150	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.149000	0.94659	1.947000	0.56498	0.477000	0.44152	TAT		0.323	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
BOD1L1	259282	broad.mit.edu	37	4	13601501	13601501	+	Silent	SNP	G	G	A	rs367990092		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:13601501G>A	ENST00000040738.5	-	10	7158	c.7023C>T	c.(7021-7023)tcC>tcT	p.S2341S		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2341						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S2341S(2)									CAATGCTGGCGGAAATTGGCA	0.522																																					p.S2341S												.	.	2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	c.C7023T	4						.	G		0,4406		0,0,2203	131.0	98.0	109.0		7023	-10.4	0.0	4		109	1,8599		0,1,4299	no	coding-synonymous	BOD1L	NM_148894.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		2341/3052	13601501	1,13005	2203	4300	6503	13210599	SO:0001819	synonymous_variant	259282	exon10			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219			31792	protein-coding gene	gene with protein product			"""family with sequence similarity 44, member A"", ""biorientation of chromosomes in cell division 1-like"""	FAM44A, BOD1L			Standard	XM_005248150		Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.7023C>T	4.37:g.13601501G>A		Somatic		Capture	Illumina HiSeq	Phase_I	13210599	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Silent	SNP	ENST00000040738.5	37	CCDS3411.2																																																																																				0.522	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
SCLT1	132320	broad.mit.edu	37	4	129891533	129891533	+	Splice_Site	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:129891533C>A	ENST00000281142.5	-	10	1280	c.777G>T	c.(775-777)aaG>aaT	p.K259N	SCLT1_ENST00000434680.1_Intron|SCLT1_ENST00000439369.2_Intron|SCLT1_ENST00000503215.1_Intron|SCLT1_ENST00000502495.1_5'UTR	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	259					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.K259N(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						TAGAAAATACCTTCTTTTTCA	0.343																																					p.K259N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G777T	4						.						80.0	81.0	81.0					4																	129891533		2203	4299	6502	130110983	SO:0001630	splice_region_variant	132320	exon10			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.777+1G>T	4.37:g.129891533C>A		Somatic		Capture	Illumina HiSeq	Phase_I	130110983	NM_144643	A4QN04|Q0VAH2|Q6P2M4	Missense_Mutation	SNP	ENST00000281142.5	37	CCDS3740.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.685871	0.47991	.	.	ENSG00000151466	ENST00000281142	T	0.10288	2.89	4.58	4.58	0.56647	.	0.162025	0.52532	D	0.000073	T	0.28433	0.0703	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00351	-1.1796	9	.	.	.	-5.8939	13.063	0.59018	0.0:1.0:0.0:0.0	.	259	Q96NL6	SCLT1_HUMAN	N	259	ENSP00000281142:K259N	.	K	-	3	2	SCLT1	130110983	1.000000	0.71417	0.818000	0.32626	0.434000	0.31775	4.108000	0.57817	2.538000	0.85594	0.460000	0.39030	AAG		0.343	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643	Missense_Mutation
PCDH10	57575	broad.mit.edu	37	4	134072678	134072678	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:134072678G>A	ENST00000264360.5	+	1	2209	c.1383G>A	c.(1381-1383)ccG>ccA	p.P461P	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	461	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.P461P(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)		ACAACGCGCCGCGTTTCAGCC	0.622																																					p.P461P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1383A	4						.						88.0	90.0	89.0					4																	134072678		2203	4300	6503	134292128	SO:0001819	synonymous_variant	57575	exon1			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.1383G>A	4.37:g.134072678G>A		Somatic		Capture	Illumina HiSeq	Phase_I	134292128	NM_032961	Q4W5F6|Q96SF0	Silent	SNP	ENST00000264360.5	37	CCDS34063.1																																																																																				0.622	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961	
CC2D2A	57545	broad.mit.edu	37	4	15517558	15517558	+	Silent	SNP	C	C	T	rs201439700		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:15517558C>T	ENST00000503292.1	+	11	1128	c.948C>T	c.(946-948)acC>acT	p.T316T	CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000413206.1_Silent_p.T316T|CC2D2A_ENST00000389652.5_Silent_p.T267T|CC2D2A_ENST00000424120.1_Silent_p.T316T	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	316					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.T267T(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						GCCTTTACACCGGGGTAAGAC	0.453													C|||	1	0.000199681	0.0	0.0	5008	,	,		16858	0.0		0.001	False		,,,				2504	0.0				p.T316T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C948T	4						.	C		0,3806		0,0,1903	43.0	43.0	43.0		948	-8.6	0.0	4		43	1,8213		0,1,4106	no	coding-synonymous	CC2D2A	NM_001080522.2		0,1,6009	TT,TC,CC		0.0122,0.0,0.0083		316/1621	15517558	1,12019	1903	4107	6010	15126656	SO:0001819	synonymous_variant	57545	exon11			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.948C>T	4.37:g.15517558C>T		Somatic		Capture	Illumina HiSeq	Phase_I	15126656	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Silent	SNP	ENST00000503292.1	37	CCDS47026.1																																																																																				0.453	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522	
POU4F2	5458	broad.mit.edu	37	4	147561756	147561756	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:147561756C>T	ENST00000281321.3	+	2	1274	c.1026C>T	c.(1024-1026)ggC>ggT	p.G342G	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	342					axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	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 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.G342G(1)		NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					TCTTCAATGGCGCGGAGAAGA	0.582																																					p.G342G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1026T	4						.						85.0	89.0	87.0					4																	147561756		2203	4300	6503	147781206	SO:0001819	synonymous_variant	5458	exon2			U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9219	protein-coding gene	gene with protein product		113725	"""POU domain, class 4, transcription factor 2"", ""POU domain class 4, transcription factor 2"""	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.1026C>T	4.37:g.147561756C>T		Somatic		Capture	Illumina HiSeq	Phase_I	147781206	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	37	CCDS34074.1																																																																																				0.582	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575	
GATB	5188	broad.mit.edu	37	4	152629229	152629229	+	Missense_Mutation	SNP	T	T	C	rs372598891		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:152629229T>C	ENST00000515812.1	-	5	681	c.665A>G	c.(664-666)aAt>aGt	p.N222S	PET112_ENST00000263985.6_Missense_Mutation_p.N263S|PET112_ENST00000512306.1_Missense_Mutation_p.N263S														p.N263S(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						CACGGATATATTGGCATCCAC	0.483																																					p.N263S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A788G	4						.	T	SER/ASN	0,4406		0,0,2203	69.0	64.0	66.0		788	5.7	1.0	4		66	1,8599	1.2+/-3.3	0,1,4299	no	missense	PET112	NM_004564.2	46	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	263/558	152629229	1,13005	2203	4300	6503	152848679	SO:0001583	missense	5188	exon6																														ENST00000515812.1:c.665A>G	4.37:g.152629229T>C	ENSP00000426859:p.Asn222Ser	Somatic		Capture	Illumina HiSeq	Phase_I	152848679	NM_004564		Missense_Mutation	SNP	ENST00000515812.1	37		.	.	.	.	.	.	.	.	.	.	T	25.1	4.602573	0.87157	0.0	1.16E-4	ENSG00000059691	ENST00000263985;ENST00000515812;ENST00000512306	T;T;T	0.69926	-0.44;0.33;0.01	5.71	5.71	0.89125	Aspartyl/Glutamyl-tRNA(Gln) amidotransferase, subunit B/E, catalytic (1);	0.000000	0.85682	D	0.000000	D	0.87261	0.6133	H	0.95745	3.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.91065	0.4888	10	0.87932	D	0	-30.0186	15.9691	0.79998	0.0:0.0:0.0:1.0	.	263;263	D6RDU9;O75879	.;GATB_HUMAN	S	263;222;263	ENSP00000263985:N263S;ENSP00000426859:N222S;ENSP00000420831:N263S	ENSP00000263985:N263S	N	-	2	0	PET112	152848679	1.000000	0.71417	0.962000	0.40283	0.785000	0.44390	7.799000	0.85936	2.185000	0.69588	0.459000	0.35465	AAT		0.483	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1		
KIAA0922	23240	broad.mit.edu	37	4	154513664	154513664	+	Missense_Mutation	SNP	C	C	T	rs201534569		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:154513664C>T	ENST00000409663.3	+	18	1899	c.1847C>T	c.(1846-1848)cCg>cTg	p.P616L	KIAA0922_ENST00000440693.1_Intron|KIAA0922_ENST00000409959.3_Missense_Mutation_p.P617L	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	616						integral component of membrane (GO:0016021)		p.P469L(1)		breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				TCCTCTTGGCCGGTCTCCTTG	0.512													C|||	1	0.000199681	0.0	0.0	5008	,	,		19250	0.0		0.001	False		,,,				2504	0.0				p.P616L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1847T	4						.						144.0	122.0	130.0					4																	154513664		2203	4300	6503	154733114	SO:0001583	missense	23240	exon18			AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.1847C>T	4.37:g.154513664C>T	ENSP00000386574:p.Pro616Leu	Somatic		Capture	Illumina HiSeq	Phase_I	154733114	NM_015196	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	16.25	3.069855	0.55539	.	.	ENSG00000121210	ENST00000409663;ENST00000409959	T;T	0.17691	2.26;2.26	4.42	4.42	0.53409	.	0.118552	0.64402	D	0.000016	T	0.46132	0.1377	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;0.995	D;P	0.73380	0.98;0.842	T	0.53767	-0.8392	10	0.66056	D	0.02	-12.4374	17.5913	0.87997	0.0:1.0:0.0:0.0	.	617;616	A2VDJ0-5;A2VDJ0	.;T131L_HUMAN	L	616;617	ENSP00000386574:P616L;ENSP00000386787:P617L	ENSP00000386574:P616L	P	+	2	0	KIAA0922	154733114	0.998000	0.40836	0.884000	0.34674	0.483000	0.33249	3.492000	0.53259	2.445000	0.82738	0.655000	0.94253	CCG		0.512	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
DCHS2	54798	broad.mit.edu	37	4	155156691	155156691	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:155156691G>A	ENST00000357232.4	-	25	7747	c.7748C>T	c.(7747-7749)gCg>gTg	p.A2583V		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2583					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A2583V(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)		TCTCAAGTCCGCATCTAAAGA	0.428																																					p.A2583V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C7748T	4						.						113.0	118.0	116.0					4																	155156691		2203	4299	6502	155376141	SO:0001583	missense	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.7748C>T	4.37:g.155156691G>A	ENSP00000349768:p.Ala2583Val	Somatic		Capture	Illumina HiSeq	Phase_I	155376141	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	A	0.405	-0.916341	0.02415	.	.	ENSG00000197410	ENST00000357232	T	0.55234	0.53	5.82	-4.68	0.03309	.	1.433700	0.04096	N	0.312070	T	0.35219	0.0924	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.21177	-1.0253	10	0.27785	T	0.31	.	10.1249	0.42643	0.2286:0.3761:0.3953:0.0	.	2583	Q6V1P9	PCD23_HUMAN	V	2583	ENSP00000349768:A2583V	ENSP00000349768:A2583V	A	-	2	0	DCHS2	155376141	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.089000	0.15002	-0.897000	0.03910	-0.516000	0.04426	GCG		0.428	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
PROM1	8842	broad.mit.edu	37	4	16010628	16010628	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:16010628G>T	ENST00000510224.1	-	12	1493	c.1245C>A	c.(1243-1245)aaC>aaA	p.N415K	RNU6-350P_ENST00000515949.1_RNA|PROM1_ENST00000505450.1_Missense_Mutation_p.N406K|PROM1_ENST00000508167.1_Missense_Mutation_p.N406K|PROM1_ENST00000539194.1_Missense_Mutation_p.N415K|PROM1_ENST00000540805.1_Missense_Mutation_p.N415K|PROM1_ENST00000543373.1_Missense_Mutation_p.N406K|PROM1_ENST00000447510.2_Missense_Mutation_p.N415K			O43490	PROM1_HUMAN	prominin 1	415					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)	p.N414K(1)|p.N414N(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						AACTTTCAGTGTTATTAACAT	0.388																																					p.N415K												PROM1,kidney,NS,Substitution - coding silent,0 	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|kidney(1)	c.C1245A	4						.						84.0	80.0	81.0					4																	16010628		1866	4100	5966	15619726	SO:0001583	missense	8842	exon11			AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"""CD molecules"""	9454	protein-coding gene	gene with protein product		604365	"""prominin (mouse)-like 1"", ""macular dystrophy, retinal 2"", ""Stargardt disease 4 (autosomal dominant)"""	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.1245C>A	4.37:g.16010628G>T	ENSP00000426809:p.Asn415Lys	Somatic		Capture	Illumina HiSeq	Phase_I	15619726	NM_001145849	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Missense_Mutation	SNP	ENST00000510224.1	37	CCDS47029.1	.	.	.	.	.	.	.	.	.	.	G	8.093	0.774987	0.16051	.	.	ENSG00000007062	ENST00000447510;ENST00000540805;ENST00000539194;ENST00000505450;ENST00000508167;ENST00000510224;ENST00000543373	T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95	5.52	-3.37	0.04898	.	0.963321	0.08721	N	0.903538	T	0.16214	0.0390	N	0.08118	0	0.09310	N	1	B;B;B;B;B;B	0.23185	0.049;0.049;0.081;0.049;0.052;0.06	B;B;B;B;B;B	0.25987	0.021;0.021;0.039;0.039;0.022;0.065	T	0.31110	-0.9955	10	0.05525	T	0.97	-7.692	5.3657	0.16113	0.2399:0.5344:0.136:0.0897	.	406;415;406;415;406;415	O43490-5;O43490-6;O43490-4;O43490-7;O43490-2;O43490	.;.;.;.;.;PROM1_HUMAN	K	415;415;415;406;406;415;406	ENSP00000415481:N415K;ENSP00000438045:N415K;ENSP00000443620:N415K;ENSP00000426090:N406K;ENSP00000427346:N406K;ENSP00000426809:N415K;ENSP00000445526:N406K	ENSP00000415481:N415K	N	-	3	2	PROM1	15619726	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.038000	0.13862	-0.551000	0.06175	-0.136000	0.14681	AAC		0.388	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017	
DCHS2	54798	broad.mit.edu	37	4	155252805	155252805	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:155252805T>C	ENST00000357232.4	-	10	2294	c.2295A>G	c.(2293-2295)acA>acG	p.T765T	DCHS2_ENST00000507542.1_5'Flank|DCHS2_ENST00000339452.1_Intron	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	765	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.T765T(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)		ATGCAAAGTCTGTCCCACTAA	0.478																																					p.T765T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2295G	4						.						78.0	66.0	70.0					4																	155252805		2203	4300	6503	155472255	SO:0001819	synonymous_variant	54798	exon10			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.2295A>G	4.37:g.155252805T>C		Somatic		Capture	Illumina HiSeq	Phase_I	155472255	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																				0.478	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
RAPGEF2	9693	broad.mit.edu	37	4	160252816	160252816	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:160252816C>T	ENST00000264431.4	+	9	1546	c.1127C>T	c.(1126-1128)gCg>gTg	p.A376V		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	376	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)	p.A364V(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		TTGAATATCGCGTGTGCTGCT	0.403																																					p.A376V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1127T	4						.						123.0	112.0	116.0					4																	160252816		1873	4110	5983	160472266	SO:0001583	missense	9693	exon9			AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"""Rap GEP"""	609530	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 1"""	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.1127C>T	4.37:g.160252816C>T	ENSP00000264431:p.Ala376Val	Somatic		Capture	Illumina HiSeq	Phase_I	160472266	NM_014247	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	37	CCDS43277.1	.	.	.	.	.	.	.	.	.	.	C	17.98	3.520206	0.64747	.	.	ENSG00000109756	ENST00000264431	T	0.29655	1.56	5.39	5.39	0.77823	PDZ/DHR/GLGF (1);Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.54319	0.1851	M	0.69523	2.12	0.80722	D	1	D	0.56968	0.978	P	0.61533	0.89	T	0.54997	-0.8209	10	0.54805	T	0.06	.	19.1678	0.93563	0.0:1.0:0.0:0.0	.	376	Q9Y4G8	RPGF2_HUMAN	V	376	ENSP00000264431:A376V	ENSP00000264431:A376V	A	+	2	0	RAPGEF2	160472266	1.000000	0.71417	0.978000	0.43139	0.070000	0.16714	7.818000	0.86416	2.535000	0.85469	0.467000	0.42956	GCG		0.403	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247	
RAPGEF2	9693	broad.mit.edu	37	4	160271428	160271428	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:160271428T>C	ENST00000264431.4	+	20	3788	c.3369T>C	c.(3367-3369)agT>agC	p.S1123S		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	1123	Ser-rich.				adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)	p.S1111S(1)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		CTCCACAGAGTTCTCCAAGGA	0.343																																					p.S1123S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3369C	4						.						69.0	66.0	67.0					4																	160271428		1820	4073	5893	160490878	SO:0001819	synonymous_variant	9693	exon20			AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"""Rap GEP"""	609530	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 1"""	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.3369T>C	4.37:g.160271428T>C		Somatic		Capture	Illumina HiSeq	Phase_I	160490878	NM_014247	D3DP27	Silent	SNP	ENST00000264431.4	37	CCDS43277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.34|10.34	1.323851|1.323851	0.24080|0.24080	.|.	.|.	ENSG00000109756|ENSG00000109756	ENST00000505026|ENST00000510253	.|.	.|.	.|.	5.45|5.45	-6.65|-6.65	0.01795|0.01795	.|.	.|.	.|.	.|.	.|.	T|T	0.68622|0.68622	0.3021|0.3021	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.71652|0.71652	-0.4528|-0.4528	4|4	.|.	.|.	.|.	.|.	20.3614|20.3614	0.98856|0.98856	0.0:0.7029:0.0:0.2971|0.0:0.7029:0.0:0.2971	.|.	.|.	.|.	.|.	L|A	17|155	.|.	.|.	F|V	+|+	1|2	0|0	RAPGEF2|RAPGEF2	160490878|160490878	0.982000|0.982000	0.34865|0.34865	0.884000|0.884000	0.34674|0.34674	0.993000|0.993000	0.82548|0.82548	0.198000|0.198000	0.17217|0.17217	-1.178000|-1.178000	0.02741|0.02741	-0.256000|-0.256000	0.11100|0.11100	TTC|GTT		0.343	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247	
RAPGEF2	9693	broad.mit.edu	37	4	160274739	160274739	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:160274739G>A	ENST00000264431.4	+	22	4128	c.3709G>A	c.(3709-3711)Gcg>Acg	p.A1237T		NM_014247.2	NP_055062.1	Q9Y4G8	RPGF2_HUMAN	Rap guanine nucleotide exchange factor (GEF) 2	1237					adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|blood vessel development (GO:0001568)|brain-derived neurotrophic factor receptor signaling pathway (GO:0031547)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|forebrain neuron development (GO:0021884)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|negative regulation of cell proliferation (GO:0008285)|negative regulation of dendrite morphogenesis (GO:0050774)|negative regulation of melanin biosynthetic process (GO:0048022)|nerve growth factor signaling pathway (GO:0038180)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein binding (GO:0032092)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of vasculogenesis (GO:2001214)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|regulation of synaptic plasticity (GO:0048167)|small GTPase mediated signal transduction (GO:0007264)|ventricular system development (GO:0021591)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	beta-1 adrenergic receptor binding (GO:0031697)|calcium ion binding (GO:0005509)|cAMP binding (GO:0030552)|diacylglycerol binding (GO:0019992)|PDZ domain binding (GO:0030165)|Rap GTPase activator activity (GO:0046582)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)	p.A1225T(2)		breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	70	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0817)		GGGGGATCGCGCGTCACTTGA	0.537																																					p.A1237T												.	.	2	Substitution - Missense(2)	large_intestine(1)|haematopoietic_and_lymphoid_tissue(1)	c.G3709A	4						.						93.0	96.0	95.0					4																	160274739		2038	4195	6233	160494189	SO:0001583	missense	9693	exon22			AB002311	CCDS43277.1	4q32.1	2004-03-01	2004-03-01	2004-03-01					16854	protein-coding gene	gene with protein product	"""Rap GEP"""	609530	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 1"""	PDZGEF1		9205841, 10934204	Standard	NM_014247		Approved	PDZ-GEF1, RA-GEF, DKFZP586O1422, KIAA0313	uc003iqg.4	Q9Y4G8		ENST00000264431.4:c.3709G>A	4.37:g.160274739G>A	ENSP00000264431:p.Ala1237Thr	Somatic		Capture	Illumina HiSeq	Phase_I	160494189	NM_014247	D3DP27	Missense_Mutation	SNP	ENST00000264431.4	37	CCDS43277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.42|13.42	2.231131|2.231131	0.39399|0.39399	.|.	.|.	ENSG00000109756|ENSG00000109756	ENST00000264431|ENST00000505026	T|T	0.37584|0.29917	1.19|1.55	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.052754|.	0.85682|.	D|.	0.000000|.	T|T	0.33702|0.33702	0.0872|0.0872	N|N	0.19112|0.19112	0.55|0.55	0.53005|0.53005	D|D	0.999965|0.999965	B|.	0.23806|.	0.091|.	B|.	0.15870|.	0.014|.	T|T	0.02491|0.02491	-1.1151|-1.1151	10|7	0.21540|0.30854	T|T	0.41|0.27	.|.	20.0544|20.0544	0.97645|0.97645	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1237|.	Q9Y4G8|.	RPGF2_HUMAN|.	T|H	1237|171	ENSP00000264431:A1237T|ENSP00000427334:R171H	ENSP00000264431:A1237T|ENSP00000427334:R171H	A|R	+|+	1|2	0|0	RAPGEF2|RAPGEF2	160494189|160494189	1.000000|1.000000	0.71417|0.71417	0.158000|0.158000	0.22627|0.22627	0.135000|0.135000	0.20990|0.20990	6.668000|6.668000	0.74457|0.74457	2.741000|2.741000	0.93983|0.93983	0.650000|0.650000	0.86243|0.86243	GCG|CGC		0.537	RAPGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364980.2	NM_014247	
KLHL2	11275	broad.mit.edu	37	4	166231811	166231811	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:166231811C>T	ENST00000226725.6	+	10	1405	c.1146C>T	c.(1144-1146)agC>agT	p.S382S	KLHL2_ENST00000509028.1_3'UTR|KLHL2_ENST00000506761.1_Silent_p.S216S|KLHL2_ENST00000421009.2_Silent_p.S285S|KLHL2_ENST00000514860.1_Silent_p.S386S|KLHL2_ENST00000538127.1_Silent_p.S294S	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	382					protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)	actin binding (GO:0003779)	p.S382S(1)		endometrium(3)|large_intestine(5)|lung(4)|prostate(1)|urinary_tract(1)	14	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		AGTGGACCAGCGTTGCTAACA	0.473																																					p.S386S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1158T	4						.						353.0	354.0	354.0					4																	166231811		2203	4300	6503	166451261	SO:0001819	synonymous_variant	11275	exon10			AF059569	CCDS34094.1, CCDS54815.1, CCDS54816.1	4q21.2	2013-01-30	2013-01-30		ENSG00000109466	ENSG00000109466		"""Kelch-like"", ""BTB/POZ domain containing"""	6353	protein-coding gene	gene with protein product	"""mayven"""	605774	"""kelch (Drosophila)-like 2 (Mayven)"", ""kelch-like 2, Mayven (Drosophila)"""			10397770, 16035103	Standard	NM_007246		Approved	MAV	uc011cjm.2	O95198	OTTHUMG00000161294	ENST00000226725.6:c.1146C>T	4.37:g.166231811C>T		Somatic		Capture	Illumina HiSeq	Phase_I	166451261	NM_001161521	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Silent	SNP	ENST00000226725.6	37	CCDS34094.1																																																																																				0.473	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364439.1		
NCAPG	64151	broad.mit.edu	37	4	17816521	17816521	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:17816521G>A	ENST00000251496.2	+	4	766	c.590G>A	c.(589-591)cGg>cAg	p.R197Q		NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	197					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)		p.R197Q(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	27				STAD - Stomach adenocarcinoma(129;0.18)		GAAGTTAGACGGGCAGTGTTA	0.358																																					p.R197Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G590A	4						.						88.0	86.0	86.0					4																	17816521		2203	4300	6503	17425619	SO:0001583	missense	64151	exon4			AF331796	CCDS3424.1	4p15.32	2014-01-15			ENSG00000109805	ENSG00000109805			24304	protein-coding gene	gene with protein product	"""chromosome condensation protein G"""	606280				10910072, 11136719	Standard	NM_022346		Approved	FLJ12450, hCAP-G, CAP-G, YCG1	uc003gpp.4	Q9BPX3	OTTHUMG00000128539	ENST00000251496.2:c.590G>A	4.37:g.17816521G>A	ENSP00000251496:p.Arg197Gln	Somatic		Capture	Illumina HiSeq	Phase_I	17425619	NM_022346	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000251496.2	37	CCDS3424.1	.	.	.	.	.	.	.	.	.	.	G	35	5.571315	0.96553	.	.	ENSG00000109805	ENST00000251496	T	0.44083	0.93	5.94	5.94	0.96194	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.64227	0.2579	L	0.58302	1.8	0.58432	D	0.999998	D	0.89917	1.0	D	0.79108	0.992	T	0.63305	-0.6667	10	0.72032	D	0.01	-12.1223	20.3736	0.98901	0.0:0.0:1.0:0.0	.	197	Q9BPX3	CND3_HUMAN	Q	197	ENSP00000251496:R197Q	ENSP00000251496:R197Q	R	+	2	0	NCAPG	17425619	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	9.096000	0.94182	2.820000	0.97059	0.650000	0.86243	CGG		0.358	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250375.1	NM_022346	
C4orf27	54969	broad.mit.edu	37	4	170663247	170663247	+	Missense_Mutation	SNP	G	G	A	rs147005968		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:170663247G>A	ENST00000393381.2	-	5	584	c.509C>T	c.(508-510)aCg>aTg	p.T170M		NM_017867.2	NP_060337.2	Q9NWY4	CD027_HUMAN	chromosome 4 open reading frame 27	170						nucleus (GO:0005634)		p.T170M(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	12		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.018)|LUSC - Lung squamous cell carcinoma(193;0.116)		AAGTTTTTTCGTCAAAAATAA	0.353													G|||	0	0.0	0.0	0.0	5008	,	,		18196	0.0		0.0	False		,,,				2504	0.0				p.T170M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C509T	4						.	G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	83.0	78.0	80.0		509	-2.2	1.0	4	dbSNP_134	80	7,8593	5.7+/-21.5	0,7,4293	yes	missense	C4orf27	NM_017867.2	81	0,8,6495	AA,AG,GG		0.0814,0.0227,0.0615	benign	170/347	170663247	8,12998	2203	4300	6503	170899822	SO:0001583	missense	54969	exon5			BC010367	CCDS3813.1	4q33	2011-01-25			ENSG00000056050	ENSG00000056050			26051	protein-coding gene	gene with protein product						11230166	Standard	NM_017867		Approved	FLJ20534	uc003isl.4	Q9NWY4	OTTHUMG00000160960	ENST00000393381.2:c.509C>T	4.37:g.170663247G>A	ENSP00000406598:p.Thr170Met	Somatic		Capture	Illumina HiSeq	Phase_I	170899822	NM_017867		Missense_Mutation	SNP	ENST00000393381.2	37	CCDS3813.1	.	.	.	.	.	.	.	.	.	.	G	2.221	-0.378368	0.05000	2.27E-4	8.14E-4	ENSG00000056050	ENST00000393381	T	0.47177	0.85	4.78	-2.21	0.06973	.	0.459860	0.26237	N	0.025524	T	0.13243	0.0321	N	0.01267	-0.92	0.22489	N	0.999051	B	0.10296	0.003	B	0.15484	0.013	T	0.11518	-1.0584	10	0.40728	T	0.16	-15.2856	1.1022	0.01686	0.4508:0.1505:0.2516:0.1472	.	170	Q9NWY4	CD027_HUMAN	M	170	ENSP00000406598:T170M	ENSP00000406598:T170M	T	-	2	0	C4orf27	170899822	1.000000	0.71417	0.992000	0.48379	0.002000	0.02628	1.413000	0.34725	-0.277000	0.09193	-2.496000	0.00192	ACG		0.353	C4orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363140.1	NM_017867	
WDR17	116966	broad.mit.edu	37	4	177082100	177082100	+	Silent	SNP	C	C	T	rs139183882		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:177082100C>T	ENST00000280190.4	+	21	2925	c.2769C>T	c.(2767-2769)tcC>tcT	p.S923S	WDR17_ENST00000507824.2_Silent_p.S906S|WDR17_ENST00000508596.1_Silent_p.S899S|WDR17_ENST00000393643.2_Silent_p.S899S			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	923								p.S923S(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)		TACATGTTTCCGTGCCTAAAG	0.343													T|||	1	0.000199681	0.0008	0.0	5008	,	,		17749	0.0		0.0	False		,,,				2504	0.0				p.S899S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2697T	4						.	T	,	1,4405	825.9+/-416.6	0,1,2202	124.0	120.0	121.0		2769,2697	-0.8	0.0	4	dbSNP_134	121	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	WDR17	NM_170710.4,NM_181265.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	923/1323,899/1284	177082100	1,13005	2203	4300	6503	177319094	SO:0001819	synonymous_variant	116966	exon20			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.2769C>T	4.37:g.177082100C>T		Somatic		Capture	Illumina HiSeq	Phase_I	177319094	NM_181265	E7EQX0|Q0QD35	Silent	SNP	ENST00000280190.4	37	CCDS3825.1	.	.	.	.	.	.	.	.	.	.	T	3.009	-0.204342	0.06180	2.27E-4	0.0	ENSG00000150627	ENST00000443118	.	.	.	4.73	-0.796	0.10912	.	.	.	.	.	T	0.19604	0.0471	.	.	.	0.24121	N	0.995805	.	.	.	.	.	.	T	0.22906	-1.0203	4	.	.	.	-13.4697	0.9954	0.01465	0.2267:0.2888:0.1166:0.3679	.	.	.	.	C	166	.	.	R	+	1	0	WDR17	177319094	0.000000	0.05858	0.003000	0.11579	0.041000	0.13682	-0.807000	0.04520	-0.468000	0.06922	-0.269000	0.10298	CGT		0.343	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		
ASB5	140458	broad.mit.edu	37	4	177138146	177138146	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:177138146T>G	ENST00000296525.3	-	6	798	c.685A>C	c.(685-687)Aaa>Caa	p.K229Q	ASB5_ENST00000512254.1_Missense_Mutation_p.K176Q	NM_080874.3	NP_543150.1	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box containing 5	229					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.K229Q(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(18)|prostate(2)|skin(2)	34		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;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		TATTTGCCTTTCTGTACGTCA	0.388																																					p.K229Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A685C	4						.						175.0	169.0	171.0					4																	177138146		2203	4300	6503	177375140	SO:0001583	missense	140458	exon6			AY057053	CCDS3827.1	4q34.1	2013-01-10	2011-01-25		ENSG00000164122	ENSG00000164122		"""Ankyrin repeat domain containing"""	17180	protein-coding gene	gene with protein product		615050	"""ankyrin repeat and SOCS box-containing 5"""				Standard	NM_080874		Approved		uc003iuq.2	Q8WWX0	OTTHUMG00000160793	ENST00000296525.3:c.685A>C	4.37:g.177138146T>G	ENSP00000296525:p.Lys229Gln	Somatic		Capture	Illumina HiSeq	Phase_I	177375140	NM_080874	Q8N7B5	Missense_Mutation	SNP	ENST00000296525.3	37	CCDS3827.1	.	.	.	.	.	.	.	.	.	.	T	14.86	2.661334	0.47572	.	.	ENSG00000164122	ENST00000296525;ENST00000512254	T;T	0.53640	0.61;0.61	5.38	5.38	0.77491	Ankyrin repeat-containing domain (4);	0.133395	0.64402	D	0.000002	T	0.41534	0.1163	N	0.12443	0.215	0.51767	D	0.999933	P;D	0.56287	0.955;0.975	P;P	0.55455	0.724;0.776	T	0.31558	-0.9939	10	0.33141	T	0.24	-38.8324	10.8681	0.46866	0.1406:0.0:0.0:0.8594	.	229;176	Q8WWX0;Q8N7B5	ASB5_HUMAN;.	Q	229;176	ENSP00000296525:K229Q;ENSP00000422877:K176Q	ENSP00000296525:K229Q	K	-	1	0	ASB5	177375140	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	4.444000	0.60001	2.163000	0.67991	0.443000	0.29094	AAA		0.388	ASB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362344.1		
AGA	175	broad.mit.edu	37	4	178355598	178355598	+	Silent	SNP	G	G	A	rs148052291	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:178355598G>A	ENST00000264595.2	-	7	871	c.744C>T	c.(742-744)gaC>gaT	p.D248D	AGA_ENST00000506853.1_5'UTR	NM_000027.3|NM_001171988.1	NP_000018.2|NP_001165459.1	P20933	ASPG_HUMAN	aspartylglucosaminidase	248					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.D248D(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)		CTGCAGTATCGTCAGCATAGG	0.468													G|||	7	0.00139776	0.0	0.0	5008	,	,		15708	0.0069		0.0	False		,,,				2504	0.0				p.D238D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C714T	4						.	G	,	1,4405	2.1+/-5.4	0,1,2202	111.0	105.0	107.0		744,714	-5.5	0.1	4	dbSNP_134	107	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	AGA	NM_000027.3,NM_001171988.1	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	248/347,238/337	178355598	1,13005	2203	4300	6503	178592592	SO:0001819	synonymous_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.744C>T	4.37:g.178355598G>A		Somatic		Capture	Illumina HiSeq	Phase_I	178592592	NM_001171988	B2R7H2|D3DP47|Q4W5Q2|Q6FHN6|Q9UCK6|Q9UCK7|Q9UCK8	Silent	SNP	ENST00000264595.2	37	CCDS3829.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	0.901	-0.722296	0.03182	2.27E-4	0.0	ENSG00000038002	ENST00000510635	.	.	.	5.68	-5.52	0.02560	.	.	.	.	.	T	0.48059	0.1479	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48186	-0.9057	4	.	.	.	-24.2725	7.2858	0.26337	0.4898:0.0:0.4016:0.1086	.	.	.	.	M	137	.	.	T	-	2	0	AGA	178592592	0.972000	0.33761	0.092000	0.20876	0.051000	0.14879	0.157000	0.16402	-1.134000	0.02899	-1.223000	0.01593	ACG		0.468	AGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361916.1	NM_000027	
TENM3	55714	broad.mit.edu	37	4	183675635	183675635	+	Missense_Mutation	SNP	G	G	A	rs543878787	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:183675635G>A	ENST00000511685.1	+	22	4238	c.4115G>A	c.(4114-4116)cGt>cAt	p.R1372H	TENM3_ENST00000406950.2_Missense_Mutation_p.R1372H|TENM3_ENST00000502950.1_3'UTR			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1372					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.R1372L(1)|p.R1372H(1)									ACTGAAAATCGTCAAGTTCGC	0.493													G|||	2	0.000399361	0.0	0.0	5008	,	,		19944	0.0		0.0	False		,,,				2504	0.002				p.R1372H												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G4115A	4						.						59.0	56.0	57.0					4																	183675635		1973	4175	6148	183912629	SO:0001583	missense	55714	exon21			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.4115G>A	4.37:g.183675635G>A	ENSP00000424226:p.Arg1372His	Somatic		Capture	Illumina HiSeq	Phase_I	183912629	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.491408	0.26774	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.90261	-2.64;-2.64	5.58	5.58	0.84498	Six-bladed beta-propeller, TolB-like (1);	.	.	.	.	T	0.80308	0.4599	N	0.05510	-0.035	0.37609	D	0.920853	B	0.02656	0.0	B	0.01281	0.0	T	0.75563	-0.3274	9	0.23302	T	0.38	.	13.0014	0.58679	0.0729:0.0:0.9271:0.0	.	1372	Q9P273	TEN3_HUMAN	H	1372	ENSP00000424226:R1372H;ENSP00000385276:R1372H	ENSP00000385276:R1372H	R	+	2	0	ODZ3	183912629	1.000000	0.71417	0.643000	0.29450	0.899000	0.52679	6.606000	0.74159	2.906000	0.99361	0.655000	0.94253	CGT		0.493	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
IRF2	3660	broad.mit.edu	37	4	185350153	185350153	+	Silent	SNP	C	C	T	rs142409473		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:185350153C>T	ENST00000393593.3	-	2	273	c.66G>A	c.(64-66)ccG>ccA	p.P22P	IRF2_ENST00000512020.1_5'UTR|SNORD79_ENST00000516069.1_RNA	NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	22					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P22P(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		ACTTGAGCCCCGGGATCGTGT	0.577																																					p.P22P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G66A	4						.	T		0,4406		0,0,2203	159.0	109.0	126.0		66	-10.7	0.0	4	dbSNP_134	126	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	IRF2	NM_002199.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		22/350	185350153	2,13004	2203	4300	6503	185587147	SO:0001819	synonymous_variant	3660	exon2				CCDS3835.1	4q34.1-q35.1	2008-07-29				ENSG00000168310			6117	protein-coding gene	gene with protein product		147576				2475256	Standard	NM_002199		Approved		uc003iwf.4	P14316		ENST00000393593.3:c.66G>A	4.37:g.185350153C>T		Somatic		Capture	Illumina HiSeq	Phase_I	185587147	NM_002199	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Silent	SNP	ENST00000393593.3	37	CCDS3835.1																																																																																				0.577	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1		
LRP2BP	55805	broad.mit.edu	37	4	186291964	186291964	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:186291964C>T	ENST00000328559.7	-	7	1619	c.808G>A	c.(808-810)Gct>Act	p.A270T	LRP2BP_ENST00000362004.3_Missense_Mutation_p.A272T|RP11-714G18.1_ENST00000514884.1_RNA|LRP2BP_ENST00000510776.1_Missense_Mutation_p.A244T|LRP2BP_ENST00000505916.1_Missense_Mutation_p.A270T	NM_018409.3	NP_060879.2	Q9P2M1	LR2BP_HUMAN	LRP2 binding protein	270						cytoplasm (GO:0005737)		p.A270T(1)		breast(1)|endometrium(2)|large_intestine(6)|lung(3)|prostate(1)|skin(2)	15		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;2.14e-25)|Epithelial(43;1.55e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-11)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000766)|Colorectal(24;0.00116)|LUSC - Lung squamous cell carcinoma(40;0.00904)|COAD - Colon adenocarcinoma(29;0.0101)|READ - Rectum adenocarcinoma(43;0.161)		TCATAGTCAGCGATCCTGAGA	0.493																																					p.A270T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G808A	4						.						114.0	94.0	101.0					4																	186291964		2203	4300	6503	186528958	SO:0001583	missense	55805	exon7			AB037746	CCDS3840.1	4q35.1	2011-05-03			ENSG00000109771	ENSG00000109771			25434	protein-coding gene	gene with protein product						10718198, 12508107	Standard	NM_018409		Approved	DKFZp761O0113	uc003ixj.2	Q9P2M1	OTTHUMG00000160460	ENST00000328559.7:c.808G>A	4.37:g.186291964C>T	ENSP00000332681:p.Ala270Thr	Somatic		Capture	Illumina HiSeq	Phase_I	186528958	NM_018409	A6NJR7|A7E219|B3KX83|Q9NSN6	Missense_Mutation	SNP	ENST00000328559.7	37	CCDS3840.1	.	.	.	.	.	.	.	.	.	.	C	9.742	1.165135	0.21538	.	.	ENSG00000109771	ENST00000362004;ENST00000328559;ENST00000510776;ENST00000505916	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	5.64	4.73	0.59995	Tetratricopeptide-like helical (1);	0.507247	0.22458	N	0.059787	T	0.26666	0.0652	N	0.04508	-0.205	0.26777	N	0.969673	B;B	0.29037	0.055;0.231	B;B	0.17722	0.009;0.019	T	0.09292	-1.0681	10	0.48119	T	0.1	-14.6102	8.9383	0.35713	0.1584:0.7605:0.0:0.0811	.	244;270	G5E9Z9;Q9P2M1	.;LR2BP_HUMAN	T	272;270;244;270	ENSP00000354846:A272T;ENSP00000332681:A270T;ENSP00000424610:A244T;ENSP00000426203:A270T	ENSP00000332681:A270T	A	-	1	0	LRP2BP	186528958	0.953000	0.32496	0.967000	0.41034	0.110000	0.19582	1.472000	0.35376	2.937000	0.99478	0.650000	0.86243	GCT		0.493	LRP2BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360679.2	NM_018409	
SORBS2	8470	broad.mit.edu	37	4	186583259	186583259	+	Splice_Site	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:186583259G>A	ENST00000284776.7	-	5	602	c.93C>T	c.(91-93)ctC>ctT	p.L31L	SORBS2_ENST00000437304.2_Splice_Site_p.L210L|SORBS2_ENST00000393528.3_Splice_Site_p.L77L|SORBS2_ENST00000449407.2_Splice_Site_p.L117L|SORBS2_ENST00000431808.1_Splice_Site_p.L31L|SORBS2_ENST00000448662.2_Splice_Site_p.L100L|SORBS2_ENST00000355634.5_Splice_Site_p.L131L|SORBS2_ENST00000319471.9_Splice_Site_p.L117L	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	31					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)	p.L100L(1)|p.L31L(1)		endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		ATTACTTACCGAGGGATGTGC	0.527																																					p.L100L	Esophageal Squamous(153;41 2433 9491 36028)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C300T	4						.						115.0	94.0	101.0					4																	186583259		2203	4300	6503	186820253	SO:0001630	splice_region_variant	8470	exon5				CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.94+1C>T	4.37:g.186583259G>A		Somatic		Capture	Illumina HiSeq	Phase_I	186820253	NM_001145672	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1																																																																																				0.527	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	Silent
FAT1	2195	broad.mit.edu	37	4	187524652	187524652	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:187524652G>A	ENST00000441802.2	-	19	11237	c.11028C>T	c.(11026-11028)aaC>aaT	p.N3676N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3676					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.N3676N(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						TCTGTATGTCGTTCCTCCTCA	0.493										HNSCC(5;0.00058)																											p.N3676N	Colon(197;1040 2055 4143 4984 49344)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C11028T	4						.						63.0	66.0	65.0					4																	187524652		2059	4216	6275	187761646	SO:0001819	synonymous_variant	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.11028C>T	4.37:g.187524652G>A		Somatic		Capture	Illumina HiSeq	Phase_I	187761646	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																				0.493	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
FAT1	2195	broad.mit.edu	37	4	187540374	187540374	+	Missense_Mutation	SNP	C	C	T	rs370340394		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:187540374C>T	ENST00000441802.2	-	10	7575	c.7366G>A	c.(7366-7368)Gcc>Acc	p.A2456T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2456	Cadherin 22. {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.A2456T(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						GGCTTCAGGGCGTGCCGGTGC	0.438										HNSCC(5;0.00058)																											p.A2456T	Colon(197;1040 2055 4143 4984 49344)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G7366A	4						.	C	THR/ALA	0,4080		0,0,2040	173.0	178.0	176.0		7366	0.0	0.9	4		176	1,8353		0,1,4176	no	missense	FAT1	NM_005245.3	58	0,1,6216	TT,TC,CC		0.012,0.0,0.0080	benign	2456/4589	187540374	1,12433	2040	4177	6217	187777368	SO:0001583	missense	2195	exon10			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.7366G>A	4.37:g.187540374C>T	ENSP00000406229:p.Ala2456Thr	Somatic		Capture	Illumina HiSeq	Phase_I	187777368	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	0.008	-1.872816	0.00542	0.0	1.2E-4	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.37915	1.17	5.24	0.0232	0.14136	Cadherin (4);Cadherin-like (1);	0.467050	0.25538	N	0.029995	T	0.13286	0.0322	N	0.04018	-0.295	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.17653	-1.0362	10	0.26408	T	0.33	.	5.4481	0.16548	0.1178:0.2847:0.0:0.5975	.	2456	Q14517	FAT1_HUMAN	T	2456;2458	ENSP00000406229:A2456T	ENSP00000260147:A2458T	A	-	1	0	FAT1	187777368	0.755000	0.28372	0.897000	0.35233	0.013000	0.08279	1.064000	0.30579	-0.037000	0.13646	-0.247000	0.11927	GCC		0.438	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
ZNF141	7700	broad.mit.edu	37	4	367516	367516	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:367516A>C	ENST00000240499.7	+	4	1439	c.1290A>C	c.(1288-1290)aaA>aaC	p.K430N	ZNF141_ENST00000505939.1_Intron|ZNF141_ENST00000512994.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	430					anatomical structure morphogenesis (GO:0009653)|limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K430N(1)		breast(1)|kidney(3)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	18						AATGTGACAAAGCCTTTAAAC	0.363																																					p.K430N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1290C	4						.						85.0	92.0	90.0					4																	367516		2203	4300	6503	357516	SO:0001583	missense	7700	exon4			L15309	CCDS33931.1	4p16.3	2013-01-08	2006-06-13			ENSG00000131127		"""Zinc fingers, C2H2-type"", ""-"""	12926	protein-coding gene	gene with protein product		194648	"""zinc finger protein 141 (clone pHZ-44)"""	D4S90		8268908	Standard	NM_003441		Approved	pHZ-44	uc003gaa.2	Q15928		ENST00000240499.7:c.1290A>C	4.37:g.367516A>C	ENSP00000240499:p.Lys430Asn	Somatic		Capture	Illumina HiSeq	Phase_I	357516	NM_003441	Q6DK07	Missense_Mutation	SNP	ENST00000240499.7	37	CCDS33931.1	.	.	.	.	.	.	.	.	.	.	A	13.86	2.363955	0.41902	.	.	ENSG00000131127	ENST00000240499	T	0.27890	1.64	1.24	1.24	0.21308	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.60715	0.2290	H	0.96518	3.835	0.20703	N	0.999863	D	0.89917	1.0	D	0.80764	0.994	T	0.49380	-0.8946	8	.	.	.	.	3.1258	0.06407	0.7198:0.0:0.2802:0.0	.	430	Q15928	ZN141_HUMAN	N	430	ENSP00000240499:K430N	.	K	+	3	2	ZNF141	357516	0.000000	0.05858	0.017000	0.16124	0.370000	0.29829	-0.241000	0.08940	0.495000	0.27882	0.260000	0.18958	AAA		0.363	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441	
PDE6B	5158	broad.mit.edu	37	4	660333	660333	+	Missense_Mutation	SNP	G	G	A	rs144727865	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:660333G>A	ENST00000496514.1	+	20	2303	c.2282G>A	c.(2281-2283)cGg>cAg	p.R761Q	PDE6B_ENST00000429163.2_Missense_Mutation_p.R482Q|PDE6B_ENST00000255622.6_Missense_Mutation_p.R761Q			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	761					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)	p.R761Q(1)		NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	ATGATGGACCGGAACAAGGCG	0.642																																					p.R482Q	GBM(71;463 1194 9848 25922 46834)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1445A	4						.	G	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	94.0	78.0	83.0		2282,2282,1445	4.2	1.0	4	dbSNP_134	83	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	PDE6B	NM_000283.3,NM_001145291.1,NM_001145292.1	43,43,43	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging	761/855,761/854,482/576	660333	2,13004	2203	4300	6503	650333	SO:0001583	missense	5158	exon18			BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"""Phosphodiesterases"""	8786	protein-coding gene	gene with protein product	"""congenital stationary night blindness 3, autosomal dominant"""	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.2282G>A	4.37:g.660333G>A	ENSP00000420295:p.Arg761Gln	Somatic		Capture	Illumina HiSeq	Phase_I	650333	NM_001145292	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Missense_Mutation	SNP	ENST00000496514.1	37	CCDS33932.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.5|27.5	4.836894|4.836894	0.91117|0.91117	0.0|0.0	2.33E-4|2.33E-4	ENSG00000133256|ENSG00000133256	ENST00000461490|ENST00000255622;ENST00000496514;ENST00000429163;ENST00000471824	.|D;D;D;D	.|0.82255	.|-1.59;-1.59;-1.59;-1.59	4.22|4.22	4.22|4.22	0.49857|0.49857	.|5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	.|0.050815	.|0.85682	.|N	.|0.000000	D|D	0.89047|0.89047	0.6604|0.6604	H|H	0.95294|0.95294	3.65|3.65	0.45354|0.45354	D|D	0.998349|0.998349	.|B;B	.|0.30605	.|0.194;0.287	.|B;B	.|0.36289	.|0.221;0.22	D|D	0.91035|0.91035	0.4867|0.4867	5|10	.|0.87932	.|D	.|0	.|.	14.5139|14.5139	0.67807|0.67807	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|761;761	.|P35913;P35913-2	.|PDE6B_HUMAN;.	R|Q	42|761;761;482;121	.|ENSP00000255622:R761Q;ENSP00000420295:R761Q;ENSP00000406334:R482Q;ENSP00000417852:R121Q	.|ENSP00000255622:R761Q	G|R	+|+	1|2	0|0	PDE6B|PDE6B	650333|650333	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.943000|0.943000	0.58893|0.58893	9.209000|9.209000	0.95087|0.95087	2.074000|2.074000	0.62210|0.62210	0.644000|0.644000	0.83932|0.83932	GGA|CGG		0.642	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283	
GAK	2580	broad.mit.edu	37	4	871523	871523	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:871523G>A	ENST00000314167.4	-	16	1846	c.1736C>T	c.(1735-1737)gCc>gTc	p.A579V	GAK_ENST00000511163.1_Missense_Mutation_p.A500V	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	579	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A579V(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		CATGACCACGGCCCTCACCAG	0.652																																					p.A579V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1736T	4						.						68.0	60.0	63.0					4																	871523		2203	4300	6503	861523	SO:0001583	missense	2580	exon16			D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.1736C>T	4.37:g.871523G>A	ENSP00000314499:p.Ala579Val	Somatic		Capture	Illumina HiSeq	Phase_I	861523	NM_005255	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	37	CCDS3340.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.948187	0.73787	.	.	ENSG00000178950	ENST00000314167;ENST00000511163	D;D	0.85339	-1.97;-1.97	5.71	5.71	0.89125	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.234157	0.44902	D	0.000415	D	0.82591	0.5070	L	0.29908	0.895	0.41018	D	0.985054	P;P;P;P	0.45768	0.866;0.737;0.661;0.776	P;B;P;P	0.45913	0.497;0.428;0.497;0.497	D	0.85048	0.0927	10	0.72032	D	0.01	-21.0568	17.3485	0.87316	0.0:0.0:1.0:0.0	.	500;500;579;475	Q5U4P5;E9PGR2;O14976;Q59HA5	.;.;GAK_HUMAN;.	V	579;500	ENSP00000314499:A579V;ENSP00000421361:A500V	ENSP00000314499:A579V	A	-	2	0	GAK	861523	1.000000	0.71417	0.049000	0.19019	0.211000	0.24417	9.111000	0.94308	2.697000	0.92050	0.655000	0.94253	GCC		0.652	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
WHSC1	7468	broad.mit.edu	37	4	1941440	1941440	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:1941440G>A	ENST00000382895.3	+	11	2247	c.1816G>A	c.(1816-1818)Gca>Aca	p.A606T	WHSC1_ENST00000398261.1_Missense_Mutation_p.A606T|WHSC1_ENST00000508803.1_Missense_Mutation_p.A606T|WHSC1_ENST00000503128.1_Missense_Mutation_p.A606T|WHSC1_ENST00000514045.1_Missense_Mutation_p.A606T|WHSC1_ENST00000482415.2_3'UTR|WHSC1_ENST00000382892.2_Missense_Mutation_p.A606T|WHSC1_ENST00000420906.2_Missense_Mutation_p.A606T|WHSC1_ENST00000382891.5_Missense_Mutation_p.A606T	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	606					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.A606T(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)		GGCTTCCACGGCAGCATCTTC	0.368			T	IGH@	MM																																p.A606T			Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1816A	4						.						81.0	77.0	78.0					4																	1941440		2203	4300	6503	1911238	SO:0001583	missense	7468	exon10			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.1816G>A	4.37:g.1941440G>A	ENSP00000372351:p.Ala606Thr	Somatic		Capture	Illumina HiSeq	Phase_I	1911238	NM_133331	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	37	CCDS33940.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.232|8.232	0.804962|0.804962	0.16467|0.16467	.|.	.|.	ENSG00000109685|ENSG00000109685	ENST00000508803;ENST00000514045;ENST00000382891;ENST00000382892;ENST00000420906;ENST00000382895;ENST00000503128;ENST00000398261|ENST00000514329	D;T;D;D;T;D;T;T|.	0.95103|.	-3.61;1.21;-3.61;-3.61;1.21;-3.61;1.19;1.19|.	5.63|5.63	2.93|2.93	0.34026|0.34026	.|.	0.392825|.	0.21571|.	N|.	0.072420|.	T|T	0.28699|0.28699	0.0711|0.0711	N|N	0.22421|0.22421	0.69|0.69	0.29668|0.29668	N|N	0.842702|0.842702	B;B;B|.	0.10296|.	0.003;0.0;0.003|.	B;B;B|.	0.12837|.	0.005;0.003;0.008|.	T|T	0.23404|0.23404	-1.0189|-1.0189	10|5	0.08599|.	T|.	0.76|.	.|.	6.3164|6.3164	0.21192|0.21192	0.2189:0.1308:0.6503:0.0|0.2189:0.1308:0.6503:0.0	.|.	606;606;606|.	O96028-3;O96028;O96028-5|.	.;NSD2_HUMAN;.|.	T|D	606|18	ENSP00000423972:A606T;ENSP00000421681:A606T;ENSP00000372347:A606T;ENSP00000372348:A606T;ENSP00000399251:A606T;ENSP00000372351:A606T;ENSP00000425761:A606T;ENSP00000381311:A606T|.	ENSP00000308780:A606T|.	A|G	+|+	1|2	0|0	WHSC1|WHSC1	1911238|1911238	0.969000|0.969000	0.33509|0.33509	0.015000|0.015000	0.15790|0.15790	0.975000|0.975000	0.68041|0.68041	1.822000|1.822000	0.39052|0.39052	0.723000|0.723000	0.32274|0.32274	-0.262000|-0.262000	0.10625|0.10625	GCA|GGC		0.368	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330	
NOP14	8602	broad.mit.edu	37	4	2959412	2959412	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:2959412C>A	ENST00000314262.6	-	2	299	c.251G>T	c.(250-252)aGa>aTa	p.R84I	NOP14_ENST00000398071.4_Missense_Mutation_p.R84I|NOP14_ENST00000502735.1_Missense_Mutation_p.R84I|NOP14_ENST00000416614.2_Missense_Mutation_p.R84I|NOP14-AS1_ENST00000503709.1_RNA	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	84					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)	p.R84I(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						GCGTTTATCTCTGAATACATT	0.403																																					p.R84I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G251T	4						.						192.0	176.0	181.0					4																	2959412		2203	4300	6503	2929210	SO:0001583	missense	8602	exon2			AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269			16821	protein-coding gene	gene with protein product	"""NOP14 homolog (S. cerevisiae)"""	611526	"""chromosome 4 open reading frame 9"", ""nucleolar protein 14"", ""nucleolar protein 14 homolog (yeast)"", ""NOP14 nucleolar protein homolog (yeast)"""	C4orf9, NOL14		9734812, 11694595	Standard	XR_241655		Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.251G>T	4.37:g.2959412C>A	ENSP00000315674:p.Arg84Ile	Somatic		Capture	Illumina HiSeq	Phase_I	2929210	NM_003703	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Missense_Mutation	SNP	ENST00000314262.6	37	CCDS33945.1	.	.	.	.	.	.	.	.	.	.	C	2.010	-0.427401	0.04701	.	.	ENSG00000087269	ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071	T;T;T;T	0.26223	1.75;1.75;1.75;1.75	5.11	-8.33	0.00992	.	1.063240	0.07262	N	0.867636	T	0.07503	0.0189	N	0.02357	-0.585	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.10450	0.005;0.003	T	0.36672	-0.9738	10	0.87932	D	0	1.3974	2.5531	0.04753	0.2082:0.3901:0.0984:0.3033	.	84;84	E9PFK5;P78316	.;NOP14_HUMAN	I	84	ENSP00000405068:R84I;ENSP00000315674:R84I;ENSP00000427415:R84I;ENSP00000381146:R84I	ENSP00000315674:R84I	R	-	2	0	NOP14	2929210	0.001000	0.12720	0.000000	0.03702	0.200000	0.23975	-0.060000	0.11712	-1.703000	0.01409	0.655000	0.94253	AGA		0.403	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703	
HTT	3064	broad.mit.edu	37	4	3230615	3230615	+	Missense_Mutation	SNP	G	G	A	rs377091390		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:3230615G>A	ENST00000355072.5	+	59	8133	c.7988G>A	c.(7987-7989)cGg>cAg	p.R2663Q	HTT_ENST00000513806.1_3'UTR	NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2663					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.R2663Q(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)		AGGAAACACCGGGCTGGAGTT	0.502																																					p.R2663Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G7988A	4						.	G	GLN/ARG	0,3918		0,0,1959	79.0	81.0	81.0		7988	5.0	1.0	4		81	1,8331		0,1,4165	no	missense	HTT	NM_002111.6	43	0,1,6124	AA,AG,GG		0.012,0.0,0.0082	probably-damaging	2663/3143	3230615	1,12249	1959	4166	6125	3200413	SO:0001583	missense	3064	exon59			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.7988G>A	4.37:g.3230615G>A	ENSP00000347184:p.Arg2663Gln	Somatic		Capture	Illumina HiSeq	Phase_I	3200413	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.920748	0.92249	0.0	1.2E-4	ENSG00000197386	ENST00000355072	T	0.06068	3.35	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.12178	0.0296	M	0.64997	1.995	0.80722	D	1	D	0.54964	0.969	B	0.44133	0.442	T	0.02477	-1.1153	10	0.51188	T	0.08	.	18.3626	0.90380	0.0:0.0:1.0:0.0	.	2663	P42858	HD_HUMAN	Q	2663	ENSP00000347184:R2663Q	ENSP00000347184:R2663Q	R	+	2	0	HTT	3200413	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	9.452000	0.97615	2.350000	0.79820	0.563000	0.77884	CGG		0.502	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
HTT	3064	broad.mit.edu	37	4	3240324	3240324	+	Silent	SNP	C	C	T	rs373377741	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:3240324C>T	ENST00000355072.5	+	65	9187	c.9042C>T	c.(9040-9042)acC>acT	p.T3014T		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	3014					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.T3014T(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)		TCATGGCCACCGTGGTGTATA	0.562																																					p.T3014T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9042T	4						.						71.0	79.0	76.0					4																	3240324		2058	4193	6251	3210122	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.9042C>T	4.37:g.3240324C>T		Somatic		Capture	Illumina HiSeq	Phase_I	3210122	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	
MSANTD1	345222	broad.mit.edu	37	4	3255096	3255096	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:3255096G>A	ENST00000438480.2	+	2	2230	c.483G>A	c.(481-483)tcG>tcA	p.S161S	MSANTD1_ENST00000510580.1_Silent_p.S161S|MSANTD1_ENST00000507492.1_Silent_p.S148S	NM_001042690.1	NP_001036155.1	Q6ZTZ1	MSD1_HUMAN	Myb/SANT-like DNA-binding domain containing 1	161								p.S161S(1)		endometrium(1)|lung(2)	3						CGTCCCTGTCGCCGCCCGCTA	0.632																																					p.S161S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G483A	4						.						86.0	88.0	87.0					4																	3255096		2203	4300	6503	3224894	SO:0001819	synonymous_variant	345222	exon2				CCDS47003.1	4p16.2	2012-03-02	2012-03-02	2012-03-02	ENSG00000188981	ENSG00000188981			33741	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 44"""	C4orf44			Standard	NM_001042690		Approved	LOC345222	uc003ggs.3	Q6ZTZ1	OTTHUMG00000159977	ENST00000438480.2:c.483G>A	4.37:g.3255096G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3224894	NM_001042690	C9J6V0	Silent	SNP	ENST00000438480.2	37	CCDS47003.1																																																																																				0.632	MSANTD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370924.1	NM_001012982	
RGS12	6002	broad.mit.edu	37	4	3318583	3318583	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:3318583C>T	ENST00000344733.5	+	2	1590	c.686C>T	c.(685-687)gCg>gTg	p.A229V	RGS12_ENST00000543385.1_Missense_Mutation_p.A229V|RGS12_ENST00000336727.3_Missense_Mutation_p.A229V|RGS12_ENST00000382788.3_Missense_Mutation_p.A229V	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	229	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.A229V(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)		TTAAACGTGGCGATGATCGTG	0.483																																					p.A229V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C686T	4						.						83.0	77.0	79.0					4																	3318583		2203	4300	6503	3288381	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.686C>T	4.37:g.3318583C>T	ENSP00000339381:p.Ala229Val	Somatic		Capture	Illumina HiSeq	Phase_I	3288381	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Missense_Mutation	SNP	ENST00000344733.5	37	CCDS3366.1	.	.	.	.	.	.	.	.	.	.	C	13.07	2.126951	0.37533	.	.	ENSG00000159788	ENST00000543385;ENST00000344733;ENST00000336727;ENST00000382788	T;T;T;T	0.13420	2.59;2.59;2.59;2.59	4.54	4.54	0.55810	Phosphotyrosine interaction domain (2);	0.060504	0.64402	D	0.000005	T	0.27169	0.0666	M	0.65975	2.015	0.80722	D	1	D;D;D	0.71674	0.986;0.998;0.989	P;P;P	0.55785	0.544;0.717;0.784	T	0.01409	-1.1362	10	0.48119	T	0.1	-31.0555	12.2142	0.54396	0.0:0.8281:0.1719:0.0	.	229;229;229	Q8WX97;O14924;O14924-4	.;RGS12_HUMAN;.	V	229	ENSP00000440566:A229V;ENSP00000339381:A229V;ENSP00000338509:A229V;ENSP00000372238:A229V	ENSP00000338509:A229V	A	+	2	0	RGS12	3288381	1.000000	0.71417	0.918000	0.36340	0.037000	0.13140	3.319000	0.51983	2.071000	0.62044	0.491000	0.48974	GCG		0.483	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926	
HGFAC	3083	broad.mit.edu	37	4	3446058	3446058	+	Missense_Mutation	SNP	C	C	A	rs377317114	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:3446058C>A	ENST00000382774.3	+	6	734	c.619C>A	c.(619-621)Cgc>Agc	p.R207S	HGFAC_ENST00000511533.1_Missense_Mutation_p.R207S	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	207	Fibronectin type-I. {ECO:0000255|PROSITE- ProRule:PRU00478}.				proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.R207S(1)		central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TGATGAGACCCGCTACGAGTA	0.687																																					p.R207S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C619A	4						.						14.0	17.0	16.0					4																	3446058		2164	4280	6444	3415856	SO:0001583	missense	3083	exon6			D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.619C>A	4.37:g.3446058C>A	ENSP00000372224:p.Arg207Ser	Somatic		Capture	Illumina HiSeq	Phase_I	3415856	NM_001528	Q14726|Q2M1W7|Q53X47	Missense_Mutation	SNP	ENST00000382774.3	37	CCDS3369.1	.	.	.	.	.	.	.	.	.	.	C	9.363	1.068469	0.20067	.	.	ENSG00000109758	ENST00000382774;ENST00000511533	T;T	0.46451	0.87;0.87	3.74	3.74	0.42951	Fibronectin, type I (4);	0.148873	0.45361	D	0.000361	T	0.48572	0.1507	L	0.45581	1.43	0.09310	N	0.999999	D;B	0.63046	0.992;0.315	P;B	0.59288	0.855;0.29	T	0.35943	-0.9768	10	0.18276	T	0.48	.	13.0704	0.59057	0.0:1.0:0.0:0.0	.	207;207	D6RAR4;Q04756	.;HGFA_HUMAN	S	207	ENSP00000372224:R207S;ENSP00000421801:R207S	ENSP00000372224:R207S	R	+	1	0	HGFAC	3415856	0.000000	0.05858	0.913000	0.36048	0.207000	0.24258	0.576000	0.23744	1.925000	0.55765	0.462000	0.41574	CGC		0.687	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
LRPAP1	4043	broad.mit.edu	37	4	3521881	3521881	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:3521881G>A	ENST00000500728.2	-	3	535	c.389C>T	c.(388-390)gCt>gTt	p.A130V	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	130					extracellular negative regulation of signal transduction (GO:1900116)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of protein binding (GO:0032091)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|protein folding (GO:0006457)|receptor-mediated endocytosis (GO:0006898)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum lumen (GO:0048237)|vesicle (GO:0031982)	asialoglycoprotein receptor activity (GO:0004873)|heparin binding (GO:0008201)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|unfolded protein binding (GO:0051082)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.A130V(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		CACCTGCCGAGCGTCCTTCTT	0.522																																					p.A130V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C389T	4						.						120.0	114.0	116.0					4																	3521881		2203	4300	6503	3491679	SO:0001583	missense	4043	exon3				CCDS3371.1	4p16.3	2008-05-02	2003-03-17		ENSG00000163956	ENSG00000163956			6701	protein-coding gene	gene with protein product		104225	"""low density lipoprotein-related protein-associated protein 1 (alpha-2-macroglobulin receptor-associated protein 1)"""	A2MRAP		1712782	Standard	NM_002337		Approved	HBP44	uc003ghh.4	P30533	OTTHUMG00000090299	ENST00000500728.2:c.389C>T	4.37:g.3521881G>A	ENSP00000421922:p.Ala130Val	Somatic		Capture	Illumina HiSeq	Phase_I	3491679	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Missense_Mutation	SNP	ENST00000500728.2	37	CCDS3371.1	.	.	.	.	.	.	.	.	.	.	G	10.14	1.269635	0.23221	.	.	ENSG00000163956	ENST00000500728	T	0.45668	0.89	4.83	3.97	0.46021	Alpha-2-macroglobulin receptor-associated protein, domain 1 (3);	0.413735	0.26522	N	0.023906	T	0.20047	0.0482	N	0.08118	0	0.27771	N	0.943491	B	0.11235	0.004	B	0.13407	0.009	T	0.11690	-1.0577	10	0.08599	T	0.76	-11.7525	11.2186	0.48842	0.0927:0.0:0.9073:0.0	.	130	P30533	AMRP_HUMAN	V	130	ENSP00000421922:A130V	ENSP00000421922:A130V	A	-	2	0	LRPAP1	3491679	0.354000	0.24912	0.072000	0.20136	0.096000	0.18686	3.307000	0.51888	2.218000	0.71995	0.563000	0.77884	GCT		0.522	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4		
LYAR	55646	broad.mit.edu	37	4	4283602	4283602	+	Missense_Mutation	SNP	C	C	T	rs151107558		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:4283602C>T	ENST00000343470.4	-	4	385	c.145G>A	c.(145-147)Gtg>Atg	p.V49M	LYAR_ENST00000452476.1_Missense_Mutation_p.V49M	NM_017816.2	NP_060286	Q9NX58	LYAR_HUMAN	Ly1 antibody reactive	49						nucleolus (GO:0005730)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.V49M(1)		endometrium(2)|large_intestine(6)|liver(2)|lung(5)|ovary(1)|prostate(1)	17				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		ATGCATTTCACGTGGTTTTTA	0.448													C|||	1	0.000199681	0.0	0.0	5008	,	,		20064	0.0		0.001	False		,,,				2504	0.0				p.V49M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G145A	4						.						327.0	291.0	303.0					4																	4283602		2203	4300	6503	4334503	SO:0001583	missense	55646	exon4			AL136750	CCDS3374.1	4p16.3	2013-01-10	2012-12-07		ENSG00000145220	ENSG00000145220		"""Zinc fingers, C2HC-type containing"""	26021	protein-coding gene	gene with protein product			"""Ly1 antibody reactive homolog (mouse)"""			11230166, 8491376	Standard	NM_001145725		Approved	ZC2HC2, ZLYAR	uc003ght.3	Q9NX58	OTTHUMG00000125477	ENST00000343470.4:c.145G>A	4.37:g.4283602C>T	ENSP00000345917:p.Val49Met	Somatic		Capture	Illumina HiSeq	Phase_I	4334503	NM_001145725	D3DVS4|Q6FI78|Q9NYS1	Missense_Mutation	SNP	ENST00000343470.4	37	CCDS3374.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	14.03	2.414350	0.42817	.	.	ENSG00000145220	ENST00000343470;ENST00000452476;ENST00000513174	T;T	0.32023	1.47;1.47	4.16	3.31	0.37934	Zinc finger, C2H2, LYAR-type (1);	0.370392	0.30142	N	0.010319	T	0.45617	0.1351	L	0.58101	1.795	0.39300	D	0.964886	D	0.89917	1.0	D	0.75020	0.985	T	0.43507	-0.9387	10	0.59425	D	0.04	-12.3642	6.9337	0.24455	0.0:0.7237:0.1771:0.0992	.	49	Q9NX58	LYAR_HUMAN	M	49	ENSP00000345917:V49M;ENSP00000397367:V49M	ENSP00000345917:V49M	V	-	1	0	LYAR	4334503	1.000000	0.71417	0.997000	0.53966	0.445000	0.32107	2.027000	0.41078	0.850000	0.35239	0.205000	0.17691	GTG		0.448	LYAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246800.2	NM_017816	
ZBTB49	166793	broad.mit.edu	37	4	4303944	4303944	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:4303944C>T	ENST00000337872.4	+	3	502	c.381C>T	c.(379-381)ggC>ggT	p.G127G	ZBTB49_ENST00000355834.3_Silent_p.G127G|ZBTB49_ENST00000538529.1_5'UTR	NM_145291.3	NP_660334.3	Q6ZSB9	ZBT49_HUMAN	zinc finger and BTB domain containing 49	127					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.G127G(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	28						AGCCACCTGGCATGCCTTGTA	0.433																																					p.G127G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C381T	4						.						129.0	122.0	124.0					4																	4303944		2203	4300	6503	4354845	SO:0001819	synonymous_variant	166793	exon3			AK095878	CCDS3375.1	4p16.2	2013-01-08	2010-01-26	2010-01-26	ENSG00000168826	ENSG00000168826		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	19883	protein-coding gene	gene with protein product			"""zinc finger protein 509"""	ZNF509		12477932	Standard	NM_145291		Approved	FLJ38559	uc003ghu.3	Q6ZSB9	OTTHUMG00000090325	ENST00000337872.4:c.381C>T	4.37:g.4303944C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4354845	NM_145291	Q59FJ4|Q5EBN0|Q8TB80	Silent	SNP	ENST00000337872.4	37	CCDS3375.1																																																																																				0.433	ZBTB49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206688.3	NM_145291	
STK32B	55351	broad.mit.edu	37	4	5141658	5141658	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:5141658C>T	ENST00000282908.5	+	2	501	c.79C>T	c.(79-81)Cgg>Tgg	p.R27W	STK32B_ENST00000512636.1_5'UTR|STK32B_ENST00000510398.1_5'UTR	NM_018401.1	NP_060871.1			serine/threonine kinase 32B									p.R27W(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	39						TCAGATTCTGCGGGCCATTGG	0.388																																					p.R27W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C79T	4						.						168.0	172.0	170.0					4																	5141658		2203	4300	6503	5192559	SO:0001583	missense	55351	exon2			AJ250839	CCDS3380.1	4p16	2009-09-30			ENSG00000152953	ENSG00000152953			14217	protein-coding gene	gene with protein product						10700184	Standard	XM_005247982		Approved	STKG6, YANK2, STK32, HSA250839	uc003gih.1	Q9NY57	OTTHUMG00000090423	ENST00000282908.5:c.79C>T	4.37:g.5141658C>T	ENSP00000282908:p.Arg27Trp	Somatic		Capture	Illumina HiSeq	Phase_I	5192559	NM_018401		Missense_Mutation	SNP	ENST00000282908.5	37	CCDS3380.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.323430	0.60634	.	.	ENSG00000152953	ENST00000282908	T	0.27256	1.68	5.69	4.83	0.62350	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	0.36482	U	0.002565	T	0.57873	0.2083	M	0.91406	3.205	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66874	-0.5813	10	0.87932	D	0	.	11.8842	0.52592	0.1743:0.8257:0.0:0.0	.	27	Q9NY57	ST32B_HUMAN	W	27	ENSP00000282908:R27W	ENSP00000282908:R27W	R	+	1	2	STK32B	5192559	1.000000	0.71417	0.999000	0.59377	0.954000	0.61252	2.946000	0.49050	1.342000	0.45619	0.655000	0.94253	CGG		0.388	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401	
EVC	2121	broad.mit.edu	37	4	5755640	5755640	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:5755640G>T	ENST00000264956.6	+	10	1628	c.1444G>T	c.(1444-1446)Gac>Tac	p.D482Y	EVC_ENST00000509451.1_Missense_Mutation_p.D482Y|EVC_ENST00000382674.2_Missense_Mutation_p.D482Y	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	482					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.D482Y(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				GCCGACTGCTGACCCGGAAAA	0.612																																					p.D482Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1444T	4						.						63.0	61.0	61.0					4																	5755640		2203	4300	6503	5806541	SO:0001583	missense	2121	exon10			AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.1444G>T	4.37:g.5755640G>T	ENSP00000264956:p.Asp482Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	5806541	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	37	CCDS3383.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.403502	0.42613	.	.	ENSG00000072840	ENST00000264956;ENST00000382674;ENST00000509451	T;T;T	0.64803	-0.12;-0.12;-0.05	5.04	0.197	0.15164	.	0.546264	0.18271	N	0.146306	T	0.54806	0.1881	L	0.53249	1.67	0.09310	N	0.999999	P	0.36183	0.542	B	0.40659	0.336	T	0.50980	-0.8763	10	0.72032	D	0.01	.	5.4467	0.16539	0.2392:0.2701:0.4907:0.0	.	482	P57679	EVC_HUMAN	Y	482	ENSP00000264956:D482Y;ENSP00000372120:D482Y;ENSP00000426774:D482Y	ENSP00000264956:D482Y	D	+	1	0	EVC	5806541	0.003000	0.15002	0.001000	0.08648	0.016000	0.09150	0.891000	0.28309	-0.320000	0.08640	0.561000	0.74099	GAC		0.612	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
ABLIM2	84448	broad.mit.edu	37	4	7986617	7986617	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:7986617C>T	ENST00000341937.5	-	17	1646	c.1582G>A	c.(1582-1584)Gcc>Acc	p.A528T	ABLIM2_ENST00000505872.1_Missense_Mutation_p.A476T|ABLIM2_ENST00000546334.1_Intron|ABLIM2_ENST00000514025.1_Missense_Mutation_p.A263T|ABLIM2_ENST00000296372.8_Intron|ABLIM2_ENST00000361737.5_Intron|ABLIM2_ENST00000361581.5_Intron|ABLIM2_ENST00000545242.1_Intron|ABLIM2_ENST00000318888.4_Missense_Mutation_p.A263T|ABLIM2_ENST00000407564.3_Intron|ABLIM2_ENST00000447017.2_Missense_Mutation_p.A562T	NM_001130084.1	NP_001123556.1	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2	528					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|myofibril (GO:0030016)	zinc ion binding (GO:0008270)	p.A562T(1)		NS(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|pancreas(3)|prostate(2)|urinary_tract(1)	25						GCCAGATTGGCATTCTGGAAG	0.657																																					p.A562T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1684A	4						.						51.0	53.0	52.0					4																	7986617		1565	3580	5145	8037517	SO:0001583	missense	84448	exon18			AB058711	CCDS47011.1, CCDS47012.1, CCDS47013.1, CCDS47014.1, CCDS47015.1, CCDS47016.1, CCDS54719.1, CCDS68669.1	4p16.1	2012-05-16			ENSG00000163995	ENSG00000163995			19195	protein-coding gene	gene with protein product		612544	"""actin binding LIM protein 2"""				Standard	NM_001130083		Approved	KIAA1808	uc003gkj.4	Q6H8Q1	OTTHUMG00000057427	ENST00000341937.5:c.1582G>A	4.37:g.7986617C>T	ENSP00000342813:p.Ala528Thr	Somatic		Capture	Illumina HiSeq	Phase_I	8037517	NM_001130083	E9PF39|Q08E71|Q19VH0|Q6H8Q0|Q6NX73|Q8N3C5|Q8N9E9|Q8N9G2|Q96JL7	Missense_Mutation	SNP	ENST00000341937.5	37	CCDS47013.1	.	.	.	.	.	.	.	.	.	.	C	9.316	1.056888	0.19907	.	.	ENSG00000163995	ENST00000400045;ENST00000318888;ENST00000514025;ENST00000447017;ENST00000341937;ENST00000505872	T;T;T;T;T	0.47869	0.83;0.83;1.72;1.8;1.53	4.36	3.51	0.40186	.	0.748628	0.11846	N	0.523811	T	0.39886	0.1095	L	0.33485	1.01	0.47949	D	0.999554	B;P;P;B	0.52061	0.01;0.568;0.95;0.127	B;B;P;B	0.47891	0.016;0.303;0.56;0.06	T	0.08493	-1.0719	10	0.08179	T	0.78	.	11.005	0.47629	0.0:0.908:0.0:0.092	.	528;476;263;562	Q6H8Q1;Q19VH0;Q6H8Q1-4;E9PF39	ABLM2_HUMAN;.;.;.	T	561;263;263;562;528;476	ENSP00000317020:A263T;ENSP00000423661:A263T;ENSP00000393511:A562T;ENSP00000342813:A528T;ENSP00000421283:A476T	ENSP00000317020:A263T	A	-	1	0	ABLIM2	8037517	1.000000	0.71417	0.996000	0.52242	0.868000	0.49771	2.445000	0.44899	1.059000	0.40554	0.563000	0.77884	GCC		0.657	ABLIM2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358862.2	NM_001130083	
WDR1	9948	broad.mit.edu	37	4	10105549	10105549	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:10105549G>A	ENST00000499869.2	-	3	393	c.200C>T	c.(199-201)gCg>gTg	p.A67V	WDR1_ENST00000382452.2_Missense_Mutation_p.A67V|WDR1_ENST00000502702.1_Intron|WDR1_ENST00000382451.2_Intron			O75083	WDR1_HUMAN	WD repeat domain 1	67					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)		p.A67V(1)		endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		TCCGCTGGGCGCATACTTGGC	0.622																																					p.A67V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C200T	4						.						58.0	62.0	61.0					4																	10105549		2068	4213	6281	9714647	SO:0001583	missense	9948	exon3			AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"""WD repeat domain containing"""	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.200C>T	4.37:g.10105549G>A	ENSP00000427687:p.Ala67Val	Somatic		Capture	Illumina HiSeq	Phase_I	9714647	NM_017491	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Missense_Mutation	SNP	ENST00000499869.2	37	CCDS54740.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.611649	0.87258	.	.	ENSG00000071127	ENST00000499869;ENST00000382452;ENST00000508079	T;T;T	0.61392	0.11;0.11;0.11	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.178262	0.49305	D	0.000147	T	0.68915	0.3053	M	0.90870	3.155	0.80722	D	1	P	0.48503	0.911	B	0.40901	0.343	T	0.78828	-0.2050	10	0.72032	D	0.01	-30.1728	18.7609	0.91851	0.0:0.0:1.0:0.0	.	67	O75083	WDR1_HUMAN	V	67;67;71	ENSP00000427687:A67V;ENSP00000371890:A67V;ENSP00000425481:A71V	ENSP00000371890:A67V	A	-	2	0	WDR1	9714647	1.000000	0.71417	0.990000	0.47175	0.976000	0.68499	7.423000	0.80229	2.682000	0.91365	0.561000	0.74099	GCG		0.622	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1		
PPARGC1A	10891	broad.mit.edu	37	4	23833277	23833277	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:23833277G>A	ENST00000264867.2	-	3	451	c.332C>T	c.(331-333)gCg>gTg	p.A111V	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	111					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.A111V(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)				ATCTGTCAGCGCATCAAATGA	0.532																																					p.A111V	Esophageal Squamous(29;694 744 13796 34866 44181)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C332T	4						.						429.0	341.0	371.0					4																	23833277		2203	4300	6503	23442375	SO:0001583	missense	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.332C>T	4.37:g.23833277G>A	ENSP00000264867:p.Ala111Val	Somatic		Capture	Illumina HiSeq	Phase_I	23442375	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Missense_Mutation	SNP	ENST00000264867.2	37	CCDS3429.1	.	.	.	.	.	.	.	.	.	.	G	36	5.675777	0.96764	.	.	ENSG00000109819	ENST00000264867	T	0.26373	1.74	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.58264	0.2110	M	0.83223	2.63	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.59936	-0.7360	10	0.72032	D	0.01	-6.033	20.5568	0.99304	0.0:0.0:1.0:0.0	.	111	Q9UBK2	PRGC1_HUMAN	V	111	ENSP00000264867:A111V	ENSP00000264867:A111V	A	-	2	0	PPARGC1A	23442375	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	9.476000	0.97823	2.861000	0.98227	0.655000	0.94253	GCG		0.532	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	
TBC1D1	23216	broad.mit.edu	37	4	38117447	38117447	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:38117447G>T	ENST00000261439.4	+	16	3029	c.2674G>T	c.(2674-2676)Ggt>Tgt	p.G892C	TBC1D1_ENST00000508802.1_Missense_Mutation_p.G986C|TBC1D1_ENST00000407365.1_3'UTR	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	892	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)	p.G892C(1)		NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						ATATTGCCAAGGTCTCAGCTT	0.463																																					p.G892C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2674T	4						.						144.0	139.0	141.0					4																	38117447		2203	4300	6503	37793842	SO:0001583	missense	23216	exon16			AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.2674G>T	4.37:g.38117447G>T	ENSP00000261439:p.Gly892Cys	Somatic		Capture	Illumina HiSeq	Phase_I	37793842	NM_015173	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	37	CCDS33972.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.0|26.0	4.695073|4.695073	0.88830|0.88830	.|.	.|.	ENSG00000065882|ENSG00000065882	ENST00000508802;ENST00000261439;ENST00000454732|ENST00000510573	T;T|.	0.47528|.	0.84;0.84|.	5.59|5.59	5.59|5.59	0.84812|0.84812	Rab-GAP/TBC domain (4);|.	0.000000|.	0.64402|.	D|.	0.000017|.	D|D	0.88043|0.88043	0.6331|0.6331	H|H	0.95745|0.95745	3.715|3.715	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	0.91130|0.91130	0.4937|0.4937	10|5	0.87932|.	D|.	0|.	-17.5862|-17.5862	19.5982|19.5982	0.95549|0.95549	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	986;624;892|.	E9PGH8;Q6PJJ8;Q86TI0|.	.;.;TBCD1_HUMAN|.	C|M	986;892;156|579	ENSP00000423651:G986C;ENSP00000261439:G892C|.	ENSP00000261439:G892C|.	G|R	+|+	1|2	0|0	TBC1D1|TBC1D1	37793842|37793842	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	9.417000|9.417000	0.97391|0.97391	2.644000|2.644000	0.89710|0.89710	0.561000|0.561000	0.74099|0.74099	GGT|AGG		0.463	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
WDR19	57728	broad.mit.edu	37	4	39217720	39217720	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:39217720T>A	ENST00000399820.3	+	12	1293	c.1139T>A	c.(1138-1140)cTa>cAa	p.L380Q	WDR19_ENST00000506503.1_Missense_Mutation_p.L380Q|WDR19_ENST00000288634.7_Missense_Mutation_p.L220Q	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	380					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)		p.L380Q(1)		large_intestine(1)	1						TTATAGGAGCTACCAATCACA	0.328																																					p.L380Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1139A	4						.						81.0	71.0	74.0					4																	39217720		1806	4071	5877	38894115	SO:0001583	missense	57728	exon12			AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	18340	protein-coding gene	gene with protein product	"""intraflagellar transport 144 homolog (Chlamydomonas)"""	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.1139T>A	4.37:g.39217720T>A	ENSP00000382717:p.Leu380Gln	Somatic		Capture	Illumina HiSeq	Phase_I	38894115	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Missense_Mutation	SNP	ENST00000399820.3	37	CCDS47042.1	.	.	.	.	.	.	.	.	.	.	T	0.353	-0.943944	0.02322	.	.	ENSG00000157796	ENST00000399820;ENST00000288634;ENST00000506503;ENST00000399836	T;T;T	0.63417	-0.04;-0.04;1.27	5.46	-3.59	0.04583	WD40 repeat-like-containing domain (1);	1.018180	0.07810	N	0.958027	T	0.49167	0.1541	M	0.62723	1.935	0.09310	N	0.999992	B;B	0.18166	0.001;0.026	B;B	0.16289	0.007;0.015	T	0.33369	-0.9871	10	0.13108	T	0.6	1.1057	4.1429	0.10201	0.245:0.3385:0.0:0.4165	.	380;380	Q8NEZ3;D6R9P6	WDR19_HUMAN;.	Q	380;220;380;379	ENSP00000382717:L380Q;ENSP00000288634:L220Q;ENSP00000423491:L380Q	ENSP00000288634:L220Q	L	+	2	0	WDR19	38894115	0.014000	0.17966	0.013000	0.15412	0.196000	0.23810	0.262000	0.18460	-0.967000	0.03582	-1.093000	0.02169	CTA		0.328	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1		
WDR19	57728	broad.mit.edu	37	4	39279779	39279779	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:39279779C>T	ENST00000399820.3	+	35	4023	c.3869C>T	c.(3868-3870)aCg>aTg	p.T1290M	WDR19_ENST00000288634.7_Missense_Mutation_p.T1130M	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	1290					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)		p.T1290M(1)		large_intestine(1)	1						GATGACTGGACGGTGTGTCCA	0.403																																					p.T1290M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3869T	4						.						84.0	79.0	80.0					4																	39279779		1963	4135	6098	38956174	SO:0001583	missense	57728	exon35			AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	18340	protein-coding gene	gene with protein product	"""intraflagellar transport 144 homolog (Chlamydomonas)"""	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.3869C>T	4.37:g.39279779C>T	ENSP00000382717:p.Thr1290Met	Somatic		Capture	Illumina HiSeq	Phase_I	38956174	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Missense_Mutation	SNP	ENST00000399820.3	37	CCDS47042.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.015071	0.75161	.	.	ENSG00000157796	ENST00000399820;ENST00000288634	T;T	0.66460	-0.21;-0.21	5.54	5.54	0.83059	.	0.188567	0.56097	D	0.000039	T	0.77980	0.4212	M	0.81341	2.54	0.40305	D	0.978651	D	0.61080	0.989	P	0.54312	0.748	T	0.81826	-0.0754	10	0.66056	D	0.02	-18.7477	15.0058	0.71510	0.0:0.858:0.142:0.0	.	1290	Q8NEZ3	WDR19_HUMAN	M	1290;1130	ENSP00000382717:T1290M;ENSP00000288634:T1130M	ENSP00000288634:T1130M	T	+	2	0	WDR19	38956174	0.969000	0.33509	0.955000	0.39395	0.889000	0.51656	2.224000	0.42945	2.616000	0.88540	0.491000	0.48974	ACG		0.403	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1		
KLB	152831	broad.mit.edu	37	4	39450177	39450177	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:39450177T>C	ENST00000257408.4	+	5	3103	c.3006T>C	c.(3004-3006)tgT>tgC	p.C1002C		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	1002					carbohydrate metabolic process (GO:0005975)|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)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.C1002C(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						TCCTGGGTTGTTGCTTCTTCT	0.398																																					p.C1002C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3006C	4						.						138.0	131.0	133.0					4																	39450177		2203	4300	6503	39126572	SO:0001819	synonymous_variant	152831	exon5			AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.3006T>C	4.37:g.39450177T>C		Somatic		Capture	Illumina HiSeq	Phase_I	39126572	NM_175737	Q2M3K8	Silent	SNP	ENST00000257408.4	37	CCDS3451.1																																																																																				0.398	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737	
UGDH	7358	broad.mit.edu	37	4	39515753	39515753	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:39515753delA	ENST00000316423.6	-	3	556	c.214delT	c.(214-216)tctfs	p.S72fs	UGDH_ENST00000515398.1_5'UTR|UGDH_ENST00000506179.1_Frame_Shift_Del_p.S72fs|UGDH_ENST00000507089.1_5'UTR|UGDH_ENST00000501493.2_Frame_Shift_Del_p.S72fs	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	72					cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)	p.S72fs*18(1)		breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						ATATTGGTAGAAAAAAAAAGA	0.299																																					p.S72fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.214delT	4						.						64.0	75.0	72.0					4																	39515753		2201	4290	6491	39192148	SO:0001589	frameshift_variant	7358	exon3			AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	"""UDP-glucose dehydrogenase"""			9737970, 10575217	Standard	NM_003359		Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.214delT	4.37:g.39515753delA	ENSP00000319501:p.Ser72fs	Somatic		Capture	Illumina HiSeq	Phase_I	39192148	NM_001184700	B3KUU2|B4DN25|O60589	Frame_Shift_Del	DEL	ENST00000316423.6	37	CCDS3455.1																																																																																				0.299	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359	
PHOX2B	8929	broad.mit.edu	37	4	41749389	41749389	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:41749389C>T	ENST00000226382.2	-	2	765	c.406G>A	c.(406-408)Gac>Aac	p.D136N	RP11-227F19.1_ENST00000508038.1_RNA|RP11-227F19.2_ENST00000510602.1_lincRNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	136					autonomic nervous system development (GO:0048483)|brainstem development (GO:0003360)|cell differentiation in hindbrain (GO:0021533)|cellular response to BMP stimulus (GO:0071773)|dopaminergic neuron differentiation (GO:0071542)|efferent axon development in a lateral line nerve (GO:0048894)|enteric nervous system development (GO:0048484)|glial cell differentiation (GO:0010001)|hindbrain tangential cell migration (GO:0021934)|inner ear development (GO:0048839)|medullary reticular formation development (GO:0021723)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron differentiation (GO:0003357)|parasympathetic nervous system development (GO:0048486)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression (GO:0010468)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory system development (GO:0060541)|retrotrapezoid nucleus neuron differentiation (GO:0061452)|skeletal muscle cell differentiation (GO:0035914)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)	p.D136N(1)		autonomic_ganglia(7)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	30						TCTGTGAGGTCGATCTTCAGG	0.642			"""Mis, F"""		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.D136N		yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G406A	4						.						42.0	46.0	45.0					4																	41749389		2203	4300	6503	41444146	SO:0001583	missense	8929	exon2	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D82344	CCDS3463.1	4p13	2014-09-17	2003-02-10	2003-02-14	ENSG00000109132	ENSG00000109132		"""Homeoboxes / PRD class"""	9143	protein-coding gene	gene with protein product		603851	"""paired mesoderm homeobox 2b"""	PMX2B		9039501, 10395798	Standard	NM_003924		Approved	Phox2b, NBPhox	uc003gwf.4	Q99453	OTTHUMG00000099379	ENST00000226382.2:c.406G>A	4.37:g.41749389C>T	ENSP00000226382:p.Asp136Asn	Somatic		Capture	Illumina HiSeq	Phase_I	41444146	NM_003924	Q6PJD9	Missense_Mutation	SNP	ENST00000226382.2	37	CCDS3463.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.385997	0.61956	.	.	ENSG00000109132	ENST00000226382	D	0.94793	-3.52	5.54	5.54	0.83059	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.92727	0.7688	N	0.02830	-0.485	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.92557	0.6055	10	0.27082	T	0.32	.	19.6787	0.95950	0.0:1.0:0.0:0.0	.	136	Q99453	PHX2B_HUMAN	N	136	ENSP00000226382:D136N	ENSP00000226382:D136N	D	-	1	0	PHOX2B	41444146	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.779000	0.62375	2.884000	0.98904	0.655000	0.94253	GAC		0.642	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2		
KCTD8	386617	broad.mit.edu	37	4	44177134	44177134	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:44177134C>A	ENST00000360029.3	-	2	1378	c.1095G>T	c.(1093-1095)gaG>gaT	p.E365D		NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	365					protein homooligomerization (GO:0051260)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)		p.E365D(1)		central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|prostate(3)|upper_aerodigestive_tract(4)	41						GAGTGCTTGCCTCTGAATGGC	0.478										HNSCC(17;0.042)																											p.E365D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1095T	4						.						143.0	133.0	137.0					4																	44177134		2203	4300	6503	43871891	SO:0001583	missense	386617	exon2			AK123347	CCDS3467.1	4p13	2013-06-20	2013-06-20		ENSG00000183783	ENSG00000183783			22394	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 8"""				Standard	NM_198353		Approved		uc003gwu.3	Q6ZWB6	OTTHUMG00000099409	ENST00000360029.3:c.1095G>T	4.37:g.44177134C>A	ENSP00000353129:p.Glu365Asp	Somatic		Capture	Illumina HiSeq	Phase_I	43871891	NM_198353	A2RU39	Missense_Mutation	SNP	ENST00000360029.3	37	CCDS3467.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.85|10.85	1.466469|1.466469	0.26335|0.26335	.|.	.|.	ENSG00000183783|ENSG00000183783	ENST00000360029|ENST00000515268	T|.	0.42131|.	0.98|.	4.65|4.65	0.988|0.988	0.19796|0.19796	.|.	0.128806|.	0.34555|.	N|.	0.003871|.	T|T	0.25494|0.25494	0.0620|0.0620	N|N	0.24115|0.24115	0.695|0.695	0.31113|0.31113	N|N	0.709761|0.709761	B|.	0.16603|.	0.018|.	B|.	0.12837|.	0.008|.	T|T	0.28681|0.28681	-1.0036|-1.0036	10|5	0.46703|.	T|.	0.11|.	.|.	3.3947|3.3947	0.07302|0.07302	0.2791:0.2999:0.0:0.421|0.2791:0.2999:0.0:0.421	.|.	365|.	Q6ZWB6|.	KCTD8_HUMAN|.	D|M	365|101	ENSP00000353129:E365D|.	ENSP00000353129:E365D|.	E|R	-|-	3|2	2|0	KCTD8|KCTD8	43871891|43871891	0.997000|0.997000	0.39634|0.39634	0.998000|0.998000	0.56505|0.56505	0.990000|0.990000	0.78478|0.78478	0.454000|0.454000	0.21827|0.21827	0.291000|0.291000	0.22468|0.22468	0.585000|0.585000	0.79938|0.79938	GAG|AGG		0.478	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1		
LRRC66	339977	broad.mit.edu	37	4	52861934	52861934	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:52861934G>A	ENST00000343457.3	-	4	1260	c.1254C>T	c.(1252-1254)aaC>aaT	p.N418N		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	418						integral component of membrane (GO:0016021)		p.N418N(1)		central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(8)|lung(34)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	58						TTGAATACGCGTTGTCCAGGC	0.532																																					p.N418N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1254T	4						.						112.0	116.0	115.0					4																	52861934		2012	4175	6187	52556691	SO:0001819	synonymous_variant	339977	exon4			BC040414	CCDS43229.1	4q12	2008-08-08			ENSG00000188993	ENSG00000188993			34299	protein-coding gene	gene with protein product							Standard	XM_005265739		Approved		uc003gzi.3	Q68CR7	OTTHUMG00000160623	ENST00000343457.3:c.1254C>T	4.37:g.52861934G>A		Somatic		Capture	Illumina HiSeq	Phase_I	52556691	NM_001024611		Silent	SNP	ENST00000343457.3	37	CCDS43229.1																																																																																				0.532	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611	
PDGFRA	5156	broad.mit.edu	37	4	55130090	55130090	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:55130090delA	ENST00000257290.5	+	4	955	c.624delA	c.(622-624)ttafs	p.L208fs	FIP1L1_ENST00000507166.1_Intron|PDGFRA_ENST00000508170.1_Frame_Shift_Del_p.L208fs	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	208	Ig-like C2-type 3.				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.A210fs*7(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)	TTTATGCTTTAAAAGGTACTT	0.378			"""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.L208fs	Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"""platelet-derived growth factor, alpha-receptor"""		"""L, M, O"""	.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.624delA	4						.						65.0	67.0	66.0					4																	55130090		2203	4300	6503	54824847	SO:0001589	frameshift_variant	5156	exon4	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.624delA	4.37:g.55130090delA	ENSP00000257290:p.Leu208fs	Somatic		Capture	Illumina HiSeq	Phase_I	54824847	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Frame_Shift_Del	DEL	ENST00000257290.5	37	CCDS3495.1																																																																																				0.378	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
CLOCK	9575	broad.mit.edu	37	4	56304549	56304549	+	Missense_Mutation	SNP	G	G	A	rs538817792		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:56304549G>A	ENST00000309964.4	-	21	2511	c.2261C>T	c.(2260-2262)aCg>aTg	p.T754M	CLOCK_ENST00000381322.1_Missense_Mutation_p.T754M|CLOCK_ENST00000513440.1_Missense_Mutation_p.T754M	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	754	Gln-rich.|Interaction with NR3C1. {ECO:0000250|UniProtKB:O08785}.				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.T754M(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)			ctgctgctgcgttactgacaa	0.522													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17400	0.0		0.0	False		,,,				2504	0.0				p.T754M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2261T	4						.						65.0	55.0	59.0					4																	56304549		2203	4300	6503	55999306	SO:0001583	missense	9575	exon22			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.2261C>T	4.37:g.56304549G>A	ENSP00000308741:p.Thr754Met	Somatic		Capture	Illumina HiSeq	Phase_I	55999306	NM_004898	A0AV01|A2I2N9|O14516|Q9UIT8	Missense_Mutation	SNP	ENST00000309964.4	37	CCDS3500.1	.	.	.	.	.	.	.	.	.	.	G	10.87	1.473664	0.26423	.	.	ENSG00000134852	ENST00000309964;ENST00000381322;ENST00000513440	T;T;T	0.04083	3.71;3.71;3.71	5.83	4.99	0.66335	.	2.580450	0.01305	N	0.010414	T	0.10551	0.0258	L	0.51422	1.61	0.09310	N	0.999999	D	0.54047	0.964	P	0.44477	0.451	T	0.49224	-0.8962	10	0.21014	T	0.42	.	14.8467	0.70264	0.0688:0.0:0.9312:0.0	.	754	O15516	CLOCK_HUMAN	M	754	ENSP00000308741:T754M;ENSP00000370723:T754M;ENSP00000426983:T754M	ENSP00000308741:T754M	T	-	2	0	CLOCK	55999306	0.482000	0.25948	0.036000	0.18154	0.017000	0.09413	3.631000	0.54280	1.478000	0.48253	0.585000	0.79938	ACG		0.522	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898	
KIAA1211	57482	broad.mit.edu	37	4	57179372	57179372	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:57179372G>A	ENST00000504228.1	+	5	469	c.364G>A	c.(364-366)Gtt>Att	p.V122I	KIAA1211_ENST00000541073.1_Missense_Mutation_p.V115I|KIAA1211_ENST00000264229.6_Missense_Mutation_p.V122I			Q6ZU35	K1211_HUMAN	KIAA1211	122								p.V122I(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)					GGTTGCTCCCGTTAAACCGTC	0.537																																					p.V122I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G364A	4						.						175.0	179.0	178.0					4																	57179372		1991	4150	6141	56874129	SO:0001583	missense	57482	exon7			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.364G>A	4.37:g.57179372G>A	ENSP00000423366:p.Val122Ile	Somatic		Capture	Illumina HiSeq	Phase_I	56874129	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.685739	0.29962	.	.	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.14266	2.52;2.52;2.53	5.26	2.61	0.31194	.	.	.	.	.	T	0.18882	0.0453	M	0.77820	2.39	0.28742	N	0.901893	B;B;B	0.22211	0.066;0.043;0.043	B;B;B	0.21360	0.023;0.034;0.034	T	0.08848	-1.0702	9	0.49607	T	0.09	-9.4259	10.2679	0.43466	0.2768:0.0:0.7232:0.0	.	115;115;122	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	I	122;122;115;32	ENSP00000264229:V122I;ENSP00000423366:V122I;ENSP00000444006:V115I	ENSP00000264229:V122I	V	+	1	0	KIAA1211	56874129	1.000000	0.71417	0.953000	0.39169	0.260000	0.26232	4.509000	0.60448	0.235000	0.21160	-1.013000	0.02462	GTT		0.537	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
KIAA1211	57482	broad.mit.edu	37	4	57181468	57181468	+	Silent	SNP	C	C	T	rs367553040		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:57181468C>T	ENST00000504228.1	+	6	1905	c.1800C>T	c.(1798-1800)ggC>ggT	p.G600G	KIAA1211_ENST00000541073.1_Silent_p.G593G|KIAA1211_ENST00000264229.6_Silent_p.G600G			Q6ZU35	K1211_HUMAN	KIAA1211	600								p.G600G(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)					TGGTCACGGGCGCGCAGCTCT	0.667																																					p.G600G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1800T	4						.						18.0	24.0	22.0					4																	57181468		2069	4195	6264	56876225	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.1800C>T	4.37:g.57181468C>T		Somatic		Capture	Illumina HiSeq	Phase_I	56876225	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	37	CCDS43230.1																																																																																				0.667	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
KIAA1211	57482	broad.mit.edu	37	4	57181855	57181855	+	Silent	SNP	C	C	T	rs267600196		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:57181855C>T	ENST00000504228.1	+	6	2292	c.2187C>T	c.(2185-2187)tcC>tcT	p.S729S	KIAA1211_ENST00000541073.1_Silent_p.S722S|KIAA1211_ENST00000264229.6_Silent_p.S729S			Q6ZU35	K1211_HUMAN	KIAA1211	729								p.S729S(2)		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)					AGAAATTTTCCGATGGTGGCA	0.572																																					p.S729S												.	.	2	Substitution - coding silent(2)	large_intestine(1)|skin(1)	c.C2187T	4						.						68.0	78.0	74.0					4																	57181855		1967	4153	6120	56876612	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.2187C>T	4.37:g.57181855C>T		Somatic		Capture	Illumina HiSeq	Phase_I	56876612	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	37	CCDS43230.1																																																																																				0.572	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
KIAA1211	57482	broad.mit.edu	37	4	57182840	57182840	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:57182840G>A	ENST00000504228.1	+	6	3277	c.3172G>A	c.(3172-3174)Gag>Aag	p.E1058K	KIAA1211_ENST00000541073.1_Missense_Mutation_p.E1051K|KIAA1211_ENST00000264229.6_Missense_Mutation_p.E1058K			Q6ZU35	K1211_HUMAN	KIAA1211	1058								p.E1058K(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)					TCAAACACCCGAGGCCGGGAG	0.582																																					p.E1058K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3172A	4						.						24.0	25.0	25.0					4																	57182840		1880	4030	5910	56877597	SO:0001583	missense	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.3172G>A	4.37:g.57182840G>A	ENSP00000423366:p.Glu1058Lys	Somatic		Capture	Illumina HiSeq	Phase_I	56877597	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.588099	0.86851	.	.	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073	T;T;T	0.29655	2.3;2.3;1.56	4.97	4.97	0.65823	.	.	.	.	.	T	0.53690	0.1812	M	0.61703	1.905	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.69307	0.963;0.963;0.963	T	0.56263	-0.8008	9	0.72032	D	0.01	-29.3986	18.4442	0.90678	0.0:0.0:1.0:0.0	.	1051;1051;1058	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	K	1058;1058;1051	ENSP00000264229:E1058K;ENSP00000423366:E1058K;ENSP00000444006:E1051K	ENSP00000264229:E1058K	E	+	1	0	KIAA1211	56877597	1.000000	0.71417	0.353000	0.25747	0.095000	0.18619	8.315000	0.89983	2.583000	0.87209	0.561000	0.74099	GAG		0.582	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
REST	5978	broad.mit.edu	37	4	57777462	57777462	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:57777462C>T	ENST00000309042.7	+	2	972	c.658C>T	c.(658-660)Cgc>Tgc	p.R220C	REST_ENST00000514063.1_3'UTR	NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	220					cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|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 factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R220C(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					TCGCTGTGACCGCTGCGGCTA	0.493																																					p.R220C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C658T	4						.						53.0	51.0	52.0					4																	57777462		2203	4300	6503	57472219	SO:0001583	missense	5978	exon2			U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.658C>T	4.37:g.57777462C>T	ENSP00000311816:p.Arg220Cys	Somatic		Capture	Illumina HiSeq	Phase_I	57472219	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	37	CCDS3509.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.989437	0.74589	.	.	ENSG00000084093	ENST00000456010;ENST00000309042;ENST00000358605	T	0.28666	1.6	5.25	4.41	0.53225	Zinc finger, C2H2-like (1);	0.000000	0.64402	D	0.000007	T	0.48909	0.1526	M	0.62154	1.92	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.949;0.998	T	0.50039	-0.8874	10	0.87932	D	0	-8.269	8.5431	0.33404	0.1518:0.771:0.0:0.0772	.	220;220	Q13127-2;Q13127	.;REST_HUMAN	C	220	ENSP00000311816:R220C	ENSP00000311816:R220C	R	+	1	0	REST	57472219	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.291000	0.43540	1.463000	0.47967	0.655000	0.94253	CGC		0.493	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
NOA1	84273	broad.mit.edu	37	4	57829783	57829783	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:57829783G>A	ENST00000264230.4	-	7	3167	c.1930C>T	c.(1930-1932)Cga>Tga	p.R644*	RP11-738E22.3_ENST00000602820.1_lincRNA	NM_032313.2	NP_115689.1	Q8NC60	NOA1_HUMAN	nitric oxide associated 1	644					apoptotic process (GO:0006915)|GTP catabolic process (GO:0006184)|mitochondrial translation (GO:0032543)|regulation of cell death (GO:0010941)|regulation of cellular respiration (GO:0043457)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)	p.R644*(1)									GTATAGCCTCGGAGATGCAGT	0.433																																					p.R644X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1930T	4						.						83.0	87.0	86.0					4																	57829783		2203	4300	6503	57524540	SO:0001587	stop_gained	84273	exon7			AK098215	CCDS3510.1	4q12	2013-05-24	2011-10-19	2011-10-19	ENSG00000084092	ENSG00000084092			28473	protein-coding gene	gene with protein product	"""nitric oxide synthase, mitochondrial (putative)"", ""mitochondrial GTPase 3 homolog (S. cerevisiae)"""	614919	"""chromosome 4 open reading frame 14"""	C4orf14		16380119, 2118999, 21771794, 22447445	Standard	NM_032313		Approved	MGC3232, hAtNOS1, hNOA1, MTG3	uc003hck.3	Q8NC60	OTTHUMG00000128773	ENST00000264230.4:c.1930C>T	4.37:g.57829783G>A	ENSP00000264230:p.Arg644*	Somatic		Capture	Illumina HiSeq	Phase_I	57524540	NM_032313	Q8N7L6|Q9BSQ9	Nonsense_Mutation	SNP	ENST00000264230.4	37	CCDS3510.1	.	.	.	.	.	.	.	.	.	.	G	49	15.142400	0.99824	.	.	ENSG00000084092	ENST00000264230	.	.	.	5.41	5.41	0.78517	.	0.064004	0.64402	D	0.000013	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.3361	0.87281	0.0:0.0:1.0:0.0	.	.	.	.	X	644	.	ENSP00000264230:R644X	R	-	1	2	C4orf14	57524540	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	3.113000	0.50376	2.681000	0.91329	0.655000	0.94253	CGA		0.433	NOA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250694.2	NM_032313	
EPHA5	2044	broad.mit.edu	37	4	66270104	66270104	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:66270104A>G	ENST00000273854.3	-	8	2378	c.1778T>C	c.(1777-1779)cTc>cCc	p.L593P	EPHA5_ENST00000354839.4_Missense_Mutation_p.L593P|EPHA5_ENST00000432638.2_Missense_Mutation_p.L430P|EPHA5_ENST00000511294.1_Missense_Mutation_p.L594P	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	593					axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)	p.L593P(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						TCCACTGAGGAGGACGCCGAT	0.488										TSP Lung(17;0.13)																											p.L593P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1778C	4						.						118.0	99.0	105.0					4																	66270104		2203	4300	6503	65952699	SO:0001583	missense	2044	exon8			L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3389	protein-coding gene	gene with protein product		600004	"""EphA5"""			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.1778T>C	4.37:g.66270104A>G	ENSP00000273854:p.Leu593Pro	Somatic		Capture	Illumina HiSeq	Phase_I	65952699	NM_004439	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	A	14.79	2.639345	0.47153	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.76448	-1.02;-1.02;2.65;-1.01	4.95	4.95	0.65309	.	0.000000	0.51477	D	0.000089	T	0.76572	0.4006	N	0.08118	0	0.80722	D	1	D;D;D;B	0.71674	0.997;0.975;0.998;0.097	D;P;D;B	0.76071	0.971;0.733;0.987;0.017	T	0.81302	-0.0994	10	0.52906	T	0.07	.	14.9102	0.70752	1.0:0.0:0.0:0.0	.	594;594;593;593	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	P	593;430;593;594	ENSP00000273854:L593P;ENSP00000389208:L430P;ENSP00000346899:L593P;ENSP00000427638:L594P	ENSP00000273854:L593P	L	-	2	0	EPHA5	65952699	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.722000	0.84778	1.988000	0.58038	0.528000	0.53228	CTC		0.488	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439	
GNRHR	2798	broad.mit.edu	37	4	68606278	68606278	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:68606278G>T	ENST00000226413.4	-	3	931	c.907C>A	c.(907-909)Cca>Aca	p.P303T	GNRHR_ENST00000420975.2_3'UTR|UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000502758.1_RNA	NM_000406.2	NP_000397.1	P30968	GNRHR_HUMAN	gonadotropin-releasing hormone receptor	303					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.P303T(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)	TGATTTACTGGGTCTGACAAC	0.383																																					p.P303T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C907A	4						.						160.0	166.0	164.0					4																	68606278		2203	4300	6503	68288873	SO:0001583	missense	2798	exon3				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.907C>A	4.37:g.68606278G>T	ENSP00000226413:p.Pro303Thr	Somatic		Capture	Illumina HiSeq	Phase_I	68288873	NM_000406	O75793|Q14D13|Q92644	Missense_Mutation	SNP	ENST00000226413.4	37	CCDS3517.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.083573	0.36758	.	.	ENSG00000109163	ENST00000226413	T	0.35973	1.28	5.43	5.43	0.79202	GPCR, rhodopsin-like superfamily (1);	0.242043	0.29806	N	0.011160	T	0.27697	0.0681	N	0.24115	0.695	0.80722	D	1	D	0.53312	0.959	P	0.49922	0.626	T	0.06534	-1.0821	10	0.05721	T	0.95	-12.638	10.5382	0.45018	0.0882:0.0:0.9118:0.0	.	303	P30968	GNRHR_HUMAN	T	303	ENSP00000226413:P303T	ENSP00000226413:P303T	P	-	1	0	GNRHR	68288873	1.000000	0.71417	0.989000	0.46669	0.918000	0.54935	3.915000	0.56409	2.718000	0.92993	0.585000	0.79938	CCA		0.383	GNRHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251432.2		
UGT2B11	10720	broad.mit.edu	37	4	70079940	70079940	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:70079940C>T	ENST00000446444.1	-	1	509	c.501G>A	c.(499-501)cgG>cgA	p.R167R	RP11-704M14.1_ENST00000504301.1_RNA|RP11-704M14.1_ENST00000505646.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	167					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.R167R(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						TGTACACAAACCGTATGTTAA	0.418																																					p.R167R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G501A	4						.						132.0	127.0	129.0					4																	70079940		2203	4299	6502	70114529	SO:0001819	synonymous_variant	10720	exon1			AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"""UDP glucuronosyltransferases"""	12545	protein-coding gene	gene with protein product		603064	"""UDP glycosyltransferase 2 family, polypeptide B11"""			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.501G>A	4.37:g.70079940C>T		Somatic		Capture	Illumina HiSeq	Phase_I	70114529	NM_001073	Q3KNV9	Silent	SNP	ENST00000446444.1	37	CCDS3527.1																																																																																				0.418	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	
UGT2A1	10941	broad.mit.edu	37	4	70455263	70455263	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:70455263C>T	ENST00000503640.1	-	6	1466	c.1411G>A	c.(1411-1413)Gcc>Acc	p.A471T	UGT2A1_ENST00000502343.1_5'Flank|UGT2A1_ENST00000514019.1_Missense_Mutation_p.A637T|UGT2A1_ENST00000286604.4_Missense_Mutation_p.A471T|UGT2A1_ENST00000512704.1_Missense_Mutation_p.A427T|UGT2A2_ENST00000457664.2_Missense_Mutation_p.A480T	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	471					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.A471T(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						AGGTGCTTGGCTCCTTTGTGG	0.488																																					p.A471T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1411A	4						.						140.0	135.0	137.0					4																	70455263		2203	4300	6503	70489852	SO:0001583	missense	10941	exon6			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.1411G>A	4.37:g.70455263C>T	ENSP00000424478:p.Ala471Thr	Somatic		Capture	Illumina HiSeq	Phase_I	70489852	NM_006798	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	37	CCDS3529.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.956344	0.92726	.	.	ENSG00000173610	ENST00000457664;ENST00000503640;ENST00000512704;ENST00000514019;ENST00000286604	T;T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58;-0.25	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	D	0.82995	0.5158	M	0.74546	2.27	.	.	.	D;D;P;B;B	0.71674	0.998;0.972;0.79;0.037;0.37	D;P;B;B;B	0.70227	0.968;0.794;0.391;0.041;0.114	D	0.86468	0.1783	9	0.87932	D	0	.	15.8962	0.79336	0.0:1.0:0.0:0.0	.	637;637;427;480;471	E9PDM7;B4E2F4;D6RFW5;Q9Y4X1-2;Q9Y4X1	.;.;.;.;UD2A1_HUMAN	T	480;471;427;637;471	ENSP00000387888:A480T;ENSP00000424478:A471T;ENSP00000421432:A427T;ENSP00000425497:A637T;ENSP00000286604:A471T	ENSP00000286604:A471T	A	-	1	0	UGT2A1	70489852	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	7.520000	0.81821	2.526000	0.85167	0.579000	0.79373	GCC		0.488	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798	
CSN3	1448	broad.mit.edu	37	4	71114913	71114913	+	Missense_Mutation	SNP	C	C	T	rs74750151	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:71114913C>T	ENST00000304954.3	+	4	372	c.286C>T	c.(286-288)Cgg>Tgg	p.R96W		NM_005212.2	NP_005203.2	Q9UNS2	CSN3_HUMAN	casein kappa	0					cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)		p.R96W(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						AATTCCTCAGCGGCAATACCT	0.463													C|||	13	0.00259585	0.0098	0.0	5008	,	,		17641	0.0		0.0	False		,,,				2504	0.0				p.R96W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C286T	4						.	C	TRP/ARG	29,4377	35.2+/-66.4	0,29,2174	116.0	103.0	107.0		286	-1.5	0.0	4	dbSNP_131	107	1,8599		0,1,4299	yes	missense	CSN3	NM_005212.2	101	0,30,6473	TT,TC,CC		0.0116,0.6582,0.2307	benign	96/183	71114913	30,12976	2203	4300	6503	71149502	SO:0001583	missense	1448	exon4			U51899	CCDS3538.1	4q21.1	2014-02-19	2003-01-24	2003-01-31	ENSG00000171209	ENSG00000171209			2446	protein-coding gene	gene with protein product		601695	"""casein, kappa"""	CSN10		8863730, 9050925	Standard	NM_005212		Approved		uc003hfe.4	P07498	OTTHUMG00000129399	ENST00000304954.3:c.286C>T	4.37:g.71114913C>T	ENSP00000304822:p.Arg96Trp	Somatic		Capture	Illumina HiSeq	Phase_I	71149502	NM_005212	B2R683|B4DY81|O43191|Q7LDR6	Missense_Mutation	SNP	ENST00000304954.3	37	CCDS3538.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.031	-1.331129	0.01298	0.006582	1.16E-4	ENSG00000171209	ENST00000304954	T	0.19250	2.16	4.52	-1.48	0.08745	.	1.105910	0.06755	N	0.780777	T	0.01695	0.0054	N	0.00065	-2.305	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41662	-0.9496	10	0.02654	T	1	-15.3993	0.6889	0.00888	0.1644:0.1902:0.1702:0.4752	.	96	P07498	CASK_HUMAN	W	96	ENSP00000304822:R96W	ENSP00000304822:R96W	R	+	1	2	CSN3	71149502	0.062000	0.20869	0.001000	0.08648	0.002000	0.02628	0.235000	0.17948	-0.125000	0.11703	-1.202000	0.01658	CGG		0.463	CSN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251555.1	NM_005212	
ENAM	10117	broad.mit.edu	37	4	71509385	71509385	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:71509385G>A	ENST00000396073.3	+	9	2523	c.2242G>A	c.(2242-2244)Gtt>Att	p.V748I	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	748					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)		p.V748I(1)		haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			GGGCTACTACGTTAATAATGC	0.458																																					p.V748I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2242A	4						.						63.0	64.0	63.0					4																	71509385		2202	4300	6502	71728249	SO:0001583	missense	10117	exon9			AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.2242G>A	4.37:g.71509385G>A	ENSP00000379383:p.Val748Ile	Somatic		Capture	Illumina HiSeq	Phase_I	71728249	NM_031889	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	37	CCDS3544.2	.	.	.	.	.	.	.	.	.	.	G	1.241	-0.621433	0.03636	.	.	ENSG00000132464	ENST00000396073	T	0.30448	1.53	6.01	-8.33	0.00992	.	1.506600	0.03689	N	0.246783	T	0.17365	0.0417	N	0.20986	0.625	0.09310	N	1	B	0.14012	0.009	B	0.10450	0.005	T	0.14587	-1.0467	10	0.19590	T	0.45	4.0835	9.5518	0.39315	0.4867:0.383:0.1303:0.0	.	748	Q9NRM1	ENAM_HUMAN	I	748	ENSP00000379383:V748I	ENSP00000379383:V748I	V	+	1	0	ENAM	71728249	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.503000	0.06383	-1.446000	0.01945	-0.819000	0.03115	GTT		0.458	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889	
ENAM	10117	broad.mit.edu	37	4	71509879	71509879	+	Silent	SNP	C	C	T	rs143333113		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:71509879C>T	ENST00000396073.3	+	9	3017	c.2736C>T	c.(2734-2736)gaC>gaT	p.D912D	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	912					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)		p.D912D(2)		haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			TGTATACAGACGGTAGTCATA	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		20689	0.001		0.0	False		,,,				2504	0.0				p.D912D												.	.	2	Substitution - coding silent(2)	large_intestine(1)|central_nervous_system(1)	c.C2736T	4						.	C		0,4406		0,0,2203	98.0	86.0	90.0		2736	3.2	0.7	4	dbSNP_134	90	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ENAM	NM_031889.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		912/1143	71509879	1,13005	2203	4300	6503	71728743	SO:0001819	synonymous_variant	10117	exon9			AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.2736C>T	4.37:g.71509879C>T		Somatic		Capture	Illumina HiSeq	Phase_I	71728743	NM_031889	Q17RI5|Q9H3D1	Silent	SNP	ENST00000396073.3	37	CCDS3544.2																																																																																				0.493	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889	
NPFFR2	10886	broad.mit.edu	37	4	72897735	72897735	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:72897735C>T	ENST00000308744.6	+	1	215	c.117C>T	c.(115-117)cgC>cgT	p.R39R	NPFFR2_ENST00000344413.5_Silent_p.R39R	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	39					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)	p.R39R(1)		NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			TCCAGCAGCGCGGCGGGCCAG	0.677																																					p.R39R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C117T	4						.						23.0	28.0	26.0					4																	72897735		2190	4277	6467	73116599	SO:0001819	synonymous_variant	10886	exon1			AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"""GPCR / Class A :  Neuropeptide receptors : FF/AF"", ""GPCR / Class A : RF amide peptide receptors"""	4525	protein-coding gene	gene with protein product	"""neuropeptide FF 2"""	607449	"""G protein-coupled receptor 74"""	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.117C>T	4.37:g.72897735C>T		Somatic		Capture	Illumina HiSeq	Phase_I	73116599	NM_004885	Q96RV1|Q9NR49	Silent	SNP	ENST00000308744.6	37	CCDS3551.1																																																																																				0.677	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885	
NPFFR2	10886	broad.mit.edu	37	4	73012885	73012885	+	Missense_Mutation	SNP	C	C	T	rs200830127		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:73012885C>T	ENST00000308744.6	+	4	1023	c.925C>T	c.(925-927)Cgg>Tgg	p.R309W	NPFFR2_ENST00000344413.5_3'UTR|NPFFR2_ENST00000395999.1_Missense_Mutation_p.R210W|NPFFR2_ENST00000358749.3_Missense_Mutation_p.R207W|NPFFR2_ENST00000506359.1_3'UTR	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	309					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)	p.R309W(1)		NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			CTACTGGTGCCGGGAAGACTG	0.458													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20271	0.0		0.0	False		,,,				2504	0.0				p.R210W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C628T	4						.						104.0	95.0	98.0					4																	73012885		2203	4300	6503	73231749	SO:0001583	missense	10886	exon5			AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"""GPCR / Class A :  Neuropeptide receptors : FF/AF"", ""GPCR / Class A : RF amide peptide receptors"""	4525	protein-coding gene	gene with protein product	"""neuropeptide FF 2"""	607449	"""G protein-coupled receptor 74"""	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.925C>T	4.37:g.73012885C>T	ENSP00000307822:p.Arg309Trp	Somatic		Capture	Illumina HiSeq	Phase_I	73231749	NM_001144756	Q96RV1|Q9NR49	Missense_Mutation	SNP	ENST00000308744.6	37	CCDS3551.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	7.865	0.726833	0.15439	.	.	ENSG00000056291	ENST00000308744;ENST00000395999;ENST00000358749	T;T;T	0.36699	1.24;1.24;1.24	5.91	5.07	0.68467	GPCR, rhodopsin-like superfamily (1);	0.543150	0.16863	N	0.196442	T	0.28896	0.0717	N	0.25890	0.77	0.58432	D	0.999999	B;B	0.22983	0.023;0.078	B;B	0.22386	0.005;0.039	T	0.03773	-1.1005	10	0.37606	T	0.19	.	14.6657	0.68907	0.0:0.9297:0.0:0.0703	.	210;309	Q9Y5X5-3;Q9Y5X5	.;NPFF2_HUMAN	W	309;210;207	ENSP00000307822:R309W;ENSP00000379321:R210W;ENSP00000351599:R207W	ENSP00000307822:R309W	R	+	1	2	NPFFR2	73231749	0.441000	0.25626	0.994000	0.49952	0.052000	0.14988	-0.055000	0.11807	1.491000	0.48482	0.655000	0.94253	CGG		0.458	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885	
RASSF6	166824	broad.mit.edu	37	4	74450915	74450915	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:74450915T>C	ENST00000342081.3	-	6	775	c.645A>G	c.(643-645)ggA>ggG	p.G215G	RASSF6_ENST00000395777.2_Silent_p.G183G|RASSF6_ENST00000335049.5_Silent_p.G171G|RASSF6_ENST00000307439.5_Silent_p.G183G	NM_201431.2	NP_958834.1	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family member 6	215					apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|signal transduction (GO:0007165)			p.G215G(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|pancreas(2)|skin(2)	17	Breast(15;0.00102)		all cancers(17;0.00104)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			TATAGAAGTGTCCATTAATAG	0.353																																					p.G183G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A549G	4						.						135.0	131.0	133.0					4																	74450915		2203	4299	6502	74669779	SO:0001819	synonymous_variant	166824	exon6			AY217664	CCDS3558.1, CCDS3559.1, CCDS58904.1, CCDS58905.1	4q21.1	2008-02-22	2008-02-22		ENSG00000169435	ENSG00000169435			20796	protein-coding gene	gene with protein product		612620					Standard	NM_177532		Approved		uc003hhd.2	Q6ZTQ3	OTTHUMG00000130007	ENST00000342081.3:c.645A>G	4.37:g.74450915T>C		Somatic		Capture	Illumina HiSeq	Phase_I	74669779	NM_177532	Q68DT2|Q6PDA6|Q86WG9|Q86WH0	Silent	SNP	ENST00000342081.3	37	CCDS3558.1																																																																																				0.353	RASSF6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252279.1	NM_177532	
BTC	685	broad.mit.edu	37	4	75681166	75681166	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:75681166G>A	ENST00000395743.3	-	3	544	c.184C>T	c.(184-186)Cgg>Tgg	p.R62W		NM_001729.2	NP_001720.1	P35070	BTC_HUMAN	betacellulin	62					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)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitosis (GO:0045840)|positive regulation of urine volume (GO:0035810)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)	p.R62W(1)		central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	10			Lung(101;0.219)			TGGCCTTTCCGCTTTGATTGT	0.433																																					p.R62W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C184T	4						.						222.0	206.0	212.0					4																	75681166		2203	4300	6503	75900190	SO:0001583	missense	685	exon3			S55606	CCDS3566.1	4q13.3	2012-09-20			ENSG00000174808	ENSG00000174808			1121	protein-coding gene	gene with protein product		600345				8439318, 11522793	Standard	NM_001729		Approved		uc003hig.2	P35070	OTTHUMG00000130107	ENST00000395743.3:c.184C>T	4.37:g.75681166G>A	ENSP00000379092:p.Arg62Trp	Somatic		Capture	Illumina HiSeq	Phase_I	75900190	NM_001729	Q96F48	Missense_Mutation	SNP	ENST00000395743.3	37	CCDS3566.1	.	.	.	.	.	.	.	.	.	.	G	12.51	1.958836	0.34565	.	.	ENSG00000174808	ENST00000395743	T	0.15372	2.43	4.69	-3.52	0.04682	.	0.483385	0.23847	N	0.043992	T	0.09069	0.0224	L	0.40543	1.245	0.09310	N	1	B	0.15473	0.013	B	0.08055	0.003	T	0.15723	-1.0427	10	0.44086	T	0.13	-8.4393	0.9664	0.01406	0.4107:0.1175:0.2326:0.2391	.	62	P35070	BTC_HUMAN	W	62	ENSP00000379092:R62W	ENSP00000379092:R62W	R	-	1	2	BTC	75900190	0.000000	0.05858	0.000000	0.03702	0.559000	0.35586	-0.266000	0.08631	-0.998000	0.03446	-0.140000	0.14226	CGG		0.433	BTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252413.1		
CCDC158	339965	broad.mit.edu	37	4	77247144	77247144	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:77247144G>A	ENST00000388914.3	-	22	3175	c.3023C>T	c.(3022-3024)gCt>gTt	p.A1008V		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	1008	Ser-rich.							p.A1008V(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						TGAACGAGAAGCTGAGTTTTT	0.363																																					p.A1008V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3023T	4						.						137.0	133.0	134.0					4																	77247144		1838	4080	5918	77466168	SO:0001583	missense	339965	exon22			BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.3023C>T	4.37:g.77247144G>A	ENSP00000373566:p.Ala1008Val	Somatic		Capture	Illumina HiSeq	Phase_I	77466168	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Missense_Mutation	SNP	ENST00000388914.3	37	CCDS43242.1	.	.	.	.	.	.	.	.	.	.	G	6.481	0.456913	0.12283	.	.	ENSG00000163749	ENST00000388914;ENST00000318586	T	0.36878	1.23	4.96	2.19	0.27852	.	0.437286	0.19387	N	0.115520	T	0.19927	0.0479	N	0.24115	0.695	0.20563	N	0.999885	B	0.02656	0.0	B	0.06405	0.002	T	0.15321	-1.0441	10	0.23302	T	0.38	.	6.012	0.19582	0.3278:0.0:0.6722:0.0	.	1008	Q5M9N0	CD158_HUMAN	V	1008;428	ENSP00000373566:A1008V	ENSP00000316815:A428V	A	-	2	0	CCDC158	77466168	0.000000	0.05858	0.708000	0.30435	0.008000	0.06430	0.222000	0.17699	0.757000	0.33036	0.555000	0.69702	GCT		0.363	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784	
SHROOM3	57619	broad.mit.edu	37	4	77691898	77691898	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:77691898C>T	ENST00000296043.6	+	10	6422	c.5469C>T	c.(5467-5469)agC>agT	p.S1823S	RP11-359D14.3_ENST00000449007.1_RNA	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	1823	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.				actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)		p.S1822S(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			CTCTGATCAGCGAGCTCTGCA	0.577																																					p.S1823S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5469T	4						.						142.0	141.0	141.0					4																	77691898		2203	4300	6503	77910922	SO:0001819	synonymous_variant	57619	exon10			AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.5469C>T	4.37:g.77691898C>T		Somatic		Capture	Illumina HiSeq	Phase_I	77910922	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	37	CCDS3579.2																																																																																				0.577	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
BMP2K	55589	broad.mit.edu	37	4	79833100	79833100	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:79833100G>A	ENST00000335016.5	+	16	3565	c.3399G>A	c.(3397-3399)gtG>gtA	p.V1133V	PAQR3_ENST00000512733.1_3'UTR|PAQR3_ENST00000295462.3_Intron|PAQR3_ENST00000515541.1_5'Flank	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	1133					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.V1133V(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						AACTTGTGGTGCAAAGCATCA	0.458																																					p.V1133V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3399A	4						.						182.0	175.0	177.0					4																	79833100		1961	4143	6104	80052124	SO:0001819	synonymous_variant	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.3399G>A	4.37:g.79833100G>A		Somatic		Capture	Illumina HiSeq	Phase_I	80052124	NM_198892	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Silent	SNP	ENST00000335016.5	37	CCDS47083.1	.	.	.	.	.	.	.	.	.	.	G	5.603	0.296064	0.10622	.	.	ENSG00000138756	ENST00000502613	.	.	.	5.25	2.16	0.27623	.	.	.	.	.	T	0.55847	0.1946	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51631	-0.8681	4	.	.	.	-12.3668	7.964	0.30087	0.16:0.0:0.7053:0.1347	.	.	.	.	T	826	.	.	A	+	1	0	BMP2K	80052124	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	1.826000	0.39092	1.217000	0.43442	0.305000	0.20034	GCA		0.458	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593	
RASGEF1B	153020	broad.mit.edu	37	4	82377897	82377897	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:82377897C>T	ENST00000264400.2	-	4	497	c.346G>A	c.(346-348)Gaa>Aaa	p.E116K	RASGEF1B_ENST00000509081.1_Missense_Mutation_p.E116K|RASGEF1B_ENST00000514889.1_5'UTR|RASGEF1B_ENST00000436139.2_Missense_Mutation_p.E116K|RASGEF1B_ENST00000335927.7_Missense_Mutation_p.E75K	NM_152545.1	NP_689758.1	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B	116	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.E116K(1)		endometrium(2)|kidney(5)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	26						TCCGTCCATTCCGTGAGGAGT	0.398																																					p.E116K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G346A	4						.						118.0	116.0	117.0					4																	82377897		2203	4300	6503	82596921	SO:0001583	missense	153020	exon4			AK056257	CCDS34022.1, CCDS75151.1, CCDS75152.1	4q21.21	2013-09-24				ENSG00000138670			24881	protein-coding gene	gene with protein product		614532				12488504	Standard	XM_005262776		Approved	GPIG4, FLJ31695	uc003hmi.1	Q0VAM2		ENST00000264400.2:c.346G>A	4.37:g.82377897C>T	ENSP00000264400:p.Glu116Lys	Somatic		Capture	Illumina HiSeq	Phase_I	82596921	NM_152545	Q0VAM1|Q4W5L7|Q4W5M3|Q96MY8	Missense_Mutation	SNP	ENST00000264400.2	37	CCDS34022.1	.	.	.	.	.	.	.	.	.	.	C	32	5.141045	0.94560	.	.	ENSG00000138670	ENST00000509081;ENST00000264400;ENST00000335927;ENST00000436139;ENST00000395570	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	5.3	5.3	0.74995	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.000000	0.85682	D	0.000000	T	0.62612	0.2442	M	0.88640	2.97	0.80722	D	1	D;D;D;P	0.89917	0.998;1.0;0.964;0.933	D;D;P;P	0.91635	0.966;0.999;0.835;0.897	T	0.62623	-0.6815	10	0.30078	T	0.28	.	18.7469	0.91797	0.0:1.0:0.0:0.0	.	75;116;116;116	Q0VAM2-2;Q8N437;Q0VAM2-3;Q0VAM2	.;.;.;RGF1B_HUMAN	K	116;116;75;116;116	ENSP00000425393:E116K;ENSP00000264400:E116K;ENSP00000338437:E75K;ENSP00000398763:E116K	ENSP00000264400:E116K	E	-	1	0	RASGEF1B	82596921	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	7.320000	0.79064	2.759000	0.94783	0.650000	0.86243	GAA		0.398	RASGEF1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362830.1	NM_152545	
SEC31A	22872	broad.mit.edu	37	4	83763465	83763465	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:83763465G>T	ENST00000395310.2	-	22	2978	c.2796C>A	c.(2794-2796)gcC>gcA	p.A932A	SEC31A_ENST00000508502.1_Silent_p.A932A|SEC31A_ENST00000505984.1_Silent_p.A893A|SEC31A_ENST00000326950.5_Silent_p.A893A|SEC31A_ENST00000513858.1_Intron|SEC31A_ENST00000432794.1_Silent_p.A932A|SEC31A_ENST00000448323.1_Silent_p.A932A|SEC31A_ENST00000264405.5_Silent_p.A696A|SEC31A_ENST00000500777.2_Intron|SEC31A_ENST00000443462.2_Silent_p.A927A|SEC31A_ENST00000355196.2_Silent_p.A932A|SEC31A_ENST00000505472.1_Silent_p.A963A|SEC31A_ENST00000348405.4_Silent_p.A893A|SEC31A_ENST00000311785.7_Intron|SEC31A_ENST00000509142.1_Intron	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	932	Interaction with PDCD6.|Pro-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)	p.A932A(1)	SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				TAGGTGAAGAGGCCTGGTGCT	0.547																																					p.A927A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2781A	4						.						97.0	80.0	86.0					4																	83763465		2203	4300	6503	83982489	SO:0001819	synonymous_variant	22872	exon21			AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"""WD repeat domain containing"""	17052	protein-coding gene	gene with protein product		610257	"""SEC31-like 1 (S. cerevisiae)"", ""Sec31 homolog A (S. cerevisiae)"""	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.2796C>A	4.37:g.83763465G>T		Somatic		Capture	Illumina HiSeq	Phase_I	83982489	NM_001191049	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Silent	SNP	ENST00000395310.2	37	CCDS3596.1	.	.	.	.	.	.	.	.	.	.	G	5.752	0.323174	0.10900	.	.	ENSG00000138674	ENST00000503937	.	.	.	5.83	3.07	0.35406	.	.	.	.	.	T	0.53045	0.1772	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42361	-0.9456	4	.	.	.	-0.1053	4.7725	0.13162	0.1324:0.1216:0.6199:0.126	.	.	.	.	H	82	.	.	P	-	2	0	SEC31A	83982489	1.000000	0.71417	0.676000	0.29932	0.626000	0.37791	2.487000	0.45268	0.324000	0.23333	0.563000	0.77884	CCT		0.547	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211	
HPSE	10855	broad.mit.edu	37	4	84230034	84230034	+	Missense_Mutation	SNP	G	G	A	rs373927587		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:84230034G>A	ENST00000405413.2	-	9	1191	c.1055C>T	c.(1054-1056)gCg>gTg	p.A352V	HPSE_ENST00000513463.1_Missense_Mutation_p.A294V|HPSE_ENST00000512196.1_Intron|HPSE_ENST00000311412.5_Missense_Mutation_p.A352V	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	352					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)	p.A352V(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	TAGCAAGGGCGCTCCGCCTCC	0.512																																					p.A352V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1055T	4						.						96.0	94.0	95.0					4																	84230034		2203	4300	6503	84449058	SO:0001583	missense	10855	exon8			AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.1055C>T	4.37:g.84230034G>A	ENSP00000384262:p.Ala352Val	Somatic		Capture	Illumina HiSeq	Phase_I	84449058	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Missense_Mutation	SNP	ENST00000405413.2	37	CCDS3602.1	.	.	.	.	.	.	.	.	.	.	G	31	5.097402	0.94197	.	.	ENSG00000173083	ENST00000311412;ENST00000405413;ENST00000454730;ENST00000513463	T;T;T	0.32272	1.46;1.46;1.46	5.16	5.16	0.70880	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.049781	0.85682	D	0.000000	T	0.58235	0.2108	M	0.85542	2.76	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.993;0.988;0.993	T	0.56469	-0.7974	10	0.13108	T	0.6	-8.4716	18.424	0.90602	0.0:0.0:1.0:0.0	.	294;294;352	A9JIG7;E9PGR1;Q9Y251	.;.;HPSE_HUMAN	V	352;352;66;294	ENSP00000308107:A352V;ENSP00000384262:A352V;ENSP00000421365:A294V	ENSP00000308107:A352V	A	-	2	0	HPSE	84449058	1.000000	0.71417	0.883000	0.34634	0.933000	0.57130	8.500000	0.90498	2.680000	0.91292	0.591000	0.81541	GCG		0.512	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665	
CDS1	1040	broad.mit.edu	37	4	85540673	85540673	+	Silent	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:85540673C>A	ENST00000295887.5	+	5	990	c.567C>A	c.(565-567)gcC>gcA	p.A189A		NM_001263.3	NP_001254.2	O96017	CHK2_HUMAN	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	0					cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.A189A(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|ovary(1)	20		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.00101)		TATCATTTGCCCTCTATCTGG	0.284																																					p.A189A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C567A	4						.						86.0	80.0	82.0					4																	85540673		2203	4295	6498	85759697	SO:0001819	synonymous_variant	1040	exon5			U65887	CCDS3608.1	4q21	2008-02-05			ENSG00000163624	ENSG00000163624	2.7.7.41		1800	protein-coding gene	gene with protein product		603548				9806839, 9115637	Standard	NM_001263		Approved		uc011ccv.2	Q92903	OTTHUMG00000130428	ENST00000295887.5:c.567C>A	4.37:g.85540673C>A		Somatic		Capture	Illumina HiSeq	Phase_I	85759697	NM_001263	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000295887.5	37	CCDS3608.1																																																																																				0.284	CDS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252817.2		
WDFY3	23001	broad.mit.edu	37	4	85600379	85600379	+	Silent	SNP	G	G	A	rs530783066		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:85600379G>A	ENST00000295888.4	-	65	10247	c.9840C>T	c.(9838-9840)gaC>gaT	p.D3280D	WDFY3_ENST00000322366.6_Silent_p.D3263D	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	3280	Interaction with ATG5.|Interaction with SQSTM1.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)	p.D3280D(1)		breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TGCTGTCCTCGTCTTGGGCTT	0.532													G|||	1	0.000199681	0.0	0.0	5008	,	,		15364	0.0		0.0	False		,,,				2504	0.001				p.D3280D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9840T	4						.						48.0	37.0	41.0					4																	85600379		2203	4295	6498	85819403	SO:0001819	synonymous_variant	23001	exon65			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.9840C>T	4.37:g.85600379G>A		Somatic		Capture	Illumina HiSeq	Phase_I	85819403	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	37	CCDS3609.1																																																																																				0.532	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
PTPN13	5783	broad.mit.edu	37	4	87653801	87653801	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:87653801C>T	ENST00000411767.2	+	12	1803	c.1740C>T	c.(1738-1740)aaC>aaT	p.N580N	PTPN13_ENST00000427191.2_Silent_p.N580N|PTPN13_ENST00000316707.6_Silent_p.N580N|PTPN13_ENST00000436978.1_Silent_p.N580N|PTPN13_ENST00000511467.1_Silent_p.N580N			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	580	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.N580N(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		TGCTTCTGAACGGGCAAAGAC	0.343																																					p.N580N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1740T	4						.						127.0	119.0	122.0					4																	87653801		1890	4120	6010	87872825	SO:0001819	synonymous_variant	5783	exon12				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.1740C>T	4.37:g.87653801C>T		Somatic		Capture	Illumina HiSeq	Phase_I	87872825	NM_080684	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																				0.343	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
HERC6	55008	broad.mit.edu	37	4	89338616	89338616	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:89338616C>T	ENST00000264346.7	+	13	1657	c.1598C>T	c.(1597-1599)cCg>cTg	p.P533L	HERC6_ENST00000380265.5_Missense_Mutation_p.P533L	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	533					hematopoietic progenitor cell differentiation (GO:0002244)|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.P533S(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		TCTCTGAATCCGCTGATCCAG	0.413																																					p.R533C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1597T	4						.						70.0	64.0	66.0					4																	89338616		1867	4093	5960	89557639	SO:0001583	missense	55008	exon13			AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"""hect domain and RLD 6"""				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.1598C>T	4.37:g.89338616C>T	ENSP00000264346:p.Pro533Leu	Somatic		Capture	Illumina HiSeq	Phase_I	89557639	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Missense_Mutation	SNP	ENST00000264346.7	37	CCDS47098.1	.	.	.	.	.	.	.	.	.	.	C	2.086	-0.409550	0.04799	.	.	ENSG00000138642	ENST00000380265;ENST00000264346	T;T	0.37411	1.21;1.2	4.79	2.01	0.26516	.	1.046430	0.07480	N	0.903636	T	0.22589	0.0545	N	0.22421	0.69	0.09310	N	1	B;B	0.26635	0.155;0.096	B;B	0.15870	0.014;0.006	T	0.25187	-1.0139	10	0.59425	D	0.04	.	4.0621	0.09843	0.1522:0.4672:0.2959:0.0847	.	533;533	Q8IVU3-2;Q8IVU3	.;HERC6_HUMAN	L	533	ENSP00000369617:P533L;ENSP00000264346:P533L	ENSP00000264346:P533L	P	+	2	0	HERC6	89557639	0.000000	0.05858	0.005000	0.12908	0.001000	0.01503	0.209000	0.17435	0.293000	0.22520	-0.282000	0.10007	CCG		0.413	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2		
HERC5	51191	broad.mit.edu	37	4	89408246	89408246	+	Silent	SNP	C	C	T	rs111323592		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:89408246C>T	ENST00000264350.3	+	15	2031	c.1878C>T	c.(1876-1878)tgC>tgT	p.C626C	HERC5_ENST00000508159.1_Silent_p.C264C	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	626					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.C626C(1)		NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		TACAATGCTGCGTCATATTCA	0.318																																					p.C626C	Esophageal Squamous(39;887 1012 34045 50514)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1878T	4						.						94.0	94.0	94.0					4																	89408246		2203	4298	6501	89627269	SO:0001819	synonymous_variant	51191	exon15			AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"""hect domain and RLD 5"""			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.1878C>T	4.37:g.89408246C>T		Somatic		Capture	Illumina HiSeq	Phase_I	89627269	NM_016323	B2RTQ1|Q69G20	Silent	SNP	ENST00000264350.3	37	CCDS3630.1																																																																																				0.318	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323	
BBS12	166379	broad.mit.edu	37	4	123664722	123664722	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:123664722delA	ENST00000314218.3	+	2	1868	c.1675delA	c.(1675-1677)aaafs	p.K560fs	BBS12_ENST00000542236.1_Frame_Shift_Del_p.K560fs	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	560					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)	p.E561fs*77(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						GCAATCTCTGAAAAAAGAAAA	0.423									Bardet-Biedl syndrome																												p.K559fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1675delA	4						.						93.0	94.0	94.0					4																	123664722		2203	4300	6503	123884172	SO:0001589	frameshift_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1675delA	4.37:g.123664722delA	ENSP00000319062:p.Lys560fs	Somatic		Capture	Illumina HiSeq	Phase_I	123884172	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Frame_Shift_Del	DEL	ENST00000314218.3	37	CCDS3728.1																																																																																				0.423	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
FAT1	2195	broad.mit.edu	37	4	187540873	187540873	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr4:187540873C>T	ENST00000441802.2	-	10	7076	c.6867G>A	c.(6865-6867)gcG>gcA	p.A2289A		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2289	Cadherin 21. {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.A2289A(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						ACAGGGTCACCGCATAAGACT	0.458										HNSCC(5;0.00058)																											p.A2289A	Colon(197;1040 2055 4143 4984 49344)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G6867A	4						.						95.0	97.0	97.0					4																	187540873		1991	4161	6152	187777867	SO:0001819	synonymous_variant	2195	exon10			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.6867G>A	4.37:g.187540873C>T		Somatic		Capture	Illumina HiSeq	Phase_I	187777867	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																				0.458	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
CMBL	134147	broad.mit.edu	37	5	10290710	10290710	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:10290710C>T	ENST00000296658.3	-	2	585	c.165G>A	c.(163-165)caG>caA	p.Q55Q	Y_RNA_ENST00000516532.1_RNA|CMBL_ENST00000510532.1_5'UTR	NM_138809.3	NP_620164.1	Q96DG6	CMBL_HUMAN	carboxymethylenebutenolidase homolog (Pseudomonas)	55						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	hydrolase activity (GO:0016787)	p.Q55Q(1)		endometrium(1)|large_intestine(1)|lung(9)|skin(1)|stomach(1)	13						TATTGGGCAACTGCCAGCCAA	0.403																																					p.Q55Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G165A	5						.						126.0	125.0	126.0					5																	10290710		2203	4300	6503	10343710	SO:0001819	synonymous_variant	134147	exon2				CCDS3878.1	5p15.2	2010-06-25	2006-09-12		ENSG00000164237	ENSG00000164237	3.1.-.-		25090	protein-coding gene	gene with protein product		613379	"""carboxymethylenebutenolidase-like (Pseudomonas)"""			3804974, 20177059	Standard	NM_138809		Approved	FLJ23617	uc003jes.3	Q96DG6	OTTHUMG00000131043	ENST00000296658.3:c.165G>A	5.37:g.10290710C>T		Somatic		Capture	Illumina HiSeq	Phase_I	10343710	NM_138809	D3DTC7|Q8TED6	Silent	SNP	ENST00000296658.3	37	CCDS3878.1																																																																																				0.403	CMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253689.1	NM_138809	
ROPN1L	83853	broad.mit.edu	37	5	10448383	10448383	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:10448383C>A	ENST00000503804.1	+	3	664	c.143C>A	c.(142-144)gCt>gAt	p.A48D	ROPN1L_ENST00000274134.4_Missense_Mutation_p.A48D|ROPN1L_ENST00000510520.1_3'UTR			Q96C74	ROP1L_HUMAN	rhophilin associated tail protein 1-like	48					epithelial cilium movement (GO:0003351)|regulation of protein phosphorylation (GO:0001932)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)		p.A48D(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)	14						TATTTTTCAGCTCTGTCGAGA	0.423																																					p.A48D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C143A	5						.						70.0	71.0	71.0					5																	10448383		2203	4300	6503	10501383	SO:0001583	missense	83853	exon2			AF239723	CCDS3879.1	5p15	2011-01-20	2011-01-20		ENSG00000145491	ENSG00000145491			24060	protein-coding gene	gene with protein product	"""radial spoke head 11 homolog (Chlamydomonas)"""	611756	"""ropporin 1-like"""			11278869	Standard	NM_031916		Approved	ASP, FLJ25776, RSPH11	uc021xwo.1	Q96C74	OTTHUMG00000090507	ENST00000503804.1:c.143C>A	5.37:g.10448383C>A	ENSP00000421405:p.Ala48Asp	Somatic		Capture	Illumina HiSeq	Phase_I	10501383	NM_031916	D3DTC9|Q9BZX0	Missense_Mutation	SNP	ENST00000503804.1	37	CCDS3879.1	.	.	.	.	.	.	.	.	.	.	C	15.94	2.980747	0.53827	.	.	ENSG00000145491	ENST00000503804;ENST00000274134	T;T	0.27402	1.67;1.67	5.48	5.48	0.80851	cAMP-dependent protein kinase, regulatory subunit, type I/II alpha/beta (1);	0.179520	0.48767	D	0.000177	T	0.56848	0.2013	M	0.80982	2.52	0.50632	D	0.999882	D	0.89917	1.0	D	0.73708	0.981	T	0.60801	-0.7191	10	0.66056	D	0.02	-5.0801	13.8379	0.63421	0.0:0.8467:0.1533:0.0	.	48	Q96C74	ROP1L_HUMAN	D	48	ENSP00000421405:A48D;ENSP00000274134:A48D	ENSP00000274134:A48D	A	+	2	0	ROPN1L	10501383	0.998000	0.40836	0.980000	0.43619	0.265000	0.26407	3.798000	0.55522	2.575000	0.86900	0.655000	0.94253	GCT		0.423	ROPN1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367033.1	NM_031916	
PAM	5066	broad.mit.edu	37	5	102295706	102295706	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:102295706G>A	ENST00000438793.3	+	12	1503	c.1033G>A	c.(1033-1035)Gcc>Acc	p.A345T	PAM_ENST00000304400.7_Missense_Mutation_p.A345T|PAM_ENST00000379787.4_5'UTR|PAM_ENST00000346918.2_Missense_Mutation_p.A345T|PAM_ENST00000274392.9_Missense_Mutation_p.A248T|PAM_ENST00000348126.2_Missense_Mutation_p.A345T|PAM_ENST00000455264.2_Missense_Mutation_p.A345T	NM_000919.3|NM_001177306.1|NM_138766.2	NP_000910.2|NP_001170777.1|NP_620121.1	P19021	AMD_HUMAN	peptidylglycine alpha-amidating monooxygenase	345	Peptidylglycine alpha-hydroxylating monooxygenase. {ECO:0000250}.				central nervous system development (GO:0007417)|heart development (GO:0007507)|lactation (GO:0007595)|limb development (GO:0060173)|long-chain fatty acid metabolic process (GO:0001676)|maternal process involved in female pregnancy (GO:0060135)|odontogenesis (GO:0042476)|ovulation cycle process (GO:0022602)|peptide amidation (GO:0001519)|protein amidation (GO:0018032)|protein homooligomerization (GO:0051260)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of protein secretion (GO:0050708)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to pH (GO:0009268)|toxin metabolic process (GO:0009404)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuron projection (GO:0043005)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)	calcium ion binding (GO:0005509)|copper ion binding (GO:0005507)|L-ascorbic acid binding (GO:0031418)|peptidylamidoglycolate lyase activity (GO:0004598)|peptidylglycine monooxygenase activity (GO:0004504)|zinc ion binding (GO:0008270)	p.A345T(2)		endometrium(2)|kidney(2)|large_intestine(10)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	25		all_cancers(142;3.12e-07)|all_epithelial(76;3.48e-10)|Prostate(80;0.00914)|Lung NSC(167;0.0213)|Ovarian(225;0.024)|Colorectal(57;0.0251)|all_lung(232;0.0284)		Epithelial(69;1.1e-13)|COAD - Colon adenocarcinoma(37;0.0127)	Vitamin C(DB00126)	ACCACCAGAGGCCAACATTCC	0.348																																					p.A345T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1033A	5						.						136.0	127.0	130.0					5																	102295706		2203	4300	6503	102323605	SO:0001583	missense	5066	exon12			AB095007	CCDS4092.1, CCDS4093.1, CCDS4094.1, CCDS43348.1, CCDS54885.1	5q	2008-02-05			ENSG00000145730	ENSG00000145730	1.14.17.3		8596	protein-coding gene	gene with protein product	"""peptidyl-alpha-hydroxyglycine alpha-amidating lyase"", ""peptidylglycine alpha-hydroxylating monooxygenase"""	170270				2357221	Standard	NM_000919		Approved	PAL, PHM	uc003knt.3	P19021	OTTHUMG00000128729	ENST00000438793.3:c.1033G>A	5.37:g.102295706G>A	ENSP00000396493:p.Ala345Thr	Somatic		Capture	Illumina HiSeq	Phase_I	102323605	NM_138822	A6NMR0|A8K293|O43211|O95080|Q16252|Q16253|Q54A45|Q86U53|Q8WVC7|Q9UCG0	Missense_Mutation	SNP	ENST00000438793.3	37	CCDS54885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.332917|5.332917	0.95758|0.95758	.|.	.|.	ENSG00000145730|ENSG00000145730	ENST00000438793;ENST00000346918;ENST00000348126;ENST00000304400;ENST00000274392;ENST00000455264|ENST00000379799	T;T;T;T;T;T|.	0.63913|.	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07|.	5.58|5.58	5.58|5.58	0.84498|0.84498	PHM/PNGase F domain (1);Copper type II, ascorbate-dependent monooxygenase-like, C-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74176|0.74176	0.3682|0.3682	M|M	0.63428|0.63428	1.95|1.95	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;0.997;1.0;0.999|.	D;D;D;D;D;D;D|.	0.97110|.	0.999;0.994;1.0;0.999;0.992;0.999;0.993|.	T|T	0.71361|0.71361	-0.4616|-0.4616	10|5	0.56958|.	D|.	0.05|.	.|.	19.5796|19.5796	0.95461|0.95461	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	248;7;345;345;345;345;345|.	F8WE90;Q13749;P19021;P19021-4;P19021-3;P19021-5;P19021-2|.	.;.;AMD_HUMAN;.;.;.;.|.	T|D	345;345;345;345;248;345|117	ENSP00000396493:A345T;ENSP00000282992:A345T;ENSP00000314638:A345T;ENSP00000306100:A345T;ENSP00000274392:A248T;ENSP00000403461:A345T|.	ENSP00000274392:A248T|.	A|G	+|+	1|2	0|0	PAM|PAM	102323605|102323605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	9.476000|9.476000	0.97823|0.97823	2.636000|2.636000	0.89361|0.89361	0.460000|0.460000	0.39030|0.39030	GCC|GGC		0.348	PAM-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250640.2	NM_000919	
SLC12A7	10723	broad.mit.edu	37	5	1057717	1057717	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:1057717T>C	ENST00000264930.5	-	22	2938	c.2895A>G	c.(2893-2895)gcA>gcG	p.A965A		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	965					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)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)	p.A965A(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	GGGTCCTGGCTGCCGCCGCGG	0.647																																					p.A965A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2895G	5						.						115.0	113.0	114.0					5																	1057717		2203	4300	6503	1110717	SO:0001819	synonymous_variant	10723	exon22			AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2895A>G	5.37:g.1057717T>C		Somatic		Capture	Illumina HiSeq	Phase_I	1110717	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	37	CCDS34129.1	.	.	.	.	.	.	.	.	.	.	T	0.116	-1.132152	0.01756	.	.	ENSG00000113504	ENST00000513223	.	.	.	3.23	-6.45	0.01914	.	.	.	.	.	T	0.16769	0.0403	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.20974	-1.0259	4	.	.	.	.	1.7898	0.03049	0.3389:0.3665:0.1668:0.1278	.	.	.	.	G	323	.	.	S	-	1	0	SLC12A7	1110717	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.245000	0.01192	-1.882000	0.01122	-1.909000	0.00523	AGC		0.647	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
CTNND2	1501	broad.mit.edu	37	5	11117571	11117571	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:11117571G>A	ENST00000304623.8	-	13	2457	c.2268C>T	c.(2266-2268)atC>atT	p.I756I	CTNND2_ENST00000359640.2_Silent_p.I756I|CTNND2_ENST00000511377.1_Silent_p.I665I|CTNND2_ENST00000458100.2_Silent_p.I323I|CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000503622.1_Silent_p.I419I	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	756					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.I756I(4)		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						CCTTGCTATCGATCTCACTGC	0.527																																					p.I756I												.	.	4	Substitution - coding silent(4)	large_intestine(3)|lung(1)	c.C2268T	5						.						190.0	168.0	176.0					5																	11117571		2203	4300	6503	11170571	SO:0001819	synonymous_variant	1501	exon13			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.2268C>T	5.37:g.11117571G>A		Somatic		Capture	Illumina HiSeq	Phase_I	11170571	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Silent	SNP	ENST00000304623.8	37	CCDS3881.1																																																																																				0.527	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332	
CAMK4	814	broad.mit.edu	37	5	110814180	110814180	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:110814180A>G	ENST00000282356.4	+	9	1201	c.803A>G	c.(802-804)gAa>gGa	p.E268G	CAMK4_ENST00000512453.1_Missense_Mutation_p.E268G	NM_001744.4	NP_001735.1	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	268	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|long-term memory (GO:0007616)|myeloid dendritic cell differentiation (GO:0043011)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleocytoplasmic transport (GO:0006913)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of osteoclast differentiation (GO:0045670)|regulation of T cell differentiation in thymus (GO:0033081)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.E268G(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	30		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		TGGTGGGATGAAGTATCTCTA	0.323																																					p.E268G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A803G	5						.						68.0	72.0	71.0					5																	110814180		2202	4299	6501	110842079	SO:0001583	missense	814	exon9			D30742	CCDS4103.1	5q22.1	2012-09-20			ENSG00000152495	ENSG00000152495	2.7.11.17		1464	protein-coding gene	gene with protein product	"""brain Ca++-calmodulin-dependent protein kinase type IV"", ""calcium/calmodulin-dependent protein kinase type IV catalytic chain"", ""CAM kinase IV"", ""CAM kinase- GR"""	114080				2536634	Standard	NM_001744		Approved	CaMK-GR	uc003kpf.3	Q16566	OTTHUMG00000128792	ENST00000282356.4:c.803A>G	5.37:g.110814180A>G	ENSP00000282356:p.Glu268Gly	Somatic		Capture	Illumina HiSeq	Phase_I	110842079	NM_001744	D3DSZ7	Missense_Mutation	SNP	ENST00000282356.4	37	CCDS4103.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.594878	0.86953	.	.	ENSG00000152495	ENST00000512453;ENST00000282356	T;T	0.66815	-0.23;-0.23	5.8	5.8	0.92144	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.411993	0.28371	N	0.015588	T	0.47783	0.1464	N	0.04203	-0.255	0.54753	D	0.999987	P	0.38395	0.629	B	0.37731	0.257	T	0.55792	-0.8085	10	0.42905	T	0.14	.	16.135	0.81476	1.0:0.0:0.0:0.0	.	268	Q16566	KCC4_HUMAN	G	268	ENSP00000422634:E268G;ENSP00000282356:E268G	ENSP00000282356:E268G	E	+	2	0	CAMK4	110842079	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.828000	0.92047	2.207000	0.71202	0.482000	0.46254	GAA		0.323	CAMK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250719.2	NM_001744	
APC	324	broad.mit.edu	37	5	112154771	112154771	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:112154771C>T	ENST00000457016.1	+	10	1422	c.1042C>T	c.(1042-1044)Cga>Tga	p.R348*	APC_ENST00000508376.2_Nonsense_Mutation_p.R348*|APC_ENST00000257430.4_Nonsense_Mutation_p.R348*			P25054	APC_HUMAN	adenomatous polyposis coli	348	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R348*(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)		TATATCCATGCGACAGTCTGG	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.R330X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C988T	5	GRCh37	CM013690	APC	M		.						159.0	134.0	142.0					5																	112154771		2202	4300	6502	112182670	SO:0001587	stop_gained	324	exon8	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1042C>T	5.37:g.112154771C>T	ENSP00000413133:p.Arg348*	Somatic		Capture	Illumina HiSeq	Phase_I	112182670	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	39	7.517929	0.98332	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.1884	19.9616	0.97254	0.0:1.0:0.0:0.0	.	.	.	.	X	348;330;348;348;348	.	ENSP00000257430:R348X	R	+	1	2	APC	112182670	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.722000	0.93159	0.650000	0.86243	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	112164616	112164616	+	Nonsense_Mutation	SNP	C	C	T	rs137854574		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:112164616C>T	ENST00000457016.1	+	14	2070	c.1690C>T	c.(1690-1692)Cga>Tga	p.R564*	APC_ENST00000508376.2_Nonsense_Mutation_p.R564*|APC_ENST00000257430.4_Nonsense_Mutation_p.R564*|CTC-554D6.1_ENST00000520401.1_Silent_p.C59C			P25054	APC_HUMAN	adenomatous polyposis coli	564	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R564*(14)|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)		AAAGACGTTGCGAGAAGTTGG	0.313		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.R546X	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 	.	15	Substitution - Nonsense(14)|Unknown(1)	large_intestine(14)|skin(1)	c.C1636T	5	GRCh37	CM920035	APC	M	rs137854574	.						126.0	137.0	134.0					5																	112164616		2202	4300	6502	112192515	SO:0001587	stop_gained	324	exon12	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.1690C>T	5.37:g.112164616C>T	ENSP00000413133:p.Arg564*	Somatic		Capture	Illumina HiSeq	Phase_I	112192515	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	7.921767	0.98563	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.62	4.73	0.59995	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.3959	14.5777	0.68262	0.2726:0.7274:0.0:0.0	.	.	.	.	X	564;546;564;564;564	.	ENSP00000257430:R564X	R	+	1	2	APC	112192515	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	2.526000	0.45607	1.313000	0.45069	0.655000	0.94253	CGA		0.313	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	broad.mit.edu	37	5	112175487	112175487	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:112175487G>A	ENST00000457016.1	+	16	4576	c.4196G>A	c.(4195-4197)cGt>cAt	p.R1399H	APC_ENST00000508376.2_Missense_Mutation_p.R1399H|APC_ENST00000257430.4_Missense_Mutation_p.R1399H|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1399	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.R1399fs*16(2)|p.R1399H(1)|p.Y1376fs*41(1)|p.K1192fs*3(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)		TTTGAGAGTCGTTCGATTGCC	0.478		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.R1381H	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"""	.	.	6	Deletion - Frameshift(4)|Substitution - Missense(1)|Unknown(1)	large_intestine(4)|soft_tissue(1)|skin(1)	c.G4142A	5						.						111.0	103.0	106.0					5																	112175487		2202	4300	6502	112203386	SO:0001583	missense	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.4196G>A	5.37:g.112175487G>A	ENSP00000413133:p.Arg1399His	Somatic		Capture	Illumina HiSeq	Phase_I	112203386	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	7.171	0.587686	0.13812	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.88509	-2.39;-2.39;-2.39	6.17	6.17	0.99709	.	0.155915	0.64402	D	0.000011	T	0.77219	0.4098	N	0.08118	0	0.35199	D	0.774073	B;B	0.15719	0.014;0.014	B;B	0.08055	0.003;0.003	T	0.74937	-0.3494	9	.	.	.	-13.807	13.6699	0.62418	0.0706:0.0:0.9294:0.0	.	1401;1399	Q4LE70;P25054	.;APC_HUMAN	H	1399	ENSP00000413133:R1399H;ENSP00000257430:R1399H;ENSP00000427089:R1399H	.	R	+	2	0	APC	112203386	1.000000	0.71417	0.992000	0.48379	0.858000	0.48976	5.443000	0.66581	2.941000	0.99782	0.655000	0.94253	CGT		0.478	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-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:112175639C>T	ENST00000457016.1	+	16	4728	c.4348C>T	c.(4348-4350)Cga>Tga	p.R1450*	APC_ENST00000508376.2_Nonsense_Mutation_p.R1450*|APC_ENST00000257430.4_Nonsense_Mutation_p.R1450*|CTC-554D6.1_ENST00000520401.1_Intron			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	
DCP2	167227	broad.mit.edu	37	5	112336865	112336865	+	Missense_Mutation	SNP	C	C	T	rs369278042		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:112336865C>T	ENST00000389063.2	+	5	715	c.517C>T	c.(517-519)Cgt>Tgt	p.R173C	DCP2_ENST00000515408.1_Missense_Mutation_p.R173C|DCP2_ENST00000543319.1_5'UTR	NM_152624.5	NP_689837	Q8IU60	DCP2_HUMAN	decapping mRNA 2	173	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)|RISC complex (GO:0016442)	exoribonuclease activity, producing 5'-phosphomonoesters (GO:0016896)|m7G(5')pppN diphosphatase activity (GO:0050072)|manganese ion binding (GO:0030145)|RNA binding (GO:0003723)	p.R173C(1)		endometrium(3)|large_intestine(6)|lung(1)	10		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)		CCAGCTTGCTCGTTTGTACAT	0.338																																					p.R173C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C517T	5						.	C	CYS/ARG,CYS/ARG	0,4404		0,0,2202	84.0	87.0	86.0		517,517	4.8	1.0	5		86	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	DCP2	NM_001242377.1,NM_152624.5	180,180	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	173/386,173/421	112336865	1,13001	2202	4299	6501	112364764	SO:0001583	missense	167227	exon5			AY135173	CCDS34210.1, CCDS56377.1	5q22	2013-05-02	2013-05-02		ENSG00000172795	ENSG00000172795	3.6.1.62	"""Nudix motif containing"""	24452	protein-coding gene	gene with protein product	"""nudix (nucleoside diphosphate linked moiety X)-type motif 20"", ""M(7)GpppN-mRNA hydrolase"""	609844	"""DCP2 decapping enzyme homolog (S. cerevisiae)"""			12218187, 12417715	Standard	NM_152624		Approved	NUDT20	uc003kqh.3	Q8IU60	OTTHUMG00000162853	ENST00000389063.2:c.517C>T	5.37:g.112336865C>T	ENSP00000373715:p.Arg173Cys	Somatic		Capture	Illumina HiSeq	Phase_I	112364764	NM_152624	C9J778|Q6P2D4|Q7Z5W5|Q8NBG5	Missense_Mutation	SNP	ENST00000389063.2	37	CCDS34210.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.6|21.6	4.169953|4.169953	0.78452|0.78452	0.0|0.0	1.16E-4|1.16E-4	ENSG00000172795|ENSG00000172795	ENST00000515408;ENST00000389063|ENST00000513585	T;T|.	0.08102|.	3.13;3.13|.	5.63|5.63	4.77|4.77	0.60923|0.60923	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76118|0.76118	0.3943|0.3943	M|M	0.80508|0.80508	2.5|2.5	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.998;0.999|.	T|T	0.78181|0.78181	-0.2304|-0.2304	10|5	0.62326|.	D|.	0.03|.	2.9753|2.9753	14.9121|14.9121	0.70767|0.70767	0.0:0.9311:0.0:0.0689|0.0:0.9311:0.0:0.0689	.|.	173;173|.	Q8IU60-2;Q8IU60|.	.;DCP2_HUMAN|.	C|L	173|154	ENSP00000425770:R173C;ENSP00000373715:R173C|.	ENSP00000373715:R173C|.	R|S	+|+	1|2	0|0	DCP2|DCP2	112364764|112364764	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.904000|0.904000	0.53231|0.53231	7.393000|7.393000	0.79851|0.79851	1.523000|1.523000	0.49018|0.49018	-0.152000|-0.152000	0.13540|0.13540	CGT|TCG		0.338	DCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370765.3	NM_152624	
SEMA6A	57556	broad.mit.edu	37	5	115815886	115815886	+	Silent	SNP	C	C	T	rs369918649		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:115815886C>T	ENST00000343348.6	-	12	1969	c.1182G>A	c.(1180-1182)acG>acA	p.T394T	CTB-118N6.3_ENST00000510682.1_RNA|CTB-118N6.3_ENST00000508640.1_RNA|SEMA6A_ENST00000257414.8_Silent_p.T394T|SEMA6A_ENST00000282394.6_5'Flank|CTB-118N6.3_ENST00000514214.1_RNA|SEMA6A_ENST00000510263.1_Silent_p.T394T	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	394	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)	p.T394T(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		TGAGCGGGTGCGTCTTGATGA	0.498																																					p.T394T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1182A	5						.	C		0,3958		0,0,1979	135.0	132.0	133.0		1182	-4.6	1.0	5		133	1,8347		0,1,4173	no	coding-synonymous	SEMA6A	NM_020796.3		0,1,6152	TT,TC,CC		0.012,0.0,0.0081		394/1031	115815886	1,12305	1979	4174	6153	115843785	SO:0001819	synonymous_variant	57556	exon12			AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"""Semaphorins"""	10738	protein-coding gene	gene with protein product	"""sema VIa"""	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.1182G>A	5.37:g.115815886C>T		Somatic		Capture	Illumina HiSeq	Phase_I	115843785	NM_020796	Q9P2H9	Silent	SNP	ENST00000343348.6	37	CCDS47256.1																																																																																				0.498	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796	
DMXL1	1657	broad.mit.edu	37	5	118513159	118513159	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:118513159C>T	ENST00000311085.8	+	27	6946	c.6866C>T	c.(6865-6867)aCg>aTg	p.T2289M	DMXL1_ENST00000539542.1_Missense_Mutation_p.T2289M	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2289								p.T2289M(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		ACTCCCAATACGTCACCAGCT	0.353																																					p.T2289M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6866T	5						.						98.0	97.0	98.0					5																	118513159		2202	4300	6502	118541058	SO:0001583	missense	1657	exon27			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.6866C>T	5.37:g.118513159C>T	ENSP00000309690:p.Thr2289Met	Somatic		Capture	Illumina HiSeq	Phase_I	118541058	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	C	18.45	3.625990	0.66901	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.14893	2.47;2.47	5.96	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.40956	0.1138	M	0.83603	2.65	0.54753	D	0.999989	D;D	0.71674	0.994;0.998	P;P	0.60068	0.868;0.8	T	0.45160	-0.9280	10	0.87932	D	0	-10.315	13.0644	0.59025	0.0:0.8673:0.0:0.1327	.	2289;2289	F5H269;Q9Y485	.;DMXL1_HUMAN	M	2289	ENSP00000309690:T2289M;ENSP00000439479:T2289M	ENSP00000309690:T2289M	T	+	2	0	DMXL1	118541058	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.559000	0.67326	1.542000	0.49330	-0.136000	0.14681	ACG		0.353	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
HSD17B4	3295	broad.mit.edu	37	5	118867006	118867006	+	Missense_Mutation	SNP	C	C	T	rs201560431		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:118867006C>T	ENST00000256216.6	+	22	2033	c.1900C>T	c.(1900-1902)Cgc>Tgc	p.R634C	HSD17B4_ENST00000509514.1_Missense_Mutation_p.R372C|HSD17B4_ENST00000510025.1_Missense_Mutation_p.R610C|HSD17B4_ENST00000513628.1_Missense_Mutation_p.R497C|HSD17B4_ENST00000515320.1_Missense_Mutation_p.R616C|HSD17B4_ENST00000522415.1_3'UTR|HSD17B4_ENST00000504811.1_Missense_Mutation_p.R659C|HSD17B4_ENST00000414835.2_Missense_Mutation_p.R494C	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	634	SCP2.				alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.R634C(1)		breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		AATAGGACGCCGCCTAAAGGA	0.403																																					p.R634C	Colon(35;490 801 34689 41394 43344)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1900T	5						.	C	CYS/ARG,CYS/ARG,CYS/ARG	0,4404		0,0,2202	93.0	93.0	93.0		1900,1975,1846	4.6	1.0	5		93	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	HSD17B4	NM_000414.3,NM_001199291.1,NM_001199292.1	180,180,180	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	634/737,659/762,616/719	118867006	1,13003	2202	4300	6502	118894905	SO:0001583	missense	3295	exon22				CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5213	protein-coding gene	gene with protein product	"""17beta-estradiol dehydrogenase type IV"", ""peroxisomal multifunctional protein 2"", ""17-beta-HSD IV"", ""17-beta-hydroxysteroid dehydrogenase 4"", ""D-bifunctional protein, peroxisomal"", ""D-3-hydroxyacyl-CoA dehydratase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase"", ""beta-keto-reductase"", ""beta-hydroxyacyl dehydrogenase"", ""short chain dehydrogenase/reductase family 8C, member 1"""	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.1900C>T	5.37:g.118867006C>T	ENSP00000256216:p.Arg634Cys	Somatic		Capture	Illumina HiSeq	Phase_I	118894905	NM_000414	B4DNV1|B4DVS5|E9PB82|F5HE57	Missense_Mutation	SNP	ENST00000256216.6	37	CCDS4126.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.326196	0.81580	0.0	1.16E-4	ENSG00000133835	ENST00000256216;ENST00000515320;ENST00000510025;ENST00000504811;ENST00000414835;ENST00000513628;ENST00000509514	T;T;T;T;T;T;T	0.25912	1.77;1.77;1.77;1.77;1.77;1.77;1.77	5.49	4.61	0.57282	SCP2 sterol-binding domain (2);	0.000000	0.85682	D	0.000000	T	0.54695	0.1874	M	0.84585	2.705	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	0.78314	0.991;0.971;0.98;0.92;0.978	T	0.62077	-0.6930	10	0.59425	D	0.04	-2.6463	14.3885	0.66963	0.1492:0.8508:0.0:0.0	.	659;616;610;372;634	F5HE57;E9PB82;E7EWE5;E7EPL9;P51659	.;.;.;.;DHB4_HUMAN	C	634;616;610;659;494;497;372	ENSP00000256216:R634C;ENSP00000424613:R616C;ENSP00000424940:R610C;ENSP00000420914:R659C;ENSP00000411960:R494C;ENSP00000425993:R497C;ENSP00000426272:R372C	ENSP00000256216:R634C	R	+	1	0	HSD17B4	118894905	1.000000	0.71417	0.997000	0.53966	0.873000	0.50193	5.059000	0.64306	1.274000	0.44362	0.650000	0.86243	CGC		0.403	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414	
FBN2	2201	broad.mit.edu	37	5	127637114	127637114	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:127637114G>A	ENST00000508053.1	-	53	6980	c.6006C>T	c.(6004-6006)aaC>aaT	p.N2002N	FBN2_ENST00000262464.4_Silent_p.N2002N			P35556	FBN2_HUMAN	fibrillin 2	2002	EGF-like 33; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.N2002N(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CATAACCTTCGTTACATAGAC	0.343																																					p.N2002N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C6006T	5						.						132.0	128.0	129.0					5																	127637114		2203	4300	6503	127665013	SO:0001819	synonymous_variant	2201	exon47			U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.6006C>T	5.37:g.127637114G>A		Somatic		Capture	Illumina HiSeq	Phase_I	127665013	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																				0.343	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
FBN2	2201	broad.mit.edu	37	5	127680079	127680079	+	Missense_Mutation	SNP	G	G	A	rs202219940		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:127680079G>A	ENST00000508053.1	-	31	4315	c.3341C>T	c.(3340-3342)aCg>aTg	p.T1114M	FBN2_ENST00000262464.4_Missense_Mutation_p.T1114M|FBN2_ENST00000508989.1_Missense_Mutation_p.T1081M			P35556	FBN2_HUMAN	fibrillin 2	1114	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.T1114M(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		CATCTTACCCGTGCAGTTTCT	0.428																																					p.T1114M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3341T	5						.						132.0	129.0	130.0					5																	127680079		2203	4300	6503	127707978	SO:0001583	missense	2201	exon25			U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.3341C>T	5.37:g.127680079G>A	ENSP00000424571:p.Thr1114Met	Somatic		Capture	Illumina HiSeq	Phase_I	127707978	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.963967	0.74131	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.87650	-2.28;-2.28;-2.28	4.32	4.32	0.51571	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.076589	0.49916	D	0.000139	D	0.91673	0.7368	L	0.55743	1.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.993;0.994	D	0.91479	0.5203	10	0.49607	T	0.09	.	18.1271	0.89589	0.0:0.0:1.0:0.0	.	1081;1114	D6RJI3;P35556	.;FBN2_HUMAN	M	1114;1114;1081	ENSP00000262464:T1114M;ENSP00000424571:T1114M;ENSP00000425596:T1081M	ENSP00000262464:T1114M	T	-	2	0	FBN2	127707978	1.000000	0.71417	0.999000	0.59377	0.565000	0.35776	9.484000	0.97940	2.695000	0.91970	0.555000	0.69702	ACG		0.428	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
IL13	3596	broad.mit.edu	37	5	131993886	131993886	+	Missense_Mutation	SNP	C	C	T	rs200168712		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:131993886C>T	ENST00000304506.3	+	1	22	c.8C>T	c.(7-9)cCg>cTg	p.P3L	AC004041.2_ENST00000458509.1_RNA|IL13_ENST00000468334.1_Intron|AC004041.2_ENST00000435042.1_RNA|AC004041.2_ENST00000417516.1_RNA	NM_002188.2	NP_002179.2	P35225	IL13_HUMAN	interleukin 13	3					cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|cellular response to cytokine stimulus (GO:0071345)|cellular response to mechanical stimulus (GO:0071260)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of lung ciliated cell differentiation (GO:1901247)|negative regulation of transforming growth factor beta production (GO:0071635)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of connective tissue growth factor production (GO:0032723)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of lung goblet cell differentiation (GO:1901251)|positive regulation of macrophage activation (GO:0043032)|positive regulation of pancreatic stellate cell proliferation (GO:2000231)|positive regulation of protein secretion (GO:0050714)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat6 protein (GO:0042526)|regulation of proton transport (GO:0010155)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)	p.P3L(1)		large_intestine(1)|lung(1)|ovary(1)|skin(3)	6		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CCTATGCATCCGCTCCTCAAT	0.582											OREG0003464	type=REGULATORY REGION|Gene=IL13|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.P3L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C8T	5						.	C	LEU/PRO	0,4406		0,0,2203	114.0	88.0	97.0		8	-5.3	0.0	5		97	1,8599	1.2+/-3.3	0,1,4299	no	missense	IL13	NM_002188.2	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	3/147	131993886	1,13005	2203	4300	6503	132021785	SO:0001583	missense	3596	exon1			U31120	CCDS4157.1	5q31	2011-07-14			ENSG00000169194	ENSG00000169194		"""Interleukins and interleukin receptors"""	5973	protein-coding gene	gene with protein product	"""allergic rhinitis"", ""Bronchial hyperresponsiveness-1 (bronchial asthma)"""	147683					Standard	NM_002188		Approved	P600, IL-13, ALRH, BHR1, MGC116786, MGC116788, MGC116789	uc003kxj.1	P35225	OTTHUMG00000059723	ENST00000304506.3:c.8C>T	5.37:g.131993886C>T	ENSP00000304915:p.Pro3Leu	Somatic	1592	Capture	Illumina HiSeq	Phase_I	132021785	NM_002188	O43644|Q4VB52|Q9UDC7	Missense_Mutation	SNP	ENST00000304506.3	37	CCDS4157.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.366156	0.41902	0.0	1.16E-4	ENSG00000169194	ENST00000304506	T	0.50001	0.76	5.13	-5.27	0.02763	.	0.841724	0.09718	N	0.764824	T	0.15955	0.0384	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15037	-1.0451	10	0.87932	D	0	0.1261	2.9356	0.05814	0.1386:0.4223:0.1425:0.2966	.	3	P35225	IL13_HUMAN	L	3	ENSP00000304915:P3L	ENSP00000304915:P3L	P	+	2	0	IL13	132021785	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	-0.323000	0.07997	-0.697000	0.05092	-0.290000	0.09829	CCG		0.582	IL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132782.1	NM_002188	
TCF7	6932	broad.mit.edu	37	5	133474706	133474706	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:133474706G>A	ENST00000321584.4	+	5	808	c.612G>A	c.(610-612)ggG>ggA	p.G204G	TCF7_ENST00000520958.1_Silent_p.G89G|TCF7_ENST00000517478.1_3'UTR|TCF7_ENST00000432532.2_Silent_p.G89G|TCF7_ENST00000378560.4_Silent_p.G89G|TCF7_ENST00000321603.6_Silent_p.G204G|TCF7_ENST00000518915.1_Silent_p.G89G|TCF7_ENST00000342854.5_Silent_p.G204G|TCF7_ENST00000395029.1_Silent_p.G204G|TCF7_ENST00000395023.1_Silent_p.G89G|TCF7_ENST00000378564.1_Silent_p.G204G			P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific, HMG-box)	204					alpha-beta T cell differentiation (GO:0046632)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cellular response to interleukin-4 (GO:0071353)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|generation of neurons (GO:0048699)|immune response (GO:0006955)|neural tube development (GO:0021915)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor V(D)J recombination (GO:0033153)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.G204G(2)		kidney(2)|large_intestine(7)|lung(2)|skin(1)	12		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GCAGCATGGGGCAGCTCCCCC	0.607																																					p.G204G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G612A	5						.						72.0	57.0	62.0					5																	133474706		2203	4300	6503	133502605	SO:0001819	synonymous_variant	6932	exon5			Z47362	CCDS4169.1, CCDS4170.1, CCDS43362.1, CCDS47263.1, CCDS47263.2	5q31	2008-02-05			ENSG00000081059	ENSG00000081059			11639	protein-coding gene	gene with protein product		189908					Standard	NM_003202		Approved	TCF-1	uc003kyt.3	P36402	OTTHUMG00000129124	ENST00000321584.4:c.612G>A	5.37:g.133474706G>A		Somatic		Capture	Illumina HiSeq	Phase_I	133502605	NM_003202	B3KSH3|Q86WR9|Q9UKI4	Silent	SNP	ENST00000321584.4	37																																																																																					0.607	TCF7-201	KNOWN	basic	protein_coding	protein_coding		NM_201634	
DNAH5	1767	broad.mit.edu	37	5	13721176	13721176	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:13721176C>T	ENST00000265104.4	-	71	12316	c.12212G>A	c.(12211-12213)cGt>cAt	p.R4071H		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4071	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R4071H(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GGACACATAACGGGTTTCTAT	0.512									Kartagener syndrome																												p.R4071H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G12212A	5						.						97.0	100.0	99.0					5																	13721176		2203	4300	6503	13774176	SO:0001583	missense	1767	exon71	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12212G>A	5.37:g.13721176C>T	ENSP00000265104:p.Arg4071His	Somatic		Capture	Illumina HiSeq	Phase_I	13774176	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	12.27	1.888028	0.33348	.	.	ENSG00000039139	ENST00000265104	T	0.07800	3.16	5.18	3.4	0.38934	Dynein heavy chain (1);	0.169666	0.53938	N	0.000056	T	0.06826	0.0174	L	0.35723	1.085	0.46356	D	0.999006	B	0.11235	0.004	B	0.18263	0.021	T	0.21965	-1.0230	10	0.10902	T	0.67	.	10.9226	0.47174	0.0:0.7886:0.0:0.2114	.	4071	Q8TE73	DYH5_HUMAN	H	4071	ENSP00000265104:R4071H	ENSP00000265104:R4071H	R	-	2	0	DNAH5	13774176	0.510000	0.26171	0.768000	0.31515	0.684000	0.39900	1.254000	0.32897	0.688000	0.31529	-0.259000	0.10710	CGT		0.512	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
KLHL3	26249	broad.mit.edu	37	5	137013264	137013264	+	Silent	SNP	G	G	A	rs151050480	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:137013264G>A	ENST00000309755.4	-	6	1049	c.606C>T	c.(604-606)agC>agT	p.S202S	KLHL3_ENST00000506491.1_Silent_p.S120S|KLHL3_ENST00000508657.1_Silent_p.S170S|KLHL3_ENST00000541417.1_Silent_p.S82S|KLHL3_ENST00000394937.3_Silent_p.S202S	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	202	BACK.				distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)	p.S202R(1)|p.S202S(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		TCAGCTTGTCGCTGGATATCA	0.478													g|||	3	0.000599042	0.0	0.0	5008	,	,		18501	0.002		0.001	False		,,,				2504	0.0				p.S202S												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|endometrium(1)	c.C606T	5						.	A		1,4405	2.1+/-5.4	0,1,2202	122.0	117.0	118.0		606	-2.2	1.0	5	dbSNP_134	118	0,8600		0,0,4300	no	coding-synonymous	KLHL3	NM_017415.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		202/588	137013264	1,13005	2203	4300	6503	137041163	SO:0001819	synonymous_variant	26249	exon6			AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021		"""Kelch-like"", ""BTB/POZ domain containing"""	6354	protein-coding gene	gene with protein product		605775	"""kelch (Drosophila)-like 3"", ""kelch-like 3 (Drosophila)"""			10843806	Standard	NM_017415		Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.606C>T	5.37:g.137013264G>A		Somatic		Capture	Illumina HiSeq	Phase_I	137041163	NM_017415	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Silent	SNP	ENST00000309755.4	37	CCDS4192.1																																																																																				0.478	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2		
ETF1	2107	broad.mit.edu	37	5	137847195	137847195	+	Silent	SNP	G	G	A	rs370063938		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:137847195G>A	ENST00000360541.5	-	7	1052	c.831C>T	c.(829-831)aaC>aaT	p.N277N	ETF1_ENST00000499810.2_Silent_p.N244N|ETF1_ENST00000503014.1_Silent_p.N263N	NM_004730.3	NP_004721.1	P62495	ERF1_HUMAN	eukaryotic translation termination factor 1	277					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational termination (GO:0006415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|translation release factor activity (GO:0003747)|translation release factor activity, codon specific (GO:0016149)|translation termination factor activity (GO:0008079)	p.N277N(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TGAATTTCACGTTGGAGAGGA	0.348													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15608	0.0		0.0	False		,,,				2504	0.0				p.N277N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C831T	5						.	G		0,4404		0,0,2202	80.0	78.0	79.0		831	5.8	1.0	5		79	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ETF1	NM_004730.2		0,1,6501	AA,AG,GG		0.0116,0.0,0.0077		277/438	137847195	1,13003	2202	4300	6502	137875094	SO:0001819	synonymous_variant	2107	exon7			AF095901	CCDS4207.1, CCDS75313.1, CCDS75314.1	5q31.2	2008-02-05			ENSG00000120705	ENSG00000120705			3477	protein-coding gene	gene with protein product	"""sup45 (yeast omnipotent suppressor 45) homolog-like 1"", ""polypeptide chain release factor 1"""	600285		SUP45L1, ERF1, ERF		1546371, 7990965	Standard	NM_004730		Approved	eRF1, TB3-1, RF1	uc003ldc.5	P62495	OTTHUMG00000129199	ENST00000360541.5:c.831C>T	5.37:g.137847195G>A		Somatic		Capture	Illumina HiSeq	Phase_I	137875094	NM_004730	B2R6B4|D3DQC1|P46055|Q5M7Z7|Q96CG1	Silent	SNP	ENST00000360541.5	37	CCDS4207.1																																																																																				0.348	ETF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251276.2	NM_004730	
DNAH5	1767	broad.mit.edu	37	5	13770875	13770875	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:13770875C>T	ENST00000265104.4	-	56	9692	c.9588G>A	c.(9586-9588)gtG>gtA	p.V3196V	DNAH5_ENST00000504001.3_5'UTR	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3196	Stalk. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.V3196V(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CCAGGGTCCGCACCTCCACAT	0.458									Kartagener syndrome																												p.V3196V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G9588A	5						.						88.0	81.0	84.0					5																	13770875		2203	4300	6503	13823875	SO:0001819	synonymous_variant	1767	exon56	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.9588G>A	5.37:g.13770875C>T		Somatic		Capture	Illumina HiSeq	Phase_I	13823875	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																				0.458	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
HSPA9	3313	broad.mit.edu	37	5	137897277	137897277	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:137897277T>C	ENST00000297185.3	-	10	1299	c.1174A>G	c.(1174-1176)Atg>Gtg	p.M392V	SNORD63_ENST00000384262.1_RNA|SNORD63_ENST00000411005.1_RNA|HSPA9_ENST00000501917.2_Intron	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	392					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.M392V(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)			ACCTTGGGCATCCTAGTCATG	0.488																																					p.M392V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1174G	5						.						106.0	87.0	94.0					5																	137897277		2203	4300	6503	137925176	SO:0001583	missense	3313	exon10			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.1174A>G	5.37:g.137897277T>C	ENSP00000297185:p.Met392Val	Somatic		Capture	Illumina HiSeq	Phase_I	137925176	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Missense_Mutation	SNP	ENST00000297185.3	37	CCDS4208.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.470781	0.63625	.	.	ENSG00000113013	ENST00000297185;ENST00000541333;ENST00000540484	T	0.00902	5.56	5.37	5.37	0.77165	Heat shock protein 70, conserved site (1);	0.074096	0.85682	D	0.000000	T	0.02807	0.0084	M	0.78344	2.41	0.80722	D	1	B;B	0.19445	0.005;0.036	B;B	0.34346	0.04;0.18	T	0.41734	-0.9492	10	0.52906	T	0.07	-18.8262	15.3358	0.74250	0.0:0.0:0.0:1.0	.	323;392	B7Z1V7;P38646	.;GRP75_HUMAN	V	392;345;378	ENSP00000297185:M392V	ENSP00000297185:M392V	M	-	1	0	HSPA9	137925176	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.930000	0.87610	2.164000	0.68074	0.533000	0.62120	ATG		0.488	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134	
CTNNA1	1495	broad.mit.edu	37	5	138260978	138260978	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:138260978C>T	ENST00000302763.7	+	13	1871	c.1781C>T	c.(1780-1782)gCc>gTc	p.A594V	CTNNA1_ENST00000540387.1_Missense_Mutation_p.A224V|CTNNA1_ENST00000518825.1_Missense_Mutation_p.A594V|CTNNA1_ENST00000355078.5_Missense_Mutation_p.A491V	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	594					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.A594V(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)			GTAGAAGCAGCCGTGGAAGCC	0.552																																					p.A594V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1781T	5						.						81.0	73.0	76.0					5																	138260978		2203	4300	6503	138288877	SO:0001583	missense	1495	exon13			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.1781C>T	5.37:g.138260978C>T	ENSP00000304669:p.Ala594Val	Somatic		Capture	Illumina HiSeq	Phase_I	138288877	NM_001903	Q12795|Q8N1C0	Missense_Mutation	SNP	ENST00000302763.7	37	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.330188	0.60743	.	.	ENSG00000044115	ENST00000355078;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518825;ENST00000540387	T;T;T;T	0.52754	0.65;0.65;0.65;0.65	5.76	5.76	0.90799	.	0.051642	0.85682	D	0.000000	T	0.44180	0.1281	L	0.47716	1.5	0.80722	D	1	B;B;B	0.28208	0.203;0.023;0.027	B;B;B	0.21917	0.037;0.026;0.026	T	0.26430	-1.0103	10	0.44086	T	0.13	-15.3312	18.0966	0.89492	0.0:1.0:0.0:0.0	.	594;471;594	G3XAM7;B4DKT9;P35221	.;.;CTNA1_HUMAN	V	491;594;594;579;594;224	ENSP00000347190:A491V;ENSP00000304669:A594V;ENSP00000427821:A594V;ENSP00000438476:A224V	ENSP00000304669:A594V	A	+	2	0	CTNNA1	138288877	1.000000	0.71417	0.244000	0.24202	0.704000	0.40688	7.776000	0.85560	2.882000	0.98803	0.655000	0.94253	GCC		0.552	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903	
DNAH5	1767	broad.mit.edu	37	5	13868029	13868029	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:13868029G>A	ENST00000265104.4	-	25	4011	c.3907C>T	c.(3907-3909)Cac>Tac	p.H1303Y	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1303	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.H1303Y(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CAAGCATAGTGCAGTGTATCA	0.408									Kartagener syndrome																												p.H1303Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3907T	5						.						121.0	104.0	109.0					5																	13868029		2203	4300	6503	13921029	SO:0001583	missense	1767	exon25	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.3907C>T	5.37:g.13868029G>A	ENSP00000265104:p.His1303Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	13921029	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	G	15.65	2.897298	0.52121	.	.	ENSG00000039139	ENST00000265104	T	0.22336	1.96	5.12	5.12	0.69794	.	0.299246	0.37261	N	0.002176	T	0.16811	0.0404	N	0.22421	0.69	0.32055	N	0.596504	B	0.12013	0.005	B	0.12156	0.007	T	0.08659	-1.0711	10	0.72032	D	0.01	.	14.9863	0.71351	0.0:0.0:0.857:0.143	.	1303	Q8TE73	DYH5_HUMAN	Y	1303	ENSP00000265104:H1303Y	ENSP00000265104:H1303Y	H	-	1	0	DNAH5	13921029	1.000000	0.71417	0.756000	0.31282	0.833000	0.47200	7.531000	0.81973	2.397000	0.81536	0.655000	0.94253	CAC		0.408	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
CTNNA1	1495	broad.mit.edu	37	5	138268313	138268313	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:138268313G>A	ENST00000302763.7	+	17	2435	c.2345G>A	c.(2344-2346)cGc>cAc	p.R782H	CTNNA1_ENST00000540387.1_Missense_Mutation_p.R412H|CTNNA1_ENST00000518825.1_Missense_Mutation_p.R782H|CTNNA1_ENST00000355078.5_Missense_Mutation_p.R679H	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	782					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.R782H(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)			TACCTGCAACGCATCGCCCTC	0.602																																					p.R782H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2345A	5						.						61.0	53.0	56.0					5																	138268313		2203	4300	6503	138296212	SO:0001583	missense	1495	exon17			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.2345G>A	5.37:g.138268313G>A	ENSP00000304669:p.Arg782His	Somatic		Capture	Illumina HiSeq	Phase_I	138296212	NM_001903	Q12795|Q8N1C0	Missense_Mutation	SNP	ENST00000302763.7	37	CCDS34243.1	.	.	.	.	.	.	.	.	.	.	G	32	5.131198	0.94473	.	.	ENSG00000044115	ENST00000355078;ENST00000302763;ENST00000537034;ENST00000541863;ENST00000518825;ENST00000540387	T;T;T;T	0.55052	0.54;0.54;0.54;0.54	5.52	4.63	0.57726	.	0.056647	0.64402	D	0.000002	T	0.71134	0.3304	M	0.70275	2.135	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.967;0.973;0.99	T	0.75690	-0.3230	10	0.87932	D	0	-4.2742	15.276	0.73742	0.0:0.0:0.8586:0.1413	.	782;659;782	G3XAM7;B4DKT9;P35221	.;.;CTNA1_HUMAN	H	679;782;782;767;782;412	ENSP00000347190:R679H;ENSP00000304669:R782H;ENSP00000427821:R782H;ENSP00000438476:R412H	ENSP00000304669:R782H	R	+	2	0	CTNNA1	138296212	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.635000	0.98437	1.524000	0.49035	0.563000	0.77884	CGC		0.602	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903	
APBB3	10307	broad.mit.edu	37	5	139940621	139940621	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:139940621G>A	ENST00000357560.4	-	10	1341	c.898C>T	c.(898-900)Cca>Tca	p.P300S	APBB3_ENST00000511201.2_Missense_Mutation_p.P298S|APBB3_ENST00000412920.3_Missense_Mutation_p.P298S|APBB3_ENST00000508496.2_Missense_Mutation_p.P77S|APBB3_ENST00000356738.2_Missense_Mutation_p.P305S|APBB3_ENST00000358580.5_Missense_Mutation_p.P300S|APBB3_ENST00000507279.1_5'Flank|SRA1_ENST00000336283.6_5'Flank|APBB3_ENST00000354402.5_Missense_Mutation_p.P307S	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	300	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.P307S(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGGTGACTGGCAGTGTCCCC	0.552																																					p.P298S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C892T	5						.						294.0	285.0	289.0					5																	139940621		2203	4300	6503	139920805	SO:0001583	missense	10307	exon9			AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.898C>T	5.37:g.139940621G>A	ENSP00000350171:p.Pro300Ser	Somatic		Capture	Illumina HiSeq	Phase_I	139920805	NM_133174	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Missense_Mutation	SNP	ENST00000357560.4	37	CCDS4229.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.868461	0.72065	.	.	ENSG00000113108	ENST00000358580;ENST00000356738;ENST00000354402;ENST00000357560;ENST00000508496;ENST00000412920;ENST00000511201	T;T;T;T;T;T;T	0.47528	0.84;2.13;2.13;2.13;2.13;2.13;0.84	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.64571	0.2610	L	0.46157	1.445	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	T	0.58434	-0.7637	9	.	.	.	-6.8181	20.0932	0.97828	0.0:0.0:1.0:0.0	.	298;298;305	D6RBA1;O95704-2;O95704-3	.;.;.	S	300;305;307;300;77;298;298	ENSP00000351389:P300S;ENSP00000349177:P305S;ENSP00000346378:P307S;ENSP00000350171:P300S;ENSP00000444013:P77S;ENSP00000402591:P298S;ENSP00000424317:P298S	.	P	-	1	0	APBB3	139920805	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	8.687000	0.91255	2.747000	0.94245	0.655000	0.94253	CCA		0.552	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
PCDHA1	56147	broad.mit.edu	37	5	140167430	140167430	+	Missense_Mutation	SNP	G	G	A	rs140204027		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140167430G>A	ENST00000504120.2	+	1	1555	c.1555G>A	c.(1555-1557)Gca>Aca	p.A519T	PCDHA1_ENST00000378133.3_Missense_Mutation_p.A519T|PCDHA1_ENST00000394633.3_Missense_Mutation_p.A519T	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	519	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A519T(4)		breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAAGGTGTACGCACTGCAGCC	0.682																																					p.A519T												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.G1555A	5						.						75.0	77.0	77.0					5																	140167430		2203	4299	6502	140147614	SO:0001583	missense	56147	exon1			AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1555G>A	5.37:g.140167430G>A	ENSP00000420840:p.Ala519Thr	Somatic		Capture	Illumina HiSeq	Phase_I	140147614	NM_031410	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	37	CCDS54913.1	.	.	.	.	.	.	.	.	.	.	g	23.9	4.473564	0.84640	.	.	ENSG00000204970	ENST00000504120;ENST00000394633;ENST00000378133	T;T;T	0.42513	0.97;0.97;0.97	3.63	2.75	0.32379	Cadherin (5);Cadherin-like (1);	0.000000	0.41097	U	0.000943	T	0.48447	0.1500	L	0.31476	0.935	0.39827	D	0.972913	D;D;D	0.89917	0.998;1.0;0.998	P;D;P	0.68943	0.737;0.961;0.766	T	0.51710	-0.8671	10	0.87932	D	0	.	11.3922	0.49822	0.0916:0.0:0.9084:0.0	.	519;519;519	Q9Y5I3;Q9Y5I3-2;Q9Y5I3-3	PCDA1_HUMAN;.;.	T	519	ENSP00000420840:A519T;ENSP00000378129:A519T;ENSP00000367373:A519T	ENSP00000367373:A519T	A	+	1	0	PCDHA1	140147614	0.989000	0.36119	1.000000	0.80357	0.949000	0.60115	3.064000	0.49986	0.661000	0.30985	-0.273000	0.10243	GCA		0.682	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
PCDHA3	56145	broad.mit.edu	37	5	140182221	140182221	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140182221G>A	ENST00000522353.2	+	1	1439	c.1439G>A	c.(1438-1440)cGg>cAg	p.R480Q	PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.R480Q|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	480	Cadherin 5. {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.R480Q(2)		NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGTCTGCGCGGGACGCGGAC	0.662																																					p.R480Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1439A	5						.						85.0	90.0	88.0					5																	140182221		2203	4298	6501	140162405	SO:0001583	missense	56145	exon1			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.1439G>A	5.37:g.140182221G>A	ENSP00000429808:p.Arg480Gln	Somatic		Capture	Illumina HiSeq	Phase_I	140162405	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	g	9.134	1.012152	0.19277	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.51071	0.72;0.72	4.75	-2.39	0.06602	Cadherin (4);Cadherin-like (1);	1.511470	0.04959	U	0.461689	T	0.27765	0.0683	N	0.25094	0.71	0.09310	N	1	B;B	0.28178	0.202;0.094	B;B	0.20384	0.029;0.015	T	0.10776	-1.0615	10	0.28530	T	0.3	.	3.6913	0.08347	0.3063:0.1658:0.4432:0.0846	.	480;480	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	Q	480	ENSP00000429808:R480Q;ENSP00000434086:R480Q	ENSP00000429808:R480Q	R	+	2	0	PCDHA3	140162405	0.000000	0.05858	0.009000	0.14445	0.937000	0.57800	-5.520000	0.00116	-0.336000	0.08438	-0.464000	0.05259	CGG		0.662	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
PCDHA4	56144	broad.mit.edu	37	5	140187268	140187268	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140187268G>A	ENST00000530339.1	+	1	496	c.496G>A	c.(496-498)Gcc>Acc	p.A166T	PCDHA4_ENST00000512229.2_Missense_Mutation_p.A166T|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.A166T|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	166	Cadherin 2. {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.A166T(2)		breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGGGAGAACGCCCTGCTCAC	0.507																																					p.A166T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G496A	5						.						57.0	62.0	61.0					5																	140187268		2203	4300	6503	140167452	SO:0001583	missense	56144	exon1			AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.496G>A	5.37:g.140187268G>A	ENSP00000435300:p.Ala166Thr	Somatic		Capture	Illumina HiSeq	Phase_I	140167452	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	g	10.78	1.445794	0.25987	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.40225	1.04;1.04;1.04	4.62	2.78	0.32641	Cadherin (4);Cadherin-like (1);	0.190034	0.24899	U	0.034702	T	0.52996	0.1769	M	0.65320	2	0.09310	N	1	D;D;D	0.67145	0.996;0.991;0.995	P;P;P	0.62298	0.863;0.9;0.9	T	0.41698	-0.9494	10	0.62326	D	0.03	.	7.3815	0.26858	0.0784:0.0:0.4803:0.4413	.	166;166;166	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	T	166	ENSP00000423470:A166T;ENSP00000349344:A166T;ENSP00000435300:A166T	ENSP00000349344:A166T	A	+	1	0	PCDHA4	140167452	0.000000	0.05858	0.008000	0.14137	0.081000	0.17604	-0.239000	0.08965	0.459000	0.27016	-0.244000	0.11960	GCC		0.507	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
PCDHA6	56142	broad.mit.edu	37	5	140207861	140207861	+	Missense_Mutation	SNP	G	G	A	rs373467207		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140207861G>A	ENST00000529310.1	+	1	299	c.185G>A	c.(184-186)cGc>cAc	p.R62H	PCDHA6_ENST00000527624.1_Missense_Mutation_p.R62H|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	62	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R62H(2)		NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGTGCCGCGCCTGTTCAGG	0.622																																					p.R62H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G185A	5						.	G	,,,,,HIS/ARG,,HIS/ARG,HIS/ARG	0,4406		0,0,2203	71.0	84.0	80.0		,,,,,185,,185,185	3.9	1.0	5		80	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,intron,intron,intron,missense,intron,missense,missense	PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_031411.1,NM_031848.1,NM_031849.1	,,,,,29,,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,,,,	,,,,,62/951,,62/804,62/687	140207861	1,13005	2203	4300	6503	140188045	SO:0001583	missense	56142	exon1			AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"""Cadherins / Protocadherins : Clustered"""	8672	other	complex locus constituent	"""KIAA0345-like 8"""	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.185G>A	5.37:g.140207861G>A	ENSP00000433378:p.Arg62His	Somatic		Capture	Illumina HiSeq	Phase_I	140188045	NM_018909	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	37	CCDS47281.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255016	0.59321	0.0	1.16E-4	ENSG00000081842	ENST00000529310;ENST00000527624	T;T	0.41400	1.0;1.0	3.87	3.87	0.44632	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.34411	U	0.003997	T	0.70422	0.3222	M	0.91972	3.26	0.38021	D	0.934833	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.70935	0.95;0.971;0.971	T	0.81600	-0.0859	10	0.62326	D	0.03	.	16.3488	0.83191	0.0:0.0:1.0:0.0	.	62;62;62	Q9UN73-3;Q9UN73;Q9UN73-2	.;PCDA6_HUMAN;.	H	62	ENSP00000433378:R62H;ENSP00000434113:R62H	ENSP00000434113:R62H	R	+	2	0	PCDHA6	140188045	0.989000	0.36119	1.000000	0.80357	0.291000	0.27294	6.298000	0.72763	2.139000	0.66308	0.313000	0.20887	CGC		0.622	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909	
PCDHA8	56140	broad.mit.edu	37	5	140223103	140223103	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140223103C>T	ENST00000531613.1	+	1	2197	c.2197C>T	c.(2197-2199)Cgg>Tgg	p.R733W	PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.R733W|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	733					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.R733W(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)			GGGCGGGTGCCGGGCGGGCAA	0.662																																					p.R733W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2197T	5						.						48.0	48.0	48.0					5																	140223103		2196	4267	6463	140203287	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.2197C>T	5.37:g.140223103C>T	ENSP00000434655:p.Arg733Trp	Somatic		Capture	Illumina HiSeq	Phase_I	140203287	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	.	.	.	.	.	.	.	.	.	.	C	6.783	0.513338	0.12944	.	.	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.11821	2.74;2.74	3.06	1.2	0.21068	.	0.432471	0.16445	U	0.214106	T	0.05868	0.0153	N	0.24115	0.695	0.20821	N	0.999848	P;P	0.47677	0.587;0.899	B;B	0.31016	0.058;0.123	T	0.35992	-0.9766	10	0.37606	T	0.19	.	6.2338	0.20752	0.111:0.1981:0.6909:0.0	.	733;733	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	W	733	ENSP00000434655:R733W;ENSP00000367363:R733W	ENSP00000367363:R733W	R	+	1	2	PCDHA8	140203287	0.000000	0.05858	0.070000	0.20053	0.001000	0.01503	-0.166000	0.09954	0.145000	0.18977	-1.542000	0.00909	CGG		0.662	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
PCDHA9	9752	broad.mit.edu	37	5	140229141	140229141	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140229141C>T	ENST00000532602.1	+	1	2094	c.1061C>T	c.(1060-1062)aCg>aTg	p.T354M	PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.T354M|PCDHA1_ENST00000394633.3_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	354	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.T354M(2)		breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTATCAAAACGCTCTCGGTT	0.502																																					p.T354M	Melanoma(55;1800 1972 14909)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1061T	5						.						140.0	127.0	131.0					5																	140229141		2196	4274	6470	140209325	SO:0001583	missense	9752	exon1			AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"""Cadherins / Protocadherins : Clustered"""	8675	other	complex locus constituent	"""KIAA0345-like 5"""	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1061C>T	5.37:g.140229141C>T	ENSP00000436042:p.Thr354Met	Somatic		Capture	Illumina HiSeq	Phase_I	140209325	NM_014005	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.074174	0.55646	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.61510	0.1;0.1	3.79	2.88	0.33553	Cadherin (2);Cadherin-like (1);	0.736438	0.10350	U	0.685174	T	0.52386	0.1731	N	0.12502	0.225	0.09310	N	1	P;D	0.67145	0.895;0.996	B;P	0.54100	0.336;0.742	T	0.50440	-0.8828	10	0.87932	D	0	.	12.6278	0.56640	0.1671:0.8328:0.0:0.0	.	354;354	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	M	354	ENSP00000436042:T354M;ENSP00000367362:T354M	ENSP00000367362:T354M	T	+	2	0	PCDHA9	140209325	0.088000	0.21588	0.001000	0.08648	0.102000	0.19082	3.707000	0.54838	0.864000	0.35578	0.313000	0.20887	ACG		0.502	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857	
PCDHA11	56138	broad.mit.edu	37	5	140249777	140249777	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140249777G>T	ENST00000398640.2	+	1	1089	c.1089G>T	c.(1087-1089)caG>caT	p.Q363H	PCDHA6_ENST00000527624.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	363	Cadherin 4. {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.Q363H(1)		breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGACGCTCAGCCCAGCACGG	0.582																																					p.Q363H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1089T	5						.						83.0	81.0	82.0					5																	140249777		2203	4300	6503	140229961	SO:0001583	missense	56138	exon1			AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"""Cadherins / Protocadherins : Clustered"""	8665	other	complex locus constituent	"""KIAA0345-like 3"", ""ortholog of mouse CNR7"""	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.1089G>T	5.37:g.140249777G>T	ENSP00000381636:p.Gln363His	Somatic		Capture	Illumina HiSeq	Phase_I	140229961	NM_031861	B2RN58|O75279	Missense_Mutation	SNP	ENST00000398640.2	37	CCDS47284.1	.	.	.	.	.	.	.	.	.	.	G	0.074	-1.196492	0.01594	.	.	ENSG00000249158	ENST00000398640	T	0.52983	0.64	5.69	-4.22	0.03800	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.32315	0.0825	L	0.39898	1.24	0.09310	N	1	B;B	0.16603	0.003;0.018	B;B	0.29353	0.023;0.101	T	0.42565	-0.9444	9	0.56958	D	0.05	.	0.7927	0.01060	0.3142:0.1539:0.3061:0.2258	.	363;363	Q9Y5I1-2;Q9Y5I1	.;PCDAB_HUMAN	H	363	ENSP00000381636:Q363H	ENSP00000381636:Q363H	Q	+	3	2	PCDHA11	140229961	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.278000	0.00135	-0.762000	0.04664	-2.576000	0.00170	CAG		0.582	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902	
PCDHA13	56136	broad.mit.edu	37	5	140262397	140262397	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140262397G>A	ENST00000289272.2	+	1	544	c.544G>A	c.(544-546)Gca>Aca	p.A182T	PCDHA12_ENST00000398631.2_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.A182T|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA7_ENST00000525929.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	182	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.A182T(1)		NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACTTTGGACGCACAAAACAG	0.433																																					p.A182T	Melanoma(147;1739 1852 5500 27947 37288)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G544A	5						.						89.0	89.0	89.0					5																	140262397		2203	4300	6503	140242581	SO:0001583	missense	56136	exon1			AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"""Cadherins / Protocadherins : Clustered"""	8667	other	complex locus constituent	"""KIAA0345-like 1"", ""ortholog of mouse CNR5"""	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.544G>A	5.37:g.140262397G>A	ENSP00000289272:p.Ala182Thr	Somatic		Capture	Illumina HiSeq	Phase_I	140242581	NM_031865	O75277	Missense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	G	8.535	0.871955	0.17322	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	T;T	0.47869	0.83;0.83	5.49	-3.3	0.05003	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.20088	0.0483	N	0.04148	-0.265	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.12156	0.004;0.003;0.007	T	0.14227	-1.0480	9	0.49607	T	0.09	.	3.3848	0.07268	0.1483:0.1274:0.4736:0.2506	.	182;182;182	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	T	182	ENSP00000386821:A182T;ENSP00000289272:A182T	ENSP00000289272:A182T	A	+	1	0	PCDHA13	140242581	0.000000	0.05858	0.000000	0.03702	0.406000	0.30931	-3.451000	0.00466	-0.519000	0.06444	-0.458000	0.05436	GCA		0.433	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904	
PCDHB4	56131	broad.mit.edu	37	5	140502954	140502954	+	Silent	SNP	C	C	T	rs148427211		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140502954C>T	ENST00000194152.1	+	1	1374	c.1374C>T	c.(1372-1374)ttC>ttT	p.F458F	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	458	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F458F(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACACCCTGTTCGTCCGCGAGA	0.627																																					p.F458F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1374T	5						.						68.0	68.0	68.0					5																	140502954		2203	4297	6500	140483138	SO:0001819	synonymous_variant	56131	exon1			AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.1374C>T	5.37:g.140502954C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140483138	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	37	CCDS4246.1																																																																																				0.627	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
PCDHB6	56130	broad.mit.edu	37	5	140530654	140530654	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140530654G>A	ENST00000231136.1	+	1	816	c.816G>A	c.(814-816)tcG>tcA	p.S272S	PCDHB6_ENST00000543635.1_Silent_p.S136S	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	272	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.S272S(2)		cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATGCAGGATCGTTTGGGAAGG	0.493																																					p.S272S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G816A	5						.						72.0	74.0	73.0					5																	140530654		2203	4300	6503	140510838	SO:0001819	synonymous_variant	56130	exon1			AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.816G>A	5.37:g.140530654G>A		Somatic		Capture	Illumina HiSeq	Phase_I	140510838	NM_018939	B2R8R9	Silent	SNP	ENST00000231136.1	37	CCDS4248.1																																																																																				0.493	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
PCDHB6	56130	broad.mit.edu	37	5	140531475	140531475	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140531475G>A	ENST00000231136.1	+	1	1637	c.1637G>A	c.(1636-1638)cGc>cAc	p.R546H	PCDHB6_ENST00000543635.1_Missense_Mutation_p.R410H	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	546	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R546H(1)		cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCGCTGGTGCGCTTGCTGGTG	0.706																																					p.R546H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1637A	5						.						46.0	54.0	51.0					5																	140531475		2202	4298	6500	140511659	SO:0001583	missense	56130	exon1			AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1637G>A	5.37:g.140531475G>A	ENSP00000231136:p.Arg546His	Somatic		Capture	Illumina HiSeq	Phase_I	140511659	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.860697	0.32884	.	.	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.01767	4.65;4.65	4.19	3.29	0.37713	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.01489	0.0048	N	0.16743	0.435	0.27106	N	0.962498	P	0.35411	0.5	B	0.37198	0.243	T	0.45673	-0.9245	9	0.72032	D	0.01	.	4.5338	0.12019	0.1744:0.0:0.626:0.1996	.	546	Q9Y5E3	PCDB6_HUMAN	H	410;546;331	ENSP00000438466:R410H;ENSP00000231136:R546H	ENSP00000231136:R546H	R	+	2	0	PCDHB6	140511659	0.000000	0.05858	0.999000	0.59377	0.857000	0.48899	-0.067000	0.11579	2.047000	0.60756	0.556000	0.70494	CGC		0.706	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
PCDHGA3	56112	broad.mit.edu	37	5	140725752	140725752	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140725752C>T	ENST00000253812.6	+	1	2152	c.2152C>T	c.(2152-2154)Cgc>Tgc	p.R718C	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	718					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R718C(1)		breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGGCTGCGGCGCTGGCACAA	0.677																																					p.R718C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2152T	5						.						65.0	72.0	70.0					5																	140725752		2203	4297	6500	140705936	SO:0001583	missense	56112	exon1			AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.2152C>T	5.37:g.140725752C>T	ENSP00000253812:p.Arg718Cys	Somatic		Capture	Illumina HiSeq	Phase_I	140705936	NM_018916	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	12.13	1.845956	0.32606	.	.	ENSG00000254245	ENST00000253812	T	0.23147	1.92	5.16	3.07	0.35406	.	0.344076	0.12505	U	0.462970	T	0.33089	0.0851	M	0.86502	2.82	0.20821	N	0.999847	B;B	0.29115	0.233;0.023	B;B	0.29176	0.099;0.049	T	0.37842	-0.9688	10	0.72032	D	0.01	.	6.2063	0.20604	0.2116:0.6186:0.0:0.1699	.	718;718	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	C	718	ENSP00000253812:R718C	ENSP00000253812:R718C	R	+	1	0	PCDHGA3	140705936	0.000000	0.05858	0.870000	0.34147	0.524000	0.34500	-0.111000	0.10807	1.314000	0.45095	0.563000	0.77884	CGC		0.677	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916	
PCDHGB1	56104	broad.mit.edu	37	5	140731553	140731553	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140731553C>T	ENST00000523390.1	+	1	1726	c.1726C>T	c.(1726-1728)Cgc>Tgc	p.R576C	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	576	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.R576C(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TATGGTGCCACGCGCCGCAGA	0.667																																					p.R576C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1726T	5						.						18.0	21.0	20.0					5																	140731553		1891	4048	5939	140711737	SO:0001583	missense	56104	exon1			AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.1726C>T	5.37:g.140731553C>T	ENSP00000429273:p.Arg576Cys	Somatic		Capture	Illumina HiSeq	Phase_I	140711737	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	37	CCDS54923.1	.	.	.	.	.	.	.	.	.	.	.	16.17	3.047302	0.55110	.	.	ENSG00000254221	ENST00000523390	T	0.59772	0.24	5.39	4.47	0.54385	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.78130	0.4235	M	0.91196	3.185	0.35335	D	0.785943	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	D	0.84819	0.0795	9	0.87932	D	0	.	9.2805	0.37725	0.1452:0.7785:0.0:0.0763	.	576;576	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	C	576	ENSP00000429273:R576C	ENSP00000429273:R576C	R	+	1	0	PCDHGB1	140711737	0.000000	0.05858	0.992000	0.48379	0.768000	0.43524	0.323000	0.19593	2.683000	0.91414	0.563000	0.77884	CGC		0.667	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922	
PCDHGA4	56111	broad.mit.edu	37	5	140735005	140735005	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140735005C>T	ENST00000571252.1	+	1	238	c.238C>T	c.(238-240)Cgc>Tgc	p.R80C	PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	80	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGAACCCGCGCAGCGGCAC	0.612																																					p.R80C												.	.	0			c.C238T	5						.						46.0	55.0	52.0					5																	140735005		2174	4294	6468	140715189	SO:0001583	missense	56111	exon1			AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.238C>T	5.37:g.140735005C>T	ENSP00000458570:p.Arg80Cys	Somatic		Capture	Illumina HiSeq	Phase_I	140715189	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	37	CCDS58979.1																																																																																				0.612	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
PCDHGA6	56109	broad.mit.edu	37	5	140754858	140754858	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140754858G>A	ENST00000517434.1	+	1	1208	c.1208G>A	c.(1207-1209)cGa>cAa	p.R403Q	PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	403	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.R403Q(1)		breast(1)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AATTATTATCGATTAGTGACA	0.458																																					p.R403Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1208A	5						.						79.0	80.0	80.0					5																	140754858		1960	4157	6117	140735042	SO:0001583	missense	56109	exon1			AF152513	CCDS54926.1, CCDS75335.1	5q31	2010-01-26				ENSG00000253731		"""Cadherins / Protocadherins : Clustered"""	8704	other	protocadherin		606293				10380929	Standard	NM_018919		Approved	PCDH-GAMMA-A6		Q9Y5G7		ENST00000517434.1:c.1208G>A	5.37:g.140754858G>A	ENSP00000429601:p.Arg403Gln	Somatic		Capture	Illumina HiSeq	Phase_I	140735042	NM_032086	A6H8K7|B2RN55|Q9Y5D1	Missense_Mutation	SNP	ENST00000517434.1	37	CCDS54926.1	.	.	.	.	.	.	.	.	.	.	.	11.86	1.766083	0.31228	.	.	ENSG00000253731	ENST00000517434	T	0.59083	0.29	5.25	0.205	0.15204	Cadherin (4);Cadherin-like (1);	309.629000	0.02287	U	0.069922	T	0.53530	0.1802	L	0.55990	1.75	0.09310	N	1	B;B	0.31581	0.282;0.329	B;B	0.32533	0.035;0.147	T	0.41197	-0.9522	10	0.51188	T	0.08	.	5.7963	0.18389	0.4185:0.198:0.3834:0.0	.	403;403	Q9Y5G7-2;Q9Y5G7	.;PCDG6_HUMAN	Q	403	ENSP00000429601:R403Q	ENSP00000429601:R403Q	R	+	2	0	PCDHGA6	140735042	0.000000	0.05858	0.997000	0.53966	0.854000	0.48673	-0.656000	0.05342	0.168000	0.19655	0.655000	0.94253	CGA		0.458	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919	
PCDHGB3	56102	broad.mit.edu	37	5	140778577	140778577	+	Intron	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140778577G>A	ENST00000576222.1	+	1	2546				PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCAAAGAGCGGAGAAATTAC	0.433																																					p.G295R												.	.	0			c.G883A	5						.						97.0	100.0	99.0					5																	140778577		1858	4107	5965	140758761	SO:0001627	intron_variant	56101	exon1			AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+26201G>A	5.37:g.140778577G>A		Somatic		Capture	Illumina HiSeq	Phase_I	140758761	NM_032099	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																				0.433	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924	
PCDHGA9	56107	broad.mit.edu	37	5	140782704	140782704	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140782704G>A	ENST00000573521.1	+	1	185	c.185G>A	c.(184-186)cGc>cAc	p.R62H	PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	62	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGCGGAGCGCCGAGTCCGC	0.602																																					p.R62H												.	.	0			c.G185A	5						.						62.0	75.0	71.0					5																	140782704		2086	4250	6336	140762888	SO:0001583	missense	56107	exon1			AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.185G>A	5.37:g.140782704G>A	ENSP00000460274:p.Arg62His	Somatic		Capture	Illumina HiSeq	Phase_I	140762888	NM_018921	A2RU65|Q9Y5C9	Missense_Mutation	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																				0.602	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921	
PCDHGB7	56099	broad.mit.edu	37	5	140798288	140798288	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140798288G>A	ENST00000398594.2	+	1	862	c.862G>A	c.(862-864)Gct>Act	p.A288T	PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGA6_ENST00000517434.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	288	Cadherin 3. {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.A288T(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCTGACAAAGCTCAGCACGT	0.468																																					p.A288T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G862A	5						.						45.0	45.0	45.0					5																	140798288		2011	4179	6190	140778472	SO:0001583	missense	56099	exon1			AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"""Cadherins / Protocadherins : Clustered"""	8714	other	protocadherin	"""cadherin ME6"""	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.862G>A	5.37:g.140798288G>A	ENSP00000381594:p.Ala288Thr	Somatic		Capture	Illumina HiSeq	Phase_I	140778472	NM_032101	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	37	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	g	0.789	-0.759696	0.03019	.	.	ENSG00000254122	ENST00000398594	T	0.50277	0.75	5.7	2.81	0.32909	Cadherin (4);Cadherin-like (1);	2.323100	0.03797	N	0.263851	T	0.36663	0.0975	N	0.21373	0.66	0.09310	N	1	B;B	0.14012	0.009;0.002	B;B	0.14023	0.01;0.003	T	0.23976	-1.0173	10	0.20046	T	0.44	.	9.9795	0.41804	0.2988:0.0:0.7012:0.0	.	288;288	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	T	288	ENSP00000381594:A288T	ENSP00000381594:A288T	A	+	1	0	PCDHGB7	140778472	0.000000	0.05858	0.002000	0.10522	0.072000	0.16883	0.255000	0.18333	0.289000	0.22422	-0.367000	0.07326	GCT		0.468	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927	
PCDHGB7	56099	broad.mit.edu	37	5	140799315	140799315	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140799315G>A	ENST00000398594.2	+	1	1889	c.1889G>A	c.(1888-1890)cGt>cAt	p.R630H	PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGA6_ENST00000517434.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	630	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.R630H(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCATGGTGCGTGCTTTGGGT	0.652																																					p.R630H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1889A	5						.						59.0	65.0	63.0					5																	140799315		2181	4289	6470	140779499	SO:0001583	missense	56099	exon1			AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"""Cadherins / Protocadherins : Clustered"""	8714	other	protocadherin	"""cadherin ME6"""	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.1889G>A	5.37:g.140799315G>A	ENSP00000381594:p.Arg630His	Somatic		Capture	Illumina HiSeq	Phase_I	140779499	NM_032101	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	37	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	g	14.47	2.544489	0.45280	.	.	ENSG00000254122	ENST00000398594	T	0.53857	0.6	5.57	5.57	0.84162	Cadherin (4);Cadherin-like (1);	0.000000	0.30639	U	0.009192	T	0.74650	0.3744	M	0.88512	2.96	0.22354	N	0.999172	D;D	0.76494	0.999;0.998	D;P	0.68483	0.958;0.876	T	0.70905	-0.4745	10	0.87932	D	0	.	12.5213	0.56060	0.0769:0.0:0.9231:0.0	.	630;630	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	H	630	ENSP00000381594:R630H	ENSP00000381594:R630H	R	+	2	0	PCDHGB7	140779499	0.958000	0.32768	0.020000	0.16555	0.284000	0.27059	4.639000	0.61361	2.619000	0.88677	0.491000	0.48974	CGT		0.652	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927	
PCDHGA11	56105	broad.mit.edu	37	5	140801354	140801354	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140801354C>T	ENST00000398587.2	+	1	593	c.560C>T	c.(559-561)aCg>aTg	p.T187M	PCDHGA11_ENST00000518882.1_Missense_Mutation_p.T187M|PCDHGA6_ENST00000517434.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	187	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.T187M(1)		breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGGGCAGAACGGATGGGGCC	0.547																																					p.T187M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C560T	5						.						38.0	40.0	40.0					5																	140801354		1959	4156	6115	140781538	SO:0001583	missense	56105	exon1			AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"""Cadherins / Protocadherins : Clustered"""	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.560C>T	5.37:g.140801354C>T	ENSP00000381589:p.Thr187Met	Somatic		Capture	Illumina HiSeq	Phase_I	140781538	NM_018914	B7ZVY8|Q9Y5D8|Q9Y5D9	Missense_Mutation	SNP	ENST00000398587.2	37	CCDS47294.1	.	.	.	.	.	.	.	.	.	.	c	0.111	-1.138391	0.01742	.	.	ENSG00000253873	ENST00000398587;ENST00000518882	T;T	0.21191	2.02;2.02	6.03	2.31	0.28768	Cadherin (3);Cadherin-like (1);	0.376486	0.14673	U	0.305202	T	0.17238	0.0414	M	0.61703	1.905	0.09310	N	1	P;B;B	0.34815	0.47;0.4;0.451	B;B;B	0.28784	0.069;0.094;0.064	T	0.21690	-1.0238	10	0.51188	T	0.08	.	3.7329	0.08500	0.0898:0.473:0.1984:0.2387	.	187;187;187	Q9Y5H2;Q9Y5H2-3;Q9Y5H2-2	PCDGB_HUMAN;.;.	M	187	ENSP00000381589:T187M;ENSP00000428333:T187M	ENSP00000381589:T187M	T	+	2	0	PCDHGA11	140781538	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.650000	0.05378	-0.044000	0.13491	-0.797000	0.03246	ACG		0.547	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914	
PCDHGC5	56097	broad.mit.edu	37	5	140870843	140870843	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:140870843A>G	ENST00000252087.1	+	1	2036	c.2036A>G	c.(2035-2037)gAc>gGc	p.D679G	PCDHGA11_ENST00000518882.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGC4_ENST00000306593.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018929.2|NM_032403.2|NM_032407.1	NP_061752.1|NP_115779.1|NP_115783.1	Q9Y5F6	PCDGM_HUMAN	protocadherin gamma subfamily C, 5	679					homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D679G(2)		breast(2)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(4)|lung(10)|ovary(4)|prostate(1)|urinary_tract(2)	35			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAATCCAGTGACTTCCTCATA	0.537																																					p.D679G												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A2036G	5						.						198.0	177.0	184.0					5																	140870843		2203	4300	6503	140851027	SO:0001583	missense	56097	exon1			AF152526	CCDS4263.1, CCDS75350.1	5q31	2010-01-26			ENSG00000240764	ENSG00000240764		"""Cadherins / Protocadherins : Clustered"""	8718	other	protocadherin		606306				10380929	Standard	NM_018929		Approved	PCDH-GAMMA-C5	uc003lla.2	Q9Y5F6	OTTHUMG00000129624	ENST00000252087.1:c.2036A>G	5.37:g.140870843A>G	ENSP00000252087:p.Asp679Gly	Somatic		Capture	Illumina HiSeq	Phase_I	140851027	NM_018929	Q9Y5C2	Missense_Mutation	SNP	ENST00000252087.1	37	CCDS4263.1	.	.	.	.	.	.	.	.	.	.	A	14.29	2.490821	0.44249	.	.	ENSG00000240764	ENST00000252087	T	0.50548	0.74	4.97	4.97	0.65823	.	0.000000	0.52532	D	0.000065	T	0.49779	0.1577	M	0.75615	2.305	0.40551	D	0.981112	P;B	0.40834	0.73;0.258	B;B	0.39531	0.302;0.11	T	0.54642	-0.8263	10	0.33141	T	0.24	.	14.7958	0.69876	1.0:0.0:0.0:0.0	.	679;679	Q9Y5F6-2;Q9Y5F6	.;PCDGM_HUMAN	G	679	ENSP00000252087:D679G	ENSP00000252087:D679G	D	+	2	0	PCDHGC5	140851027	0.252000	0.23972	1.000000	0.80357	0.905000	0.53344	2.091000	0.41691	2.083000	0.62718	0.459000	0.35465	GAC		0.537	PCDHGC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251819.1	NM_018929	
FCHSD1	89848	broad.mit.edu	37	5	141026985	141026985	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:141026985C>T	ENST00000435817.2	-	9	858	c.808G>A	c.(808-810)Ggg>Agg	p.G270R	FCHSD1_ENST00000522126.1_Missense_Mutation_p.G194R|FCHSD1_ENST00000523856.1_5'UTR|FCHSD1_ENST00000522783.1_Missense_Mutation_p.G268R	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	270								p.G270R(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)			GTCTGCTCCCCGCGGTGGGCA	0.617																																					p.G270R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G808A	5						.						24.0	27.0	26.0					5																	141026985		1909	4124	6033	141007169	SO:0001583	missense	89848	exon9			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.808G>A	5.37:g.141026985C>T	ENSP00000399259:p.Gly270Arg	Somatic		Capture	Illumina HiSeq	Phase_I	141007169	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	37	CCDS47295.1	.	.	.	.	.	.	.	.	.	.	C	13.69	2.312729	0.40895	.	.	ENSG00000197948	ENST00000435817;ENST00000522126;ENST00000522783	T;T;T	0.13420	2.59;2.59;2.59	5.48	3.66	0.41972	.	0.308092	0.27831	N	0.017661	T	0.05547	0.0146	N	0.08118	0	0.19300	N	0.999973	P	0.36909	0.573	B	0.28232	0.087	T	0.27468	-1.0073	10	0.72032	D	0.01	-16.6508	7.4324	0.27134	0.0:0.8036:0.0:0.1964	.	270	Q86WN1	FCSD1_HUMAN	R	270;194;268	ENSP00000399259:G270R;ENSP00000427796:G194R;ENSP00000428677:G268R	ENSP00000399259:G270R	G	-	1	0	FCHSD1	141007169	0.009000	0.17119	0.036000	0.18154	0.218000	0.24690	1.109000	0.31135	2.578000	0.87016	0.455000	0.32223	GGG		0.617	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449	
ARAP3	64411	broad.mit.edu	37	5	141059793	141059793	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:141059793C>T	ENST00000239440.4	-	2	326	c.261G>A	c.(259-261)ccG>ccA	p.P87P	ARAP3_ENST00000508305.1_Silent_p.P9P	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	87	Pro-rich.				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.P87P(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						GCTGGGCTTGCGGGGCTGGGC	0.642																																					p.P87P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G261A	5						.						54.0	63.0	60.0					5																	141059793		2203	4300	6503	141039977	SO:0001819	synonymous_variant	64411	exon2			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.261G>A	5.37:g.141059793C>T		Somatic		Capture	Illumina HiSeq	Phase_I	141039977	NM_022481	B4DIT1|D3DQE3	Silent	SNP	ENST00000239440.4	37	CCDS4266.1																																																																																				0.642	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
PCDH12	51294	broad.mit.edu	37	5	141335160	141335160	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:141335160G>A	ENST00000231484.3	-	1	3467	c.2257C>T	c.(2257-2259)Cgg>Tgg	p.R753W	PCDH12_ENST00000512221.1_5'Flank|AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	753				R -> W (in Ref. 4; BAB14677). {ECO:0000305}.	calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R753W(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCGGCCTCCCGACAGTTGTAG	0.582																																					p.R753W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2257T	5						.						67.0	59.0	62.0					5																	141335160		2203	4300	6503	141315344	SO:0001583	missense	51294	exon1			AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2257C>T	5.37:g.141335160G>A	ENSP00000231484:p.Arg753Trp	Somatic		Capture	Illumina HiSeq	Phase_I	141315344	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.891794	0.52014	.	.	ENSG00000113555	ENST00000231484	T	0.57273	0.41	4.9	2.93	0.34026	.	0.000000	0.85682	D	0.000000	T	0.67646	0.2915	M	0.74881	2.28	0.45852	D	0.998715	D	0.89917	1.0	D	0.91635	0.999	T	0.66666	-0.5866	10	0.36615	T	0.2	.	10.1729	0.42922	0.0:0.0:0.5097:0.4903	.	753	Q9NPG4	PCD12_HUMAN	W	753	ENSP00000231484:R753W	ENSP00000231484:R753W	R	-	1	2	PCDH12	141315344	0.998000	0.40836	1.000000	0.80357	0.993000	0.82548	0.591000	0.23969	1.279000	0.44446	0.561000	0.74099	CGG		0.582	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
TRIO	7204	broad.mit.edu	37	5	14364857	14364857	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:14364857G>A	ENST00000344204.4	+	15	2710	c.2686G>A	c.(2686-2688)Gca>Aca	p.A896T	TRIO_ENST00000537187.1_Missense_Mutation_p.A896T|TRIO_ENST00000509967.2_Missense_Mutation_p.A847T	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	896					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A896T(1)		NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					GGATTTAGCCGCAGAGCAGCA	0.547											OREG0016458	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A896T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2686A	5						.						77.0	77.0	77.0					5																	14364857		2203	4300	6503	14417857	SO:0001583	missense	7204	exon15			AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"""	12303	protein-coding gene	gene with protein product		601893	"""triple functional domain (PTPRF interacting)"""			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.2686G>A	5.37:g.14364857G>A	ENSP00000339299:p.Ala896Thr	Somatic	694	Capture	Illumina HiSeq	Phase_I	14417857	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.999640	0.74818	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967;ENST00000513206	T;T;T	0.41758	0.99;0.99;0.99	5.36	4.43	0.53597	.	0.053683	0.85682	D	0.000000	T	0.50565	0.1623	L	0.55990	1.75	0.80722	D	1	D;D;B	0.58970	0.967;0.984;0.414	P;P;B	0.52710	0.572;0.707;0.093	T	0.52711	-0.8539	10	0.56958	D	0.05	.	15.1558	0.72739	0.0:0.0:0.8583:0.1417	.	847;896;896	F5H228;O75962-5;O75962	.;.;TRIO_HUMAN	T	896;896;847;583	ENSP00000339299:A896T;ENSP00000446348:A896T;ENSP00000445592:A847T	ENSP00000339299:A896T	A	+	1	0	TRIO	14417857	1.000000	0.71417	0.131000	0.22000	0.904000	0.53231	6.536000	0.73842	2.656000	0.90262	0.655000	0.94253	GCA		0.547	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
TRIO	7204	broad.mit.edu	37	5	14482709	14482709	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:14482709G>A	ENST00000344204.4	+	46	6508	c.6484G>A	c.(6484-6486)Ggt>Agt	p.G2162S	TRIO_ENST00000537187.1_Missense_Mutation_p.G2162S	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	2162	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.G2162S(1)		NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					CGTTGCCCAGGGTAAACTGCT	0.458																																					p.G2162S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6484A	5						.						68.0	63.0	64.0					5																	14482709		2203	4300	6503	14535709	SO:0001583	missense	7204	exon46			AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"""	12303	protein-coding gene	gene with protein product		601893	"""triple functional domain (PTPRF interacting)"""			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.6484G>A	5.37:g.14482709G>A	ENSP00000339299:p.Gly2162Ser	Somatic		Capture	Illumina HiSeq	Phase_I	14535709	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	G	34	5.384125	0.95967	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000513206	T;T	0.52526	0.66;0.66	5.14	5.14	0.70334	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.79233	0.4411	H	0.95151	3.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.85926	0.1449	10	0.87932	D	0	.	18.9682	0.92704	0.0:0.0:1.0:0.0	.	2162;2162	O75962-5;O75962	.;TRIO_HUMAN	S	2162;2162;1849	ENSP00000339299:G2162S;ENSP00000446348:G2162S	ENSP00000339299:G2162S	G	+	1	0	TRIO	14535709	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.809000	0.99208	2.512000	0.84698	0.655000	0.94253	GGT		0.458	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
YIPF5	81555	broad.mit.edu	37	5	143543718	143543718	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:143543718C>T	ENST00000274496.5	-	4	520	c.386G>A	c.(385-387)gGt>gAt	p.G129D	YIPF5_ENST00000448443.2_Missense_Mutation_p.G129D|YIPF5_ENST00000513112.1_Missense_Mutation_p.G75D	NM_001271732.1|NM_030799.7	NP_001258661.1|NP_110426.4	Q969M3	YIPF5_HUMAN	Yip1 domain family, member 5	129					protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum exit site (GO:0070971)|ER to Golgi transport vesicle (GO:0030134)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)		p.G129D(1)		large_intestine(2)|lung(5)|ovary(1)|skin(1)	9		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			AACCATTGGACCTGCCAAATC	0.368																																					p.G129D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G386A	5						.						165.0	151.0	156.0					5																	143543718		2203	4300	6503	143523911	SO:0001583	missense	81555	exon4			AF318329	CCDS4279.1, CCDS64277.1	5q31.3	2009-01-12			ENSG00000145817	ENSG00000145817		"""Yip1 domain family"""	24877	protein-coding gene	gene with protein product		611483				12975309, 18718466	Standard	NM_001024947		Approved	SMAP-5, FinGER5	uc003lnl.5	Q969M3	OTTHUMG00000129679	ENST00000274496.5:c.386G>A	5.37:g.143543718C>T	ENSP00000274496:p.Gly129Asp	Somatic		Capture	Illumina HiSeq	Phase_I	143523911	NM_030799	D3DQF5|Q4VSN6|Q53EX4|Q8NHE5|Q9H338|Q9H3U4	Missense_Mutation	SNP	ENST00000274496.5	37	CCDS4279.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.1|29.1	4.973560|4.973560	0.92919|0.92919	.|.	.|.	ENSG00000145817|ENSG00000145817	ENST00000536767|ENST00000274496;ENST00000377986;ENST00000448443;ENST00000513112;ENST00000519064;ENST00000522203	.|T;T;T;T	.|0.50548	.|0.74;0.74;0.74;0.74	6.03|6.03	5.16|5.16	0.70880|0.70880	.|Yip1 domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.77391	.|0.4123	H|H	0.94462|0.94462	3.54|3.54	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	.|D	.|0.84639	.|0.0694	.|10	.|0.87932	.|D	.|0	.|-26.8217	15.4719|15.4719	0.75446|0.75446	0.0:0.9337:0.0:0.0663|0.0:0.9337:0.0:0.0663	.|.	.|129	.|Q969M3	.|YIPF5_HUMAN	.|D	-1|129;129;129;75;75;75	.|ENSP00000274496:G129D;ENSP00000397704:G129D;ENSP00000425422:G75D;ENSP00000429777:G75D	.|ENSP00000274496:G129D	.|G	-|-	.|2	.|0	YIPF5|YIPF5	143523911|143523911	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	7.741000|7.741000	0.84997|0.84997	1.557000|1.557000	0.49525|0.49525	0.655000|0.655000	0.94253|0.94253	.|GGT		0.368	YIPF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251882.1	NM_030799	
RBM27	54439	broad.mit.edu	37	5	145664188	145664188	+	Missense_Mutation	SNP	G	G	A	rs368491992		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:145664188G>A	ENST00000265271.5	+	20	3158	c.2992G>A	c.(2992-2994)Gca>Aca	p.A998T	RBM27_ENST00000506502.1_Intron	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	998					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A998T(1)		NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATTTTAGACCGCAAACCAAGG	0.363																																					p.A998T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2992A	5						.	G	THR/ALA	3,3133		0,3,1565	91.0	89.0	89.0		2992	-2.1	0.9	5		89	0,7164		0,0,3582	no	missense	RBM27	NM_018989.1	58	0,3,5147	AA,AG,GG		0.0,0.0957,0.0291	benign	998/1061	145664188	3,10297	1568	3582	5150	145644381	SO:0001583	missense	54439	exon20			AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.2992G>A	5.37:g.145664188G>A	ENSP00000265271:p.Ala998Thr	Somatic		Capture	Illumina HiSeq	Phase_I	145644381	NM_018989	Q8IYW9	Missense_Mutation	SNP	ENST00000265271.5	37	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	G	13.43	2.234806	0.39498	9.57E-4	0.0	ENSG00000091009	ENST00000265271	T	0.53857	0.6	6.03	-2.07	0.07276	.	0.486738	0.21690	N	0.070583	T	0.40145	0.1105	L	0.47716	1.5	0.58432	D	0.999998	B	0.09022	0.002	B	0.06405	0.002	T	0.09930	-1.0652	10	0.29301	T	0.29	-0.0905	11.3049	0.49329	0.504:0.0:0.496:0.0	.	998	Q9P2N5	RBM27_HUMAN	T	998	ENSP00000265271:A998T	ENSP00000265271:A998T	A	+	1	0	RBM27	145644381	1.000000	0.71417	0.858000	0.33744	0.690000	0.40134	1.052000	0.30429	-0.805000	0.04404	-0.734000	0.03567	GCA		0.363	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128	
JAKMIP2	9832	broad.mit.edu	37	5	147040952	147040952	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:147040952C>T	ENST00000265272.5	-	3	653	c.186G>A	c.(184-186)gaG>gaA	p.E62E	JAKMIP2_ENST00000333010.6_Silent_p.E20E|JAKMIP2_ENST00000507386.1_Silent_p.E62E	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	62						Golgi apparatus (GO:0005794)		p.E62E(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)			GCTTGCGCTGCTCCAGCTCAC	0.488																																					p.E62E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G186A	5						.						133.0	124.0	127.0					5																	147040952		2203	4300	6503	147021145	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.186G>A	5.37:g.147040952C>T		Somatic		Capture	Illumina HiSeq	Phase_I	147021145	NM_014790	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Silent	SNP	ENST00000265272.5	37	CCDS4285.1																																																																																				0.488	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	
SH3TC2	79628	broad.mit.edu	37	5	148406592	148406592	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:148406592C>A	ENST00000515425.1	-	11	2804	c.2703G>T	c.(2701-2703)caG>caT	p.Q901H	SH3TC2_ENST00000513340.1_5'Flank|SH3TC2_ENST00000394358.2_Missense_Mutation_p.Q786H|SH3TC2_ENST00000538184.1_Missense_Mutation_p.Q448H|SH3TC2_ENST00000512049.1_Missense_Mutation_p.Q894H	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	901					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.Q901H(1)|p.Q786H(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)			GTCGTACAGCCTGCAGGAGAT	0.522																																					p.Q901H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2703T	5						.						110.0	113.0	112.0					5																	148406592		2203	4300	6503	148386785	SO:0001583	missense	79628	exon11			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.2703G>T	5.37:g.148406592C>A	ENSP00000423660:p.Gln901His	Somatic		Capture	Illumina HiSeq	Phase_I	148386785	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	37	CCDS4293.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.120255	0.37436	.	.	ENSG00000169247	ENST00000538184;ENST00000515425;ENST00000512049;ENST00000394358	D;D;D;D	0.95001	-3.58;-3.58;-3.58;-3.58	6.02	4.24	0.50183	Tetratricopeptide-like helical (1);	0.286229	0.35124	N	0.003437	D	0.96188	0.8757	M	0.69823	2.125	0.28074	N	0.932444	D;D;D;D	0.56035	0.974;0.96;0.96;0.96	P;P;D;P	0.65233	0.789;0.894;0.933;0.894	D	0.92008	0.5616	10	0.72032	D	0.01	-6.8945	12.1228	0.53902	0.0:0.8634:0.0:0.1366	.	786;894;901;901	C9JLC3;Q14CC0;E9PDF1;Q8TF17	.;.;.;S3TC2_HUMAN	H	448;901;894;786	ENSP00000441427:Q448H;ENSP00000423660:Q901H;ENSP00000421860:Q894H;ENSP00000377886:Q786H	ENSP00000377886:Q786H	Q	-	3	2	SH3TC2	148386785	0.021000	0.18746	0.198000	0.23420	0.608000	0.37181	0.910000	0.28571	1.558000	0.49541	0.650000	0.86243	CAG		0.522	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577	
SH3TC2	79628	broad.mit.edu	37	5	148427439	148427439	+	Missense_Mutation	SNP	G	G	A	rs142488510		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:148427439G>A	ENST00000515425.1	-	3	366	c.265C>T	c.(265-267)Cgc>Tgc	p.R89C	SH3TC2_ENST00000394358.2_5'UTR|SH3TC2_ENST00000512049.1_Missense_Mutation_p.R89C	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	89					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.R89C(3)		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)			AACAGCATGCGCACCTCCTGG	0.532													G|||	1	0.000199681	0.0	0.0	5008	,	,		17872	0.0		0.001	False		,,,				2504	0.0				p.R89C												.	.	3	Substitution - Missense(3)	large_intestine(2)|lung(1)	c.C265T	5						.						114.0	105.0	108.0					5																	148427439		2203	4300	6503	148407632	SO:0001583	missense	79628	exon3			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.265C>T	5.37:g.148427439G>A	ENSP00000423660:p.Arg89Cys	Somatic		Capture	Illumina HiSeq	Phase_I	148407632	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	37	CCDS4293.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	5.946	0.358618	0.11239	.	.	ENSG00000169247	ENST00000515425;ENST00000512049	T;T	0.75589	-0.94;-0.95	5.38	2.46	0.29980	.	0.705245	0.13816	N	0.360745	T	0.47655	0.1457	N	0.08118	0	0.09310	N	0.999998	B;B;B	0.18310	0.001;0.027;0.001	B;B;B	0.12837	0.0;0.008;0.0	T	0.23226	-1.0194	10	0.35671	T	0.21	.	1.8063	0.03082	0.1796:0.1588:0.4973:0.1644	.	89;89;89	Q14CC0;D6RFX2;Q8TF17	.;.;S3TC2_HUMAN	C	89	ENSP00000423660:R89C;ENSP00000421860:R89C	ENSP00000313025:R89C	R	-	1	0	SH3TC2	148407632	0.005000	0.15991	0.413000	0.26509	0.305000	0.27757	0.456000	0.21859	1.403000	0.46800	0.655000	0.94253	CGC		0.532	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577	
PCYOX1L	78991	broad.mit.edu	37	5	148748111	148748111	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:148748111C>T	ENST00000274569.4	+	6	1441	c.1379C>T	c.(1378-1380)gCc>gTc	p.A460V	PCYOX1L_ENST00000514349.1_Missense_Mutation_p.A370V	NM_024028.3	NP_076933.3	Q8NBM8	PCYXL_HUMAN	prenylcysteine oxidase 1 like	460					prenylcysteine catabolic process (GO:0030328)	extracellular region (GO:0005576)|membrane (GO:0016020)	prenylcysteine oxidase activity (GO:0001735)	p.A460V(1)		breast(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGGTGATGGCCGTGGCTGCC	0.562																																					p.A460V	Ovarian(62;1136 1477 27277 27495)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1379T	5						.						88.0	89.0	89.0					5																	148748111		2203	4300	6503	148728304	SO:0001583	missense	78991	exon6				CCDS4296.1	5q33.1	2008-02-05			ENSG00000145882	ENSG00000145882			28477	protein-coding gene	gene with protein product						12477932	Standard	NM_024028		Approved	MGC3265	uc003lqk.2	Q8NBM8	OTTHUMG00000130052	ENST00000274569.4:c.1379C>T	5.37:g.148748111C>T	ENSP00000274569:p.Ala460Val	Somatic		Capture	Illumina HiSeq	Phase_I	148728304	NM_024028	Q7Z4S2|Q8NCY5|Q8NF69|Q9BTE8|Q9BWS3	Missense_Mutation	SNP	ENST00000274569.4	37	CCDS4296.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.404322	0.83230	.	.	ENSG00000145882	ENST00000274569;ENST00000514349	T;T	0.17691	2.26;2.26	5.51	5.51	0.81932	Prenylcysteine lyase (1);	0.123452	0.56097	D	0.000027	T	0.32645	0.0836	M	0.63843	1.955	0.52099	D	0.999949	P;B;B	0.47253	0.892;0.334;0.304	P;B;B	0.51055	0.657;0.095;0.173	T	0.00904	-1.1520	10	0.41790	T	0.15	-15.6131	19.427	0.94746	0.0:1.0:0.0:0.0	.	342;370;460	B3KXF9;E7EVZ5;Q8NBM8	.;.;PCYXL_HUMAN	V	460;370	ENSP00000274569:A460V;ENSP00000428512:A370V	ENSP00000274569:A460V	A	+	2	0	PCYOX1L	148728304	1.000000	0.71417	0.960000	0.40013	0.974000	0.67602	5.974000	0.70465	2.577000	0.86979	0.561000	0.74099	GCC		0.562	PCYOX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252331.2	NM_024028	
CSNK1A1	1452	broad.mit.edu	37	5	148886602	148886602	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:148886602C>T	ENST00000377843.2	-	8	1324	c.845G>A	c.(844-846)cGc>cAc	p.R282H	CSNK1A1_ENST00000504676.1_Missense_Mutation_p.R193H|CSNK1A1_ENST00000606299.1_Missense_Mutation_p.R42H|CSNK1A1_ENST00000261798.5_Missense_Mutation_p.R282H|CSNK1A1_ENST00000515435.1_Missense_Mutation_p.R221H|CSNK1A1_ENST00000606719.1_Missense_Mutation_p.R79H|CSNK1A1_ENST00000515768.1_Missense_Mutation_p.R310H	NM_001025105.1|NM_001892.4	NP_001020276.1|NP_001883.4	P48729	KC1A_HUMAN	casein kinase 1, alpha 1	282	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell surface receptor signaling pathway (GO:0007166)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear speck (GO:0016607)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R310H(1)|p.R282H(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(4)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;0.0407)		GAAAAGAATGCGGAATAGCTG	0.363																																					p.R282H	Colon(5;64 69 1309 10383)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G845A	5						.						47.0	48.0	47.0					5																	148886602		2202	4300	6502	148866795	SO:0001583	missense	1452	exon8			AF119911	CCDS47303.1, CCDS47304.1, CCDS64291.1	5q32	2013-01-17			ENSG00000113712	ENSG00000113712			2451	protein-coding gene	gene with protein product	"""clock regulator kinase"""	600505				8050587	Standard	NM_001025105		Approved	CK1, CK1a, CK1alpha, CKIa, CKIalpha	uc003lqw.2	P48729	OTTHUMG00000163463	ENST00000377843.2:c.845G>A	5.37:g.148886602C>T	ENSP00000367074:p.Arg282His	Somatic		Capture	Illumina HiSeq	Phase_I	148866795	NM_001892	D3DQG0|D3DQG1|Q4JJA0|Q5U046|Q5U047|Q6FGA2|Q71TU5|Q96HD2|Q9UDK3	Missense_Mutation	SNP	ENST00000377843.2	37	CCDS47303.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.2|24.2	4.508292|4.508292	0.85282|0.85282	.|.	.|.	ENSG00000113712|ENSG00000113712	ENST00000503350|ENST00000261798;ENST00000377843;ENST00000504676;ENST00000515435;ENST00000322237;ENST00000515768	.|T;T;T;T;T	.|0.10288	.|2.89;2.89;2.89;2.89;2.89	5.84|5.84	5.84|5.84	0.93424|0.93424	.|Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|U	.|0.000000	T|T	0.24851|0.24851	0.0603|0.0603	M|M	0.87456|0.87456	2.885|2.885	0.80722|0.80722	D|D	1|1	.|B;B;B;B;B;B	.|0.28820	.|0.224;0.154;0.13;0.14;0.194;0.053	.|B;B;B;B;B;B	.|0.30782	.|0.12;0.077;0.062;0.036;0.063;0.026	T|T	0.03761|0.03761	-1.1006|-1.1006	5|10	.|0.56958	.|D	.|0.05	.|.	20.1535|20.1535	0.98095|0.98095	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|221;221;282;282;310;193	.|B4DER9;E7ETM0;Q71TU5;P48729;P48729-2;D6REM4	.|.;.;.;KC1A_HUMAN;.;.	T|H	113|282;282;193;221;282;310	.|ENSP00000261798:R282H;ENSP00000367074:R282H;ENSP00000426747:R193H;ENSP00000427031:R221H;ENSP00000421689:R310H	.|ENSP00000261798:R282H	A|R	-|-	1|2	0|0	CSNK1A1|CSNK1A1	148866795|148866795	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.463000|7.463000	0.80869|0.80869	2.764000|2.764000	0.94973|0.94973	0.650000|0.650000	0.86243|0.86243	GCA|CGC		0.363	CSNK1A1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001892	
ARHGEF37	389337	broad.mit.edu	37	5	149001380	149001380	+	Missense_Mutation	SNP	C	C	T	rs552298903		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:149001380C>T	ENST00000333677.6	+	9	1253	c.1090C>T	c.(1090-1092)Cgt>Tgt	p.R364C		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	364	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R364C(1)		large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GATCAAGAAGCGTCTGGACAA	0.607													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19085	0.0		0.0	False		,,,				2504	0.0				p.R364C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1090T	5						.						75.0	84.0	81.0					5																	149001380		2029	4188	6217	148981573	SO:0001583	missense	389337	exon9			BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"""Rho guanine nucleotide exchange factors"""	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1090C>T	5.37:g.149001380C>T	ENSP00000328083:p.Arg364Cys	Somatic		Capture	Illumina HiSeq	Phase_I	148981573	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	37	CCDS43385.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.827591	0.90955	.	.	ENSG00000183111	ENST00000333677	T	0.71222	-0.55	6.17	6.17	0.99709	BAR (2);	0.048695	0.85682	D	0.000000	D	0.86522	0.5953	M	0.83012	2.62	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86390	0.1735	10	0.66056	D	0.02	-2.9272	20.4745	0.99168	0.0:1.0:0.0:0.0	.	364	A1IGU5	ARH37_HUMAN	C	364	ENSP00000328083:R364C	ENSP00000328083:R364C	R	+	1	0	ARHGEF37	148981573	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.112000	0.71547	2.941000	0.99782	0.655000	0.94253	CGT		0.607	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
ARHGEF37	389337	broad.mit.edu	37	5	149003590	149003590	+	Missense_Mutation	SNP	G	G	A	rs200439928	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:149003590G>A	ENST00000333677.6	+	10	1514	c.1351G>A	c.(1351-1353)Gtc>Atc	p.V451I		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	451	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V451I(1)		large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						CCACCACCACGTCCCAGAGCC	0.552																																					p.V451I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1351A	5						.						67.0	71.0	70.0					5																	149003590		1985	4168	6153	148983783	SO:0001583	missense	389337	exon10			BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"""Rho guanine nucleotide exchange factors"""	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1351G>A	5.37:g.149003590G>A	ENSP00000328083:p.Val451Ile	Somatic		Capture	Illumina HiSeq	Phase_I	148983783	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	37	CCDS43385.1	.	.	.	.	.	.	.	.	.	.	G	6.743	0.505877	0.12883	.	.	ENSG00000183111	ENST00000333677	T	0.58940	0.3	5.76	-11.5	0.00074	BAR (1);	1.173460	0.05981	N	0.644203	T	0.29652	0.0740	N	0.22421	0.69	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.16660	-1.0395	10	0.02654	T	1	-0.0111	8.4881	0.33084	0.333:0.0874:0.5141:0.0655	.	451	A1IGU5	ARH37_HUMAN	I	451	ENSP00000328083:V451I	ENSP00000328083:V451I	V	+	1	0	ARHGEF37	148983783	0.000000	0.05858	0.000000	0.03702	0.682000	0.39822	-1.801000	0.01743	-2.489000	0.00518	-0.410000	0.06199	GTC		0.552	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
ARHGEF37	389337	broad.mit.edu	37	5	149008392	149008392	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:149008392G>A	ENST00000333677.6	+	12	1844	c.1681G>A	c.(1681-1683)Gct>Act	p.A561T		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	561	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A561T(1)		large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GTATGTGCCGGCTGGGAAACT	0.567																																					p.A561T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1681A	5						.						33.0	38.0	36.0					5																	149008392		2019	4181	6200	148988585	SO:0001583	missense	389337	exon12			BC041325	CCDS43385.1	5q33.1	2012-07-24			ENSG00000183111	ENSG00000183111		"""Rho guanine nucleotide exchange factors"""	34430	protein-coding gene	gene with protein product							Standard	XM_005268448		Approved	FLJ41603	uc003lra.1	A1IGU5	OTTHUMG00000163491	ENST00000333677.6:c.1681G>A	5.37:g.149008392G>A	ENSP00000328083:p.Ala561Thr	Somatic		Capture	Illumina HiSeq	Phase_I	148988585	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	37	CCDS43385.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.220555	0.79464	.	.	ENSG00000183111	ENST00000333677	T	0.45276	0.9	5.47	5.47	0.80525	Src homology-3 domain (2);Variant SH3 (1);	0.165964	0.53938	D	0.000055	T	0.59487	0.2197	M	0.72894	2.215	0.48975	D	0.999738	D	0.54207	0.965	P	0.58620	0.842	T	0.61676	-0.7014	10	0.59425	D	0.04	-2.492	14.8177	0.70048	0.0:0.0:1.0:0.0	.	561	A1IGU5	ARH37_HUMAN	T	561	ENSP00000328083:A561T	ENSP00000328083:A561T	A	+	1	0	ARHGEF37	148988585	0.999000	0.42202	0.983000	0.44433	0.493000	0.33554	3.578000	0.53892	2.576000	0.86940	0.491000	0.48974	GCT		0.567	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
PDGFRB	5159	broad.mit.edu	37	5	149497261	149497261	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:149497261G>A	ENST00000261799.4	-	22	3526	c.3057C>T	c.(3055-3057)aaC>aaT	p.N1019N		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	1019					adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|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 chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|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 metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)	p.N1019N(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGATATAGTCGTTGTCACCCT	0.642			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""																																p.N1019N			Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3057T	5						.						101.0	98.0	99.0					5																	149497261		2203	4300	6503	149477454	SO:0001819	synonymous_variant	5159	exon22			M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.3057C>T	5.37:g.149497261G>A		Somatic		Capture	Illumina HiSeq	Phase_I	149477454	NM_002609	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	37	CCDS4303.1																																																																																				0.642	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
RBM22	55696	broad.mit.edu	37	5	150078095	150078095	+	Silent	SNP	A	A	G	rs546304328		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:150078095A>G	ENST00000199814.4	-	4	358	c.237T>C	c.(235-237)aaT>aaC	p.N79N	RBM22_ENST00000540000.1_Intron|RBM22_ENST00000447771.2_Intron	NM_018047.2	NP_060517.1	Q9NW64	RBM22_HUMAN	RNA binding motif protein 22	79					cellular response to drug (GO:0035690)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of RNA splicing (GO:0033120)|protein import into nucleus, translocation (GO:0000060)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium-dependent protein binding (GO:0048306)|metal ion binding (GO:0046872)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|snRNA binding (GO:0017069)	p.N79N(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|ovary(1)	17		Medulloblastoma(196;0.167)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTGACAGACATTCTTCAATT	0.463													A|||	1	0.000199681	0.0	0.0	5008	,	,		20569	0.0		0.0	False		,,,				2504	0.001				p.N79N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T237C	5						.						124.0	111.0	115.0					5																	150078095		2203	4300	6503	150058288	SO:0001819	synonymous_variant	55696	exon4			AL136933	CCDS34278.1	5q33.1	2013-02-12			ENSG00000086589	ENSG00000086589		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	25503	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 47"""	612430				20013661, 19133299	Standard	NM_018047		Approved	FLJ10290, ZC3H16, fSAP47, Cwc2	uc031slu.1	Q9NW64	OTTHUMG00000163589	ENST00000199814.4:c.237T>C	5.37:g.150078095A>G		Somatic		Capture	Illumina HiSeq	Phase_I	150058288	NM_018047	A6NDM5|B4DLI9|O95607	Silent	SNP	ENST00000199814.4	37	CCDS34278.1																																																																																				0.463	RBM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374431.2	NM_018047	
ANXA6	309	broad.mit.edu	37	5	150510809	150510809	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:150510809G>T	ENST00000354546.5	-	11	1005	c.778C>A	c.(778-780)Ctc>Atc	p.L260I	ANXA6_ENST00000523714.1_Missense_Mutation_p.L228I|ANXA6_ENST00000521512.1_Intron|ANXA6_ENST00000377751.5_Intron|ANXA6_ENST00000356496.5_Missense_Mutation_p.L260I	NM_001155.4	NP_001146.2	P08133	ANXA6_HUMAN	annexin A6	260					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|protein homooligomerization (GO:0051260)|regulation of muscle contraction (GO:0006937)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|cholesterol binding (GO:0015485)|GTP binding (GO:0005525)|ligand-gated ion channel activity (GO:0015276)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)	p.L260I(1)		endometrium(2)|kidney(1)|lung(9)	12		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCCTTGAAGAGCCTTTCAGCA	0.527																																					p.L260I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C778A	5						.						147.0	150.0	149.0					5																	150510809		1896	4127	6023	150491002	SO:0001583	missense	309	exon11			J03578	CCDS47315.1, CCDS54941.1	5q33.1	2008-02-05			ENSG00000197043	ENSG00000197043		"""Annexins"""	544	protein-coding gene	gene with protein product		114070		ANX6		3258820	Standard	NM_001155		Approved		uc003ltl.2	P08133	OTTHUMG00000164179	ENST00000354546.5:c.778C>A	5.37:g.150510809G>T	ENSP00000346550:p.Leu260Ile	Somatic		Capture	Illumina HiSeq	Phase_I	150491002	NM_001155	B7Z8A7|D3DQH4|E9PGK1|Q6ZT79	Missense_Mutation	SNP	ENST00000354546.5	37	CCDS47315.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.983585	0.93044	.	.	ENSG00000197043	ENST00000354546;ENST00000523714;ENST00000356496;ENST00000540153	T;T;T	0.19250	2.16;2.16;2.16	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.48021	0.1477	M	0.70108	2.13	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.91635	0.999;0.999	T	0.48115	-0.9063	10	0.72032	D	0.01	.	17.794	0.88564	0.0:0.0:1.0:0.0	.	260;260	A6NN80;P08133	.;ANXA6_HUMAN	I	260;228;260;134	ENSP00000346550:L260I;ENSP00000430517:L228I;ENSP00000348889:L260I	ENSP00000346550:L260I	L	-	1	0	ANXA6	150491002	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.379000	0.90146	2.496000	0.84212	0.655000	0.94253	CTC		0.527	ANXA6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377668.2	NM_001155	
GM2A	2760	broad.mit.edu	37	5	150632814	150632814	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:150632814C>A	ENST00000357164.3	+	1	362	c.37C>A	c.(37-39)Ctg>Atg	p.L13M		NM_000405.4|NM_001167607.1	NP_000396.2|NP_001161079.1	P17900	SAP3_HUMAN	GM2 ganglioside activator	13					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|learning or memory (GO:0007611)|lipid storage (GO:0019915)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|positive regulation of hydrolase activity (GO:0051345)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	apical cortex (GO:0045179)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|mitochondrion (GO:0005739)	beta-N-acetylhexosaminidase activity (GO:0004563)|lipid transporter activity (GO:0005319)|phospholipase activator activity (GO:0016004)	p.L13M(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|upper_aerodigestive_tract(2)	8		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTGATCGCCCTGGGCTTGCT	0.607																																					p.L13M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C37A	5						.						59.0	57.0	58.0					5																	150632814		2203	4300	6503	150613007	SO:0001583	missense	2760	exon1				CCDS4313.1	5q33.1	2010-03-17	2004-05-20		ENSG00000196743	ENSG00000196743			4367	protein-coding gene	gene with protein product	"""cerebroside sulfate activator protein"", ""sphingolipid activator protein 3"""	613109	"""GM2 ganglioside activator protein"""			115863, 1915857	Standard	NM_000405		Approved	SAP-3	uc003ltr.4	P17900	OTTHUMG00000130124	ENST00000357164.3:c.37C>A	5.37:g.150632814C>A	ENSP00000349687:p.Leu13Met	Somatic		Capture	Illumina HiSeq	Phase_I	150613007	NM_001167607	B2R699|D3DQH6|Q14426|Q14428|Q6LBL5	Missense_Mutation	SNP	ENST00000357164.3	37	CCDS4313.1	.	.	.	.	.	.	.	.	.	.	C	11.31	1.602227	0.28534	.	.	ENSG00000196743	ENST00000357164	T	0.69806	-0.43	3.26	0.292	0.15737	.	0.527792	0.18038	N	0.153715	T	0.72985	0.3529	M	0.62723	1.935	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.73380	0.98;0.98	T	0.60687	-0.7214	10	0.54805	T	0.06	-15.6936	5.4856	0.16747	0.0:0.5784:0.0:0.4216	.	13;13	B4DQM5;P17900	.;SAP3_HUMAN	M	13	ENSP00000349687:L13M	ENSP00000349687:L13M	L	+	1	2	GM2A	150613007	0.162000	0.22906	0.153000	0.22517	0.077000	0.17291	0.121000	0.15667	0.040000	0.15660	0.462000	0.41574	CTG		0.607	GM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252432.1	NM_000405	
FAT2	2196	broad.mit.edu	37	5	150911198	150911198	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:150911198C>T	ENST00000261800.5	-	13	9773	c.9761G>A	c.(9760-9762)cGc>cAc	p.R3254H		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3254	Cadherin 29. {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.R3254H(1)|p.R3254L(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)			GCTGACCACGCGGTAGCCGGT	0.672																																					p.R3254H												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G9761A	5						.						32.0	28.0	29.0					5																	150911198		2203	4300	6503	150891391	SO:0001583	missense	2196	exon13			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.9761G>A	5.37:g.150911198C>T	ENSP00000261800:p.Arg3254His	Somatic		Capture	Illumina HiSeq	Phase_I	150891391	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	C	8.212	0.800446	0.16397	.	.	ENSG00000086570	ENST00000261800	T	0.53640	0.61	5.21	3.04	0.35103	Cadherin (4);Cadherin-like (1);	0.697244	0.12889	N	0.430811	T	0.33177	0.0854	L	0.35793	1.09	0.09310	N	1	B	0.25272	0.122	B	0.22601	0.04	T	0.16129	-1.0413	10	0.25751	T	0.34	.	5.9105	0.19025	0.0:0.568:0.0:0.432	.	3254	Q9NYQ8	FAT2_HUMAN	H	3254	ENSP00000261800:R3254H	ENSP00000261800:R3254H	R	-	2	0	FAT2	150891391	0.238000	0.23825	0.550000	0.28217	0.076000	0.17211	0.654000	0.24918	1.173000	0.42796	0.555000	0.69702	CGC		0.672	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
FAT2	2196	broad.mit.edu	37	5	150923775	150923775	+	Missense_Mutation	SNP	G	G	A	rs200330283	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:150923775G>A	ENST00000261800.5	-	9	6925	c.6913C>T	c.(6913-6915)Cgt>Tgt	p.R2305C		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2305	Cadherin 20. {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.R2305C(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)			GAGACGTCACGGTTCCGCCCT	0.502													G|||	5	0.000998403	0.0	0.0014	5008	,	,		21891	0.004		0.0	False		,,,				2504	0.0				p.R2305C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6913T	5						.						112.0	111.0	111.0					5																	150923775		2203	4300	6503	150903968	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.6913C>T	5.37:g.150923775G>A	ENSP00000261800:p.Arg2305Cys	Somatic		Capture	Illumina HiSeq	Phase_I	150903968	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	14.15	2.449545	0.43531	.	.	ENSG00000086570	ENST00000261800	T	0.20598	2.06	5.68	1.56	0.23342	Cadherin (4);Cadherin-like (1);	0.829177	0.10793	N	0.633470	T	0.21307	0.0513	L	0.38175	1.15	0.31660	N	0.645748	D	0.67145	0.996	P	0.51101	0.659	T	0.31364	-0.9946	10	0.72032	D	0.01	.	4.1085	0.10049	0.0822:0.1018:0.326:0.49	.	2305	Q9NYQ8	FAT2_HUMAN	C	2305	ENSP00000261800:R2305C	ENSP00000261800:R2305C	R	-	1	0	FAT2	150903968	0.991000	0.36638	0.998000	0.56505	0.868000	0.49771	0.903000	0.28475	0.731000	0.32448	0.561000	0.74099	CGT		0.502	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
FAT2	2196	broad.mit.edu	37	5	150925038	150925038	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:150925038G>A	ENST00000261800.5	-	9	5662	c.5650C>T	c.(5650-5652)Cct>Tct	p.P1884S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1884					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.P1884S(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)			GGATGGATAGGCCCGACTATT	0.473																																					p.P1884S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5650T	5						.						98.0	105.0	103.0					5																	150925038		2203	4300	6503	150905231	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.5650C>T	5.37:g.150925038G>A	ENSP00000261800:p.Pro1884Ser	Somatic		Capture	Illumina HiSeq	Phase_I	150905231	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.274986	0.40194	.	.	ENSG00000086570	ENST00000261800	T	0.59224	0.28	5.01	5.01	0.66863	Cadherin (1);Cadherin-like (1);	0.000000	0.53938	D	0.000046	T	0.64360	0.2591	N	0.25245	0.725	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62590	-0.6822	10	0.28530	T	0.3	.	18.3202	0.90236	0.0:0.0:1.0:0.0	.	1884	Q9NYQ8	FAT2_HUMAN	S	1884	ENSP00000261800:P1884S	ENSP00000261800:P1884S	P	-	1	0	FAT2	150905231	1.000000	0.71417	0.074000	0.20217	0.020000	0.10135	9.787000	0.99055	2.330000	0.79161	0.467000	0.42956	CCT		0.473	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
G3BP1	10146	broad.mit.edu	37	5	151183531	151183531	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:151183531G>A	ENST00000394123.3	+	12	1425	c.1280G>A	c.(1279-1281)cGc>cAc	p.R427H	G3BP1_ENST00000356245.3_Missense_Mutation_p.R427H|G3BP1_ENST00000543466.1_Missense_Mutation_p.R245H			Q13283	G3BP1_HUMAN	GTPase activating protein (SH3 domain) binding protein 1	427					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Ras protein signal transduction (GO:0007265)|transport (GO:0006810)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)	p.R427H(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|skin(3)|urinary_tract(2)	29		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)			CGAGATAATCGCCTTCGGGGA	0.587																																					p.R427H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1280A	5						.						83.0	87.0	86.0					5																	151183531		2203	4300	6503	151163724	SO:0001583	missense	10146	exon12			BC006997	CCDS4319.1	5q33.1	2013-02-12	2006-11-01		ENSG00000145907	ENSG00000145907		"""RNA binding motif (RRM) containing"""	30292	protein-coding gene	gene with protein product	"""Ras-GTPase-activating protein SH3-domain-binding protein"""	608431				8649363, 9889278	Standard	NM_005754		Approved	HDH-VIII, G3BP	uc003lum.3	Q13283	OTTHUMG00000130123	ENST00000394123.3:c.1280G>A	5.37:g.151183531G>A	ENSP00000377681:p.Arg427His	Somatic		Capture	Illumina HiSeq	Phase_I	151163724	NM_005754	Q5HYE9	Missense_Mutation	SNP	ENST00000394123.3	37	CCDS4319.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.259497	0.59321	.	.	ENSG00000145907	ENST00000394123;ENST00000543466;ENST00000356245;ENST00000274596	T;T;T	0.76709	-0.94;-1.04;-0.94	5.36	5.36	0.76844	.	0.043814	0.85682	D	0.000000	T	0.76463	0.3991	L	0.57536	1.79	0.80722	D	1	B	0.13145	0.007	B	0.08055	0.003	T	0.71293	-0.4636	10	0.42905	T	0.14	-1.4343	19.4633	0.94927	0.0:0.0:1.0:0.0	.	427	Q13283	G3BP1_HUMAN	H	427;245;427;269	ENSP00000377681:R427H;ENSP00000445035:R245H;ENSP00000348578:R427H	ENSP00000274596:R269H	R	+	2	0	G3BP1	151163724	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.156000	0.89645	2.666000	0.90696	0.655000	0.94253	CGC		0.587	G3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252431.1	NM_005754	
KIF4B	285643	broad.mit.edu	37	5	154394112	154394112	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:154394112C>T	ENST00000435029.4	+	1	853	c.693C>T	c.(691-693)agC>agT	p.S231S		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	231	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)	p.S231S(2)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AGAATTGCAGCTTTCGCTCCA	0.453																																					p.S231S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C693T	5						.						102.0	101.0	101.0					5																	154394112		2203	4300	6503	154374305	SO:0001819	synonymous_variant	285643	exon1			AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"""Kinesins"""	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.693C>T	5.37:g.154394112C>T		Somatic		Capture	Illumina HiSeq	Phase_I	154374305	NM_001099293		Silent	SNP	ENST00000435029.4	37	CCDS47324.1																																																																																				0.453	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1		
CYFIP2	26999	broad.mit.edu	37	5	156760449	156760449	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:156760449A>G	ENST00000521420.1	+	20	2393	c.2302A>G	c.(2302-2304)Att>Gtt	p.I768V	CYFIP2_ENST00000347377.6_Missense_Mutation_p.I794V|CYFIP2_ENST00000435847.2_Missense_Mutation_p.I493V|CYFIP2_ENST00000522463.1_Missense_Mutation_p.I598V|CYFIP2_ENST00000442283.2_Missense_Mutation_p.I79V|CYFIP2_ENST00000318218.6_Missense_Mutation_p.I819V|CYFIP2_ENST00000541131.1_Missense_Mutation_p.I719V|CYFIP2_ENST00000377576.3_Missense_Mutation_p.I794V					cytoplasmic FMR1 interacting protein 2									p.I819V(1)		breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCTGACCTCCATTGTGGTAAG	0.493																																					p.I794V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2380G	5						.						189.0	187.0	188.0					5																	156760449		1954	4154	6108	156693027	SO:0001583	missense	26999	exon21			AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"""p53 inducible protein"""	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.2302A>G	5.37:g.156760449A>G	ENSP00000430904:p.Ile768Val	Somatic		Capture	Illumina HiSeq	Phase_I	156693027	NM_001037333		Missense_Mutation	SNP	ENST00000521420.1	37		.	.	.	.	.	.	.	.	.	.	A	15.85	2.954688	0.53293	.	.	ENSG00000055163	ENST00000318218;ENST00000442283;ENST00000522463;ENST00000521420;ENST00000347377;ENST00000377576;ENST00000541131;ENST00000435847	T;T;T;T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84;1.84;1.84;1.84	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.39145	0.1067	L	0.28458	0.855	0.80722	D	1	B;B;B;D;B;B	0.76494	0.05;0.124;0.033;0.999;0.049;0.0	B;B;B;D;B;B	0.85130	0.076;0.232;0.092;0.997;0.097;0.001	T	0.09292	-1.0681	10	0.29301	T	0.29	-20.1818	16.0916	0.81094	1.0:0.0:0.0:0.0	.	658;598;768;794;794;819	A8MUM2;E7EW33;E7EVJ5;E7EVF4;Q96F07-2;Q96F07	.;.;.;.;.;CYFP2_HUMAN	V	819;79;598;768;794;794;719;493	ENSP00000325817:I819V;ENSP00000390948:I79V;ENSP00000428009:I598V;ENSP00000430904:I768V;ENSP00000313567:I794V;ENSP00000366799:I794V;ENSP00000444645:I719V;ENSP00000403793:I493V	ENSP00000325817:I819V	I	+	1	0	CYFIP2	156693027	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.527000	0.81931	2.186000	0.69663	0.533000	0.62120	ATT		0.493	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332	
ADAM19	8728	broad.mit.edu	37	5	156946941	156946941	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:156946941G>A	ENST00000517905.1	-	6	550	c.506C>T	c.(505-507)cCg>cTg	p.P169L	ADAM19_ENST00000394020.1_Missense_Mutation_p.P171L|ADAM19_ENST00000257527.4_Missense_Mutation_p.P169L|ADAM19_ENST00000430702.2_5'UTR			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	169					heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.P170L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TCCCGGGGGCGGCTTGAGATG	0.562																																					p.P169L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C506T	5						.						121.0	124.0	123.0					5																	156946941		2203	4300	6503	156879519	SO:0001583	missense	8728	exon6			AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"""ADAM metallopeptidase domain containing"""	197	protein-coding gene	gene with protein product	"""meltrin beta"""	603640	"""a disintegrin and metalloproteinase domain 19 (meltrin beta)"""			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.506C>T	5.37:g.156946941G>A	ENSP00000428654:p.Pro169Leu	Somatic		Capture	Illumina HiSeq	Phase_I	156879519	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	37		.	.	.	.	.	.	.	.	.	.	G	3.537	-0.094423	0.07053	.	.	ENSG00000135074	ENST00000257527;ENST00000394020;ENST00000517905	T;T;T	0.01560	4.78;4.79;4.77	5.72	4.5	0.54988	.	0.370692	0.23125	N	0.051660	T	0.00637	0.0021	N	0.00237	-1.79	0.37434	D	0.914138	B	0.02656	0.0	B	0.01281	0.0	T	0.53809	-0.8386	10	0.20519	T	0.43	.	9.3972	0.38410	0.9174:0.0:0.0826:0.0	.	169	Q9H013-2	.	L	169;171;169	ENSP00000257527:P169L;ENSP00000377588:P171L;ENSP00000428654:P169L	ENSP00000257527:P169L	P	-	2	0	ADAM19	156879519	0.955000	0.32602	1.000000	0.80357	0.839000	0.47603	3.997000	0.57016	1.001000	0.39076	-0.290000	0.09829	CCG		0.562	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274	
SOX30	11063	broad.mit.edu	37	5	157065584	157065584	+	Missense_Mutation	SNP	G	G	A	rs571563119		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:157065584G>A	ENST00000265007.6	-	4	1875	c.1534C>T	c.(1534-1536)Cgc>Tgc	p.R512C	SOX30_ENST00000519442.1_Missense_Mutation_p.R207C|SOX30_ENST00000311371.5_Intron	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	512					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R512C(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCAGTAAAGCGTTGGGGTGGG	0.562													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17687	0.0		0.0	False		,,,				2504	0.0				p.R512C	Esophageal Squamous(31;525 799 19355 21125 41744)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1534T	5						.						77.0	77.0	77.0					5																	157065584		2203	4300	6503	156998162	SO:0001583	missense	11063	exon4			AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"""SRY (sex determining region Y)-boxes"""	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.1534C>T	5.37:g.157065584G>A	ENSP00000265007:p.Arg512Cys	Somatic		Capture	Illumina HiSeq	Phase_I	156998162	NM_178424	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	37	CCDS4339.1	.	.	.	.	.	.	.	.	.	.	G	5.097	0.203594	0.09704	.	.	ENSG00000039600	ENST00000265007;ENST00000519442	D;D	0.97791	-4.26;-4.54	5.49	3.7	0.42460	.	0.769759	0.12145	N	0.495419	D	0.93900	0.8048	N	0.19112	0.55	0.29475	N	0.856775	B;B	0.11235	0.004;0.004	B;B	0.04013	0.001;0.001	D	0.89635	0.3858	10	0.72032	D	0.01	.	9.8799	0.41227	0.0736:0.1381:0.7884:0.0	.	207;512	B4DXW7;O94993	.;SOX30_HUMAN	C	512;207	ENSP00000265007:R512C;ENSP00000427984:R207C	ENSP00000265007:R512C	R	-	1	0	SOX30	156998162	1.000000	0.71417	0.327000	0.25402	0.004000	0.04260	3.653000	0.54446	0.680000	0.31366	-0.181000	0.13052	CGC		0.562	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017	
SOX30	11063	broad.mit.edu	37	5	157073761	157073761	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:157073761A>G	ENST00000265007.6	-	3	1612	c.1271T>C	c.(1270-1272)tTt>tCt	p.F424S	SOX30_ENST00000519442.1_Missense_Mutation_p.F119S|SOX30_ENST00000311371.5_Missense_Mutation_p.F424S	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	424					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.F424S(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGTACCAGAAAATACATTGGA	0.418																																					p.F424S	Esophageal Squamous(31;525 799 19355 21125 41744)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1271C	5						.						146.0	143.0	144.0					5																	157073761		2203	4300	6503	157006339	SO:0001583	missense	11063	exon3			AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"""SRY (sex determining region Y)-boxes"""	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.1271T>C	5.37:g.157073761A>G	ENSP00000265007:p.Phe424Ser	Somatic		Capture	Illumina HiSeq	Phase_I	157006339	NM_007017	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	37	CCDS4339.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.227755	0.79576	.	.	ENSG00000039600	ENST00000311371;ENST00000265007;ENST00000519442	D;D;D	0.97924	-4.61;-4.28;-4.55	5.39	5.39	0.77823	.	0.075924	0.56097	D	0.000026	D	0.97167	0.9074	L	0.27053	0.805	0.40478	D	0.980411	D;D;D	0.62365	0.964;0.991;0.985	P;D;D	0.66602	0.601;0.945;0.942	D	0.98268	1.0502	10	0.59425	D	0.04	.	14.2795	0.66202	1.0:0.0:0.0:0.0	.	119;424;424	B4DXW7;O94993-2;O94993	.;.;SOX30_HUMAN	S	424;424;119	ENSP00000309343:F424S;ENSP00000265007:F424S;ENSP00000427984:F119S	ENSP00000265007:F424S	F	-	2	0	SOX30	157006339	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.993000	0.70616	2.171000	0.68590	0.528000	0.53228	TTT		0.418	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017	
SOX30	11063	broad.mit.edu	37	5	157078573	157078573	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:157078573C>T	ENST00000265007.6	-	1	855	c.514G>A	c.(514-516)Ggg>Agg	p.G172R	SOX30_ENST00000519442.1_Intron|SOX30_ENST00000311371.5_Missense_Mutation_p.G172R	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	172					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.G172R(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			AGGGCCGGCCCGGGGCCTTCC	0.672																																					p.G172R	Esophageal Squamous(31;525 799 19355 21125 41744)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G514A	5						.						31.0	39.0	36.0					5																	157078573		2167	4238	6405	157011151	SO:0001583	missense	11063	exon1			AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"""SRY (sex determining region Y)-boxes"""	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.514G>A	5.37:g.157078573C>T	ENSP00000265007:p.Gly172Arg	Somatic		Capture	Illumina HiSeq	Phase_I	157011151	NM_007017	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	37	CCDS4339.1	.	.	.	.	.	.	.	.	.	.	C	9.995	1.231788	0.22626	.	.	ENSG00000039600	ENST00000311371;ENST00000265007	D;D	0.99405	-5.84;-5.18	4.62	4.62	0.57501	.	0.333064	0.21615	N	0.071721	D	0.96651	0.8907	L	0.29908	0.895	0.20196	N	0.999927	P;B	0.36974	0.576;0.27	B;B	0.26517	0.07;0.01	D	0.93730	0.7040	10	0.87932	D	0	.	4.7466	0.13040	0.1973:0.6558:0.0:0.1469	.	172;172	O94993-2;O94993	.;SOX30_HUMAN	R	172	ENSP00000309343:G172R;ENSP00000265007:G172R	ENSP00000265007:G172R	G	-	1	0	SOX30	157011151	0.049000	0.20398	0.019000	0.16419	0.001000	0.01503	1.848000	0.39309	2.098000	0.63641	0.305000	0.20034	GGG		0.672	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017	
GABRB2	2561	broad.mit.edu	37	5	160753376	160753376	+	Splice_Site	SNP	G	G	A	rs375083192		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:160753376G>A	ENST00000393959.1	-	9	1189	c.1190C>T	c.(1189-1191)aCg>aTg	p.T397M	GABRB2_ENST00000274547.2_Splice_Site_p.T397M|GABRB2_ENST00000517547.1_Intron|GABRB2_ENST00000517901.1_Intron|GABRB2_ENST00000520240.1_Intron|GABRB2_ENST00000353437.6_Intron			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	397					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)	p.T397M(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CTATCTAACCGTATACAGAGA	0.398													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17657	0.0		0.0	False		,,,				2504	0.0				p.T397M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1190T	5						.	G	,MET/THR	0,4406		0,0,2203	105.0	102.0	103.0		,1190	4.5	1.0	5		103	1,8597	1.2+/-3.3	0,1,4298	no	intron,missense-near-splice	GABRB2	NM_000813.2,NM_021911.2	,81	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,benign	,397/513	160753376	1,13003	2203	4299	6502	160685954	SO:0001630	splice_region_variant	2561	exon10				CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4082	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 2"""	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.1191+1C>T	5.37:g.160753376G>A		Somatic		Capture	Illumina HiSeq	Phase_I	160685954	NM_021911	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Missense_Mutation	SNP	ENST00000393959.1	37	CCDS4355.1	.	.	.	.	.	.	.	.	.	.	G	12.39	1.924486	0.34002	0.0	1.16E-4	ENSG00000145864	ENST00000393959;ENST00000274547	T;T	0.71817	-0.6;-0.6	5.36	4.48	0.54585	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.981946	0.08234	U	0.977049	T	0.53077	0.1774	N	0.08118	0	0.32987	D	0.524401	B	0.23377	0.084	B	0.15870	0.014	T	0.53655	-0.8408	10	0.42905	T	0.14	.	11.6461	0.51261	0.085:0.0:0.915:0.0	.	397	P47870	GBRB2_HUMAN	M	397	ENSP00000377531:T397M;ENSP00000274547:T397M	ENSP00000274547:T397M	T	-	2	0	GABRB2	160685954	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.076000	0.41548	1.245000	0.43885	0.655000	0.94253	ACG		0.398	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1		Missense_Mutation
GABRA6	2559	broad.mit.edu	37	5	161117215	161117215	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:161117215G>A	ENST00000274545.5	+	7	1115	c.682G>A	c.(682-684)Gtt>Att	p.V228I	RP11-348M17.2_ENST00000521984.1_RNA|GABRA6_ENST00000523217.1_Missense_Mutation_p.V218I			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	228					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.V228I(1)		breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	AGGTGAATACGTTATAATGAC	0.358										TCGA Ovarian(5;0.080)																											p.V228I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G682A	5						.						129.0	114.0	119.0					5																	161117215		2203	4300	6503	161049793	SO:0001583	missense	2559	exon7				CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4080	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 6"""	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.682G>A	5.37:g.161117215G>A	ENSP00000274545:p.Val228Ile	Somatic		Capture	Illumina HiSeq	Phase_I	161049793	NM_000811	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	37	CCDS4356.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.900045	0.33535	.	.	ENSG00000145863	ENST00000274545;ENST00000523217;ENST00000517823;ENST00000523691	T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23	5.56	4.68	0.58851	Neurotransmitter-gated ion-channel ligand-binding (3);	0.236515	0.43110	D	0.000612	T	0.61362	0.2341	N	0.20445	0.575	0.45227	D	0.998237	B	0.13594	0.008	B	0.16722	0.016	T	0.55535	-0.8126	10	0.21014	T	0.42	.	10.1013	0.42507	0.1491:0.0:0.8509:0.0	.	228	Q16445	GBRA6_HUMAN	I	228;218;175;148	ENSP00000274545:V228I;ENSP00000430527:V218I;ENSP00000430212:V175I;ENSP00000427989:V148I	ENSP00000274545:V228I	V	+	1	0	GABRA6	161049793	1.000000	0.71417	0.991000	0.47740	0.976000	0.68499	3.534000	0.53568	2.607000	0.88179	0.655000	0.94253	GTT		0.358	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2		
TENM2	57451	broad.mit.edu	37	5	167675280	167675280	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:167675280A>G	ENST00000518659.1	+	27	7375	c.7336A>G	c.(7336-7338)Aaa>Gaa	p.K2446E	TENM2_ENST00000519204.1_Missense_Mutation_p.K2325E|TENM2_ENST00000520394.1_Missense_Mutation_p.K2207E|TENM2_ENST00000403607.2_Missense_Mutation_p.K2270E|TENM2_ENST00000545108.1_Missense_Mutation_p.K2445E	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2446					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.K2279E(1)									TACCATGTGGAAAAACGTGGG	0.517																																					p.K2437E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A7309G	5						.						64.0	65.0	64.0					5																	167675280		1957	4148	6105	167607858	SO:0001583	missense	57451	exon27			AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.7336A>G	5.37:g.167675280A>G	ENSP00000429430:p.Lys2446Glu	Somatic		Capture	Illumina HiSeq	Phase_I	167607858	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	A	7.285	0.609865	0.14066	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.88896	-1.97;-1.96;-2.07;-2.42;-2.44	4.74	4.74	0.60224	Rhs repeat-associated core (1);	0.417330	0.30999	N	0.008456	T	0.76564	0.4005	N	0.10664	0.02	0.40201	D	0.977518	B;B;B	0.11235	0.001;0.001;0.004	B;B;B	0.09377	0.003;0.001;0.004	T	0.71695	-0.4515	10	0.11485	T	0.65	.	14.5822	0.68300	1.0:0.0:0.0:0.0	.	2445;2446;2207	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	E	2446;2445;2325;2207;2270	ENSP00000429430:K2446E;ENSP00000438635:K2445E;ENSP00000428964:K2325E;ENSP00000427874:K2207E;ENSP00000384905:K2270E	ENSP00000384905:K2270E	K	+	1	0	ODZ2	167607858	1.000000	0.71417	0.992000	0.48379	0.960000	0.62799	5.433000	0.66520	1.915000	0.55452	0.454000	0.30748	AAA		0.517	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
DOCK2	1794	broad.mit.edu	37	5	169116272	169116272	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:169116272C>T	ENST00000256935.8	+	9	858	c.778C>T	c.(778-780)Cga>Tga	p.R260*		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	260					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.R260*(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTACCTAGTGCGATGGGGCAG	0.522																																					p.R260X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C778T	5						.						116.0	101.0	106.0					5																	169116272		2203	4300	6503	169048850	SO:0001587	stop_gained	1794	exon9			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.778C>T	5.37:g.169116272C>T	ENSP00000256935:p.Arg260*	Somatic		Capture	Illumina HiSeq	Phase_I	169048850	NM_004946	Q2M3I0|Q96AK7	Nonsense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	39	7.668199	0.98422	.	.	ENSG00000134516	ENST00000256935	.	.	.	5.96	5.1	0.69264	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.5321	0.61627	0.4227:0.5773:0.0:0.0	.	.	.	.	X	260	.	ENSP00000256935:R260X	R	+	1	2	DOCK2	169048850	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.462000	0.35266	1.530000	0.49136	-0.152000	0.13540	CGA		0.522	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
FBXW11	23291	broad.mit.edu	37	5	171337585	171337585	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:171337585C>T	ENST00000265094.5	-	3	501	c.364G>A	c.(364-366)Gct>Act	p.A122T	FBXW11_ENST00000296933.6_Missense_Mutation_p.A109T|FBXW11_ENST00000425623.2_Missense_Mutation_p.A90T|FBXW11_ENST00000393802.2_Missense_Mutation_p.A88T|FBXW11_ENST00000522891.1_5'Flank	NM_012300.2	NP_036432.2	Q9UKB1	FBW1B_HUMAN	F-box and WD repeat domain containing 11	122					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.A122T(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	21	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CCTGGTAAAGCGGTAATAAAG	0.408																																					p.A88T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G262A	5						.						49.0	46.0	47.0					5																	171337585		2203	4300	6503	171270190	SO:0001583	missense	23291	exon2			AB014596	CCDS34289.1, CCDS47340.1, CCDS47341.1	5q35.1	2013-01-09	2007-02-08	2004-06-16	ENSG00000072803	ENSG00000072803		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13607	protein-coding gene	gene with protein product		605651	"""F-box and WD-40 domain protein 1B"", ""F-box and WD-40 domain protein 11"""	FBXW1B		10531035, 10694485	Standard	NM_033644		Approved	KIAA0696, Fbw1b, BTRCP2, BTRC2, Hos, Fbw11	uc003mbm.1	Q9UKB1	OTTHUMG00000163267	ENST00000265094.5:c.364G>A	5.37:g.171337585C>T	ENSP00000265094:p.Ala122Thr	Somatic		Capture	Illumina HiSeq	Phase_I	171270190	NM_033645	B2RC98|Q9P2S8|Q9P2S9|Q9Y4C6	Missense_Mutation	SNP	ENST00000265094.5	37	CCDS34289.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.538722	0.85917	.	.	ENSG00000072803	ENST00000296933;ENST00000265094;ENST00000393802;ENST00000425623;ENST00000517395	T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96	6.16	6.16	0.99307	F-box domain, Skp2-like (1);	0.000000	0.85682	D	0.000000	T	0.17619	0.0423	L	0.35854	1.095	0.80722	D	1	P;P;P;P	0.48089	0.847;0.838;0.847;0.905	B;B;B;B	0.35550	0.11;0.149;0.154;0.205	T	0.02991	-1.1085	10	0.22109	T	0.4	-16.5552	20.4549	0.99139	0.0:1.0:0.0:0.0	.	90;88;122;109	B4DH70;Q9UKB1-2;Q9UKB1;Q9UKB1-3	.;.;FBW1B_HUMAN;.	T	109;122;88;90;143	ENSP00000296933:A109T;ENSP00000265094:A122T;ENSP00000377391:A88T;ENSP00000444929:A90T;ENSP00000428753:A143T	ENSP00000265094:A122T	A	-	1	0	FBXW11	171270190	1.000000	0.71417	0.982000	0.44146	0.997000	0.91878	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	GCT		0.408	FBXW11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372382.1	NM_012300	
NKX2-5	1482	broad.mit.edu	37	5	172660062	172660062	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:172660062T>C	ENST00000329198.4	-	2	758	c.485A>G	c.(484-486)tAc>tGc	p.Y162C	NKX2-5_ENST00000424406.2_3'UTR|NKX2-5_ENST00000521848.1_3'UTR	NM_001166175.1|NM_001166176.1|NM_004387.3	NP_001159647.1|NP_001159648.1|NP_004378.1	P52952	NKX25_HUMAN	NK2 homeobox 5	162					adult heart development (GO:0007512)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial cardiac muscle cell development (GO:0055014)|atrial septum morphogenesis (GO:0060413)|atrioventricular node cell development (GO:0060928)|atrioventricular node cell fate commitment (GO:0060929)|BMP signaling pathway (GO:0030509)|bundle of His development (GO:0003166)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac ventricle formation (GO:0003211)|cell differentiation (GO:0030154)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|hemopoiesis (GO:0030097)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|pharyngeal system development (GO:0060037)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart contraction (GO:0045823)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of voltage-gated calcium channel activity (GO:1901387)|proepicardium development (GO:0003342)|pulmonary myocardium development (GO:0003350)|Purkinje myocyte differentiation (GO:0003168)|regulation of cardiac muscle cell proliferation (GO:0060043)|regulation of cardiac muscle contraction (GO:0055117)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|sarcomere organization (GO:0045214)|septum secundum development (GO:0003285)|spleen development (GO:0048536)|thyroid gland development (GO:0030878)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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 transcription cofactor activity (GO:0001104)|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)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Y162C(1)		breast(1)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)	12	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GGCCGACAGGTACCGCTGCTG	0.677																																					p.Y162C	Esophageal Squamous(72;810 1219 2387 13420 44943)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A485G	5						.						17.0	15.0	15.0					5																	172660062		2202	4298	6500	172592668	SO:0001583	missense	1482	exon2			AB021133	CCDS4387.1, CCDS54949.1, CCDS54950.1	5q34	2014-09-17	2011-06-01	2002-10-04	ENSG00000183072	ENSG00000183072		"""Homeoboxes / ANTP class : NKL subclass"""	2488	protein-coding gene	gene with protein product	"""tinman paralog (Drosophila)"""	600584	"""cardiac-specific homeo box"", ""NK2 transcription factor related, locus 5 (Drosophila)"""	CSX, NKX2E		7665173, 8900537	Standard	NM_004387		Approved	CSX1, NKX2.5, NKX4-1	uc003mcm.2	P52952	OTTHUMG00000130522	ENST00000329198.4:c.485A>G	5.37:g.172660062T>C	ENSP00000327758:p.Tyr162Cys	Somatic		Capture	Illumina HiSeq	Phase_I	172592668	NM_004387	A8K3K0|B4DNB6|E9PBU6	Missense_Mutation	SNP	ENST00000329198.4	37	CCDS4387.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.253152	0.80135	.	.	ENSG00000183072	ENST00000329198	D	0.97430	-4.38	4.12	4.12	0.48240	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.47852	D	0.000203	D	0.98861	0.9615	H	0.96239	3.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99376	1.0921	10	0.87932	D	0	.	13.5702	0.61843	0.0:0.0:0.0:1.0	.	162	P52952	NKX25_HUMAN	C	162	ENSP00000327758:Y162C	ENSP00000327758:Y162C	Y	-	2	0	NKX2-5	172592668	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.797000	0.85911	1.870000	0.54199	0.379000	0.24179	TAC		0.677	NKX2-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252942.2		
FAF2	23197	broad.mit.edu	37	5	175921028	175921028	+	Missense_Mutation	SNP	G	G	A	rs146584253		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:175921028G>A	ENST00000261942.6	+	6	565	c.512G>A	c.(511-513)cGc>cAc	p.R171H		NM_014613.2	NP_055428.1	Q96CS3	FAF2_HUMAN	Fas associated factor family member 2	171					lipid particle organization (GO:0034389)|negative regulation of catalytic activity (GO:0043086)|response to unfolded protein (GO:0006986)	Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	lipase binding (GO:0035473)|lipase inhibitor activity (GO:0055102)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.R171H(1)		breast(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						AGGGAGCTTCGCTTTCTTTTG	0.403																																					p.R171H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G512A	5						.	G	HIS/ARG	0,4406		0,0,2203	163.0	155.0	158.0		512	5.4	1.0	5	dbSNP_134	158	1,8599	1.2+/-3.3	0,1,4299	no	missense	FAF2	NM_014613.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	171/446	175921028	1,13005	2203	4300	6503	175853634	SO:0001583	missense	23197	exon6			BC015791	CCDS34296.1	5q35.2	2011-06-28	2008-07-25	2008-07-25	ENSG00000113194	ENSG00000113194		"""UBX domain containing"""	24666	protein-coding gene	gene with protein product	"""expressed in T cells and eosinophils in atopic dermatitis"", ""UBX domain protein 3B"""		"""UBX domain containing 8"""	UBXD8		10048485, 12372427	Standard	NM_014613		Approved	ETEA, KIAA0887, UBXN3B	uc003mej.4	Q96CS3	OTTHUMG00000163228	ENST00000261942.6:c.512G>A	5.37:g.175921028G>A	ENSP00000261942:p.Arg171His	Somatic		Capture	Illumina HiSeq	Phase_I	175853634	NM_014613	O94963|Q8IUF2|Q9BRP2|Q9BVM7	Missense_Mutation	SNP	ENST00000261942.6	37	CCDS34296.1	.	.	.	.	.	.	.	.	.	.	G	33	5.289300	0.95517	0.0	1.16E-4	ENSG00000113194	ENST00000261942;ENST00000540174	T	0.52057	0.68	5.36	5.36	0.76844	UAS (1);	0.000000	0.85682	D	0.000000	T	0.71888	0.3393	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.75513	-0.3291	10	0.87932	D	0	-10.9117	19.4543	0.94882	0.0:0.0:1.0:0.0	.	171	Q96CS3	FAF2_HUMAN	H	171	ENSP00000261942:R171H	ENSP00000261942:R171H	R	+	2	0	FAF2	175853634	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	9.378000	0.97191	2.664000	0.90586	0.650000	0.86243	CGC		0.403	FAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372194.1	NM_014613	
TSPAN17	26262	broad.mit.edu	37	5	176083806	176083806	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:176083806G>A	ENST00000503045.1	+	7	731	c.676G>A	c.(676-678)Gcc>Acc	p.A226T	TSPAN17_ENST00000508164.1_Missense_Mutation_p.A246T|TSPAN17_ENST00000405525.2_Missense_Mutation_p.A249T|TSPAN17_ENST00000515708.1_Missense_Mutation_p.A246T|TSPAN17_ENST00000310032.8_Missense_Mutation_p.A249T|TSPAN17_ENST00000298564.10_Missense_Mutation_p.A138T			Q96FV3	TSN17_HUMAN	tetraspanin 17	246					establishment of protein localization to organelle (GO:0072594)|protein ubiquitination (GO:0016567)	integral component of membrane (GO:0016021)|ubiquitin ligase complex (GO:0000151)	enzyme binding (GO:0019899)|ubiquitin-protein transferase activity (GO:0004842)	p.A246T(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	13	all_cancers(89;0.00141)|Renal(175;0.000269)|Lung NSC(126;0.00814)|all_lung(126;0.0133)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CATGGGCATCGCCCTCCTCCA	0.622																																					p.A246T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G736A	5						.						136.0	122.0	126.0					5																	176083806		2203	4300	6503	176016412	SO:0001583	missense	26262	exon7			AF174603	CCDS34298.1, CCDS47346.1, CCDS47346.2, CCDS54952.1	5q35.3	2013-02-14	2005-03-21	2005-03-21	ENSG00000048140	ENSG00000048140		"""Tetraspanins"""	13594	protein-coding gene	gene with protein product			"""F-box only protein 23, transmembrane 4 superfamily member 17"""	FBXO23, TM4SF17		10531035, 10531037	Standard	NM_012171		Approved	FBX23	uc003met.3	Q96FV3	OTTHUMG00000163230	ENST00000503045.1:c.676G>A	5.37:g.176083806G>A	ENSP00000425212:p.Ala226Thr	Somatic		Capture	Illumina HiSeq	Phase_I	176016412	NM_001006616	Q6NXF7|Q96S98|Q9UKB9	Missense_Mutation	SNP	ENST00000503045.1	37		.	.	.	.	.	.	.	.	.	.	G	22.0	4.229363	0.79688	.	.	ENSG00000048140	ENST00000310032;ENST00000405525;ENST00000298564;ENST00000508164;ENST00000504168;ENST00000503045;ENST00000515708	D;D;D;D;D;D;D	0.81996	-1.56;-1.56;-1.56;-1.56;-1.56;-1.56;-1.56	4.71	3.83	0.44106	.	0.000000	0.85682	D	0.000000	D	0.91610	0.7349	M	0.89601	3.045	0.58432	D	0.999996	D;D;D;D;D	0.89917	0.958;1.0;0.973;1.0;1.0	P;D;P;D;D	0.83275	0.493;0.978;0.476;0.987;0.996	D	0.91575	0.5274	10	0.49607	T	0.09	-9.2282	11.8573	0.52446	0.0873:0.0:0.9127:0.0	.	246;249;246;246;138	Q96FV3-3;C9J7R4;Q96FV3-4;Q96FV3;Q96FV3-2	.;.;.;TSN17_HUMAN;.	T	249;249;138;246;234;226;246	ENSP00000309036:A249T;ENSP00000385665:A249T;ENSP00000298564:A138T;ENSP00000422053:A246T;ENSP00000423957:A234T;ENSP00000425212:A226T;ENSP00000426650:A246T	ENSP00000298564:A138T	A	+	1	0	TSPAN17	176016412	1.000000	0.71417	0.969000	0.41365	0.575000	0.36095	9.791000	0.99081	0.971000	0.38288	0.491000	0.48974	GCC		0.622	TSPAN17-008	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372215.1		
HK3	3101	broad.mit.edu	37	5	176314527	176314527	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:176314527C>A	ENST00000292432.5	-	11	1616	c.1525G>T	c.(1525-1527)Gcc>Tcc	p.A509S		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	509	Catalytic.|Hexokinase type-1 2.				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.A509S(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)			AGCCCCTTGGCCATGGCCTTC	0.667																																					p.A509S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1525T	5						.						35.0	34.0	34.0					5																	176314527		2203	4300	6503	176247133	SO:0001583	missense	3101	exon11				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.1525G>T	5.37:g.176314527C>A	ENSP00000292432:p.Ala509Ser	Somatic		Capture	Illumina HiSeq	Phase_I	176247133	NM_002115	Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	37	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	C	13.24	2.177694	0.38413	.	.	ENSG00000160883	ENST00000292432	D	0.98207	-4.79	4.3	2.48	0.30137	Hexokinase, N-terminal (1);	1.847160	0.03314	N	0.190844	D	0.95252	0.8460	N	0.20807	0.61	0.27933	N	0.93779	B	0.09022	0.002	B	0.20184	0.028	D	0.88865	0.3329	10	0.32370	T	0.25	.	7.703	0.28634	0.0:0.7952:0.0:0.2048	.	509	P52790	HXK3_HUMAN	S	509	ENSP00000292432:A509S	ENSP00000292432:A509S	A	-	1	0	HK3	176247133	0.439000	0.25610	0.463000	0.27130	0.903000	0.53119	1.075000	0.30716	0.265000	0.21872	0.462000	0.41574	GCC		0.667	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
DDX41	51428	broad.mit.edu	37	5	176938921	176938921	+	Silent	SNP	G	G	A	rs148650463		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:176938921G>A	ENST00000507955.1	-	17	2263	c.1740C>T	c.(1738-1740)cgC>cgT	p.R580R	DOK3_ENST00000357198.4_5'Flank|DOK3_ENST00000312943.6_5'Flank|DOK3_ENST00000501403.2_5'Flank|DOK3_ENST00000377112.4_5'Flank	NM_016222.2	NP_057306.2	Q9UJV9	DDX41_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	580					apoptotic process (GO:0006915)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)|RNA processing (GO:0006396)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.R580R(1)				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)|Epithelial(233;0.191)			AGGCACAGCCGCGCTCTCCTG	0.642																																					p.R580R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1740T	5						.	G		2,4402	4.2+/-10.8	0,2,2200	48.0	50.0	49.0		1740	-11.8	0.7	5	dbSNP_134	49	0,8600		0,0,4300	no	coding-synonymous	DDX41	NM_016222.2		0,2,6500	AA,AG,GG		0.0,0.0454,0.0154		580/623	176938921	2,13002	2202	4300	6502	176871527	SO:0001819	synonymous_variant	51428	exon17			AF195417	CCDS4427.1	5q35.3	2008-02-05			ENSG00000183258	ENSG00000183258		"""DEAD-boxes"""	18674	protein-coding gene	gene with protein product		608170				10607561	Standard	NM_016222		Approved	ABS, MGC8828	uc003mho.3	Q9UJV9	OTTHUMG00000130858	ENST00000507955.1:c.1740C>T	5.37:g.176938921G>A		Somatic		Capture	Illumina HiSeq	Phase_I	176871527	NM_016222	B2RDC8|Q96BK6|Q96K05|Q9NT96|Q9NW04	Silent	SNP	ENST00000507955.1	37	CCDS4427.1																																																																																				0.642	DDX41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253432.2	NM_016222	
FAM193B	54540	broad.mit.edu	37	5	176963388	176963388	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:176963388C>T	ENST00000514747.1	-	4	1095	c.1047G>A	c.(1045-1047)ccG>ccA	p.P349P	FAM193B_ENST00000508298.1_Intron|FAM193B_ENST00000329540.5_5'UTR|FAM193B_ENST00000443375.2_Silent_p.P236P	NM_001190946.1	NP_001177875.1	Q96PV7	F193B_HUMAN	family with sequence similarity 193, member B	349	Pro-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.P236P(1)		kidney(1)|large_intestine(3)	4						GCTGAGAGCTCGGGGGTGGGA	0.587																																					p.P349P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1047A	5						.						15.0	16.0	16.0					5																	176963388		1994	4137	6131	176895994	SO:0001819	synonymous_variant	54540	exon4				CCDS54954.1	5q35	2010-02-17			ENSG00000146067	ENSG00000146067			25524	protein-coding gene	gene with protein product		615813				11572484	Standard	NR_024019		Approved	KIAA1931, FLJ10404	uc003mhu.3	Q96PV7	OTTHUMG00000163396	ENST00000514747.1:c.1047G>A	5.37:g.176963388C>T		Somatic		Capture	Illumina HiSeq	Phase_I	176895994	NM_001190946	E9PET5|Q9NW00	Silent	SNP	ENST00000514747.1	37	CCDS54954.1																																																																																				0.587	FAM193B-003	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373121.1	NM_019057	
COL23A1	91522	broad.mit.edu	37	5	177715339	177715339	+	Nonsense_Mutation	SNP	G	G	A	rs373614230		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:177715339G>A	ENST00000390654.3	-	5	784	c.427C>T	c.(427-429)Cga>Tga	p.R143*	COL23A1_ENST00000407622.1_Intron	NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	143	Collagen-like 1.|Gly-rich.				collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R143*(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(89;0.00188)|Renal(175;0.000159)|Lung NSC(126;0.00814)|all_lung(126;0.0129)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.153)|all cancers(165;0.172)		TAGCCATCTCGTCCTGATTGC	0.413																																					p.R143X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C427T	5						.	G	stop/ARG	0,3758		0,0,1879	150.0	147.0	148.0		427	4.7	1.0	5		148	1,8233		0,1,4116	no	stop-gained	COL23A1	NM_173465.3		0,1,5995	AA,AG,GG		0.0121,0.0,0.0083		143/541	177715339	1,11991	1879	4117	5996	177647945	SO:0001587	stop_gained	91522	exon5			AL137461	CCDS4436.1	5q35.3	2013-01-16			ENSG00000050767	ENSG00000050767		"""Collagens"""	22990	protein-coding gene	gene with protein product		610043				12644459	Standard	NM_173465		Approved	DKFZp434K0621	uc021yiz.1	Q86Y22	OTTHUMG00000130890	ENST00000390654.3:c.427C>T	5.37:g.177715339G>A	ENSP00000375069:p.Arg143*	Somatic		Capture	Illumina HiSeq	Phase_I	177647945	NM_173465	Q8IVR4|Q9NT93	Nonsense_Mutation	SNP	ENST00000390654.3	37	CCDS4436.1	.	.	.	.	.	.	.	.	.	.	G	36	5.822439	0.96989	0.0	1.21E-4	ENSG00000050767	ENST00000390654	.	.	.	5.59	4.72	0.59763	.	0.308460	0.20082	N	0.099630	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-0.5113	12.7033	0.57046	0.0:0.1653:0.8346:0.0	.	.	.	.	X	143	.	ENSP00000375069:R143X	R	-	1	2	COL23A1	177647945	1.000000	0.71417	1.000000	0.80357	0.177000	0.22998	3.370000	0.52372	1.364000	0.46038	-0.127000	0.14921	CGA		0.413	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253475.1	NM_173465	
ZNF354B	117608	broad.mit.edu	37	5	178310208	178310208	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:178310208G>A	ENST00000322434.3	+	5	981	c.755G>A	c.(754-756)aGc>aAc	p.S252N	RNU1-39P_ENST00000383897.1_RNA	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	252					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.S252N(1)		breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAAGCTTTCAGCCAAAGTTCT	0.353																																					p.S252N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G755A	5						.						62.0	72.0	69.0					5																	178310208		2200	4298	6498	178242814	SO:0001583	missense	117608	exon5			AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"""Zinc fingers, C2H2-type"", ""-"""	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.755G>A	5.37:g.178310208G>A	ENSP00000327143:p.Ser252Asn	Somatic		Capture	Illumina HiSeq	Phase_I	178242814	NM_058230	A8K0V2|Q5U5Z4	Missense_Mutation	SNP	ENST00000322434.3	37	CCDS4439.1	.	.	.	.	.	.	.	.	.	.	G	6.582	0.475744	0.12521	.	.	ENSG00000178338	ENST00000322434	T	0.07567	3.18	3.44	-1.27	0.09347	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04724	0.0128	N	0.25286	0.73	0.18873	N	0.999988	B	0.02656	0.0	B	0.04013	0.001	T	0.42137	-0.9469	9	0.31617	T	0.26	.	3.7171	0.08442	0.1036:0.4435:0.3013:0.1516	.	252	Q96LW1	Z354B_HUMAN	N	252	ENSP00000327143:S252N	ENSP00000327143:S252N	S	+	2	0	ZNF354B	178242814	0.000000	0.05858	0.987000	0.45799	0.966000	0.64601	-0.326000	0.07965	-0.126000	0.11682	-0.305000	0.09177	AGC		0.353	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230	
ZNF354C	30832	broad.mit.edu	37	5	178505831	178505831	+	Missense_Mutation	SNP	A	A	G	rs57271258	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:178505831A>G	ENST00000315475.6	+	5	704	c.398A>G	c.(397-399)gAg>gGg	p.E133G		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	133					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.E133G(1)		endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		TTTGAGAGCGAGATAGAAGAA	0.378													G|||	122	0.024361	0.0862	0.0115	5008	,	,		20349	0.0		0.0	False		,,,				2504	0.0				p.E133G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A398G	5						.	G	GLY/GLU	312,4094	788.4+/-414.9	9,294,1900	90.0	95.0	93.0		398	1.0	0.0	5	dbSNP_129	93	0,8600		0,0,4300	yes	missense	ZNF354C	NM_014594.1	98	9,294,6200	GG,GA,AA		0.0,7.0813,2.3989	benign	133/555	178505831	312,12694	2203	4300	6503	178438437	SO:0001583	missense	30832	exon5				CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.398A>G	5.37:g.178505831A>G	ENSP00000324064:p.Glu133Gly	Somatic		Capture	Illumina HiSeq	Phase_I	178438437	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	30	0.013736263736263736	27	0.054878048780487805	3	0.008287292817679558	0	0.0	0	0.0	G	7.305	0.613748	0.14066	0.070813	0.0	ENSG00000177932	ENST00000315475	T	0.05786	3.39	3.87	1.04	0.20106	.	.	.	.	.	T	0.00241	0.0007	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48747	-0.9008	9	0.16896	T	0.51	1.603	3.2954	0.06964	0.3129:0.0:0.505:0.182	rs57271258	133	Q86Y25	Z354C_HUMAN	G	133	ENSP00000324064:E133G	ENSP00000324064:E133G	E	+	2	0	ZNF354C	178438437	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.082000	0.03400	-0.148000	0.11234	-0.930000	0.02707	GAG		0.378	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
ZNF354C	30832	broad.mit.edu	37	5	178506440	178506440	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:178506440C>T	ENST00000315475.6	+	5	1313	c.1007C>T	c.(1006-1008)gCc>gTc	p.A336V		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	336					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.A336V(1)		endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		TGTGAGAAGGCCTTCAACTGT	0.433																																					p.A336V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1007T	5						.						171.0	182.0	178.0					5																	178506440		2203	4300	6503	178439046	SO:0001583	missense	30832	exon5				CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.1007C>T	5.37:g.178506440C>T	ENSP00000324064:p.Ala336Val	Somatic		Capture	Illumina HiSeq	Phase_I	178439046	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.477358	0.63849	.	.	ENSG00000177932	ENST00000315475	T	0.19105	2.17	4.04	3.09	0.35607	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.33469	0.0864	L	0.53249	1.67	0.29560	N	0.850703	D	0.56287	0.975	P	0.57425	0.82	T	0.06023	-1.0850	9	0.46703	T	0.11	-9.1708	10.8397	0.46708	0.1887:0.8113:0.0:0.0	.	336	Q86Y25	Z354C_HUMAN	V	336	ENSP00000324064:A336V	ENSP00000324064:A336V	A	+	2	0	ZNF354C	178439046	0.226000	0.23696	1.000000	0.80357	0.990000	0.78478	0.856000	0.27818	2.226000	0.72624	0.591000	0.81541	GCC		0.433	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
ADAMTS2	9509	broad.mit.edu	37	5	178562942	178562942	+	Missense_Mutation	SNP	C	C	T	rs367549580		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:178562942C>T	ENST00000251582.7	-	13	2154	c.2053G>A	c.(2053-2055)Gcc>Acc	p.A685T		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	685	Cys-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.A685T(2)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		AGGCTGAAGGCGTCCTTGTAG	0.637																																					p.A685T												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G2053A	5						.	C	THR/ALA	0,4406		0,0,2203	83.0	76.0	78.0		2053	2.5	1.0	5		78	1,8599	1.2+/-3.3	0,1,4299	no	missense	ADAMTS2	NM_014244.4	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	685/1212	178562942	1,13005	2203	4300	6503	178495548	SO:0001583	missense	9509	exon13			AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.2053G>A	5.37:g.178562942C>T	ENSP00000251582:p.Ala685Thr	Somatic		Capture	Illumina HiSeq	Phase_I	178495548	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.679603	0.47886	0.0	1.16E-4	ENSG00000087116	ENST00000251582	T	0.69685	-0.42	5.37	2.45	0.29901	.	0.233607	0.29900	N	0.010906	T	0.33760	0.0874	N	0.04203	-0.255	0.80722	D	1	P	0.45986	0.87	B	0.33846	0.171	T	0.16630	-1.0396	10	0.49607	T	0.09	.	5.4769	0.16700	0.1167:0.498:0.3025:0.0828	.	685	O95450	ATS2_HUMAN	T	685	ENSP00000251582:A685T	ENSP00000251582:A685T	A	-	1	0	ADAMTS2	178495548	0.279000	0.24239	0.995000	0.50966	0.962000	0.63368	0.634000	0.24614	0.606000	0.29965	0.462000	0.41574	GCC		0.637	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
MGAT4B	11282	broad.mit.edu	37	5	179225961	179225961	+	Missense_Mutation	SNP	C	C	T	rs146867088		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:179225961C>T	ENST00000292591.7	-	11	1660	c.1310G>A	c.(1309-1311)cGc>cAc	p.R437H	MGAT4B_ENST00000337755.5_Missense_Mutation_p.R452H|MIR1229_ENST00000408467.1_RNA|MGAT4B_ENST00000521305.1_5'Flank	NM_014275.4	NP_055090.1	Q9UQ53	MGT4B_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme B	437					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)	p.R452H(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	13	all_cancers(89;0.000201)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0525)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAAGCGGAAGCGGATGAAGTC	0.632																																					p.R437H	GBM(13;414 434 4098 22176 23230)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1310A	5						.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	72.0	74.0	73.0		1310,1355	3.3	1.0	5	dbSNP_134	73	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	MGAT4B	NM_014275.4,NM_054013.3	29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging	437/549,452/564	179225961	2,13004	2203	4300	6503	179158567	SO:0001583	missense	11282	exon11			AB000624	CCDS4448.1, CCDS4449.1	5q35	2013-02-25	2005-11-16		ENSG00000161013	ENSG00000161013	2.4.1.145	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7048	protein-coding gene	gene with protein product		604561	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme B"""			10372966	Standard	NM_014275		Approved	GnT-Ivb	uc003mks.3	Q9UQ53	OTTHUMG00000130912	ENST00000292591.7:c.1310G>A	5.37:g.179225961C>T	ENSP00000292591:p.Arg437His	Somatic		Capture	Illumina HiSeq	Phase_I	179158567	NM_014275	A8MPR0|Q86TF1|Q96GH4|Q9NSK6	Missense_Mutation	SNP	ENST00000292591.7	37	CCDS4448.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.91|19.91	3.914485|3.914485	0.72983|0.72983	0.0|0.0	2.33E-4|2.33E-4	ENSG00000161013|ENSG00000161013	ENST00000520969;ENST00000518980|ENST00000337755;ENST00000292591;ENST00000519836	.|T;T	.|0.32023	.|1.47;1.49	4.17|4.17	3.29|3.29	0.37713|0.37713	.|.	.|0.063524	.|0.64402	.|D	.|0.000010	T|T	0.46171|0.46171	0.1379|0.1379	L|L	0.47716|0.47716	1.5|1.5	0.58432|0.58432	D|D	0.999995|0.999995	.|D;D;D	.|0.76494	.|0.989;0.996;0.999	.|P;P;D	.|0.78314	.|0.548;0.549;0.991	T|T	0.34453|0.34453	-0.9828|-0.9828	5|10	.|0.44086	.|T	.|0.13	-29.7862|-29.7862	13.2476|13.2476	0.60031|0.60031	0.16:0.84:0.0:0.0|0.16:0.84:0.0:0.0	.|.	.|437;452;436	.|Q9UQ53;A8MPR0;Q9UQ53-2	.|MGT4B_HUMAN;.;.	T|H	134;183|452;437;305	.|ENSP00000338487:R452H;ENSP00000292591:R437H	.|ENSP00000292591:R437H	A|R	-|-	1|2	0|0	MGAT4B|MGAT4B	179158567|179158567	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	1.684000|1.684000	0.37649|0.37649	0.941000|0.941000	0.37499|0.37499	0.561000|0.561000	0.74099|0.74099	GCT|CGC		0.632	MGAT4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253503.3	NM_014275	
SDHA	6389	broad.mit.edu	37	5	251567	251567	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:251567C>T	ENST00000264932.6	+	13	1893	c.1778C>T	c.(1777-1779)gCc>gTc	p.A593V	SDHA_ENST00000507522.1_3'UTR|SDHA_ENST00000504309.1_Intron|SDHA_ENST00000510361.1_Missense_Mutation_p.A545V	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	593					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.A593V(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)	GGCGCGCATGCCAGGGAAGAC	0.627									Familial Paragangliomas																												p.A593V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1778T	5						.						46.0	52.0	50.0					5																	251567		2203	4300	6503	304567	SO:0001583	missense	6389	exon13	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.1778C>T	5.37:g.251567C>T	ENSP00000264932:p.Ala593Val	Somatic		Capture	Illumina HiSeq	Phase_I	304567	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	.	.	.	.	.	.	.	.	.	.	N	17.17	3.321478	0.60634	.	.	ENSG00000073578	ENST00000264932;ENST00000327872;ENST00000510361;ENST00000509564	T;T;T	0.80566	-1.39;-1.39;-1.39	3.79	3.79	0.43588	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal (2);Fumarate reductase/succinate dehydrogenase flavoprotein, C-terminal (1);	0.148160	0.44902	U	0.000408	D	0.89508	0.6735	M	0.88450	2.955	0.80722	D	1	D;D;D;D	0.69078	0.992;0.989;0.997;0.989	D;P;P;P	0.63113	0.911;0.791;0.789;0.793	D	0.91683	0.5360	10	0.87932	D	0	.	13.5022	0.61462	0.0:1.0:0.0:0.0	.	545;593;187;593	E9PBJ5;B4DYN5;B3KYA5;P31040	.;.;.;DHSA_HUMAN	V	593;448;545;39	ENSP00000264932:A593V;ENSP00000427703:A545V;ENSP00000421911:A39V	ENSP00000264932:A593V	A	+	2	0	SDHA	304567	1.000000	0.71417	0.979000	0.43373	0.060000	0.15804	7.033000	0.76504	1.853000	0.53794	0.305000	0.20034	GCC		0.627	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
SDHA	6389	broad.mit.edu	37	5	256514	256514	+	Silent	SNP	G	G	C	rs1042446	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:256514G>C	ENST00000264932.6	+	15	2089	c.1974G>C	c.(1972-1974)ccG>ccC	p.P658P	SDHA_ENST00000507522.1_3'UTR|SDHA_ENST00000504309.1_Silent_p.P577P|SDHA_ENST00000510361.1_Silent_p.P610P	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	658					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)			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)	CCACCGTCCCGCCAGCCATTC	0.443									Familial Paragangliomas																												p.P658P												.	.	0			c.G1974C	5						.						69.0	74.0	72.0					5																	256514		2203	4300	6503	309514	SO:0001819	synonymous_variant	6389	exon15	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.1974G>C	5.37:g.256514G>C		None		Capture	Illumina HiSeq	Phase_I	309514	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																				0.443	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
PDCD6	10016	broad.mit.edu	37	5	311467	311467	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:311467C>T	ENST00000264933.4	+	5	527	c.427C>T	c.(427-429)Cgg>Tgg	p.R143W	AHRR_ENST00000505113.1_Intron|PDCD6_ENST00000507528.1_Missense_Mutation_p.R141W|AHRR_ENST00000512529.1_Intron|AHRR_ENST00000316418.5_Intron|PDCD6_ENST00000505221.1_Intron|PDCD6_ENST00000511482.1_3'UTR	NM_001267556.1|NM_001267558.1|NM_013232.3	NP_001254485.1|NP_001254487.1|NP_037364.1	O75340	PDCD6_HUMAN	programmed cell death 6	143	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|proteolysis (GO:0006508)|response to calcium ion (GO:0051592)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|calcium-dependent protein binding (GO:0048306)|protein dimerization activity (GO:0046983)	p.R143W(1)		breast(2)|endometrium(1)|large_intestine(4)|lung(1)	8			Epithelial(17;0.00193)|OV - Ovarian serous cystadenocarcinoma(19;0.00489)|all cancers(22;0.00511)|Lung(60;0.113)			CAGGCAGGGACGGGGGCAGAT	0.577																																					p.R143W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C427T	5						.						103.0	85.0	91.0					5																	311467		2203	4299	6502	364467	SO:0001583	missense	10016	exon5			AF035606	CCDS3854.1, CCDS58940.1, CCDS58941.1, CCDS75222.1, CCDS75223.1	5p15.33	2013-01-10			ENSG00000249915	ENSG00000249915		"""EF-hand domain containing"""	8765	protein-coding gene	gene with protein product	"""apoptosis-linked gene-2"""	601057				8560270	Standard	NM_013232		Approved	ALG-2, PEF1B	uc003jat.1	O75340	OTTHUMG00000090283	ENST00000264933.4:c.427C>T	5.37:g.311467C>T	ENSP00000264933:p.Arg143Trp	Somatic		Capture	Illumina HiSeq	Phase_I	364467	NM_013232	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Missense_Mutation	SNP	ENST00000264933.4	37	CCDS3854.1	.	.	.	.	.	.	.	.	.	.	c	18.17	3.565360	0.65651	.	.	ENSG00000249915	ENST00000264933;ENST00000507528;ENST00000507473	T;T;T	0.78816	-0.59;-0.59;-1.21	5.83	3.84	0.44239	EF-hand-like domain (1);	.	.	.	.	D	0.86756	0.6009	M	0.89095	3.005	0.80722	D	1	D;D	0.69078	0.997;0.996	P;P	0.57244	0.816;0.668	D	0.88129	0.2837	9	0.87932	D	0	.	12.2987	0.54862	0.332:0.668:0.0:0.0	.	141;143	Q2YDC2;O75340	.;PDCD6_HUMAN	W	143;141;56	ENSP00000264933:R143W;ENSP00000423815:R141W;ENSP00000425370:R56W	ENSP00000264933:R143W	R	+	1	2	PDCD6	364467	1.000000	0.71417	0.815000	0.32552	0.360000	0.29518	3.523000	0.53488	0.736000	0.32559	0.655000	0.94253	CGG		0.577	PDCD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206609.2	NM_013232	
SLC9A3	6550	broad.mit.edu	37	5	477552	477552	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:477552C>T	ENST00000264938.3	-	11	1664	c.1655G>A	c.(1654-1656)cGc>cAc	p.R552H	CTD-2228K2.7_ENST00000607286.1_RNA|CTD-2228K2.7_ENST00000606319.1_RNA|SLC9A3_ENST00000514375.1_Missense_Mutation_p.R543H|CTD-2228K2.7_ENST00000606288.1_RNA|CTD-2228K2.7_ENST00000607005.1_RNA	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	552					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.R552H(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)			GGACCCGCGGCGCTCTCCCTG	0.672																																					p.R552H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1655A	5						.						55.0	43.0	47.0					5																	477552		2203	4300	6503	530552	SO:0001583	missense	6550	exon11				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.1655G>A	5.37:g.477552C>T	ENSP00000264938:p.Arg552His	Somatic		Capture	Illumina HiSeq	Phase_I	530552	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Missense_Mutation	SNP	ENST00000264938.3	37	CCDS3855.1	.	.	.	.	.	.	.	.	.	.	C	17.84	3.487257	0.63962	.	.	ENSG00000066230	ENST00000264938;ENST00000514375	T;T	0.79141	-1.24;-1.24	4.88	4.88	0.63580	.	0.053634	0.85682	D	0.000000	D	0.84325	0.5447	L	0.52573	1.65	0.48236	D	0.999617	D;D	0.89917	1.0;1.0	D;D	0.83275	0.98;0.996	T	0.81169	-0.1055	10	0.21540	T	0.41	.	17.6513	0.88164	0.0:1.0:0.0:0.0	.	543;552	E9PF67;P48764	.;SL9A3_HUMAN	H	552;543	ENSP00000264938:R552H;ENSP00000422983:R543H	ENSP00000264938:R552H	R	-	2	0	SLC9A3	530552	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	4.805000	0.62561	2.251000	0.74343	0.561000	0.74099	CGC		0.672	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174	
ICE1	23379	broad.mit.edu	37	5	5461142	5461142	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:5461142G>A	ENST00000296564.7	+	13	1917	c.1695G>A	c.(1693-1695)aaG>aaA	p.K565K		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		565					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.K565K(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						AGTTTACTAAGTGGACACGAA	0.388																																					p.K565K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1695A	5						.						148.0	146.0	146.0					5																	5461142		1871	4105	5976	5514142	SO:0001819	synonymous_variant	23379	exon13																														ENST00000296564.7:c.1695G>A	5.37:g.5461142G>A		Somatic		Capture	Illumina HiSeq	Phase_I	5514142	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	37	CCDS47187.1																																																																																				0.388	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
FLJ33360	401172	broad.mit.edu	37	5	6337303	6337303	+	lincRNA	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:6337303G>A	ENST00000507444.1	-	0	102					NR_028351.1																						TGCAGGTGCCGTCCATGCTGT	0.527																																					.												.	.	0			.	5						.						204.0	189.0	194.0					5																	6337303		1983	4166	6149	6390303			401172	.																															5.37:g.6337303G>A		Somatic		Capture	Illumina HiSeq	Phase_I	6390303	.		Silent	SNP	ENST00000507444.1	37																																																																																					0.527	CTD-2324F15.2-001	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000365707.1		
FAM173B	134145	broad.mit.edu	37	5	10227605	10227605	+	Frame_Shift_Del	DEL	C	C	-	rs200573104		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:10227605delC	ENST00000511437.1	-	5	662	c.650delG	c.(649-651)cgtfs	p.R217fs	FAM173B_ENST00000280330.8_Frame_Shift_Del_p.R53fs|FAM173B_ENST00000510047.1_Frame_Shift_Del_p.R200fs|FAM173B_ENST00000510052.1_5'Flank	NM_199133.3	NP_954584.2	Q6P4H8	F173B_HUMAN	family with sequence similarity 173, member B	217						integral component of membrane (GO:0016021)		p.R217L(1)|p.R217fs*>17(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	16						CCTCTTTTCACGGCCTCTAAA	0.488																																					p.R217fs												.	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|lung(1)	c.650delG	5						.						121.0	119.0	120.0					5																	10227605		1953	4137	6090	10280605	SO:0001589	frameshift_variant	134145	exon5				CCDS43301.1, CCDS58942.1	5p15.2	2008-08-08			ENSG00000150756	ENSG00000150756			27029	protein-coding gene	gene with protein product						12477932	Standard	NM_199133		Approved		uc003jeo.3	Q6P4H8	OTTHUMG00000161771	ENST00000511437.1:c.650delG	5.37:g.10227605delC	ENSP00000422338:p.Arg217fs	Somatic		Capture	Illumina HiSeq	Phase_I	10280605	NM_199133	B4DT41|B4DXK2|E9PBZ4	Frame_Shift_Del	DEL	ENST00000511437.1	37	CCDS43301.1																																																																																				0.488	FAM173B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366048.2	NM_199133	
PRDM9	56979	broad.mit.edu	37	5	23527586	23527586	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:23527586A>G	ENST00000296682.3	+	11	2571	c.2389A>G	c.(2389-2391)Aca>Gca	p.T797A		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	797					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.T797A(1)		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						TCACCAGAGGACACACACAGG	0.567										HNSCC(3;0.000094)																											p.T797A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2389G	5						.						86.0	84.0	84.0					5																	23527586		2196	4296	6492	23563343	SO:0001583	missense	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.2389A>G	5.37:g.23527586A>G	ENSP00000296682:p.Thr797Ala	Somatic		Capture	Illumina HiSeq	Phase_I	23563343	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	A	11.58	1.682069	0.29872	.	.	ENSG00000164256	ENST00000296682	T	0.20332	2.08	3.07	3.07	0.35406	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20373	0.0490	L	0.39692	1.235	0.22591	N	0.998959	P	0.42785	0.79	B	0.43225	0.412	T	0.07347	-1.0777	9	0.48119	T	0.1	.	9.8449	0.41021	1.0:0.0:0.0:0.0	.	797	Q9NQV7	PRDM9_HUMAN	A	797	ENSP00000296682:T797A	ENSP00000296682:T797A	T	+	1	0	PRDM9	23563343	0.000000	0.05858	1.000000	0.80357	0.643000	0.38383	0.570000	0.23653	1.649000	0.50652	0.381000	0.24937	ACA		0.567	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
CDH10	1008	broad.mit.edu	37	5	24511608	24511608	+	Missense_Mutation	SNP	C	C	T	rs149518689		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:24511608C>T	ENST00000264463.4	-	6	1337	c.830G>A	c.(829-831)cGa>cAa	p.R277Q		NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	277	Cadherin 3. {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.R277Q(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)		TTCAAGAACTCGAAGATGAAT	0.418										HNSCC(23;0.051)																											p.R277Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G830A	5						.	C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	67.0	62.0	64.0		830	4.1	0.9	5	dbSNP_134	64	1,8599	1.2+/-3.3	0,1,4299	no	missense	CDH10	NM_006727.3	43	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	possibly-damaging	277/789	24511608	3,13003	2203	4300	6503	24547365	SO:0001583	missense	1008	exon6			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.830G>A	5.37:g.24511608C>T	ENSP00000264463:p.Arg277Gln	Somatic		Capture	Illumina HiSeq	Phase_I	24547365	NM_006727	Q9ULB3	Missense_Mutation	SNP	ENST00000264463.4	37	CCDS3892.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.316727	0.81469	4.54E-4	1.16E-4	ENSG00000040731	ENST00000264463	T	0.51325	0.71	4.98	4.11	0.48088	Cadherin (4);Cadherin-like (1);	0.191286	0.42294	D	0.000724	T	0.38453	0.1041	L	0.33792	1.035	0.39061	D	0.960525	P	0.50272	0.933	B	0.42138	0.377	T	0.41251	-0.9519	10	0.62326	D	0.03	.	12.5016	0.55957	0.0:0.9186:0.0:0.0814	.	277	Q9Y6N8	CAD10_HUMAN	Q	277	ENSP00000264463:R277Q	ENSP00000264463:R277Q	R	-	2	0	CDH10	24547365	0.998000	0.40836	0.874000	0.34290	0.942000	0.58702	3.983000	0.56916	1.082000	0.41137	0.650000	0.86243	CGA		0.418	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727	
CDH9	1007	broad.mit.edu	37	5	26881280	26881280	+	Missense_Mutation	SNP	C	C	T	rs368164243		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:26881280C>T	ENST00000231021.4	-	12	2507	c.2335G>A	c.(2335-2337)Gat>Aat	p.D779N		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	779					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.D779N(1)		breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						CCATACATATCGGCAAGTTTT	0.413																																					p.D779N	Melanoma(8;187 585 15745 40864 52829)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2335A	5						.	C	ASN/ASP	0,4406		0,0,2203	140.0	135.0	136.0		2335	5.3	0.9	5		136	1,8597	1.2+/-3.3	0,1,4298	no	missense	CDH9	NM_016279.3	23	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	779/790	26881280	1,13003	2203	4299	6502	26917037	SO:0001583	missense	1007	exon12			AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.2335G>A	5.37:g.26881280C>T	ENSP00000231021:p.Asp779Asn	Somatic		Capture	Illumina HiSeq	Phase_I	26917037	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	C	19.58	3.854070	0.71719	0.0	1.16E-4	ENSG00000113100	ENST00000231021	T	0.78481	-1.18	5.26	5.26	0.73747	Cadherin, cytoplasmic domain (1);	0.090887	0.85682	D	0.000000	T	0.81039	0.4740	M	0.80422	2.495	0.50632	D	0.999889	P;P	0.38110	0.476;0.618	B;B	0.40009	0.316;0.292	T	0.81665	-0.0830	9	.	.	.	.	17.4441	0.87574	0.0:1.0:0.0:0.0	.	372;779	B4DFP0;Q9ULB4	.;CADH9_HUMAN	N	779	ENSP00000231021:D779N	.	D	-	1	0	CDH9	26917037	1.000000	0.71417	0.910000	0.35882	0.917000	0.54804	7.792000	0.85828	2.456000	0.83038	0.557000	0.71058	GAT		0.413	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
CDH6	1004	broad.mit.edu	37	5	31323125	31323125	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:31323125G>A	ENST00000265071.2	+	12	2348	c.2083G>A	c.(2083-2085)Gaa>Aaa	p.E695K		NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	695					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)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E695K(1)		NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CATTGTGCCCGAAGCCCTTTT	0.517																																					p.E695K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2083A	5						.						85.0	79.0	81.0					5																	31323125		2203	4300	6503	31358882	SO:0001583	missense	1004	exon12			D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"""Cadherins / Major cadherins"""	1765	protein-coding gene	gene with protein product	"""K-Cadherin"""	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.2083G>A	5.37:g.31323125G>A	ENSP00000265071:p.Glu695Lys	Somatic		Capture	Illumina HiSeq	Phase_I	31358882	NM_004932	A8K5H5|Q9BWS0	Missense_Mutation	SNP	ENST00000265071.2	37	CCDS3894.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.829697	0.91036	.	.	ENSG00000113361	ENST00000265071	T	0.76709	-1.04	5.66	5.66	0.87406	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.89030	0.6599	M	0.85630	2.765	0.80722	D	1	D	0.63880	0.993	P	0.61874	0.895	D	0.89885	0.4033	10	0.87932	D	0	.	20.1253	0.97977	0.0:0.0:1.0:0.0	.	695	P55285	CADH6_HUMAN	K	695	ENSP00000265071:E695K	ENSP00000265071:E695K	E	+	1	0	CDH6	31358882	1.000000	0.71417	1.000000	0.80357	0.274000	0.26718	9.721000	0.98766	2.832000	0.97577	0.655000	0.94253	GAA		0.517	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932	
DROSHA	29102	broad.mit.edu	37	5	31472171	31472171	+	Splice_Site	SNP	G	G	A	rs202101007		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:31472171G>A	ENST00000511367.2	-	16	2484	c.2240C>T	c.(2239-2241)aCg>aTg	p.T747M	DROSHA_ENST00000513349.1_Splice_Site_p.T710M|DROSHA_ENST00000442743.1_Splice_Site_p.T710M|DROSHA_ENST00000344624.3_Splice_Site_p.T747M	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	747	Necessary for interaction with DGCR8 and pri-miRNA processing activity.				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.T747M(2)		breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						AGAACATACCGTCCCAGGGTT	0.443																																					p.T747M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2240T	5						.	G	MET/THR,MET/THR	0,3972		0,0,1986	140.0	136.0	138.0		2129,2240	4.8	1.0	5		138	1,8299		0,1,4149	no	missense-near-splice,missense-near-splice	DROSHA	NM_001100412.1,NM_013235.4	81,81	0,1,6135	AA,AG,GG		0.012,0.0,0.0081	benign,benign	710/1338,747/1375	31472171	1,12271	1986	4150	6136	31507928	SO:0001630	splice_region_variant	29102	exon16			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.2241+1C>T	5.37:g.31472171G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31507928	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	.	.	.	.	.	.	.	.	.	.	G	8.521	0.868785	0.17322	0.0	1.2E-4	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188	T;T;T;T	0.39592	1.65;1.65;1.07;1.07	5.81	4.84	0.62591	.	0.084366	0.85682	D	0.000000	T	0.12050	0.0293	N	0.00633	-1.31	0.45648	D	0.998571	B;B	0.14805	0.011;0.006	B;B	0.10450	0.004;0.005	T	0.17531	-1.0366	10	0.30854	T	0.27	-11.2848	3.8438	0.08926	0.3268:0.0:0.6732:0.0	.	710;747	E7EMP9;Q9NRR4	.;RNC_HUMAN	M	747;747;710;710;672;703	ENSP00000425979:T747M;ENSP00000339845:T747M;ENSP00000409335:T710M;ENSP00000424161:T710M	ENSP00000265075:T672M	T	-	2	0	DROSHA	31507928	1.000000	0.71417	0.994000	0.49952	0.831000	0.47069	6.044000	0.71012	2.746000	0.94184	0.655000	0.94253	ACG		0.443	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	Missense_Mutation
PDZD2	23037	broad.mit.edu	37	5	32037370	32037370	+	Missense_Mutation	SNP	G	G	A	rs529949435		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:32037370G>A	ENST00000438447.1	+	7	1829	c.1441G>A	c.(1441-1443)Ggt>Agt	p.G481S	PDZD2_ENST00000282493.3_Missense_Mutation_p.G481S			O15018	PDZD2_HUMAN	PDZ domain containing 2	481					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.G481S(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						AGATGTGTGCGGTGCTGAGGA	0.537													G|||	1	0.000199681	0.0	0.0	5008	,	,		21198	0.0		0.0	False		,,,				2504	0.001				p.G481S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1441A	5						.						79.0	76.0	77.0					5																	32037370		2203	4300	6503	32073127	SO:0001583	missense	23037	exon6			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.1441G>A	5.37:g.32037370G>A	ENSP00000402033:p.Gly481Ser	Somatic		Capture	Illumina HiSeq	Phase_I	32073127	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	2.288	-0.363099	0.05103	.	.	ENSG00000133401	ENST00000438447;ENST00000282493	T;T	0.06371	3.31;3.31	5.37	2.44	0.29823	.	0.123056	0.37623	N	0.002014	T	0.01730	0.0055	N	0.04508	-0.205	0.09310	N	1	B;P	0.36874	0.123;0.572	B;B	0.23574	0.003;0.047	T	0.41698	-0.9494	10	0.07175	T	0.84	.	4.9949	0.14233	0.1905:0.0:0.6413:0.1682	.	307;481	B4E3P2;O15018	.;PDZD2_HUMAN	S	481	ENSP00000402033:G481S;ENSP00000282493:G481S	ENSP00000282493:G481S	G	+	1	0	PDZD2	32073127	0.397000	0.25270	0.019000	0.16419	0.087000	0.18053	1.164000	0.31810	0.749000	0.32854	-0.136000	0.14681	GGT		0.537	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
PDZD2	23037	broad.mit.edu	37	5	32090400	32090400	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:32090400G>A	ENST00000438447.1	+	20	7234	c.6846G>A	c.(6844-6846)ccG>ccA	p.P2282P	PDZD2_ENST00000282493.3_Silent_p.P2282P			O15018	PDZD2_HUMAN	PDZ domain containing 2	2282					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.P2282P(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						GTGTAAAGCCGCTGCTGGACA	0.527																																					p.P2282P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G6846A	5						.						88.0	94.0	92.0					5																	32090400		2203	4300	6503	32126157	SO:0001819	synonymous_variant	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.6846G>A	5.37:g.32090400G>A		Somatic		Capture	Illumina HiSeq	Phase_I	32126157	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																				0.527	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
GOLPH3	64083	broad.mit.edu	37	5	32126511	32126511	+	Missense_Mutation	SNP	C	C	T	rs192633198		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:32126511C>T	ENST00000265070.6	-	4	1019	c.704G>A	c.(703-705)cGc>cAc	p.R235H	GOLPH3_ENST00000512668.1_5'Flank	NM_022130.3	NP_071413.1	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3 (coat-protein)	235					cell adhesion molecule production (GO:0060352)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|gene expression (GO:0010467)|glycoprotein biosynthetic process (GO:0009101)|Golgi organization (GO:0007030)|Golgi to plasma membrane protein transport (GO:0043001)|Golgi vesicle budding (GO:0048194)|lamellipodium assembly (GO:0030032)|leukocyte tethering or rolling (GO:0050901)|positive regulation of protein secretion (GO:0050714)|positive regulation of TOR signaling (GO:0032008)|protein retention in Golgi apparatus (GO:0045053)|protein secretion (GO:0009306)|regulation of mitochondrion organization (GO:0010821)	cytosol (GO:0005829)|endosome (GO:0005768)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	enzyme binding (GO:0019899)|phosphatidylinositol-4-phosphate binding (GO:0070273)	p.R235H(1)		kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11						GGCCAGCAAGCGCCTGTCCAT	0.517													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19176	0.0		0.0	False		,,,				2504	0.0				p.R235H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G704A	5						.	C	HIS/ARG	0,4406		0,0,2203	160.0	142.0	148.0		704	5.3	1.0	5		148	2,8598	2.2+/-6.3	0,2,4298	yes	missense	GOLPH3	NM_022130.3	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	235/299	32126511	2,13004	2203	4300	6503	32162268	SO:0001583	missense	64083	exon4			AK075156	CCDS3896.1	5p13.2	2008-07-18			ENSG00000113384	ENSG00000113384			15452	protein-coding gene	gene with protein product	"""golgi peripheral membrane protein 1, 34 kDa"", ""golgi protein"", ""coat-protein"", ""golgi-associated protein"""	612207				11042173, 16263763	Standard	NM_022130		Approved	GPP34, GOPP1, MIDAS	uc003jhp.1	Q9H4A6	OTTHUMG00000090679	ENST00000265070.6:c.704G>A	5.37:g.32126511C>T	ENSP00000265070:p.Arg235His	Somatic		Capture	Illumina HiSeq	Phase_I	32162268	NM_022130	Q9UIW5	Missense_Mutation	SNP	ENST00000265070.6	37	CCDS3896.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	15.33	2.801010	0.50315	0.0	2.33E-4	ENSG00000113384	ENST00000265070;ENST00000542582	.	.	.	6.17	5.3	0.74995	.	0.000000	0.85682	D	0.000000	D	0.86049	0.5840	M	0.93197	3.39	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.88846	0.3316	9	0.87932	D	0	-10.5279	15.9972	0.80260	0.0:0.935:0.0:0.065	.	235	Q9H4A6	GOLP3_HUMAN	H	235;218	.	ENSP00000265070:R235H	R	-	2	0	GOLPH3	32162268	1.000000	0.71417	1.000000	0.80357	0.048000	0.14542	5.730000	0.68546	2.941000	0.99782	0.655000	0.94253	CGC		0.517	GOLPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207363.2	NM_022130	
SLC1A3	6507	broad.mit.edu	37	5	36677049	36677049	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:36677049C>T	ENST00000265113.4	+	6	1099	c.623C>T	c.(622-624)aCg>aTg	p.T208M	SLC1A3_ENST00000381918.3_Missense_Mutation_p.T208M|CTD-2353F22.1_ENST00000510740.1_RNA	NM_004172.4	NP_004163.3	P43003	EAA1_HUMAN	solute carrier family 1 (glial high affinity glutamate transporter), member 3	208					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.T208M(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)			GCCAACGAAACGCTTGTGGGT	0.428																																					p.T208M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C623T	5						.						80.0	74.0	76.0					5																	36677049		2203	4300	6503	36712806	SO:0001583	missense	6507	exon5				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.623C>T	5.37:g.36677049C>T	ENSP00000265113:p.Thr208Met	Somatic		Capture	Illumina HiSeq	Phase_I	36712806	NM_001166695	B2R5T3|Q4JCQ8	Missense_Mutation	SNP	ENST00000265113.4	37	CCDS3919.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.898502	0.52227	.	.	ENSG00000079215	ENST00000265113;ENST00000427100;ENST00000381918	T;T	0.57752	0.38;0.38	6.02	5.15	0.70609	.	0.140170	0.64402	D	0.000004	T	0.63757	0.2538	L	0.45352	1.415	0.41548	D	0.988552	D;D	0.65815	0.995;0.972	P;P	0.60886	0.88;0.667	T	0.67094	-0.5757	10	0.59425	D	0.04	-13.5837	17.2911	0.87157	0.0:0.8745:0.1255:0.0	.	208;208	Q4JCQ8;P43003	.;EAA1_HUMAN	M	208;156;208	ENSP00000265113:T208M;ENSP00000371343:T208M	ENSP00000265113:T208M	T	+	2	0	SLC1A3	36712806	1.000000	0.71417	0.877000	0.34402	0.070000	0.16714	5.389000	0.66255	1.538000	0.49270	0.655000	0.94253	ACG		0.428	SLC1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207579.2	NM_004172	
NIPBL	25836	broad.mit.edu	37	5	37052509	37052509	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:37052509A>G	ENST00000282516.8	+	42	7603	c.7104A>G	c.(7102-7104)caA>caG	p.Q2368Q	NIPBL_ENST00000448238.2_Silent_p.Q2368Q	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	2368					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.Q2368Q(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)			ACCAGGTACAACAGGCAATCA	0.393																																					p.Q2368Q												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A7104G	5						.						89.0	90.0	89.0					5																	37052509		2203	4300	6503	37088266	SO:0001819	synonymous_variant	25836	exon42			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.7104A>G	5.37:g.37052509A>G		Somatic		Capture	Illumina HiSeq	Phase_I	37088266	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	CCDS3920.1																																																																																				0.393	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
OSMR	9180	broad.mit.edu	37	5	38904525	38904525	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:38904525C>T	ENST00000274276.3	+	9	1607	c.1205C>T	c.(1204-1206)gCg>gTg	p.A402V		NM_003999.2	NP_003990.1	Q99650	OSMR_HUMAN	oncostatin M receptor	402	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	oncostatin-M receptor complex (GO:0005900)	growth factor binding (GO:0019838)|oncostatin-M receptor activity (GO:0004924)	p.A402V(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	46	all_lung(31;0.000365)					GAGTACATGGCGCGAGTACGG	0.468																																					p.A402V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1205T	5						.						107.0	95.0	99.0					5																	38904525		2203	4300	6503	38940282	SO:0001583	missense	9180	exon9			U60805	CCDS3928.1, CCDS54847.1	5p13.2	2013-02-11			ENSG00000145623	ENSG00000145623		"""Fibronectin type III domain containing"""	8507	protein-coding gene	gene with protein product		601743				8999038	Standard	NM_001168355		Approved	OSMRB	uc003jln.2	Q99650	OTTHUMG00000090811	ENST00000274276.3:c.1205C>T	5.37:g.38904525C>T	ENSP00000274276:p.Ala402Val	Somatic		Capture	Illumina HiSeq	Phase_I	38940282	NM_003999	Q6P4E8|Q96QJ6	Missense_Mutation	SNP	ENST00000274276.3	37	CCDS3928.1	.	.	.	.	.	.	.	.	.	.	C	1.689	-0.504625	0.04261	.	.	ENSG00000145623	ENST00000274276;ENST00000513831	T;T	0.49139	0.79;0.79	5.7	2.98	0.34508	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.625326	0.16645	N	0.205455	T	0.36936	0.0985	M	0.72118	2.19	0.09310	N	1	B	0.25312	0.123	B	0.15484	0.013	T	0.39251	-0.9623	10	0.02654	T	1	.	6.6002	0.22697	0.0:0.7202:0.0:0.2798	.	402	Q99650	OSMR_HUMAN	V	402;9	ENSP00000274276:A402V;ENSP00000423913:A9V	ENSP00000274276:A402V	A	+	2	0	OSMR	38940282	0.000000	0.05858	0.006000	0.13384	0.014000	0.08584	0.031000	0.13710	0.782000	0.33613	0.650000	0.86243	GCG		0.468	OSMR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000207609.2	NM_003999	
HMGCS1	3157	broad.mit.edu	37	5	43295930	43295930	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:43295930G>A	ENST00000325110.6	-	6	1035	c.829C>T	c.(829-831)Cgg>Tgg	p.R277W	HMGCS1_ENST00000433297.2_Missense_Mutation_p.R277W	NM_001098272.2	NP_001091742.1	Q01581	HMCS1_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)	277					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|lipid metabolic process (GO:0006629)|liver development (GO:0001889)|male gonad development (GO:0008584)|response to acid chemical (GO:0001101)|response to drug (GO:0042493)|response to lipoprotein particle (GO:0055094)|response to low light intensity stimulus (GO:0009645)|response to purine-containing compound (GO:0014074)|response to tellurium ion (GO:0046690)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hydroxymethylglutaryl-CoA synthase activity (GO:0004421)|isomerase activity (GO:0016853)|organic acid binding (GO:0043177)	p.R277W(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|stomach(1)|urinary_tract(1)	15						AGCAACATCCGAGCTAGAGAT	0.363																																					p.R277W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C829T	5						.						83.0	86.0	85.0					5																	43295930		2203	4300	6503	43331687	SO:0001583	missense	3157	exon5				CCDS34154.1	5p14-p13	2012-10-02	2010-04-30			ENSG00000112972	2.3.3.10		5007	protein-coding gene	gene with protein product	"""3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase"""	142940	"""3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble)"""	HMGCS			Standard	NM_001098272		Approved		uc003jnq.5	Q01581		ENST00000325110.6:c.829C>T	5.37:g.43295930G>A	ENSP00000322706:p.Arg277Trp	Somatic		Capture	Illumina HiSeq	Phase_I	43331687	NM_002130	B2RDL8	Missense_Mutation	SNP	ENST00000325110.6	37	CCDS34154.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.074699	0.76415	.	.	ENSG00000112972	ENST00000325110;ENST00000433297;ENST00000545275	T;T	0.81415	-1.49;-1.49	5.66	4.78	0.61160	Hydroxymethylglutaryl-coenzyme A synthase C-terminal (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	D	0.90130	0.6916	M	0.92169	3.28	0.80722	D	1	D	0.69078	0.997	P	0.57324	0.818	D	0.92458	0.5975	10	0.87932	D	0	-2.1255	14.7138	0.69251	0.0:0.0:0.7243:0.2757	.	277	Q01581	HMCS1_HUMAN	W	277;277;266	ENSP00000322706:R277W;ENSP00000399402:R277W	ENSP00000322706:R277W	R	-	1	2	HMGCS1	43331687	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.868000	0.48436	1.372000	0.46190	0.585000	0.79938	CGG		0.363	HMGCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368022.1		
NNT	23530	broad.mit.edu	37	5	43656075	43656075	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:43656075G>A	ENST00000264663.5	+	15	2414	c.2193G>A	c.(2191-2193)acG>acA	p.T731T	NNT_ENST00000344920.4_Silent_p.T731T|NNT_ENST00000512996.2_Silent_p.T600T	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	731				T -> P (in Ref. 1; AAC51914). {ECO:0000305}.	cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)	p.T731T(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					ATTTTGCTACGGATGCAGCAG	0.438																																					p.T731T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2193A	5						.						123.0	109.0	114.0					5																	43656075		2203	4300	6503	43691832	SO:0001819	synonymous_variant	23530	exon15			U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.2193G>A	5.37:g.43656075G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43691832	NM_182977	Q16796|Q2TB60|Q8N3V4	Silent	SNP	ENST00000264663.5	37	CCDS3949.1																																																																																				0.438	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977	
HCN1	348980	broad.mit.edu	37	5	45262787	45262787	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:45262787C>T	ENST00000303230.4	-	8	1966	c.1909G>A	c.(1909-1911)Gct>Act	p.A637T		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	637					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.A637S(1)|p.A637T(1)		NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						TTGATGGGAGCGATTGCCTGC	0.483																																					p.A637T												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G1909A	5						.						177.0	158.0	164.0					5																	45262787		2203	4300	6503	45298544	SO:0001583	missense	348980	exon8			AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.1909G>A	5.37:g.45262787C>T	ENSP00000307342:p.Ala637Thr	Somatic		Capture	Illumina HiSeq	Phase_I	45298544	NM_021072		Missense_Mutation	SNP	ENST00000303230.4	37	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	C	2.952	-0.216592	0.06101	.	.	ENSG00000164588	ENST00000303230	T	0.41758	0.99	5.91	3.12	0.35913	.	0.284783	0.29653	N	0.011551	T	0.27866	0.0686	L	0.27053	0.805	0.25682	N	0.985789	B	0.13145	0.007	B	0.06405	0.002	T	0.14924	-1.0455	10	0.32370	T	0.25	.	9.9165	0.41436	0.0:0.6591:0.271:0.0699	.	637	O60741	HCN1_HUMAN	T	637	ENSP00000307342:A637T	ENSP00000307342:A637T	A	-	1	0	HCN1	45298544	0.920000	0.31207	0.793000	0.32043	0.385000	0.30292	1.198000	0.32223	0.376000	0.24707	-0.140000	0.14226	GCT		0.483	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072	
HCN1	348980	broad.mit.edu	37	5	45462053	45462053	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:45462053G>A	ENST00000303230.4	-	3	963	c.906C>T	c.(904-906)atC>atT	p.I302I		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	302					apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)	p.I302I(1)		NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						GCATCATGCCGATGAGATTAA	0.393																																					p.I302I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C906T	5						.						73.0	73.0	73.0					5																	45462053		2203	4300	6503	45497810	SO:0001819	synonymous_variant	348980	exon3			AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.906C>T	5.37:g.45462053G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45497810	NM_021072		Silent	SNP	ENST00000303230.4	37	CCDS3952.1																																																																																				0.393	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072	
ITGA2	3673	broad.mit.edu	37	5	52356865	52356865	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:52356865C>T	ENST00000296585.5	+	12	1590	c.1447C>T	c.(1447-1449)Cga>Tga	p.R483*		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	483					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)	p.R483*(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				TCAGGCTCACCGAGGTGACCA	0.463																																					p.R483X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1447T	5						.						94.0	88.0	90.0					5																	52356865		2203	4300	6503	52392622	SO:0001587	stop_gained	3673	exon12				CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.1447C>T	5.37:g.52356865C>T	ENSP00000296585:p.Arg483*	Somatic		Capture	Illumina HiSeq	Phase_I	52392622	NM_002203	Q14595	Nonsense_Mutation	SNP	ENST00000296585.5	37	CCDS3957.1	.	.	.	.	.	.	.	.	.	.	C	36	5.938484	0.97122	.	.	ENSG00000164171	ENST00000296585	.	.	.	6.06	2.33	0.28932	.	0.083486	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.9092	0.63855	0.6235:0.3765:0.0:0.0	.	.	.	.	X	483	.	ENSP00000296585:R483X	R	+	1	2	ITGA2	52392622	1.000000	0.71417	0.998000	0.56505	0.715000	0.41141	3.860000	0.55995	0.159000	0.19401	-0.271000	0.10264	CGA		0.463	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
SNX18	112574	broad.mit.edu	37	5	53815027	53815027	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:53815027C>T	ENST00000326277.3	+	1	1435	c.1245C>T	c.(1243-1245)ccC>ccT	p.P415P	SNX18_ENST00000343017.6_Silent_p.P415P|SNX18_ENST00000381410.4_Silent_p.P415P	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	415					cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.P415P(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				GCACGCCCCCCGCCGCTGCCC	0.622																																					p.P415P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1245T	5						.						41.0	49.0	46.0					5																	53815027		2203	4300	6503	53850784	SO:0001819	synonymous_variant	112574	exon1			AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"""Sorting nexins"""	19245	protein-coding gene	gene with protein product			"""sorting nexin associated golgi protein 1"""	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000326277.3:c.1245C>T	5.37:g.53815027C>T		Somatic		Capture	Illumina HiSeq	Phase_I	53850784	NM_001145427	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Silent	SNP	ENST00000326277.3	37	CCDS3962.1																																																																																				0.622	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2		
PPAP2A	8611	broad.mit.edu	37	5	54721148	54721148	+	Silent	SNP	C	C	T	rs143095107	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:54721148C>T	ENST00000307259.8	-	6	1161	c.741G>A	c.(739-741)tcG>tcA	p.S247S	PPAP2A_ENST00000264775.5_Silent_p.S248S|SKIV2L2_ENST00000230640.5_3'UTR	NM_003711.2	NP_003702.2	O14494	LPP1_HUMAN	phosphatidic acid phosphatase type 2A	247					androgen receptor signaling pathway (GO:0030521)|germ cell migration (GO:0008354)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|lipid metabolic process (GO:0006629)|negative regulation of cell proliferation (GO:0008285)|phospholipid dephosphorylation (GO:0046839)|protein dephosphorylation (GO:0006470)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of lipid metabolic process (GO:0019216)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)	p.S248S(1)		breast(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	9		Lung NSC(810;4.08e-05)|Prostate(74;0.0181)|Breast(144;0.0544)				TGAAGAAATCCGATACATATA	0.333													C|||	3	0.000599042	0.0023	0.0	5008	,	,		18156	0.0		0.0	False		,,,				2504	0.0				p.S248S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G744A	5						.	C	,,	10,4396	16.8+/-37.8	0,10,2193	86.0	82.0	84.0		741,,744	-11.0	0.2	5	dbSNP_134	84	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,utr-3,coding-synonymous	PPAP2A,SKIV2L2	NM_003711.2,NM_015360.4,NM_176895.1	,,	0,12,6491	TT,TC,CC		0.0233,0.227,0.0923	,,	247/285,,248/286	54721148	12,12994	2203	4300	6503	54756905	SO:0001819	synonymous_variant	8611	exon6			AB000888	CCDS34159.1, CCDS34160.1	5q11	2009-05-27			ENSG00000067113	ENSG00000067113	3.1.3.4		9228	protein-coding gene	gene with protein product		607124				9305923	Standard	NM_003711		Approved	PAP-2a, LPP1	uc003jpz.4	O14494	OTTHUMG00000162240	ENST00000307259.8:c.741G>A	5.37:g.54721148C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54756905	NM_176895	B7ZKN8|G3XA95|O60457|O60463|Q17RZ4	Silent	SNP	ENST00000307259.8	37	CCDS34159.1																																																																																				0.333	PPAP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368073.1		
SLC38A9	153129	broad.mit.edu	37	5	54968510	54968510	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:54968510C>T	ENST00000396865.2	-	4	718	c.127G>A	c.(127-129)Gag>Aag	p.E43K	SLC38A9_ENST00000416547.2_Intron|SLC38A9_ENST00000539768.1_Missense_Mutation_p.E43K|SLC38A9_ENST00000318672.3_Missense_Mutation_p.E43K|SLC38A9_ENST00000512595.1_Missense_Mutation_p.E16K|SLC38A9_ENST00000515629.1_5'UTR	NM_173514.3	NP_775785.2	Q8NBW4	S38A9_HUMAN	solute carrier family 38, member 9	43					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)		p.E43K(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	8		Lung NSC(810;0.00122)|Prostate(74;0.0376)|Breast(144;0.181)				TTTGTGGGCTCTATACAGAAA	0.418																																					p.E43K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G127A	5						.						104.0	89.0	94.0					5																	54968510		2203	4300	6503	55004267	SO:0001583	missense	153129	exon4				CCDS3968.1, CCDS58947.1, CCDS58948.1, CCDS75243.1	5q11.2	2013-05-22			ENSG00000177058	ENSG00000177058		"""Solute carriers"""	26907	protein-coding gene	gene with protein product							Standard	NM_173514		Approved	FLJ90709	uc003jqf.3	Q8NBW4	OTTHUMG00000131189	ENST00000396865.2:c.127G>A	5.37:g.54968510C>T	ENSP00000380074:p.Glu43Lys	Somatic		Capture	Illumina HiSeq	Phase_I	55004267	NM_173514	B3KXV1|B7Z7D0|Q0P5S0|Q6MZJ8	Missense_Mutation	SNP	ENST00000396865.2	37	CCDS3968.1	.	.	.	.	.	.	.	.	.	.	C	34	5.363804	0.95877	.	.	ENSG00000177058	ENST00000396865;ENST00000318672;ENST00000539768;ENST00000512595;ENST00000511233;ENST00000503891;ENST00000513993	T;T;T;T;T	0.55234	1.55;1.55;0.53;0.81;1.06	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.66147	0.2760	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.994;0.996	T	0.66456	-0.5919	10	0.56958	D	0.05	-11.847	19.6439	0.95769	0.0:1.0:0.0:0.0	.	16;43	B3KXV1;Q8NBW4	.;S38A9_HUMAN	K	43;43;43;16;43;43;43	ENSP00000380074:E43K;ENSP00000316596:E43K;ENSP00000437771:E43K;ENSP00000427335:E16K;ENSP00000423219:E43K	ENSP00000316596:E43K	E	-	1	0	SLC38A9	55004267	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.202000	0.77856	2.716000	0.92895	0.650000	0.86243	GAG		0.418	SLC38A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253912.2	NM_173514	
MAP3K1	4214	broad.mit.edu	37	5	56177644	56177644	+	Missense_Mutation	SNP	G	G	A	rs149242419	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:56177644G>A	ENST00000399503.3	+	14	2617	c.2617G>A	c.(2617-2619)Gta>Ata	p.V873I		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	873					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.V710I(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)		CCAGTTGGGCGTAGAAGACAC	0.502													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		19928	0.0		0.0	False		,,,				2504	0.0				p.V873I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2617A	5						.						84.0	79.0	81.0					5																	56177644		1964	4147	6111	56213401	SO:0001583	missense	4214	exon14			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.2617G>A	5.37:g.56177644G>A	ENSP00000382423:p.Val873Ile	Somatic		Capture	Illumina HiSeq	Phase_I	56213401	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	G	1.041	-0.678736	0.03378	.	.	ENSG00000095015	ENST00000399503	T	0.32272	1.46	5.41	-10.0	0.00425	.	1.424960	0.03880	N	0.277031	T	0.14614	0.0353	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10382	-1.0632	10	0.27785	T	0.31	.	4.109	0.10050	0.2399:0.2941:0.3704:0.0957	.	873	Q13233	M3K1_HUMAN	I	873	ENSP00000382423:V873I	ENSP00000382423:V873I	V	+	1	0	MAP3K1	56213401	0.000000	0.05858	0.000000	0.03702	0.228000	0.25075	-0.877000	0.04197	-1.629000	0.01546	-0.302000	0.09304	GTA		0.502	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
MIER3	166968	broad.mit.edu	37	5	56219756	56219761	+	In_Frame_Del	DEL	ATGGTT	ATGGTT	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	ATGGTT	ATGGTT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:56219756_56219761delATGGTT	ENST00000381199.3	-	11	1043_1048	c.1033_1038delAACCAT	c.(1033-1038)aaccatdel	p.NH345del	MIER3_ENST00000381213.3_In_Frame_Del_p.NH344del|SETD9_ENST00000541720.1_Intron|MIER3_ENST00000381226.3_In_Frame_Del_p.NH350del|MIER3_ENST00000409421.1_In_Frame_Del_p.NH282del			Q7Z3K6	MIER3_HUMAN	mesoderm induction early response 1, family member 3	345					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.N344_H345delNH(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(2)|urinary_tract(1)	19		Lung NSC(810;4.65e-05)|Prostate(74;0.0253)|Breast(144;0.0503)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;1.24e-37)		CTCCAGGGTGATGGTTATATCTTTTT	0.369																																					p.344_345del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.1030_1035del	5						.																																			56255518	SO:0001651	inframe_deletion	166968	exon11			BX537798	CCDS3973.2, CCDS75248.1	5q11.2	2009-03-19			ENSG00000155545	ENSG00000155545			26678	protein-coding gene	gene with protein product						12477932	Standard	XM_005248448		Approved	FLJ35954, DKFZp686L09111, DKFZp781I1119	uc003jra.1	Q7Z3K6	OTTHUMG00000059589	ENST00000381199.3:c.1033_1038delAACCAT	5.37:g.56219756_56219761delATGGTT	ENSP00000370596:p.Asn345_His346del	Somatic		Capture	Illumina HiSeq	Phase_I	56255513	NM_152622	B4DRI9|B8ZZQ0|Q5CZI0|Q68CS3|Q6MZS7|Q86YG8|Q8NA13	In_Frame_Del	DEL	ENST00000381199.3	37																																																																																					0.369	MIER3-004	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000132523.2	NM_152622	
ACTBL2	345651	broad.mit.edu	37	5	56778423	56778423	+	Missense_Mutation	SNP	G	G	A	rs78342986	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:56778423G>A	ENST00000423391.1	-	1	213	c.112C>T	c.(112-114)Cgt>Tgt	p.R38C	CTD-2023N9.1_ENST00000506106.1_RNA|AC025470.1_ENST00000584598.1_RNA	NM_001017992.3	NP_001017992.1	Q562R1	ACTBL_HUMAN	actin, beta-like 2	38						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.R38C(2)		breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(3)|pancreas(1)|prostate(2)	28		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		TGTCGAGGACGCCCTATCATG	0.592																																					p.R38C												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C112T	5						.						84.0	58.0	67.0					5																	56778423		2203	4300	6503	56814180	SO:0001583	missense	345651	exon1				CCDS34163.1	5q11.2	2014-08-08			ENSG00000169067	ENSG00000169067			17780	protein-coding gene	gene with protein product		614835					Standard	NM_001017992		Approved	DKFZp686D0972	uc003jrm.3	Q562R1	OTTHUMG00000162330	ENST00000423391.1:c.112C>T	5.37:g.56778423G>A	ENSP00000416706:p.Arg38Cys	Somatic		Capture	Illumina HiSeq	Phase_I	56814180	NM_001017992	B2RPJ1|Q562R2|Q562S9|Q562X8	Missense_Mutation	SNP	ENST00000423391.1	37	CCDS34163.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.186492	0.38609	.	.	ENSG00000169067	ENST00000423391	D	0.92149	-2.98	5.16	5.16	0.70880	.	0.000000	0.64402	D	0.000004	D	0.94000	0.8078	M	0.91354	3.2	0.80722	D	1	B	0.33103	0.397	B	0.35859	0.212	D	0.94452	0.7668	10	0.87932	D	0	.	16.1712	0.81817	0.0:0.0:1.0:0.0	.	38	Q562R1	ACTBL_HUMAN	C	38	ENSP00000416706:R38C	ENSP00000416706:R38C	R	-	1	0	ACTBL2	56814180	1.000000	0.71417	0.993000	0.49108	0.918000	0.54935	5.240000	0.65378	2.669000	0.90835	0.563000	0.77884	CGT		0.592	ACTBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368579.1	NM_001017992	
ERCC8	1161	broad.mit.edu	37	5	60214197	60214197	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:60214197G>A	ENST00000265038.5	-	4	336	c.294C>T	c.(292-294)caC>caT	p.H98H	AC104113.3_ENST00000457499.1_RNA|ERCC8_ENST00000426742.2_Silent_p.H40H|ERCC8_ENST00000543101.1_5'UTR	NM_000082.3	NP_000073.1	Q13216	ERCC8_HUMAN	excision repair cross-complementation group 8	98					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|positive regulation of DNA repair (GO:0045739)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|response to X-ray (GO:0010165)|transcription-coupled nucleotide-excision repair (GO:0006283)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|protein complex (GO:0043234)	protein complex binding (GO:0032403)	p.H98H(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14		Lung NSC(810;1.51e-06)|Prostate(74;0.0322)|Ovarian(174;0.0481)|Breast(144;0.077)				CACTGTATCTGTGAACATCAG	0.353																																					p.H98H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C294T	5						.						108.0	102.0	104.0					5																	60214197		2203	4299	6502	60249954	SO:0001819	synonymous_variant	1161	exon4			U28413	CCDS3978.1	5q12.1	2014-09-17	2014-03-07		ENSG00000049167	ENSG00000049167		"""WD repeat domain containing"""	3439	protein-coding gene	gene with protein product		609412	"""Cockayne syndrome 1 (classical)"", ""excision repair cross-complementing rodent repair deficiency, complementation group 8"""	CKN1		8596535	Standard	NM_000082		Approved	CSA	uc003jsm.3	Q13216	OTTHUMG00000097741	ENST00000265038.5:c.294C>T	5.37:g.60214197G>A		Somatic		Capture	Illumina HiSeq	Phase_I	60249954	NM_000082	B2RB64|Q6FHX5|Q96GB9	Silent	SNP	ENST00000265038.5	37	CCDS3978.1																																																																																				0.353	ERCC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214971.2	NM_000082	
ADAMTS6	11174	broad.mit.edu	37	5	64558758	64558758	+	IGR	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:64558758C>T								ADAMTS6 (64166 upstream) : ADAMTS6 (34276 downstream)														p.G551D(1)									GGGCCAAGTGCCAAAAGGAAC	0.507																																					p.G551D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1652A	5						.						70.0	61.0	64.0					5																	64558758		2203	4300	6503	64594514	SO:0001628	intergenic_variant	11174	exon13																															5.37:g.64558758C>T		Somatic		Capture	Illumina HiSeq	Phase_I	64594514	NM_197941		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	C	21.4	4.144958	0.77888	.	.	ENSG00000049192	ENST00000381055;ENST00000261306;ENST00000464680	T;T	0.60040	0.22;0.32	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.72661	0.3488	L	0.51853	1.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.69213	-0.5204	10	0.40728	T	0.16	.	19.9313	0.97120	0.0:1.0:0.0:0.0	.	551;551	D6R9L6;Q9UKP5	.;ATS6_HUMAN	D	551;501;551	ENSP00000370443:G551D;ENSP00000423551:G551D	ENSP00000261306:G501D	G	-	2	0	ADAMTS6	64594514	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.395000	0.79876	2.778000	0.95560	0.655000	0.94253	GGC	0	0.507								
ERBB2IP	55914	broad.mit.edu	37	5	65321329	65321329	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:65321329C>T	ENST00000284037.5	+	11	1228	c.839C>T	c.(838-840)aCg>aTg	p.T280M	ERBB2IP_ENST00000508515.1_Missense_Mutation_p.T280M|ERBB2IP_ENST00000511297.1_Missense_Mutation_p.T280M|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.T280M|ERBB2IP_ENST00000380936.1_Missense_Mutation_p.T280M|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.T280M|ERBB2IP_ENST00000416865.2_Missense_Mutation_p.T280M|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.T280M|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.T280M|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.T280M	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	280					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)	p.T280M(1)		breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		AATATAACAACGCTTAAAATA	0.353																																					p.T280M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C839T	5						.						169.0	164.0	166.0					5																	65321329		2203	4300	6503	65357085	SO:0001583	missense	55914	exon11				CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"""densin-180-like protein"", ""ERBB2-interacting protein"""	606944	"""erbb2-interacting protein"""			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.839C>T	5.37:g.65321329C>T	ENSP00000284037:p.Thr280Met	Somatic		Capture	Illumina HiSeq	Phase_I	65357085	NM_018695	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	37	CCDS58953.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.395099	0.83011	.	.	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000416865;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	T;T;T;T;T;T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75	5.11	5.11	0.69529	.	0.047869	0.85682	D	0.000000	T	0.39860	0.1094	L	0.37630	1.12	0.58432	D	0.999993	D;D;B;D;D;D;D;D	0.89917	1.0;0.991;0.368;0.998;0.983;0.974;0.98;1.0	D;P;B;P;P;P;P;D	0.74023	0.981;0.901;0.087;0.8;0.682;0.572;0.897;0.982	T	0.16571	-1.0398	10	0.72032	D	0.01	.	13.2636	0.60120	0.0:0.9232:0.0:0.0768	.	280;280;280;280;280;280;280;280	B4DIP2;Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2	.;.;.;.;.;LAP2_HUMAN;.;.	M	280	ENSP00000284037:T280M;ENSP00000370330:T280M;ENSP00000397833:T280M;ENSP00000370326:T280M;ENSP00000370323:T280M;ENSP00000370322:T280M;ENSP00000370325:T280M;ENSP00000422766:T280M;ENSP00000426632:T280M;ENSP00000422015:T280M	ENSP00000284037:T280M	T	+	2	0	ERBB2IP	65357085	0.996000	0.38824	1.000000	0.80357	0.992000	0.81027	2.822000	0.48073	2.535000	0.85469	0.650000	0.86243	ACG		0.353	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	
SREK1	140890	broad.mit.edu	37	5	65473410	65473410	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:65473410G>A	ENST00000380918.3	+	12	1961	c.1301G>A	c.(1300-1302)cGt>cAt	p.R434H	SREK1_ENST00000334121.6_Missense_Mutation_p.R550H|SREK1_ENST00000284041.3_3'UTR	NM_139168.3	NP_631907.1	Q8WXA9	SREK1_HUMAN	splicing regulatory glutamine/lysine-rich protein 1	434	Arg/Glu/Lys/Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R434H(1)		breast(1)|kidney(3)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)	9						GAGAGAGAACGTTCAACGTCT	0.363																																					p.R434H	GBM(10;31 347 27684 38976 41583)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1301A	5						.						144.0	128.0	133.0					5																	65473410		2203	4300	6503	65509166	SO:0001583	missense	140890	exon12			AF459094	CCDS3991.1, CCDS43323.1, CCDS75253.1	5q11.2-q12.1	2013-02-12	2010-09-08	2010-09-08	ENSG00000153914	ENSG00000153914		"""RNA binding motif (RRM) containing"""	17882	protein-coding gene	gene with protein product	"""serine-arginine-rich splicing regulatory protein 508"""	609268	"""splicing factor, arginine/serine-rich 12"""	SFRS12		12043562	Standard	NM_001077199		Approved	DKFZp564B176, SRrp86, SRrp508	uc003jun.4	Q8WXA9	OTTHUMG00000097809	ENST00000380918.3:c.1301G>A	5.37:g.65473410G>A	ENSP00000370305:p.Arg434His	Somatic		Capture	Illumina HiSeq	Phase_I	65509166	NM_139168	A4FTW3|Q2M1J0|Q86X37	Missense_Mutation	SNP	ENST00000380918.3	37	CCDS3991.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.517824	0.85495	.	.	ENSG00000153914	ENST00000334121;ENST00000380918	T;T	0.11495	2.77;2.77	5.6	5.6	0.85130	.	0.418357	0.25538	N	0.029996	T	0.07818	0.0196	N	0.19112	0.55	0.27816	N	0.941972	B;B	0.17852	0.024;0.01	B;B	0.09377	0.002;0.004	T	0.15435	-1.0437	10	0.37606	T	0.19	.	11.6332	0.51187	0.0815:0.0:0.9185:0.0	.	434;550	Q8WXA9;Q8WXA9-2	SREK1_HUMAN;.	H	550;434	ENSP00000334538:R550H;ENSP00000370305:R434H	ENSP00000334538:R550H	R	+	2	0	SREK1	65509166	0.727000	0.28069	1.000000	0.80357	0.958000	0.62258	1.605000	0.36815	2.628000	0.89032	0.655000	0.94253	CGT		0.363	SREK1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381118.1	NM_001077199	
MAST4	375449	broad.mit.edu	37	5	66426055	66426055	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:66426055G>A	ENST00000403625.2	+	15	2058	c.1763G>A	c.(1762-1764)cGg>cAg	p.R588Q	MAST4_ENST00000261569.7_Missense_Mutation_p.R394Q|MAST4_ENST00000405643.1_Missense_Mutation_p.R409Q|MAST4_ENST00000404260.3_Missense_Mutation_p.R591Q|MAST4_ENST00000403666.1_Missense_Mutation_p.R399Q	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	591	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.R591Q(1)		breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		TACTTTGTTCGGCATAAAGAA	0.443																																					p.R399Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1196A	5						.						30.0	30.0	30.0					5																	66426055		1968	4173	6141	66461811	SO:0001583	missense	375449	exon14			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.1763G>A	5.37:g.66426055G>A	ENSP00000385727:p.Arg588Gln	Somatic		Capture	Illumina HiSeq	Phase_I	66461811	NM_015183	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	G	35	5.557093	0.96514	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569;ENST00000432399	T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74	5.33	5.33	0.75918	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	0.34279	0.0892	N	0.05554	-0.025	0.54753	D	0.999983	D;D;D;D	0.89917	0.991;1.0;1.0;0.999	D;D;D;D	0.91635	0.944;0.999;0.997;0.988	T	0.48927	-0.8991	10	0.87932	D	0	-18.8264	19.382	0.94540	0.0:0.0:1.0:0.0	.	409;591;394;399	E7EWQ5;O15021;O15021-2;O15021-3	.;MAST4_HUMAN;.;.	Q	591;588;399;409;409;394;394	ENSP00000385048:R591Q;ENSP00000385727:R588Q;ENSP00000384313:R399Q;ENSP00000384099:R409Q;ENSP00000261569:R394Q	ENSP00000261569:R394Q	R	+	2	0	MAST4	66461811	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.636000	0.89361	0.655000	0.94253	CGG		0.443	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2		
RAD17	5884	broad.mit.edu	37	5	68692228	68692228	+	Missense_Mutation	SNP	G	G	A	rs17236478	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:68692228G>A	ENST00000509734.1	+	15	2138	c.1460G>A	c.(1459-1461)cGc>cAc	p.R487H	RAD17_ENST00000354312.3_Missense_Mutation_p.R476H|RAD17_ENST00000358030.2_Missense_Mutation_p.R311H|RAD17_ENST00000282891.6_Missense_Mutation_p.R390H|RAD17_ENST00000305138.4_Missense_Mutation_p.R476H|RAD17_ENST00000345306.6_Missense_Mutation_p.R476H|RAD17_ENST00000504177.1_Intron|RAD17_ENST00000521422.1_Missense_Mutation_p.R311H|RAD17_ENST00000361732.2_Missense_Mutation_p.R476H|RAD17_ENST00000354868.5_Missense_Mutation_p.R476H|RAD17_ENST00000380774.3_Missense_Mutation_p.R487H			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)	487	Interaction with MCM7.		R -> L (in dbSNP:rs17236478). {ECO:0000269|Ref.13}.		cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|regulation of phosphorylation (GO:0042325)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)	p.R476H(1)					Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		TGTTAGACACGCTCTTTACTC	0.373								Other conserved DNA damage response genes																													p.R390H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1169A	5						.						67.0	61.0	63.0					5																	68692228		2203	4300	6503	68727984	SO:0001583	missense	5884	exon13			AF085736	CCDS4003.1, CCDS4004.1, CCDS4005.1, CCDS47226.1	5q13	2010-09-24	2001-11-28		ENSG00000152942	ENSG00000152942			9807	protein-coding gene	gene with protein product		603139	"""RAD1 (S. pombe) homolog"""			9869296, 9660800	Standard	NM_133343		Approved	Rad24, RAD17Sp, CCYC	uc003jwo.3	O75943	OTTHUMG00000099357	ENST00000509734.1:c.1460G>A	5.37:g.68692228G>A	ENSP00000426191:p.Arg487His	Somatic		Capture	Illumina HiSeq	Phase_I	68727984	NM_133341	A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Missense_Mutation	SNP	ENST00000509734.1	37	CCDS4003.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.067050	0.55539	.	.	ENSG00000152942	ENST00000361732;ENST00000509734;ENST00000354868;ENST00000521422;ENST00000354312;ENST00000345306;ENST00000305138;ENST00000282891;ENST00000358030;ENST00000380774;ENST00000513214	T;T;T;T;T;T;T;T;T;T;T	0.24538	1.85;1.85;1.85;1.85;1.85;1.85;1.85;1.85;1.85;1.85;1.85	5.24	4.36	0.52297	.	0.051159	0.85682	D	0.000000	T	0.50871	0.1641	M	0.83312	2.635	0.36053	D	0.840922	D;D;D	0.71674	0.998;0.998;0.998	D;P;P	0.65233	0.933;0.815;0.855	T	0.66630	-0.5875	10	0.66056	D	0.02	-13.3579	12.9413	0.58345	0.0808:0.0:0.9192:0.0	.	487;390;476	O75943;O75943-4;O75943-2	RAD17_HUMAN;.;.	H	476;487;476;311;476;476;476;390;311;487;95	ENSP00000355226:R476H;ENSP00000426191:R487H;ENSP00000346938:R476H;ENSP00000427743:R311H;ENSP00000346271:R476H;ENSP00000311227:R476H;ENSP00000303134:R476H;ENSP00000282891:R390H;ENSP00000350725:R311H;ENSP00000370151:R487H;ENSP00000425005:R95H	ENSP00000282891:R390H	R	+	2	0	RAD17	68727984	0.991000	0.36638	0.909000	0.35828	0.854000	0.48673	2.816000	0.48026	1.321000	0.45227	0.557000	0.71058	CGC		0.373	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369171.1	NM_133344	
FAM169A	26049	broad.mit.edu	37	5	74100362	74100362	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:74100362C>T	ENST00000389156.4	-	8	958	c.868G>A	c.(868-870)Gaa>Aaa	p.E290K	FAM169A_ENST00000510496.1_Missense_Mutation_p.E230K|FAM169A_ENST00000380515.3_3'UTR	NM_015566.2	NP_056381.1	Q9Y6X4	F169A_HUMAN	family with sequence similarity 169, member A	290						membrane (GO:0016020)|nucleus (GO:0005634)		p.E290K(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	27						GTTCTTGCTTCGTATTCTGGA	0.338																																					p.E290K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G868A	5						.						143.0	135.0	137.0					5																	74100362		1853	4099	5952	74136118	SO:0001583	missense	26049	exon8				CCDS43330.1	5q13.3	2008-08-08			ENSG00000198780	ENSG00000198780			29138	protein-coding gene	gene with protein product		615769				10048485	Standard	NM_015566		Approved	KIAA0888	uc003kdm.4	Q9Y6X4	OTTHUMG00000162930	ENST00000389156.4:c.868G>A	5.37:g.74100362C>T	ENSP00000373808:p.Glu290Lys	Somatic		Capture	Illumina HiSeq	Phase_I	74136118	NM_015566	A8K1T9|Q6MZT0|Q9H989	Missense_Mutation	SNP	ENST00000389156.4	37	CCDS43330.1	.	.	.	.	.	.	.	.	.	.	C	16.75	3.210235	0.58343	.	.	ENSG00000198780	ENST00000389156;ENST00000510496	T	0.52057	0.68	5.58	5.58	0.84498	.	0.225652	0.31747	N	0.007129	T	0.39835	0.1093	L	0.32530	0.975	0.80722	D	1	P;P	0.52577	0.954;0.907	B;B	0.42245	0.381;0.123	T	0.27157	-1.0082	10	0.44086	T	0.13	-10.3063	15.053	0.71891	0.0:1.0:0.0:0.0	.	230;290	D6RB01;Q9Y6X4	.;F169A_HUMAN	K	290;230	ENSP00000373808:E290K	ENSP00000373808:E290K	E	-	1	0	FAM169A	74136118	0.991000	0.36638	0.942000	0.38095	0.358000	0.29455	3.942000	0.56614	2.613000	0.88420	0.650000	0.86243	GAA		0.338	FAM169A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371092.2		
COL4A3BP	10087	broad.mit.edu	37	5	74681787	74681787	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:74681787C>T	ENST00000405807.4	-	13	1778	c.1357G>A	c.(1357-1359)Gtc>Atc	p.V453I	COL4A3BP_ENST00000261415.7_Missense_Mutation_p.V427I|COL4A3BP_ENST00000380494.5_Missense_Mutation_p.V581I|COL4A3BP_ENST00000508692.1_5'Flank	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	453	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|ceramide metabolic process (GO:0006672)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi ceramide transport (GO:0035621)|heart morphogenesis (GO:0003007)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lipid homeostasis (GO:0055088)|mitochondrion morphogenesis (GO:0070584)|muscle contraction (GO:0006936)|protein phosphorylation (GO:0006468)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ceramide binding (GO:0097001)|ceramide transporter activity (GO:0035620)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein kinase activity (GO:0004672)	p.V453I(1)		breast(1)|kidney(1)|large_intestine(5)|lung(4)|skin(3)|stomach(1)|urinary_tract(1)	16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		TGTCCTGTGACGCCTTTAACT	0.343																																					p.V581I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1741A	5						.						67.0	61.0	63.0					5																	74681787		2202	4298	6500	74717543	SO:0001583	missense	10087	exon14			AF136450	CCDS4028.1, CCDS4029.1, CCDS47235.1	5q13.3	2013-01-10	2007-06-08	2007-06-08	ENSG00000113163	ENSG00000113163		"""StAR-related lipid transfer (START) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2205	protein-coding gene	gene with protein product	"""ceramide transporter"", ""StAR-related lipid transfer (START) domain containing 11"""	604677				10212244	Standard	NM_001130105		Approved	GPBP, STARD11, CERT	uc003kdt.3	Q9Y5P4	OTTHUMG00000102068	ENST00000405807.4:c.1357G>A	5.37:g.74681787C>T	ENSP00000383996:p.Val453Ile	Somatic		Capture	Illumina HiSeq	Phase_I	74717543	NM_001130105	A8K7S2|B3KUB7|Q53YV1|Q53YV2|Q96Q85|Q96Q88|Q9H2S7|Q9H2S8	Missense_Mutation	SNP	ENST00000405807.4	37	CCDS4028.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.493777	0.84962	.	.	ENSG00000113163	ENST00000357457;ENST00000405807;ENST00000380494;ENST00000261415	D;D;D	0.84589	-1.87;-1.87;-1.87	5.85	4.99	0.66335	Lipid-binding START (3);START-like domain (1);	0.108239	0.64402	D	0.000007	D	0.89822	0.6826	L	0.49778	1.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.80764	0.994;0.99;0.844	D	0.89996	0.4111	10	0.51188	T	0.08	-0.6187	15.1693	0.72858	0.0:0.9322:0.0:0.0678	.	453;581;427	Q9Y5P4;Q9Y5P4-3;Q9Y5P4-2	C43BP_HUMAN;.;.	I	58;453;581;427	ENSP00000383996:V453I;ENSP00000369862:V581I;ENSP00000261415:V427I	ENSP00000261415:V427I	V	-	1	0	COL4A3BP	74717543	1.000000	0.71417	0.982000	0.44146	0.992000	0.81027	7.794000	0.85869	1.478000	0.48253	0.655000	0.94253	GTC		0.343	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	NM_005713	
POLK	51426	broad.mit.edu	37	5	74865196	74865196	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:74865196G>T	ENST00000241436.4	+	4	459	c.287G>T	c.(286-288)aGc>aTc	p.S96I	POLK_ENST00000515295.1_Missense_Mutation_p.S96I|POLK_ENST00000504026.1_Missense_Mutation_p.S96I|POLK_ENST00000506928.1_3'UTR|POLK_ENST00000380481.3_Missense_Mutation_p.S6I|POLK_ENST00000508526.1_Missense_Mutation_p.S96I|POLK_ENST00000352007.5_Missense_Mutation_p.S96I	NM_016218.2	NP_057302.1	Q9UBT6	POLK_HUMAN	polymerase (DNA directed) kappa	96					DNA repair (GO:0006281)|nucleotide-excision repair, DNA gap filling (GO:0006297)	nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.S96I(1)		endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	27		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		TTAGAACAAAGCCGAAATTTG	0.333								DNA polymerases (catalytic subunits)																													p.S96I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G287T	5						.						87.0	83.0	84.0					5																	74865196		2203	4300	6503	74900952	SO:0001583	missense	51426	exon4			AB027564	CCDS4030.1	5q13	2012-05-18			ENSG00000122008	ENSG00000122008		"""DNA polymerases"""	9183	protein-coding gene	gene with protein product	"""polymerase (DNA-directed) kappa"", ""DINB protein"", ""DNA polymerase kappa"""	605650		DINB1		10887153, 10518552	Standard	NM_016218		Approved	POLQ, DINP	uc003kdw.3	Q9UBT6	OTTHUMG00000102107	ENST00000241436.4:c.287G>T	5.37:g.74865196G>T	ENSP00000241436:p.Ser96Ile	Somatic		Capture	Illumina HiSeq	Phase_I	74900952	NM_016218	B2RBD2|Q5Q9G5|Q5Q9G6|Q5Q9G7|Q5Q9G8|Q86VJ8|Q8IZY0|Q8IZY1|Q8NB30|Q96L01|Q96Q86|Q96Q87|Q9UHC5	Missense_Mutation	SNP	ENST00000241436.4	37	CCDS4030.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.022236	0.35701	.	.	ENSG00000122008	ENST00000241436;ENST00000352007;ENST00000514296;ENST00000515295;ENST00000504026;ENST00000508526;ENST00000380481	T;T;T;T;T;T;T	0.71579	-0.58;-0.58;-0.58;-0.58;-0.58;-0.58;-0.58	5.51	2.73	0.32206	.	0.319150	0.45361	D	0.000368	T	0.79616	0.4476	M	0.76170	2.325	0.37800	D	0.927678	D;P;P;P	0.59357	0.985;0.585;0.565;0.923	D;B;P;P	0.63283	0.913;0.187;0.568;0.729	T	0.80692	-0.1269	10	0.87932	D	0	-0.7073	9.0674	0.36471	0.4354:0.0:0.5646:0.0	.	96;96;96;96	Q9UBT6-3;Q5Q9G5;Q9UBT6-2;Q9UBT6	.;.;.;POLK_HUMAN	I	96;96;96;96;96;96;6	ENSP00000241436:S96I;ENSP00000342256:S96I;ENSP00000425208:S96I;ENSP00000424174:S96I;ENSP00000425075:S96I;ENSP00000426853:S96I;ENSP00000369848:S6I	ENSP00000241436:S96I	S	+	2	0	POLK	74900952	1.000000	0.71417	0.913000	0.36048	0.524000	0.34500	1.301000	0.33447	0.359000	0.24239	0.460000	0.39030	AGC		0.333	POLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219945.3	NM_016218	
OTP	23440	broad.mit.edu	37	5	76932681	76932681	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:76932681C>T	ENST00000306422.3	-	2	1550	c.412G>A	c.(412-414)Gca>Aca	p.A138T	OTP_ENST00000515716.1_5'UTR	NM_032109.2	NP_115485.1	Q5XKR4	OTP_HUMAN	orthopedia homeobox	138					forebrain neuron differentiation (GO:0021879)|hypothalamus cell differentiation (GO:0021979)|neurohypophysis development (GO:0021985)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.A138T(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|pancreas(1)	13		all_lung(232;0.00051)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;9.04e-51)|Epithelial(54;1.62e-45)|all cancers(79;4.4e-41)		ATACGCAGTGCCAGCTCCTCA	0.622																																					p.A138T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G412A	5						.						89.0	84.0	86.0					5																	76932681		2203	4300	6503	76968437	SO:0001583	missense	23440	exon2				CCDS4039.1	5q14.1	2011-06-20	2007-02-15		ENSG00000171540	ENSG00000171540		"""Homeoboxes / PRD class"""	8518	protein-coding gene	gene with protein product		604529	"""orthopedia homolog (Drosophila)"""			10458915	Standard	NM_032109		Approved		uc003kfg.3	Q5XKR4	OTTHUMG00000102171	ENST00000306422.3:c.412G>A	5.37:g.76932681C>T	ENSP00000302814:p.Ala138Thr	Somatic		Capture	Illumina HiSeq	Phase_I	76968437	NM_032109		Missense_Mutation	SNP	ENST00000306422.3	37	CCDS4039.1	.	.	.	.	.	.	.	.	.	.	C	33	5.281915	0.95489	.	.	ENSG00000171540	ENST00000306422	D	0.98164	-4.76	5.21	5.21	0.72293	Homeodomain-related (1);Helix-turn-helix motif, lambda-like repressor (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99269	0.9745	H	0.96048	3.76	0.80722	D	1	D	0.63046	0.992	P	0.62885	0.908	D	0.98936	1.0789	10	0.87932	D	0	.	18.712	0.91661	0.0:1.0:0.0:0.0	.	138	Q5XKR4	OTP_HUMAN	T	138	ENSP00000302814:A138T	ENSP00000302814:A138T	A	-	1	0	OTP	76968437	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.703000	0.84585	2.597000	0.87782	0.655000	0.94253	GCA		0.622	OTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220016.2		
AP3B1	8546	broad.mit.edu	37	5	77334907	77334907	+	Frame_Shift_Del	DEL	T	T	-	rs201179527	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:77334907delT	ENST00000255194.6	-	23	2944	c.2769delA	c.(2767-2769)aaafs	p.K923fs	AP3B1_ENST00000523204.1_5'UTR|AP3B1_ENST00000519295.1_Frame_Shift_Del_p.K874fs	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	923					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.K923fs*4(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)		CTATAGGAAGTTTTTTTTCCC	0.289									Hermansky-Pudlak syndrome																												p.K923fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2769delA	5						.						103.0	98.0	100.0					5																	77334907		2203	4299	6502	77370663	SO:0001589	frameshift_variant	8546	exon23	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.2769delA	5.37:g.77334907delT	ENSP00000255194:p.Lys923fs	Somatic		Capture	Illumina HiSeq	Phase_I	77370663	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Frame_Shift_Del	DEL	ENST00000255194.6	37	CCDS4041.1																																																																																				0.289	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
DMGDH	29958	broad.mit.edu	37	5	78340335	78340335	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:78340335T>G	ENST00000255189.3	-	6	814	c.786A>C	c.(784-786)gaA>gaC	p.E262D	DMGDH_ENST00000540686.1_Intron|DMGDH_ENST00000380311.4_Missense_Mutation_p.E61D	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	262					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)	p.E262D(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		TGAGAGGATGTTCTAGTCCAA	0.383																																					p.E262D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A786C	5						.						98.0	88.0	91.0					5																	78340335		2203	4300	6503	78376091	SO:0001583	missense	29958	exon6			AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.786A>C	5.37:g.78340335T>G	ENSP00000255189:p.Glu262Asp	Somatic		Capture	Illumina HiSeq	Phase_I	78376091	NM_013391	B2RBN0|B4E1J9	Missense_Mutation	SNP	ENST00000255189.3	37	CCDS4044.1	.	.	.	.	.	.	.	.	.	.	T	7.533	0.659030	0.14645	.	.	ENSG00000132837	ENST00000255189;ENST00000523732;ENST00000380311;ENST00000539598	D;D;D	0.84944	-1.92;-1.92;-1.92	5.29	-6.83	0.01693	FAD dependent oxidoreductase (1);	0.413393	0.27730	N	0.018093	T	0.63757	0.2538	N	0.17082	0.46	0.80722	D	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.002	T	0.45542	-0.9254	10	0.10111	T	0.7	.	9.5327	0.39205	0.0925:0.5972:0.0978:0.2125	.	61;112;262	F8W6P8;F5H1C7;Q9UI17	.;.;M2GD_HUMAN	D	262;101;61;112	ENSP00000255189:E262D;ENSP00000430972:E101D;ENSP00000369667:E61D	ENSP00000255189:E262D	E	-	3	2	DMGDH	78376091	0.000000	0.05858	0.077000	0.20336	0.985000	0.73830	-2.032000	0.01426	-1.310000	0.02312	0.529000	0.55759	GAA		0.383	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391	
JMY	133746	broad.mit.edu	37	5	78595989	78595989	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:78595989G>A	ENST00000396137.4	+	5	2003	c.1541G>A	c.(1540-1542)cGg>cAg	p.R514Q		NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	514	Interaction with p300/EP300. {ECO:0000250}.				'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.R160Q(1)		endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		CAGAGTTTGCGGGGTGGTACA	0.343																																					p.R514Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1541A	5						.						107.0	99.0	102.0					5																	78595989		1849	4099	5948	78631745	SO:0001583	missense	133746	exon5			AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.1541G>A	5.37:g.78595989G>A	ENSP00000379441:p.Arg514Gln	Somatic		Capture	Illumina HiSeq	Phase_I	78631745	NM_152405	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	37	CCDS4047.3	.	.	.	.	.	.	.	.	.	.	G	4.373	0.068778	0.08436	.	.	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.07021	3.23	5.19	3.95	0.45737	.	0.341865	0.32068	N	0.006626	T	0.01765	0.0056	N	0.00268	-1.735	0.21064	N	0.999799	B	0.02656	0.0	B	0.04013	0.001	T	0.43686	-0.9376	10	0.05620	T	0.96	.	11.0241	0.47734	0.9252:0.0:0.0748:0.0	.	514	Q8N9B5	JMY_HUMAN	Q	514	ENSP00000379441:R514Q	ENSP00000282259:R514Q	R	+	2	0	JMY	78631745	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.141000	0.50593	0.904000	0.36572	-0.455000	0.05494	CGG		0.343	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405	
RPS23	6228	broad.mit.edu	37	5	81572269	81572269	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:81572269C>T	ENST00000296674.8	-	3	486	c.233G>A	c.(232-234)gGc>gAc	p.G78D	RPS23_ENST00000510210.1_Missense_Mutation_p.G78D|RPS23_ENST00000503605.1_5'UTR|ATG10_ENST00000514253.2_3'UTR|RPS23_ENST00000507980.1_Missense_Mutation_p.G78D|RPS23_ENST00000512493.1_Missense_Mutation_p.G78D|RPS23_ENST00000510019.1_Splice_Site	NM_001025.4	NP_001016.1	P62266	RS23_HUMAN	ribosomal protein S23	78					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|membrane (GO:0016020)|nucleolus (GO:0005730)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.G78D(1)		prostate(1)	1		Lung NSC(167;0.0025)|all_lung(232;0.00278)|Ovarian(174;0.0336)		OV - Ovarian serous cystadenocarcinoma(54;1.94e-42)|Epithelial(54;8.38e-37)|all cancers(79;1.42e-31)		GATTTTCTTGCCATTCTTGAT	0.458																																					p.G78D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G233A	5						.						105.0	95.0	98.0					5																	81572269		1913	4117	6030	81608025	SO:0001583	missense	6228	exon3			AB007158	CCDS47241.1	5q14.2	2013-05-09			ENSG00000186468	ENSG00000186468		"""S ribosomal proteins"""	10410	protein-coding gene	gene with protein product		603683				9582194	Standard	NM_001025		Approved	S23	uc003khu.3	P62266	OTTHUMG00000162557	ENST00000296674.8:c.233G>A	5.37:g.81572269C>T	ENSP00000296674:p.Gly78Asp	Somatic		Capture	Illumina HiSeq	Phase_I	81608025	NM_001025	P39028|Q6IB08	Missense_Mutation	SNP	ENST00000296674.8	37	CCDS47241.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.2|26.2	4.713541|4.713541	0.89112|0.89112	.|.	.|.	ENSG00000186468|ENSG00000186468	ENST00000510019|ENST00000296674;ENST00000510210;ENST00000512493;ENST00000507980	.|.	.|.	.|.	5.4|5.4	5.4|5.4	0.78164|0.78164	.|Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	.|0.052348	.|0.85682	.|D	.|0.000000	.|T	.|0.81113	.|0.4755	H|H	0.96720|0.96720	3.87|3.87	0.80722|0.80722	D|D	1|1	.|P	.|0.36535	.|0.557	.|B	.|0.39152	.|0.292	.|D	.|0.86031	.|0.1513	.|9	.|0.62326	.|D	.|0.03	.|.	18.7651|18.7651	0.91869|0.91869	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|78	.|P62266	.|RS23_HUMAN	.|D	-1|78	.|.	.|ENSP00000296674:G78D	.|G	-|-	.|2	.|0	RPS23|RPS23	81608025|81608025	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.978000|0.978000	0.69477|0.69477	5.977000|5.977000	0.70492|0.70492	2.541000|2.541000	0.85698|0.85698	0.655000|0.655000	0.94253|0.94253	.|GGC		0.458	RPS23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369546.2	NM_001025	
MEF2C	4208	broad.mit.edu	37	5	88100464	88100464	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:88100464G>A	ENST00000437473.2	-	3	626	c.209C>T	c.(208-210)aCg>aTg	p.T70M	MEF2C_ENST00000504921.2_Missense_Mutation_p.T70M|MEF2C_ENST00000506554.1_Missense_Mutation_p.T70M|MEF2C_ENST00000340208.5_Missense_Mutation_p.T70M|MEF2C_ENST00000539796.1_Missense_Mutation_p.T70M|MEF2C_ENST00000508569.1_Missense_Mutation_p.T70M|MEF2C_ENST00000424173.2_Missense_Mutation_p.T70M|MEF2C_ENST00000510942.1_Missense_Mutation_p.T70M|MEF2C_ENST00000514028.1_Missense_Mutation_p.T70M|MEF2C_ENST00000514015.1_Missense_Mutation_p.T70M	NM_001193350.1|NM_002397.4	NP_001180279.1|NP_002388.2	Q06413	MEF2C_HUMAN	myocyte enhancer factor 2C	70					apoptotic process (GO:0006915)|B cell homeostasis (GO:0001782)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac ventricle formation (GO:0003211)|cartilage morphogenesis (GO:0060536)|cell morphogenesis involved in neuron differentiation (GO:0048667)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to fluid shear stress (GO:0071498)|cellular response to glucose stimulus (GO:0071333)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cellular response to trichostatin A (GO:0035984)|chondrocyte differentiation (GO:0002062)|dentate gyrus development (GO:0021542)|embryonic viscerocranium morphogenesis (GO:0048703)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|germinal center formation (GO:0002467)|glomerulus morphogenesis (GO:0072102)|heart development (GO:0007507)|heart looping (GO:0001947)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|MAPK cascade (GO:0000165)|melanocyte differentiation (GO:0030318)|monocyte differentiation (GO:0030224)|muscle cell differentiation (GO:0042692)|muscle cell fate determination (GO:0007521)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myotube differentiation (GO:0014902)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nephron tubule epithelial cell differentiation (GO:0072160)|nervous system development (GO:0007399)|neural crest cell differentiation (GO:0014033)|neuron development (GO:0048666)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoblast differentiation (GO:0001649)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|platelet formation (GO:0030220)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation in bone marrow (GO:0071864)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primary heart field specification (GO:0003138)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of dendritic spine development (GO:0060998)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of germinal center formation (GO:0002634)|regulation of megakaryocyte differentiation (GO:0045652)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron apoptotic process (GO:0043523)|regulation of neurotransmitter secretion (GO:0046928)|regulation of sarcomere organization (GO:0060297)|regulation of synapse assembly (GO:0051963)|regulation of synaptic activity (GO:0060025)|regulation of synaptic plasticity (GO:0048167)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|renal tubule morphogenesis (GO:0061333)|response to ischemia (GO:0002931)|response to virus (GO:0009615)|response to vitamin E (GO:0033197)|secondary heart field specification (GO:0003139)|sinoatrial valve morphogenesis (GO:0003185)|skeletal muscle tissue development (GO:0007519)|smooth muscle cell differentiation (GO:0051145)|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)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|sarcomere (GO:0030017)	activating transcription factor binding (GO:0033613)|AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|miRNA binding (GO:0035198)|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 core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|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 positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.T70M(2)		breast(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	40		all_cancers(142;6.67e-05)|all_epithelial(76;7.77e-07)|Lung NSC(167;0.00566)|all_lung(232;0.00732)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;1.04e-33)|Epithelial(54;1.6e-28)|all cancers(79;2.9e-25)		GTTGTACTCCGTGTACTTGAG	0.547										HNSCC(66;0.2)																											p.T70M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C209T	5						.						157.0	142.0	147.0					5																	88100464		2203	4300	6503	88136220	SO:0001583	missense	4208	exon3			AL833268	CCDS47244.1, CCDS47245.1, CCDS54877.1, CCDS54878.1	5q14.3	2013-07-03	2007-04-24		ENSG00000081189	ENSG00000081189		"""Myocyte enhancer factors"""	6996	protein-coding gene	gene with protein product		600662				8455629	Standard	NM_002397		Approved		uc003kjl.3	Q06413	OTTHUMG00000162634	ENST00000437473.2:c.209C>T	5.37:g.88100464G>A	ENSP00000396219:p.Thr70Met	Somatic		Capture	Illumina HiSeq	Phase_I	88136220	NM_001193350	C9JMZ0|D7F7N5|F8W7V7	Missense_Mutation	SNP	ENST00000437473.2	37	CCDS47245.1	.	.	.	.	.	.	.	.	.	.	G	34	5.339001	0.95783	.	.	ENSG00000081189	ENST00000340208;ENST00000424173;ENST00000504921;ENST00000514028;ENST00000437473;ENST00000510942;ENST00000506554;ENST00000508569;ENST00000514015;ENST00000539796;ENST00000513252;ENST00000506716;ENST00000507984;ENST00000502983;ENST00000508610;ENST00000502831;ENST00000503075	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61;-1.61	5.5	5.5	0.81552	Transcription factor, MADS-box (1);	0.000000	0.85682	D	0.000000	D	0.90717	0.7087	M	0.65498	2.005	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.997;0.996	D	0.91271	0.5044	10	0.87932	D	0	-6.2641	19.4018	0.94632	0.0:0.0:1.0:0.0	.	70;70;70;70	C9JMZ0;F8W7V7;Q06413;Q06413-2	.;.;MEF2C_HUMAN;.	M	70	ENSP00000340874:T70M;ENSP00000389610:T70M;ENSP00000421925:T70M;ENSP00000426665:T70M;ENSP00000396219:T70M;ENSP00000422390:T70M;ENSP00000425636:T70M;ENSP00000423597:T70M;ENSP00000424606:T70M;ENSP00000441153:T70M;ENSP00000423826:T70M;ENSP00000423656:T70M;ENSP00000424331:T70M;ENSP00000427163:T70M;ENSP00000426442:T70M;ENSP00000427286:T70M;ENSP00000426465:T70M	ENSP00000340874:T70M	T	-	2	0	MEF2C	88136220	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.578000	0.87016	0.655000	0.94253	ACG		0.547	MEF2C-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369817.1	NM_002397	
GPR98	84059	broad.mit.edu	37	5	89923448	89923448	+	Missense_Mutation	SNP	G	G	T	rs372147148		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:89923448G>T	ENST00000405460.2	+	7	1189	c.1093G>T	c.(1093-1095)Gat>Tat	p.D365Y		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	365					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.D365Y(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)		GTTACTAAAAGATACCTTACA	0.363																																					p.D365Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1093T	5						.						160.0	155.0	157.0					5																	89923448		1872	4100	5972	89959204	SO:0001583	missense	84059	exon7			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.1093G>T	5.37:g.89923448G>T	ENSP00000384582:p.Asp365Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	89959204	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.024206	0.75390	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.29655	1.56	5.85	4.76	0.60689	.	0.231809	0.50627	D	0.000109	T	0.52757	0.1754	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.55068	-0.8198	10	0.62326	D	0.03	.	12.2879	0.54803	0.1028:0.0:0.8972:0.0	.	365	Q8WXG9	GPR98_HUMAN	Y	365	ENSP00000384582:D365Y	ENSP00000296619:D365Y	D	+	1	0	GPR98	89959204	1.000000	0.71417	0.874000	0.34290	0.968000	0.65278	7.705000	0.84606	1.136000	0.42199	0.585000	0.79938	GAT		0.363	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
GPR98	84059	broad.mit.edu	37	5	89924637	89924637	+	Silent	SNP	C	C	T	rs201377512		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:89924637C>T	ENST00000405460.2	+	8	1593	c.1497C>T	c.(1495-1497)agC>agT	p.S499S		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	499					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.S499S(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)		CAGAAGTGAGCGAGCCAGCGG	0.403													C|||	1	0.000199681	0.0	0.0	5008	,	,		17345	0.0		0.0	False		,,,				2504	0.001				p.S499S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1497T	5						.						69.0	72.0	71.0					5																	89924637		1992	4158	6150	89960393	SO:0001819	synonymous_variant	84059	exon8			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.1497C>T	5.37:g.89924637C>T		Somatic		Capture	Illumina HiSeq	Phase_I	89960393	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	8.539	0.872760	0.17322	.	.	ENSG00000164199	ENST00000504142	.	.	.	5.78	2.69	0.31865	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.5444	0.00651	0.2011:0.3565:0.195:0.2474	.	.	.	.	X	88	.	.	R	+	1	2	GPR98	89960393	0.978000	0.34361	1.000000	0.80357	0.815000	0.46073	0.169000	0.16641	1.455000	0.47813	-0.145000	0.13849	CGA		0.403	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
GPR98	84059	broad.mit.edu	37	5	89939729	89939729	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:89939729G>A	ENST00000405460.2	+	14	2759	c.2663G>A	c.(2662-2664)gGc>gAc	p.G888D		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	888	Calx-beta 7. {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.G888D(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)		GATCCTCATGGCATTATAGAA	0.383																																					p.G888D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2663A	5						.						107.0	104.0	105.0					5																	89939729		1886	4104	5990	89975485	SO:0001583	missense	84059	exon14			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.2663G>A	5.37:g.89939729G>A	ENSP00000384582:p.Gly888Asp	Somatic		Capture	Illumina HiSeq	Phase_I	89975485	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.7|29.7	5.029096|5.029096	0.93518|0.93518	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043|ENST00000504142	T|.	0.35236|.	1.32|.	5.2|5.2	5.2|5.2	0.72013|0.72013	Na-Ca exchanger/integrin-beta4 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.86948|.	0.6056|.	M|M	0.93420|0.93420	3.415|3.415	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|.	0.90456|.	0.4442|.	10|.	0.87932|.	D|.	0|.	.|.	18.7179|18.7179	0.91682|0.91682	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	888|.	Q8WXG9|.	GPR98_HUMAN|.	D|X	888|476	ENSP00000384582:G888D|.	ENSP00000296619:G888D|.	G|W	+|+	2|3	0|0	GPR98|GPR98	89975485|89975485	1.000000|1.000000	0.71417|0.71417	0.976000|0.976000	0.42696|0.42696	0.859000|0.859000	0.49053|0.49053	8.871000|8.871000	0.92346|0.92346	2.425000|2.425000	0.82216|0.82216	0.655000|0.655000	0.94253|0.94253	GGC|TGG		0.383	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
CHD1	1105	broad.mit.edu	37	5	98212142	98212142	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:98212142G>A	ENST00000284049.3	-	23	3507	c.3358C>T	c.(3358-3360)Cgg>Tgg	p.R1120W		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1120					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)	p.R1120W(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	ATATTCTCCCGAGGAATAGTC	0.418																																					p.R1120W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3358T	5						.						212.0	213.0	213.0					5																	98212142		2203	4300	6503	98240042	SO:0001583	missense	1105	exon23			AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.3358C>T	5.37:g.98212142G>A	ENSP00000284049:p.Arg1120Trp	Somatic		Capture	Illumina HiSeq	Phase_I	98240042	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	37	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	G	17.54	3.414403	0.62511	.	.	ENSG00000153922	ENST00000284049	D	0.90444	-2.67	5.14	5.14	0.70334	.	0.000000	0.29876	U	0.010966	D	0.93661	0.7975	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.66351	0.943	D	0.93997	0.7272	10	0.87932	D	0	.	13.8972	0.63781	0.0:0.0:0.8475:0.1524	.	1120	O14646	CHD1_HUMAN	W	1120	ENSP00000284049:R1120W	ENSP00000284049:R1120W	R	-	1	2	CHD1	98240042	1.000000	0.71417	0.999000	0.59377	0.691000	0.40173	2.860000	0.48372	2.546000	0.85860	0.650000	0.86243	CGG		0.418	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
H2AFY	9555	broad.mit.edu	37	5	134705285	134705285	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:134705285delT	ENST00000511689.1	-	4	881	c.288delA	c.(286-288)aaafs	p.K96fs	H2AFY_ENST00000312469.4_Frame_Shift_Del_p.K96fs|H2AFY_ENST00000510038.1_Frame_Shift_Del_p.K96fs|H2AFY_ENST00000304332.4_Frame_Shift_Del_p.K96fs|H2AFY_ENST00000423969.2_Intron	NM_001040158.1|NM_138610.2	NP_001035248.1|NP_613258.2	O75367	H2AY_HUMAN	H2A histone family, member Y	96	Histone H2A.				chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of cell cycle G2/M phase transition (GO:1902750)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|condensed chromosome (GO:0000793)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleosome (GO:0000786)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|sex chromatin (GO:0001739)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|rDNA binding (GO:0000182)|transcription regulatory region DNA binding (GO:0044212)	p.G97fs*4(2)		endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGGTGACTCCTTTTAGCAGCT	0.517																																					p.K96fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.288delA	5						.						64.0	67.0	66.0					5																	134705285		2203	4300	6503	134733184	SO:0001589	frameshift_variant	9555	exon4			AF054174	CCDS4183.1, CCDS4184.1, CCDS4185.1	5q31.1	2011-01-27			ENSG00000113648	ENSG00000113648		"""Histones / Replication-independent"""	4740	protein-coding gene	gene with protein product		610054				9653160, 9714746	Standard	NM_004893		Approved	macroH2A1.2	uc003lam.1	O75367	OTTHUMG00000129141	ENST00000511689.1:c.288delA	5.37:g.134705285delT	ENSP00000423563:p.Lys96fs	Somatic		Capture	Illumina HiSeq	Phase_I	134733184	NM_004893	O75377|Q503A8|Q7Z5E3|Q96D41|Q9H8P3|Q9UP96	Frame_Shift_Del	DEL	ENST00000511689.1	37	CCDS4185.1																																																																																				0.517	H2AFY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251196.3	NM_004893	
SPINK7	84651	broad.mit.edu	37	5	147692956	147692956	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:147692956delA	ENST00000274565.4	+	2	142	c.81delA	c.(79-81)ccafs	p.P27fs	SPINK7_ENST00000523535.1_5'Flank|SPINK7_ENST00000514394.1_Intron|RP11-373N22.3_ENST00000501695.3_RNA	NM_032566.2	NP_115955.1	P58062	ISK7_HUMAN	serine peptidase inhibitor, Kazal type 7 (putative)	27	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.V30fs*42(1)		large_intestine(2)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCTGTCTCCAAAAAAAGTAA	0.279																																					p.P27fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.81delA	5						.						70.0	74.0	73.0					5																	147692956		2202	4294	6496	147673149	SO:0001589	frameshift_variant	84651	exon2				CCDS4289.1	5q32	2011-08-31			ENSG00000145879	ENSG00000145879		"""Serine peptidase inhibitors, Kazal type"""	24643	protein-coding gene	gene with protein product	"""esophagus cancer related gene 2"""					12646258, 12970870	Standard	NM_032566		Approved	ECG2, ECRG2	uc003lpd.3	P58062	OTTHUMG00000163522	ENST00000274565.4:c.81delA	5.37:g.147692956delA	ENSP00000274565:p.Pro27fs	Somatic		Capture	Illumina HiSeq	Phase_I	147673149	NM_032566	Q32LY0	Frame_Shift_Del	DEL	ENST00000274565.4	37	CCDS4289.1																																																																																				0.279	SPINK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251944.5	NM_032566	
FLT4	2324	broad.mit.edu	37	5	180041117	180041117	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr5:180041117C>G	ENST00000261937.6	-	24	3360	c.3282G>C	c.(3280-3282)caG>caC	p.Q1094H	FLT4_ENST00000393347.3_Missense_Mutation_p.Q1094H|FLT4_ENST00000502649.1_Missense_Mutation_p.Q1094H	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	1094	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|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 JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.Q1094H(2)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ACACGTCACTCTGCGTGGTGT	0.627																																					p.Q1094H	Colon(97;1075 1466 27033 27547 35871)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3282C	5						.						161.0	143.0	150.0					5																	180041117		2203	4300	6503	179973723	SO:0001583	missense	2324	exon24			X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.3282G>C	5.37:g.180041117C>G	ENSP00000261937:p.Gln1094His	Somatic		Capture	Illumina HiSeq	Phase_I	179973723	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Missense_Mutation	SNP	ENST00000261937.6	37	CCDS4457.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.686712	0.48097	.	.	ENSG00000037280	ENST00000261937;ENST00000393347;ENST00000502649;ENST00000512795	D;D;D;D	0.89270	-2.49;-2.49;-2.49;-2.49	3.57	1.73	0.24493	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.83626	0.5295	L	0.28344	0.845	0.54753	D	0.999981	B;B	0.25390	0.053;0.125	B;B	0.39503	0.301;0.301	T	0.77424	-0.2593	9	0.66056	D	0.02	.	6.4385	0.21837	0.0:0.6235:0.1454:0.2311	.	1094;1094	E9PD35;P35916	.;VGFR3_HUMAN	H	1094;1094;1094;132	ENSP00000261937:Q1094H;ENSP00000377016:Q1094H;ENSP00000426057:Q1094H;ENSP00000421535:Q132H	ENSP00000261937:Q1094H	Q	-	3	2	FLT4	179973723	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	1.608000	0.36847	0.464000	0.27142	0.542000	0.68232	CAG		0.627	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
CCNC	892	broad.mit.edu	37	6	100009269	100009269	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:100009269A>G	ENST00000520429.1	-	4	713	c.268T>C	c.(268-270)Tgt>Cgt	p.C90R	CCNC_ENST00000520371.1_Missense_Mutation_p.C90R|CCNC_ENST00000518714.1_Missense_Mutation_p.C90R|CCNC_ENST00000523985.1_Missense_Mutation_p.C5R|CCNC_ENST00000482541.2_Missense_Mutation_p.C90R|CCNC_ENST00000523799.1_Missense_Mutation_p.C5R|CCNC_ENST00000521017.1_5'UTR|CCNC_ENST00000369220.4_Missense_Mutation_p.C90R	NM_001013399.1|NM_005190.3	NP_001013417.1|NP_005181.2	P24863	CCNC_HUMAN	cyclin C	90	Cyclin N-terminal.				gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|mediator complex (GO:0016592)|nucleoplasm (GO:0005654)		p.C90R(1)					all_cancers(76;8.46e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.064)		AAAAACACACATGTAGGAGCC	0.323																																					p.C90R	GBM(57;273 1020 40094 44454 49348)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T268C	6						.						92.0	98.0	96.0					6																	100009269		2203	4297	6500	100115990	SO:0001583	missense	892	exon4				CCDS34502.1, CCDS47461.1	6q21	2008-02-05			ENSG00000112237	ENSG00000112237			1581	protein-coding gene	gene with protein product		123838				1833066	Standard	XM_005267202		Approved	CycC	uc003pqe.3	P24863	OTTHUMG00000015268	ENST00000520429.1:c.268T>C	6.37:g.100009269A>G	ENSP00000428982:p.Cys90Arg	Somatic		Capture	Illumina HiSeq	Phase_I	100115990	NM_005190	B4DPZ1|Q9H543	Missense_Mutation	SNP	ENST00000520429.1	37	CCDS34502.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.502250	0.85176	.	.	ENSG00000112237	ENST00000520429;ENST00000369220;ENST00000520371;ENST00000523799;ENST00000486428;ENST00000523985;ENST00000518714;ENST00000524049;ENST00000369217;ENST00000482541	T;T;T;T;T;T;T;T;T;T	0.61040	2.0;2.0;2.0;0.14;2.0;0.14;2.0;0.38;2.0;2.0	5.76	5.76	0.90799	Cyclin, N-terminal (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.81014	0.4735	H	0.96833	3.89	0.80722	D	1	D;D;D	0.76494	0.975;0.999;0.975	P;D;P	0.65987	0.639;0.94;0.639	D	0.87710	0.2566	9	.	.	.	-9.5531	16.3695	0.83350	1.0:0.0:0.0:0.0	.	90;123;90	Q7Z4L3;Q05CF7;P24863	.;.;CCNC_HUMAN	R	90;90;90;5;36;5;90;5;137;90	ENSP00000428982:C90R;ENSP00000358222:C90R;ENSP00000430381:C90R;ENSP00000430014:C5R;ENSP00000430077:C36R;ENSP00000430119:C5R;ENSP00000430294:C90R;ENSP00000427885:C5R;ENSP00000428472:C137R;ENSP00000417072:C90R	.	C	-	1	0	CCNC	100115990	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.172000	0.94808	2.315000	0.78130	0.533000	0.62120	TGT		0.323	CCNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041613.2	NM_005190	
C6orf203	51250	broad.mit.edu	37	6	107361391	107361391	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:107361391C>T	ENST00000405204.2	+	2	1034	c.427C>T	c.(427-429)Cgg>Tgg	p.R143W	C6orf203_ENST00000489790.1_3'UTR|C6orf203_ENST00000443043.1_Missense_Mutation_p.R148W|C6orf203_ENST00000311381.5_Missense_Mutation_p.R143W	NM_001142468.1	NP_001135940.1	Q9P0P8	CF203_HUMAN	chromosome 6 open reading frame 203	143						mitochondrion (GO:0005739)		p.R143W(1)		large_intestine(4)|lung(2)|prostate(1)|urinary_tract(1)	8	Breast(9;0.00124)|all_epithelial(6;0.0729)	all_cancers(87;0.00461)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|Colorectal(196;0.171)|all_epithelial(87;0.23)	BRCA - Breast invasive adenocarcinoma(8;0.000395)|all cancers(7;0.00065)|Epithelial(6;0.000834)|OV - Ovarian serous cystadenocarcinoma(5;0.244)	BRCA - Breast invasive adenocarcinoma(108;0.117)		TCAGTCTTTTCGGTATGATGT	0.393																																					p.R148W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C442T	6						.						105.0	102.0	103.0					6																	107361391		2203	4300	6503	107468084	SO:0001583	missense	51250	exon3			AF151064	CCDS5058.1	6q21	2012-02-22			ENSG00000130349	ENSG00000130349			17971	protein-coding gene	gene with protein product						11042152, 11707072	Standard	XM_005267008		Approved	HSPC230, PRED31	uc003prq.3	Q9P0P8	OTTHUMG00000015307	ENST00000405204.2:c.427C>T	6.37:g.107361391C>T	ENSP00000384867:p.Arg143Trp	Somatic		Capture	Illumina HiSeq	Phase_I	107468084	NM_001142470	B3KRG9	Missense_Mutation	SNP	ENST00000405204.2	37	CCDS5058.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.360654	0.41801	.	.	ENSG00000130349	ENST00000443043;ENST00000405204;ENST00000311381	T;T;T	0.38560	1.13;1.13;1.13	6.08	6.08	0.98989	.	0.000000	0.64402	D	0.000001	T	0.40546	0.1121	M	0.88241	2.94	0.80722	D	1	P	0.38420	0.63	B	0.26202	0.067	T	0.55866	-0.8073	10	0.56958	D	0.05	-8.8607	20.6647	0.99678	0.0:1.0:0.0:0.0	.	143	Q9P0P8	CF203_HUMAN	W	148;143;143	ENSP00000390153:R148W;ENSP00000384867:R143W;ENSP00000310951:R143W	ENSP00000310951:R143W	R	+	1	2	C6orf203	107468084	1.000000	0.71417	0.954000	0.39281	0.018000	0.09664	5.310000	0.65780	2.890000	0.99128	0.655000	0.94253	CGG		0.393	C6orf203-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041684.1	NM_016487	
BEND3	57673	broad.mit.edu	37	6	107390103	107390103	+	Silent	SNP	G	G	A	rs146594050	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:107390103G>A	ENST00000369042.1	-	4	2482	c.2292C>T	c.(2290-2292)tcC>tcT	p.S764S	BEND3_ENST00000429433.2_Silent_p.S764S			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	764	BEN 4. {ECO:0000255|PROSITE- ProRule:PRU00784}.							p.S764S(1)		central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						TGCAAGCCCCGGAATGGTTGT	0.637													G|||	11	0.00219649	0.0076	0.0014	5008	,	,		15844	0.0		0.0	False		,,,				2504	0.0				p.S764S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2292T	6						.	G		21,4385	29.0+/-57.7	0,21,2182	53.0	54.0	53.0		2292	-9.2	0.7	6	dbSNP_134	53	0,8600		0,0,4300	no	coding-synonymous	BEND3	NM_001080450.2		0,21,6482	AA,AG,GG		0.0,0.4766,0.1615		764/829	107390103	21,12985	2203	4300	6503	107496796	SO:0001819	synonymous_variant	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.2292C>T	6.37:g.107390103G>A		Somatic		Capture	Illumina HiSeq	Phase_I	107496796	NM_001080450	A2RRH2|Q9HCL9	Silent	SNP	ENST00000369042.1	37	CCDS34507.1																																																																																				0.637	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913	
BEND3	57673	broad.mit.edu	37	6	107419895	107419895	+	Missense_Mutation	SNP	C	C	T	rs150744696		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:107419895C>T	ENST00000369042.1	-	3	290	c.100G>A	c.(100-102)Gtg>Atg	p.V34M	BEND3_ENST00000429433.2_Missense_Mutation_p.V34M			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	34								p.V34M(1)		central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						CTGGAATTCACGGAGCAGTCC	0.517																																					p.V34M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G100A	6						.	C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	115.0	109.0	111.0		100	5.0	0.6	6	dbSNP_134	111	0,8600		0,0,4300	no	missense	BEND3	NM_001080450.2	21	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	34/829	107419895	1,13005	2203	4300	6503	107526588	SO:0001583	missense	57673	exon4			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.100G>A	6.37:g.107419895C>T	ENSP00000358038:p.Val34Met	Somatic		Capture	Illumina HiSeq	Phase_I	107526588	NM_001080450	A2RRH2|Q9HCL9	Missense_Mutation	SNP	ENST00000369042.1	37	CCDS34507.1	.	.	.	.	.	.	.	.	.	.	C	12.04	1.817266	0.32145	2.27E-4	0.0	ENSG00000178409	ENST00000369042;ENST00000429433	.	.	.	5.86	5.0	0.66597	.	0.350509	0.22519	N	0.058994	T	0.14570	0.0352	N	0.24115	0.695	0.23594	N	0.997332	B	0.31655	0.334	B	0.26770	0.073	T	0.10314	-1.0635	9	0.66056	D	0.02	10.7489	13.3604	0.60652	0.0:0.8103:0.1897:0.0	.	34	Q5T5X7	BEND3_HUMAN	M	34	.	ENSP00000358038:V34M	V	-	1	0	BEND3	107526588	0.992000	0.36948	0.623000	0.29173	0.332000	0.28634	3.136000	0.50554	1.480000	0.48289	0.655000	0.94253	GTG		0.517	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913	
MICAL1	64780	broad.mit.edu	37	6	109770006	109770006	+	Silent	SNP	G	G	A	rs150407538		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:109770006G>A	ENST00000358807.3	-	12	1904	c.1593C>T	c.(1591-1593)tcC>tcT	p.S531S	MICAL1_ENST00000368952.4_Silent_p.S550S|MICAL1_ENST00000483856.1_5'Flank|MICAL1_ENST00000358577.3_Silent_p.S445S	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	531	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein phosphorylation (GO:0001933)|oxidation-reduction process (GO:0055114)|signal transduction (GO:0007165)|sulfur oxidation (GO:0019417)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	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)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.S531S(1)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		AAGACAAATCGGAGACGTGGA	0.642													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16854	0.0		0.0	False		,,,				2504	0.0				p.S445S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1335T	6						.						114.0	112.0	113.0					6																	109770006		2203	4300	6503	109876699	SO:0001819	synonymous_variant	64780	exon11			AB048948	CCDS5076.1, CCDS55047.1	6q21	2013-03-26	2013-03-26	2005-02-16	ENSG00000135596	ENSG00000135596			20619	protein-coding gene	gene with protein product		607129	"""NEDD9 interacting protein with calponin homology and LIM domains"""	NICAL		11827972	Standard	NM_022765		Approved	MICAL, FLJ11937, DKFZp434B1517, FLJ21739	uc003ptk.3	Q8TDZ2	OTTHUMG00000015350	ENST00000358807.3:c.1593C>T	6.37:g.109770006G>A		Somatic		Capture	Illumina HiSeq	Phase_I	109876699	NM_001159291	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Silent	SNP	ENST00000358807.3	37	CCDS5076.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	1.121	-0.655237	0.03480	.	.	ENSG00000135596	ENST00000433205	.	.	.	5.62	-9.19	0.00685	.	.	.	.	.	.	.	.	.	.	.	0.52501	D	0.999952	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.5576	0.04764	0.428:0.1813:0.2901:0.1006	.	.	.	.	X	93	.	.	R	-	1	2	MICAL1	109876699	0.000000	0.05858	0.012000	0.15200	0.070000	0.16714	-3.746000	0.00377	-1.775000	0.01287	-0.291000	0.09656	CGA		0.642	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765	
MICAL1	64780	broad.mit.edu	37	6	109775022	109775022	+	Silent	SNP	G	G	A	rs147861991	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:109775022G>A	ENST00000358807.3	-	3	596	c.285C>T	c.(283-285)tgC>tgT	p.C95C	MICAL1_ENST00000368952.4_Silent_p.C114C|MICAL1_ENST00000483856.1_5'Flank|MICAL1_ENST00000358577.3_Silent_p.C95C	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	95	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein phosphorylation (GO:0001933)|oxidation-reduction process (GO:0055114)|signal transduction (GO:0007165)|sulfur oxidation (GO:0019417)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	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)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.C95C(1)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		CCCGCAGCCCGCAAGGTCCAG	0.657																																					p.C95C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C285T	6						.	G	,	0,4406		0,0,2203	70.0	65.0	67.0		285,285	-10.8	0.2	6	dbSNP_134	67	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	MICAL1	NM_001159291.1,NM_022765.3	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	95/982,95/1068	109775022	2,13004	2203	4300	6503	109881715	SO:0001819	synonymous_variant	64780	exon3			AB048948	CCDS5076.1, CCDS55047.1	6q21	2013-03-26	2013-03-26	2005-02-16	ENSG00000135596	ENSG00000135596			20619	protein-coding gene	gene with protein product		607129	"""NEDD9 interacting protein with calponin homology and LIM domains"""	NICAL		11827972	Standard	NM_022765		Approved	MICAL, FLJ11937, DKFZp434B1517, FLJ21739	uc003ptk.3	Q8TDZ2	OTTHUMG00000015350	ENST00000358807.3:c.285C>T	6.37:g.109775022G>A		Somatic		Capture	Illumina HiSeq	Phase_I	109881715	NM_001159291	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Silent	SNP	ENST00000358807.3	37	CCDS5076.1																																																																																				0.657	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765	
ZBTB24	9841	broad.mit.edu	37	6	109798128	109798128	+	Nonsense_Mutation	SNP	G	G	A	rs387907104		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:109798128G>A	ENST00000230122.3	-	3	1125	c.958C>T	c.(958-960)Cga>Tga	p.R320*		NM_001164313.1|NM_014797.2	NP_001157785.1|NP_055612.2	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24	320					hematopoietic progenitor cell differentiation (GO:0002244)|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.R320*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)		TTGAAAGGTCGCTCCCCTGGA	0.458																																					p.R320X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C958T	6						.						49.0	45.0	47.0					6																	109798128		2203	4300	6503	109904821	SO:0001587	stop_gained	9841	exon3			AB007901	CCDS34509.1	6q21	2014-09-17	2004-04-15	2004-04-16	ENSG00000112365	ENSG00000112365		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	21143	protein-coding gene	gene with protein product	"""POZ (BTB) and AT hook containing zinc finger 2"""	614064	"""zinc finger protein 450"""	ZNF450		9455477	Standard	NM_014797		Approved	KIAA0441, BIF1, PATZ2	uc003ptl.1	O43167	OTTHUMG00000015349	ENST00000230122.3:c.958C>T	6.37:g.109798128G>A	ENSP00000230122:p.Arg320*	Somatic		Capture	Illumina HiSeq	Phase_I	109904821	NM_014797	Q17RC6|Q5TED5|Q8N455	Nonsense_Mutation	SNP	ENST00000230122.3	37	CCDS34509.1	.	.	.	.	.	.	.	.	.	.	G	38	6.862964	0.97893	.	.	ENSG00000112365	ENST00000230122	.	.	.	5.04	4.15	0.48705	.	0.203205	0.42172	D	0.000752	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	-3.3806	15.1108	0.72355	0.0:0.0:0.8575:0.1425	.	.	.	.	X	320	.	ENSP00000230122:R320X	R	-	1	2	ZBTB24	109904821	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.942000	0.70203	1.431000	0.47355	0.650000	0.86243	CGA		0.458	ZBTB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041758.1	NM_014797	
FIG4	9896	broad.mit.edu	37	6	110056501	110056501	+	Splice_Site	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:110056501G>A	ENST00000230124.3	+	6	770	c.646G>A	c.(646-648)Ggg>Agg	p.G216R	FIG4_ENST00000368941.1_Splice_Site_p.G139R|FIG4_ENST00000441478.2_Splice_Site_p.V70M	NM_014845.5	NP_055660.1	Q92562	FIG4_HUMAN	FIG4 phosphoinositide 5-phosphatase	216	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				cell death (GO:0008219)|locomotory behavior (GO:0007626)|myelin assembly (GO:0032288)|negative regulation of myelination (GO:0031642)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of neuron projection development (GO:0010976)|small molecule metabolic process (GO:0044281)|vacuole organization (GO:0007033)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)	phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)	p.G216R(1)		central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)	32		all_cancers(87;8.63e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000124)|all_lung(197;0.0187)|Colorectal(196;0.0492)|Lung SC(18;0.0548)		OV - Ovarian serous cystadenocarcinoma(136;0.0355)|Epithelial(106;0.038)|all cancers(137;0.0425)|BRCA - Breast invasive adenocarcinoma(108;0.079)		AGGTGGAAGCGGTAGGTGGTC	0.388																																					p.G216R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G646A	6						.						105.0	104.0	104.0					6																	110056501		2203	4300	6503	110163194	SO:0001630	splice_region_variant	9896	exon6			D87464	CCDS5078.1	6q21	2014-09-17	2014-08-04	2007-07-30	ENSG00000112367	ENSG00000112367			16873	protein-coding gene	gene with protein product		609390	"""KIAA0274"", ""FIG4 homolog (S. cerevisiae)"", ""FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)"""	KIAA0274		9039502, 11274189, 17572665	Standard	NM_014845		Approved	SAC3, hSac3, dJ249I4.1, ALS11, CMT4J	uc003ptt.2	Q92562	OTTHUMG00000015352	ENST00000230124.3:c.646+1G>A	6.37:g.110056501G>A		Somatic		Capture	Illumina HiSeq	Phase_I	110163194	NM_014845	Q53H49|Q5TCS6	Missense_Mutation	SNP	ENST00000230124.3	37	CCDS5078.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.50|17.50	3.404018|3.404018	0.62288|0.62288	.|.	.|.	ENSG00000112367|ENSG00000112367	ENST00000230124;ENST00000454215;ENST00000368941|ENST00000441478	T;T|T	0.71579|0.23348	0.66;-0.58|1.91	5.68|5.68	5.68|5.68	0.88126|0.88126	Synaptojanin, N-terminal (2);|.	0.061302|.	0.64402|.	D|.	0.000004|.	T|T	0.16171|0.16171	0.0389|0.0389	L|L	0.48642|0.48642	1.525|1.525	0.25532|0.25532	N|N	0.987266|0.987266	B|P	0.17852|0.46656	0.024|0.882	B|B	0.20767|0.37943	0.031|0.261	T|T	0.14727|0.14727	-1.0462|-1.0462	10|9	0.15952|0.87932	T|D	0.53|0	-11.0859|-11.0859	20.1615|20.1615	0.98135|0.98135	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	216|70	Q92562|F5H8L9	FIG4_HUMAN|.	R|M	216;195;139|70	ENSP00000230124:G216R;ENSP00000412156:G195R|ENSP00000399443:V70M	ENSP00000230124:G216R|ENSP00000399443:V70M	G|V	+|+	1|1	0|0	FIG4|FIG4	110163194|110163194	1.000000|1.000000	0.71417|0.71417	0.969000|0.969000	0.41365|0.41365	0.869000|0.869000	0.49853|0.49853	4.013000|4.013000	0.57138|0.57138	2.835000|2.835000	0.97688|0.97688	0.650000|0.650000	0.86243|0.86243	GGG|GTG		0.388	FIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041768.1	NM_014845	Missense_Mutation
CDK19	23097	broad.mit.edu	37	6	110948234	110948234	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:110948234C>T	ENST00000368911.3	-	7	940	c.761G>A	c.(760-762)cGg>cAg	p.R254Q	CDK19_ENST00000413605.2_Missense_Mutation_p.R130Q|CDK19_ENST00000323817.3_Missense_Mutation_p.R194Q	NM_015076.3	NP_055891.1	Q9BWU1	CDK19_HUMAN	cyclin-dependent kinase 19	254	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.R254Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)	22						ACTAAATATCCGATCCAGTTG	0.328																																					p.R254Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G761A	6						.						116.0	111.0	113.0					6																	110948234		2203	4300	6503	111054927	SO:0001583	missense	23097	exon7			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.761G>A	6.37:g.110948234C>T	ENSP00000357907:p.Arg254Gln	Somatic		Capture	Illumina HiSeq	Phase_I	111054927	NM_015076	Q5JQZ7|Q5JR00|Q8TC78|Q9UPX2	Missense_Mutation	SNP	ENST00000368911.3	37	CCDS5085.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.960313	0.92791	.	.	ENSG00000155111	ENST00000368911;ENST00000323817;ENST00000392576;ENST00000413605;ENST00000457688	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	5.11	5.11	0.69529	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	0.65048	0.2654	N	0.17564	0.495	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.72982	0.979;0.971	T	0.73072	-0.4098	10	0.72032	D	0.01	-25.4413	18.5489	0.91056	0.0:1.0:0.0:0.0	.	130;254	B4DUB1;Q9BWU1	.;CDK19_HUMAN	Q	254;194;193;130;194	ENSP00000357907:R254Q;ENSP00000317665:R194Q;ENSP00000410604:R130Q;ENSP00000415621:R194Q	ENSP00000317665:R194Q	R	-	2	0	CDK19	111054927	1.000000	0.71417	1.000000	0.80357	0.777000	0.43975	7.487000	0.81328	2.394000	0.81467	0.455000	0.32223	CGG		0.328	CDK19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041804.1	NM_015076	
REV3L	5980	broad.mit.edu	37	6	111694339	111694339	+	Missense_Mutation	SNP	C	C	T	rs376133263		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:111694339C>T	ENST00000358835.3	-	14	5673	c.5219G>A	c.(5218-5220)cGc>cAc	p.R1740H	REV3L_ENST00000368805.1_Missense_Mutation_p.R1740H|REV3L_ENST00000368802.3_Missense_Mutation_p.R1740H|REV3L_ENST00000435970.1_Missense_Mutation_p.R1662H			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1740					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.R1662H(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CTGGTTGTGGCGACGATTCTC	0.408								DNA polymerases (catalytic subunits)																													p.R1740H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5219A	6						.	C	HIS/ARG	0,4406		0,0,2203	239.0	224.0	229.0		5219	3.0	1.0	6		229	1,8599	1.2+/-3.3	0,1,4299	no	missense	REV3L	NM_002912.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	1740/3131	111694339	1,13005	2203	4300	6503	111801032	SO:0001583	missense	5980	exon13			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.5219G>A	6.37:g.111694339C>T	ENSP00000351697:p.Arg1740His	Somatic		Capture	Illumina HiSeq	Phase_I	111801032	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	C	5.474	0.272574	0.10349	0.0	1.16E-4	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.01505	4.92;4.92;4.92;4.82	5.93	3.05	0.35203	Ribonuclease H-like (1);	0.265833	0.30649	N	0.009168	T	0.00695	0.0023	L	0.47716	1.5	0.22858	N	0.998647	B	0.06786	0.001	B	0.01281	0.0	T	0.48352	-0.9043	10	0.44086	T	0.13	0.0478	6.5103	0.22218	0.2896:0.5715:0.0:0.1389	.	1740	O60673	DPOLZ_HUMAN	H	1740;1740;1740;1662	ENSP00000357792:R1740H;ENSP00000357795:R1740H;ENSP00000351697:R1740H;ENSP00000402003:R1662H	ENSP00000351697:R1740H	R	-	2	0	REV3L	111801032	0.960000	0.32886	0.995000	0.50966	0.431000	0.31685	0.160000	0.16462	0.837000	0.34925	0.655000	0.94253	CGC		0.408	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
FYN	2534	broad.mit.edu	37	6	112041195	112041195	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:112041195G>A	ENST00000354650.3	-	4	666	c.60C>T	c.(58-60)ggC>ggT	p.G20G	FYN_ENST00000356013.2_Silent_p.G20G|FYN_ENST00000538466.1_Silent_p.G20G|FYN_ENST00000368667.2_Silent_p.G20G|FYN_ENST00000229471.4_Silent_p.G20G|FYN_ENST00000368678.4_Silent_p.G20G|FYN_ENST00000368682.3_Silent_p.G20G|FYN_ENST00000229470.5_Silent_p.G20G	NM_002037.5	NP_002028.1	P06241	FYN_HUMAN	FYN proto-oncogene, Src family tyrosine kinase	20					activated T cell proliferation (GO:0050798)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular response to peptide hormone stimulus (GO:0071375)|dendrite morphogenesis (GO:0048813)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|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)|feeding behavior (GO:0007631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|leukocyte migration (GO:0050900)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein localization to nucleus (GO:1900182)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of defense response to virus by virus (GO:0050690)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|glycoprotein binding (GO:0001948)|growth factor receptor binding (GO:0070851)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.G20G(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(17)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	30		all_cancers(87;1.37e-05)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.00125)|Colorectal(196;0.0211)		all cancers(137;0.0451)|OV - Ovarian serous cystadenocarcinoma(136;0.0476)|Epithelial(106;0.102)	Dasatinib(DB01254)	GGTTCAGGCTGCCGTCCCTCT	0.527																																					p.G20G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C60T	6						.						153.0	111.0	125.0					6																	112041195		2203	4300	6503	112147888	SO:0001819	synonymous_variant	2534	exon4			AK056699	CCDS5094.1, CCDS5095.1, CCDS5096.1	6q21	2014-06-25	2014-06-25		ENSG00000010810	ENSG00000010810		"""SH2 domain containing"""	4037	protein-coding gene	gene with protein product		137025	"""FYN oncogene related to SRC, FGR, YES"""			3526330	Standard	NM_002037		Approved	SYN, SLK, MGC45350	uc003pvh.3	P06241	OTTHUMG00000016305	ENST00000354650.3:c.60C>T	6.37:g.112041195G>A		Somatic		Capture	Illumina HiSeq	Phase_I	112147888	NM_002037	B5BU57|E1P557|H0UI48|Q16248|Q5R3A6|Q5R3A7|Q8N5D7	Silent	SNP	ENST00000354650.3	37	CCDS5094.1																																																																																				0.527	FYN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043655.1		
ROS1	6098	broad.mit.edu	37	6	117706881	117706881	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:117706881C>T	ENST00000368508.3	-	15	2467	c.2269G>A	c.(2269-2271)Ggt>Agt	p.G757S	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.G752S	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	757					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.G757S(2)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AGAAAGTGACCCAGCCACTCA	0.473			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																p.G757S			Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2269A	6						.						104.0	96.0	99.0					6																	117706881		2203	4300	6503	117813574	SO:0001583	missense	6098	exon15			M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.2269G>A	6.37:g.117706881C>T	ENSP00000357494:p.Gly757Ser	Somatic		Capture	Illumina HiSeq	Phase_I	117813574	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.993713	0.74703	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	D;D	0.92647	-3.08;-3.08	5.23	5.23	0.72850	.	0.086092	0.50627	D	0.000111	D	0.91402	0.7287	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.72075	0.976	D	0.89785	0.3964	10	0.29301	T	0.29	.	17.9688	0.89107	0.0:1.0:0.0:0.0	.	757	P08922	ROS1_HUMAN	S	757;752	ENSP00000357494:G757S;ENSP00000357493:G752S	ENSP00000357493:G752S	G	-	1	0	ROS1	117813574	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.773000	0.55333	2.717000	0.92951	0.655000	0.94253	GGT		0.473	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
MCM9	254394	broad.mit.edu	37	6	119245073	119245073	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:119245073A>G	ENST00000316316.6	-	3	810	c.524T>C	c.(523-525)tTg>tCg	p.L175S	MCM9_ENST00000316068.3_Missense_Mutation_p.L175S	NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	175					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)	MCM8-MCM9 complex (GO:0097362)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.L175S(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)		ACAGCTCTCCAAGCTGGGACA	0.463																																					p.L175S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T524C	6						.						133.0	125.0	128.0					6																	119245073		2203	4300	6503	119286772	SO:0001583	missense	254394	exon3			BC031658	CCDS5121.1, CCDS56447.1	6q22.31	2009-11-16	2007-04-04	2007-04-04	ENSG00000111877	ENSG00000111877			21484	protein-coding gene	gene with protein product		610098	"""minichromosome maintenance deficient domain containing 1"", ""chromosome 6 open reading frame 61"""	MCMDC1, C6orf61		16226853, 15850810, 16495042	Standard	NM_153255		Approved	MGC35304, dJ329L24.3, FLJ20170	uc021zeh.1	Q9NXL9	OTTHUMG00000015468	ENST00000316316.6:c.524T>C	6.37:g.119245073A>G	ENSP00000314505:p.Leu175Ser	Somatic		Capture	Illumina HiSeq	Phase_I	119286772	NM_153255	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Missense_Mutation	SNP	ENST00000316316.6	37	CCDS56447.1	.	.	.	.	.	.	.	.	.	.	A	7.385	0.629512	0.14257	.	.	ENSG00000111877	ENST00000316316;ENST00000316068	T;T	0.05258	3.92;3.47	5.78	-1.43	0.08884	.	.	.	.	.	T	0.00580	0.0019	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.47005	-0.9150	9	0.09843	T	0.71	.	4.8279	0.13425	0.4114:0.0:0.3417:0.2469	.	175	Q9NXL9-2	.	S	175	ENSP00000314505:L175S;ENSP00000312870:L175S	ENSP00000312870:L175S	L	-	2	0	MCM9	119286772	0.157000	0.22836	0.956000	0.39512	0.996000	0.88848	1.613000	0.36900	0.095000	0.17434	0.460000	0.39030	TTG		0.463	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255	
FAM184A	79632	broad.mit.edu	37	6	119295653	119295653	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:119295653C>T	ENST00000338891.7	-	14	3298	c.2855G>A	c.(2854-2856)cGg>cAg	p.R952Q	FAM184A_ENST00000368475.4_Intron|RP11-351A11.1_ENST00000518570.1_RNA|FAM184A_ENST00000521531.1_Intron|FAM184A_ENST00000352896.5_Intron	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	952						extracellular space (GO:0005615)		p.R952Q(2)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						AAAATCTGCCCGCATGATATT	0.338																																					p.R952Q												.	.	2	Substitution - Missense(2)	large_intestine(1)|breast(1)	c.G2855A	6						.						251.0	238.0	242.0					6																	119295653		1811	4082	5893	119337352	SO:0001583	missense	79632	exon14			BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 60"""	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.2855G>A	6.37:g.119295653C>T	ENSP00000342604:p.Arg952Gln	Somatic		Capture	Illumina HiSeq	Phase_I	119337352	NM_024581	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.552658	0.65425	.	.	ENSG00000111879	ENST00000521043;ENST00000338891;ENST00000368472	T;T	0.41758	2.53;0.99	5.3	4.37	0.52481	.	0.233245	0.37437	N	0.002081	T	0.14013	0.0339	L	0.34521	1.04	0.80722	D	1	P	0.50710	0.938	B	0.37480	0.251	T	0.02885	-1.1098	10	0.13470	T	0.59	-4.7423	11.695	0.51538	0.3422:0.6578:0.0:0.0	.	952	Q8NB25	F184A_HUMAN	Q	115;952;13	ENSP00000342604:R952Q;ENSP00000357457:R13Q	ENSP00000342604:R952Q	R	-	2	0	FAM184A	119337352	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.947000	0.63583	2.650000	0.89964	0.585000	0.79938	CGG		0.338	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581	
GJA1	2697	broad.mit.edu	37	6	121769078	121769078	+	Missense_Mutation	SNP	G	G	A	rs2227885		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:121769078G>A	ENST00000282561.3	+	2	1242	c.1085G>A	c.(1084-1086)cGa>cAa	p.R362Q		NM_000165.3	NP_000156.1	P17302	CXA1_HUMAN	gap junction protein, alpha 1, 43kDa	362			R -> Q (in HLHS1 and AVSD3; associated with Gln-376 in one individual with atrioventricular septal defect; abolishes phosphorylation by PKA and PKC; dbSNP:rs2227885). {ECO:0000269|PubMed:11470490}.		adult heart development (GO:0007512)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|atrial cardiac muscle cell action potential (GO:0086014)|atrial ventricular junction remodeling (GO:0003294)|blood vessel morphogenesis (GO:0048514)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|cell-cell signaling (GO:0007267)|cellular response to mechanical stimulus (GO:0071260)|chronic inflammatory response (GO:0002544)|embryonic digit morphogenesis (GO:0042733)|endothelium development (GO:0003158)|epithelial cell maturation (GO:0002070)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lens development in camera-type eye (GO:0002088)|membrane organization (GO:0061024)|milk ejection (GO:0060156)|muscle contraction (GO:0006936)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of gene expression (GO:0010629)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|osteoblast differentiation (GO:0001649)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of cell communication by chemical coupling (GO:0010652)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein oligomerization (GO:0051259)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of bone mineralization (GO:0030500)|regulation of bone remodeling (GO:0046850)|regulation of calcium ion transport (GO:0051924)|regulation of tight junction assembly (GO:2000810)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to fluid shear stress (GO:0034405)|response to peptide hormone (GO:0043434)|response to pH (GO:0009268)|signal transduction (GO:0007165)|skeletal muscle tissue regeneration (GO:0043403)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vascular transport (GO:0010232)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|contractile fiber (GO:0043292)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gap junction (GO:0005921)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial outer membrane (GO:0005741)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion transmembrane transporter activity (GO:0015075)|signal transducer activity (GO:0004871)	p.R362Q(1)		autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(2)|large_intestine(10)|liver(2)|lung(13)|ovary(2)	33				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)	GTGGACCAGCGACCTTCAAGC	0.488													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17974	0.0		0.0	False		,,,				2504	0.0				p.R362Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1085A	6	GRCh37	CM014191	GJA1	M	rs2227885	.						65.0	70.0	68.0					6																	121769078		2201	4295	6496	121810777	SO:0001583	missense	2697	exon2			BC026329	CCDS5123.1	6q22.31	2013-05-10	2007-01-16		ENSG00000152661	ENSG00000152661		"""Ion channels / Gap junction proteins (connexins)"""	4274	protein-coding gene	gene with protein product	"""oculodentodigital dysplasia (syndactyly type III)"", ""connexin 43"""	121014	"""gap junction protein, alpha-like"", ""gap junction protein, alpha 1, 43kDa (connexin 43)"""	ODDD, GJAL		10331943, 1646158	Standard	NM_000165		Approved	CX43, ODD, ODOD, SDTY3	uc003pyr.3	P17302	OTTHUMG00000015479	ENST00000282561.3:c.1085G>A	6.37:g.121769078G>A	ENSP00000282561:p.Arg362Gln	None		Capture	Illumina HiSeq	Phase_I	121810777	NM_000165	B2R5U9|Q6FHU1|Q9Y5I8	Missense_Mutation	SNP	ENST00000282561.3	37	CCDS5123.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.999333	0.74818	.	.	ENSG00000152661	ENST00000440608;ENST00000282561	D	0.84800	-1.9	4.75	3.88	0.44766	.	0.072279	0.49916	D	0.000127	T	0.79329	0.4427	L	0.27053	0.805	0.49051	A	0.999741	D	0.60575	0.988	P	0.57057	0.812	T	0.82319	-0.0516	9	0.54805	T	0.06	.	13.2872	0.60249	0.0768:0.0:0.9232:0.0	.	362	P17302	CXA1_HUMAN	Q	346;362	ENSP00000282561:R362Q	ENSP00000282561:R362Q	R	+	2	0	GJA1	121810777	1.000000	0.71417	0.976000	0.42696	0.959000	0.62525	7.258000	0.78371	1.365000	0.46057	0.484000	0.47621	CGA		0.488	GJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042023.1	NM_000165	
CLVS2	134829	broad.mit.edu	37	6	123319088	123319088	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:123319088C>T	ENST00000275162.5	+	2	1501	c.166C>T	c.(166-168)Cgc>Tgc	p.R56C	CLVS2_ENST00000368438.1_Intron	NM_001010852.3	NP_001010852.2	Q5SYC1	CLVS2_HUMAN	clavesin 2	56					lysosome organization (GO:0007040)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|transporter activity (GO:0005215)	p.R56C(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	40						CTTCATCTTACGCTTCTTGCG	0.542																																					p.R56C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C166T	6						.						186.0	151.0	163.0					6																	123319088		2203	4300	6503	123360787	SO:0001583	missense	134829	exon2			AK095527	CCDS34525.1	6q22.31	2009-10-14	2009-10-14	2009-10-14	ENSG00000146352	ENSG00000146352			23046	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 212"", ""chromosome 6 open reading frame 213"", ""retinaldehyde binding protein 1-like 2"""	C6orf212, C6orf213, RLBP1L2		19651769	Standard	NM_001010852		Approved	bA160A10.4	uc003pzi.1	Q5SYC1	OTTHUMG00000015495	ENST00000275162.5:c.166C>T	6.37:g.123319088C>T	ENSP00000275162:p.Arg56Cys	Somatic		Capture	Illumina HiSeq	Phase_I	123360787	NM_001010852	B3KTG5|B4DHL0|C8UZT4|Q5SYC0	Missense_Mutation	SNP	ENST00000275162.5	37	CCDS34525.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.992176	0.74703	.	.	ENSG00000146352	ENST00000275162	D	0.95171	-3.63	5.39	5.39	0.77823	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.051477	0.85682	D	0.000000	D	0.97312	0.9121	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97558	1.0096	10	0.87932	D	0	-9.6722	14.2164	0.65795	0.1491:0.8509:0.0:0.0	.	56	Q5SYC1	CLVS2_HUMAN	C	56	ENSP00000275162:R56C	ENSP00000275162:R56C	R	+	1	0	CLVS2	123360787	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.400000	0.44504	2.814000	0.96858	0.585000	0.79938	CGC		0.542	CLVS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042042.2	NM_001010852	
NKAIN2	154215	broad.mit.edu	37	6	124125371	124125371	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:124125371C>T	ENST00000368417.1	+	1	86	c.26C>T	c.(25-27)aCg>aTg	p.T9M	NKAIN2_ENST00000546092.1_Missense_Mutation_p.T9M|NKAIN2_ENST00000368416.1_Missense_Mutation_p.T9M|NKAIN2_ENST00000476571.1_3'UTR	NM_001040214.1	NP_001035304.1	Q5VXU1	NKAI2_HUMAN	Na+/K+ transporting ATPase interacting 2	9						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T9M(1)		cervix(1)|endometrium(1)|large_intestine(3)|lung(12)|skin(2)	19				GBM - Glioblastoma multiforme(226;0.104)		GGCAGGTGCACGCTTATCTTT	0.537																																					p.T9M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C26T	6						.						168.0	152.0	158.0					6																	124125371		2203	4300	6503	124167070	SO:0001583	missense	154215	exon1			AB070452	CCDS34526.1	6q21	2008-02-05	2007-10-04	2007-10-04	ENSG00000188580	ENSG00000188580		"""Na+/K+ transporting ATPase interacting"""	16443	protein-coding gene	gene with protein product		609758	"""T-cell lymphoma breakpoint associated target 1"""	TCBA1		17606467	Standard	XM_005266833		Approved	FAM77B	uc003pzo.3	Q5VXU1	OTTHUMG00000015500	ENST00000368417.1:c.26C>T	6.37:g.124125371C>T	ENSP00000357402:p.Thr9Met	Somatic		Capture	Illumina HiSeq	Phase_I	124167070	NM_153355	Q8IYR4|Q8TF67	De_novo_Start_OutOfFrame	SNP	ENST00000368417.1	37	CCDS34526.1	.	.	.	.	.	.	.	.	.	.	C	12.67	2.006324	0.35415	.	.	ENSG00000188580	ENST00000368416;ENST00000368417;ENST00000546092	T;T;T	0.15139	2.45;2.45;2.45	4.17	4.17	0.49024	.	1.284680	0.05326	U	0.527453	T	0.27027	0.0662	L	0.52905	1.665	0.80722	D	1	D;D;D	0.89917	1.0;0.995;0.997	D;D;P	0.70227	0.968;0.938;0.83	T	0.01413	-1.1361	10	0.34782	T	0.22	.	12.9921	0.58625	0.0:0.8363:0.1637:0.0	.	9;9;9	F5GY48;Q5VXU1;Q5VXU1-2	.;NKAI2_HUMAN;.	M	9	ENSP00000357401:T9M;ENSP00000357402:T9M;ENSP00000440287:T9M	ENSP00000357401:T9M	T	+	2	0	NKAIN2	124167070	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.464000	0.53057	2.143000	0.66587	0.491000	0.48974	ACG		0.537	NKAIN2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042057.1	NM_001040214	
SOGA3	387104	broad.mit.edu	37	6	127797480	127797480	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:127797480T>A	ENST00000525778.1	-	6	2436	c.1691A>T	c.(1690-1692)tAt>tTt	p.Y564F	SOGA3_ENST00000556132.1_Missense_Mutation_p.Y564F|SOGA3_ENST00000465909.2_Missense_Mutation_p.Y564F|SOGA3_ENST00000368268.2_Missense_Mutation_p.Y564F|SOGA3_ENST00000474293.2_5'Flank|SOGA3_ENST00000481848.2_Missense_Mutation_p.Y564F			Q5TF21	SOGA3_HUMAN	SOGA family member 3	564					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.Y564F(1)									CAGATCCCCATAAAAGGATCT	0.493																																					p.Y564F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1691T	6						.						86.0	85.0	85.0					6																	127797480		1905	4130	6035	127839173	SO:0001583	missense	387104	exon6			AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1691A>T	6.37:g.127797480T>A	ENSP00000434570:p.Tyr564Phe	Somatic		Capture	Illumina HiSeq	Phase_I	127839173	NM_001012279		Missense_Mutation	SNP	ENST00000525778.1	37	CCDS43505.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.219621	0.79464	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.46639	0.1403	L	0.52759	1.655	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.49670	-0.8915	10	0.66056	D	0.02	-8.5364	15.6545	0.77124	0.0:0.0:0.0:1.0	.	564	Q5TF21	CF174_HUMAN	F	564	ENSP00000451768:Y564F;ENSP00000357251:Y564F;ENSP00000434570:Y564F;ENSP00000435559:Y564F	ENSP00000435559:Y564F	Y	-	2	0	C6orf174	127839173	1.000000	0.71417	0.949000	0.38748	0.975000	0.68041	8.007000	0.88571	2.112000	0.64535	0.459000	0.35465	TAT		0.493	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279	
LAMA2	3908	broad.mit.edu	37	6	129637186	129637186	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:129637186G>A	ENST00000421865.2	+	27	3977	c.3928G>A	c.(3928-3930)Gaa>Aaa	p.E1310K		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1310	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)	p.E1310K(1)		NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		TTAACAGAAAGAATGGAAATA	0.348																																					p.E1310K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3928A	6						.						84.0	89.0	87.0					6																	129637186		2203	4299	6502	129678879	SO:0001583	missense	3908	exon27			Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.3928G>A	6.37:g.129637186G>A	ENSP00000400365:p.Glu1310Lys	Somatic		Capture	Illumina HiSeq	Phase_I	129678879	NM_001079823	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	G	10.05	1.244521	0.22796	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.35236	1.32	5.4	3.63	0.41609	Laminin B type IV (2);Laminin B, subgroup (1);	0.054018	0.64402	D	0.000001	T	0.20577	0.0495	L	0.39898	1.24	0.51482	D	0.99992	P;P	0.52170	0.916;0.951	P;P	0.53954	0.674;0.738	T	0.07712	-1.0758	10	0.06236	T	0.91	.	12.3084	0.54915	0.1382:0.0:0.8618:0.0	.	1310;1310	A6NF00;P24043	.;LAMA2_HUMAN	K	1310	ENSP00000400365:E1310K	ENSP00000346769:E1310K	E	+	1	0	LAMA2	129678879	1.000000	0.71417	1.000000	0.80357	0.575000	0.36095	6.114000	0.71560	0.772000	0.33382	-0.136000	0.14681	GAA		0.348	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
TAAR5	9038	broad.mit.edu	37	6	132910663	132910663	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:132910663C>T	ENST00000258034.2	-	1	214	c.163G>A	c.(163-165)Gtg>Atg	p.V55M		NM_003967.2	NP_003958.2	O14804	TAAR5_HUMAN	trace amine associated receptor 5	55					G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|trimethylamine receptor activity (GO:1990081)	p.V55M(1)		breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	32	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00604)|GBM - Glioblastoma multiforme(226;0.015)		GCAAATGCCACAAATACATTC	0.547																																					p.V55M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G163A	6						.						183.0	177.0	179.0					6																	132910663		2203	4300	6503	132952356	SO:0001583	missense	9038	exon1			AF021818	CCDS5156.1	6q23.2	2012-08-08			ENSG00000135569	ENSG00000135569		"""GPCR / Class A : Trace amine associated receptors"""	30236	protein-coding gene	gene with protein product		607405				9464258, 15718104	Standard	NM_003967		Approved	PNR	uc003qdk.2	O14804	OTTHUMG00000015581	ENST00000258034.2:c.163G>A	6.37:g.132910663C>T	ENSP00000258034:p.Val55Met	Somatic		Capture	Illumina HiSeq	Phase_I	132952356	NM_003967	D8KZS1|Q2M1V1|Q4VBL1|Q5VUQ3|Q6NTA8	Missense_Mutation	SNP	ENST00000258034.2	37	CCDS5156.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.246799	0.80024	.	.	ENSG00000135569	ENST00000258034	D	0.84800	-1.9	5.43	5.43	0.79202	GPCR, rhodopsin-like superfamily (1);	0.109190	0.37955	N	0.001870	D	0.95262	0.8463	H	0.97440	4.005	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.95380	0.8472	10	0.49607	T	0.09	-12.1766	19.4464	0.94849	0.0:1.0:0.0:0.0	.	55	O14804	TAAR5_HUMAN	M	55	ENSP00000258034:V55M	ENSP00000258034:V55M	V	-	1	0	TAAR5	132952356	0.993000	0.37304	1.000000	0.80357	0.836000	0.47400	3.129000	0.50500	2.827000	0.97445	0.655000	0.94253	GTG		0.547	TAAR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042257.1	NM_003967	
VNN2	8875	broad.mit.edu	37	6	133070852	133070852	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:133070852C>T	ENST00000326499.6	-	6	1477	c.1353G>A	c.(1351-1353)ctG>ctA	p.L451L	VNN2_ENST00000525270.1_Silent_p.L398L|RP1-55C23.7_ENST00000430895.1_RNA|VNN2_ENST00000525289.1_Silent_p.L230L	NM_004665.2	NP_004656	O95498	VNN2_HUMAN	vanin 2	451					cellular component movement (GO:0006928)|pantothenate metabolic process (GO:0015939)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)	p.L451L(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		TTCCAGGTGACAGATGAATTT	0.368																																					p.L451L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1353A	6						.						58.0	55.0	56.0					6																	133070852		2203	4300	6503	133112545	SO:0001819	synonymous_variant	8875	exon6			AB026705	CCDS5161.1, CCDS5162.1, CCDS56451.1	6q23-q24	2013-02-13			ENSG00000112303	ENSG00000112303	3.5.1.92	"""Vanins"""	12706	protein-coding gene	gene with protein product	"""pantetheinase"""	603571				9790769, 11491533	Standard	NM_078488		Approved	FOAP-4, GPI-80	uc003qdt.3	O95498	OTTHUMG00000015588	ENST00000326499.6:c.1353G>A	6.37:g.133070852C>T		Somatic		Capture	Illumina HiSeq	Phase_I	133112545	NM_004665	A0AUZ3|A6NDY1|A8K4E3|A8K7W0|B2DFZ0|B2DFZ1|B2DFZ2|B2DFZ3|F6XL73|Q2XUN1|Q9UJF3|Q9UMW2	Silent	SNP	ENST00000326499.6	37	CCDS5161.1																																																																																				0.368	VNN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042264.2		
TBC1D7	51256	broad.mit.edu	37	6	13321193	13321193	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:13321193G>A	ENST00000379300.3	-	4	571	c.328C>T	c.(328-330)Cgc>Tgc	p.R110C	TBC1D7_ENST00000607532.1_5'UTR|TBC1D7_ENST00000607658.1_Missense_Mutation_p.R83C|TBC1D7_ENST00000343141.4_Missense_Mutation_p.R110C|TBC1D7_ENST00000356436.4_Missense_Mutation_p.R110C|TBC1D7_ENST00000379307.2_Missense_Mutation_p.R83C	NM_001143964.2|NM_016495.4	NP_001137436.1|NP_057579.1	Q9P0N9	TBCD7_HUMAN	TBC1 domain family, member 7	110	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				activation of Rho GTPase activity (GO:0032862)|negative regulation of cilium assembly (GO:1902018)|negative regulation of TOR signaling (GO:0032007)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of Rab GTPase activity (GO:0032851)|response to growth factor (GO:0070848)	ciliary basal body (GO:0036064)|cytoplasmic vesicle (GO:0031410)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)	p.R110C(2)|p.R110S(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)	22	Breast(50;0.0296)|Ovarian(93;0.0339)	all_hematologic(90;0.135)	Epithelial(50;0.0784)|BRCA - Breast invasive adenocarcinoma(129;0.13)|all cancers(50;0.21)			TGATACATGCGGAGATAGACT	0.488																																					p.R110C												.	.	3	Substitution - Missense(3)	ovary(1)|lung(1)|large_intestine(1)	c.C328T	6						.						254.0	219.0	231.0					6																	13321193		2203	4300	6503	13429172	SO:0001583	missense	51256	exon4			AF151073	CCDS4523.1, CCDS47376.1, CCDS58995.1	6p23	2013-07-10			ENSG00000145979	ENSG00000145979			21066	protein-coding gene	gene with protein product		612655				11042152, 17646400	Standard	XM_005249163		Approved	dJ257A7.3, FLJ32666	uc003nan.3	Q9P0N9	OTTHUMG00000014272	ENST00000379300.3:c.328C>T	6.37:g.13321193G>A	ENSP00000368602:p.Arg110Cys	Somatic		Capture	Illumina HiSeq	Phase_I	13429172	NM_001143965	E7EV96|Q2TU37|Q53F44|Q5SZL7|Q86VM8|Q96MB8	Missense_Mutation	SNP	ENST00000379300.3	37	CCDS4523.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.122642	0.77436	.	.	ENSG00000145979	ENST00000334971;ENST00000421203;ENST00000356436;ENST00000379300;ENST00000379307;ENST00000343141;ENST00000452989;ENST00000450347;ENST00000422136;ENST00000446018;ENST00000420456;ENST00000428109;ENST00000416436;ENST00000379291	T;T;T;T;T;T;T;T;T;T;T;T;T	0.47528	2.15;2.15;2.15;1.41;1.44;1.41;1.41;2.15;1.45;1.45;2.15;2.15;0.84	5.85	4.94	0.65067	Rab-GAP/TBC domain (1);	0.185905	0.64402	D	0.000012	T	0.56262	0.1973	M	0.75447	2.3	0.80722	D	1	D;D;D;D;D	0.89917	0.992;0.983;0.99;0.992;1.0	P;P;P;P;D	0.73380	0.785;0.707;0.53;0.785;0.98	T	0.62737	-0.6791	10	0.59425	D	0.04	-3.4931	10.0087	0.41972	0.1598:0.0:0.8402:0.0	.	110;83;83;83;110	Q2TU37;Q5JPB9;Q5SZL5;Q9P0N9-2;Q9P0N9	.;.;.;.;TBCD7_HUMAN	C	51;110;110;110;83;110;83;83;110;83;83;110;110;110	ENSP00000401438:R110C;ENSP00000348813:R110C;ENSP00000368602:R110C;ENSP00000368609:R83C;ENSP00000343100:R110C;ENSP00000414292:R83C;ENSP00000404680:R83C;ENSP00000394425:R110C;ENSP00000417005:R83C;ENSP00000412102:R83C;ENSP00000414101:R110C;ENSP00000401339:R110C;ENSP00000368593:R110C	ENSP00000334212:R51C	R	-	1	0	TBC1D7	13429172	1.000000	0.71417	0.995000	0.50966	0.987000	0.75469	5.390000	0.66261	1.385000	0.46445	0.555000	0.69702	CGC		0.488	TBC1D7-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039896.2	NM_016495	
SLC18B1	116843	broad.mit.edu	37	6	133118215	133118215	+	Missense_Mutation	SNP	G	G	A	rs200561155	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:133118215G>A	ENST00000275227.4	-	2	185	c.89C>T	c.(88-90)tCg>tTg	p.S30L	SLC18B1_ENST00000367918.1_Missense_Mutation_p.S30L|SLC18B1_ENST00000538764.1_5'UTR|SLC18B1_ENST00000460518.1_5'UTR	NM_052831.2	NP_439896.1	Q6NT16	S18B1_HUMAN	solute carrier family 18, subfamily B, member 1	30			S -> P (in dbSNP:rs41286192).		transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.S30L(1)									CTGTTCTCTCGAAAGCCACCC	0.443													G|||	2	0.000399361	0.0	0.0014	5008	,	,		15042	0.001		0.0	False		,,,				2504	0.0				p.S30L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C89T	6						.						99.0	99.0	99.0					6																	133118215		2203	4300	6503	133159908	SO:0001583	missense	116843	exon2			AK124442	CCDS5163.1	6q22.3-q23.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000146409	ENSG00000146409		"""Solute carriers"""	21573	protein-coding gene	gene with protein product		613361	"""chromosome 6 open reading frame 192"""	C6orf192		19697161	Standard	XM_006715328		Approved	dJ55C23.6	uc003qdw.1	Q6NT16	OTTHUMG00000015595	ENST00000275227.4:c.89C>T	6.37:g.133118215G>A	ENSP00000275227:p.Ser30Leu	Somatic		Capture	Illumina HiSeq	Phase_I	133159908	NM_052831	A8K1K3|B3KW77|Q6ISF2	Missense_Mutation	SNP	ENST00000275227.4	37	CCDS5163.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	G	15.07	2.722864	0.48728	.	.	ENSG00000146409	ENST00000367919;ENST00000275227;ENST00000367918	T;T	0.59224	0.28;0.28	5.28	5.28	0.74379	Major facilitator superfamily domain, general substrate transporter (1);	0.396299	0.26761	N	0.022625	T	0.47432	0.1445	M	0.82323	2.585	0.80722	D	1	P	0.47762	0.9	B	0.38683	0.279	T	0.57969	-0.7719	10	0.44086	T	0.13	-15.4061	12.2128	0.54389	0.0:0.1716:0.8284:0.0	.	30	Q6NT16	CF192_HUMAN	L	30	ENSP00000275227:S30L;ENSP00000356895:S30L	ENSP00000275227:S30L	S	-	2	0	C6orf192	133159908	0.998000	0.40836	0.368000	0.25939	0.022000	0.10575	5.483000	0.66838	2.484000	0.83849	0.650000	0.86243	TCG		0.443	SLC18B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042273.1	NM_052831	
SGK1	6446	broad.mit.edu	37	6	134583094	134583094	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:134583094A>C	ENST00000367858.5	-	2	859	c.262T>G	c.(262-264)Tgg>Ggg	p.W88G	SGK1_ENST00000524929.1_Missense_Mutation_p.W88G	NM_001143676.1	NP_001137148.1	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	0					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)	p.W88G(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		TGAGTTTCCCATGAACATGAC	0.468																																					p.W88G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T262G	6						.						137.0	123.0	127.0					6																	134583094		1568	3582	5150	134624787	SO:0001583	missense	6446	exon2			AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000367858.5:c.262T>G	6.37:g.134583094A>C	ENSP00000356832:p.Trp88Gly	Somatic		Capture	Illumina HiSeq	Phase_I	134624787	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000367858.5	37	CCDS47476.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.96|16.96	3.266037|3.266037	0.59540|0.59540	.|.	.|.	ENSG00000118515|ENSG00000118515	ENST00000460769|ENST00000367858;ENST00000461976;ENST00000524929	.|T	.|0.73575	.|-0.76	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	.|0.270348	.|0.27289	.|N	.|0.020046	T|T	0.74496|0.74496	0.3724|0.3724	L|L	0.34521|0.34521	1.04|1.04	0.41536|0.41536	D|D	0.98848|0.98848	.|D;D	.|0.89917	.|1.0;0.981	.|D;D	.|0.91635	.|0.999;0.954	T|T	0.77125|0.77125	-0.2703|-0.2703	5|10	.|0.46703	.|T	.|0.11	.|.	14.6388|14.6388	0.68708|0.68708	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|88;88	.|Q7Z3I4;O00141-2	.|.;.	R|G	35|88;57;88	.|ENSP00000356832:W88G	.|ENSP00000356832:W88G	M|W	-|-	2|1	0|0	SGK1|SGK1	134624787|134624787	1.000000|1.000000	0.71417|0.71417	0.962000|0.962000	0.40283|0.40283	0.729000|0.729000	0.41735|0.41735	5.979000|5.979000	0.70508|0.70508	2.185000|2.185000	0.69588|0.69588	0.460000|0.460000	0.39030|0.39030	ATG|TGG		0.468	SGK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042304.2		
MYB	4602	broad.mit.edu	37	6	135513605	135513605	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:135513605C>T	ENST00000367814.4	+	6	857	c.671C>T	c.(670-672)gCt>gTt	p.A224V	MYB_ENST00000528774.1_Missense_Mutation_p.A224V|MYB_ENST00000316528.8_Missense_Mutation_p.A224V|MYB_ENST00000531845.1_3'UTR|MYB_ENST00000534044.1_Missense_Mutation_p.A224V|MYB_ENST00000341911.5_Missense_Mutation_p.A224V|MYB_ENST00000527615.1_Missense_Mutation_p.A224V|MYB_ENST00000420123.2_Missense_Mutation_p.A200V|MYB_ENST00000534121.1_Missense_Mutation_p.A224V|MYB-AS1_ENST00000455534.1_RNA|MYB_ENST00000442647.2_Missense_Mutation_p.A224V|MYB_ENST00000533624.1_Missense_Mutation_p.A224V|MYB_ENST00000525369.1_Missense_Mutation_p.A224V	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog	224					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.A224V(4)		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)		ATGGGTTTTGCTCAGGCTCCG	0.502			T	NFIB	adenoid cystic carcinoma																																p.A224V			Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	.	.	4	Substitution - Missense(4)	large_intestine(2)|lung(2)	c.C671T	6						.						130.0	123.0	125.0					6																	135513605		2203	4300	6503	135555298	SO:0001583	missense	4602	exon6				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.671C>T	6.37:g.135513605C>T	ENSP00000356788:p.Ala224Val	Somatic		Capture	Illumina HiSeq	Phase_I	135555298	NM_001161657	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	37	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.074772	0.55646	.	.	ENSG00000118513	ENST00000341911;ENST00000442647;ENST00000316528;ENST00000237302;ENST00000367814;ENST00000527615;ENST00000420123;ENST00000525369;ENST00000528774;ENST00000534121;ENST00000534044;ENST00000533624;ENST00000430686	T;T;T;T;T;T;T;T;T;T	0.33654	2.64;2.16;2.15;2.16;1.4;1.85;2.64;2.64;1.82;2.14	5.43	4.56	0.56223	.	0.419396	0.30686	N	0.009083	T	0.11153	0.0272	N	0.14661	0.345	0.36982	D	0.894333	B;B;B;B;B;B;B;P;B;B	0.36959	0.232;0.025;0.054;0.043;0.306;0.046;0.306;0.575;0.032;0.236	B;B;B;B;B;B;B;B;B;B	0.33042	0.121;0.022;0.034;0.073;0.05;0.028;0.05;0.157;0.028;0.11	T	0.04781	-1.0927	10	0.29301	T	0.29	-0.7256	16.4595	0.84032	0.0:0.869:0.131:0.0	.	224;224;200;224;224;224;224;224;224;224	E9PI07;E9PLZ5;E9PMQ0;P10242-2;E9PNL6;E9PRS2;E9PNA4;P10242-4;P10242;Q708E1	.;.;.;.;.;.;.;.;MYB_HUMAN;.	V	224;224;224;224;224;224;200;224;224;224;224;224;178	ENSP00000339992:A224V;ENSP00000410825:A224V;ENSP00000326328:A224V;ENSP00000356788:A224V;ENSP00000433227:A224V;ENSP00000435938:A224V;ENSP00000434723:A224V;ENSP00000432851:A224V;ENSP00000435055:A224V;ENSP00000436605:A224V	ENSP00000237302:A224V	A	+	2	0	MYB	135555298	1.000000	0.71417	0.953000	0.39169	0.985000	0.73830	3.680000	0.54641	1.259000	0.44117	0.655000	0.94253	GCT		0.502	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4		
KIAA1244	57221	broad.mit.edu	37	6	138559696	138559696	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:138559696T>C	ENST00000251691.4	+	6	637	c.471T>C	c.(469-471)acT>acC	p.T157T		NM_020340.4	NP_065073.3			KIAA1244									p.T86T(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		GCATAAACACTGCTGTGCGGG	0.468																																					p.T157T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T471C	6						.						176.0	155.0	162.0					6																	138559696		2203	4300	6503	138601389	SO:0001819	synonymous_variant	57221	exon6			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.471T>C	6.37:g.138559696T>C		Somatic		Capture	Illumina HiSeq	Phase_I	138601389	NM_020340		Silent	SNP	ENST00000251691.4	37	CCDS5189.2																																																																																				0.468	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
KIAA1244	57221	broad.mit.edu	37	6	138615205	138615205	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:138615205G>A	ENST00000251691.4	+	20	3610	c.3444G>A	c.(3442-3444)tcG>tcA	p.S1148S		NM_020340.4	NP_065073.3			KIAA1244									p.S1077S(1)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		AGAAAGCATCGCAGTCTCAGC	0.433																																					p.S1148S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3444A	6						.						141.0	127.0	132.0					6																	138615205		2203	4300	6503	138656898	SO:0001819	synonymous_variant	57221	exon20			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.3444G>A	6.37:g.138615205G>A		Somatic		Capture	Illumina HiSeq	Phase_I	138656898	NM_020340		Silent	SNP	ENST00000251691.4	37	CCDS5189.2																																																																																				0.433	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
REPS1	85021	broad.mit.edu	37	6	139266436	139266436	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:139266436C>T	ENST00000450536.2	-	4	1122	c.548G>A	c.(547-549)cGt>cAt	p.R183H	REPS1_ENST00000415951.2_Missense_Mutation_p.R183H|REPS1_ENST00000367663.4_Missense_Mutation_p.R183H|REPS1_ENST00000531675.1_5'Flank|REPS1_ENST00000258062.5_Missense_Mutation_p.R183H|REPS1_ENST00000409812.2_Missense_Mutation_p.R183H			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	183					receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)	p.R131H(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		GCTGGGATGACGGCTGTGCTT	0.473																																					p.R183H												.	.	2	Substitution - Missense(2)	large_intestine(1)|breast(1)	c.G548A	6						.						54.0	53.0	53.0					6																	139266436		2203	4300	6503	139308129	SO:0001583	missense	85021	exon4				CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"""EF-hand domain containing"""	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.548G>A	6.37:g.139266436C>T	ENSP00000392065:p.Arg183His	Somatic		Capture	Illumina HiSeq	Phase_I	139308129	NM_031922	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Missense_Mutation	SNP	ENST00000450536.2	37		.	.	.	.	.	.	.	.	.	.	C	32	5.172883	0.94807	.	.	ENSG00000135597	ENST00000450536;ENST00000367663;ENST00000529597;ENST00000409812;ENST00000258062;ENST00000415951;ENST00000367668	T;T;T;T;T;T	0.34667	1.36;1.38;1.38;1.38;1.35;1.37	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.40094	0.1103	L	0.40543	1.245	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.83275	0.996;0.996;0.932;0.991	T	0.04413	-1.0953	10	0.14252	T	0.57	-8.7454	18.201	0.89838	0.0:1.0:0.0:0.0	.	183;183;183;183	Q96D71-3;Q96D71-2;Q96D71;E9PMG1	.;.;REPS1_HUMAN;.	H	183;183;169;183;183;183;131	ENSP00000392065:R183H;ENSP00000356635:R183H;ENSP00000434251:R169H;ENSP00000386699:R183H;ENSP00000258062:R183H;ENSP00000397941:R183H	ENSP00000258062:R183H	R	-	2	0	REPS1	139308129	1.000000	0.71417	0.653000	0.29593	0.854000	0.48673	7.143000	0.77348	2.740000	0.93945	0.561000	0.74099	CGT		0.473	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3		
ABRACL	58527	broad.mit.edu	37	6	139363897	139363897	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:139363897C>T	ENST00000367660.3	+	3	303	c.103C>T	c.(103-105)Cgt>Tgt	p.R35C		NM_021243.2	NP_067066.1	Q9P1F3	ABRAL_HUMAN	ABRA C-terminal like	35								p.R35C(1)									GGTCCTCTTCCGTGATGATAA	0.403																																					p.R35C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C103T	6						.						257.0	234.0	241.0					6																	139363897		1894	4115	6009	139405590	SO:0001583	missense	58527	exon3			BC014953	CCDS43509.1	6q24.1	2012-03-05	2012-03-05	2012-03-05	ENSG00000146386	ENSG00000146386			21230	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 115"""	C6orf115		21082705	Standard	NM_021243		Approved	PRO2013, HSPC280, Costars	uc003qil.2	Q9P1F3	OTTHUMG00000015684	ENST00000367660.3:c.103C>T	6.37:g.139363897C>T	ENSP00000356632:p.Arg35Cys	Somatic		Capture	Illumina HiSeq	Phase_I	139405590	NM_021243	Q5SZC8|Q9P0A1	Missense_Mutation	SNP	ENST00000367660.3	37	CCDS43509.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.638260	0.47153	.	.	ENSG00000146386	ENST00000367660	.	.	.	5.73	4.84	0.62591	.	0.986139	0.08291	N	0.968368	T	0.38108	0.1028	.	.	.	0.80722	D	1	P	0.35844	0.524	B	0.36186	0.219	T	0.38824	-0.9643	8	0.66056	D	0.02	-13.8255	9.3425	0.38089	0.0:0.5691:0.3536:0.0773	.	35	Q9P1F3	CF115_HUMAN	C	35	.	ENSP00000356632:R35C	R	+	1	0	C6orf115	139405590	0.904000	0.30761	0.970000	0.41538	0.958000	0.62258	2.153000	0.42282	1.371000	0.46172	0.655000	0.94253	CGT		0.403	ABRACL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042445.1	NM_021243	
GPR126	57211	broad.mit.edu	37	6	142741125	142741125	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:142741125G>A	ENST00000230173.6	+	22	3679	c.3203G>A	c.(3202-3204)cGc>cAc	p.R1068H	GPR126_ENST00000367608.2_Missense_Mutation_p.R1040H|GPR126_ENST00000296932.8_Missense_Mutation_p.R1040H|GPR126_ENST00000367609.3_Missense_Mutation_p.R1068H	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	1068					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R1039H(1)|p.R1068H(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		AGGAACCTGCGCAGTGTGGTT	0.488																																					p.R1040H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3119A	6						.						281.0	278.0	279.0					6																	142741125		1955	4149	6104	142782818	SO:0001583	missense	57211	exon21			AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"""-"", ""GPCR / Class B : Orphans"""	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.3203G>A	6.37:g.142741125G>A	ENSP00000230173:p.Arg1068His	Somatic		Capture	Illumina HiSeq	Phase_I	142782818	NM_001032394	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	37	CCDS47490.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.552380	0.86127	.	.	ENSG00000112414	ENST00000230173;ENST00000367608;ENST00000296932;ENST00000367609	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.55	5.55	0.83447	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000002	T	0.69637	0.3133	M	0.91300	3.195	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	1.0;1.0;1.0;1.0;1.0	T	0.76961	-0.2765	10	0.87932	D	0	.	19.5048	0.95111	0.0:0.0:1.0:0.0	.	128;1040;1068;1040;1068	B4DSK4;Q86SQ4-4;Q86SQ4-3;Q86SQ4-2;Q86SQ4	.;.;.;.;GP126_HUMAN	H	1068;1040;1040;1068	ENSP00000230173:R1068H;ENSP00000356580:R1040H;ENSP00000296932:R1040H;ENSP00000356581:R1068H	ENSP00000230173:R1068H	R	+	2	0	GPR126	142782818	1.000000	0.71417	1.000000	0.80357	0.495000	0.33615	9.471000	0.97696	2.600000	0.87896	0.650000	0.86243	CGC		0.488	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2		
HIVEP2	3097	broad.mit.edu	37	6	143091583	143091583	+	Silent	SNP	G	G	A	rs34191067	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:143091583G>A	ENST00000367604.1	-	4	4932	c.4293C>T	c.(4291-4293)agC>agT	p.S1431S	HIVEP2_ENST00000012134.2_Silent_p.S1431S|HIVEP2_ENST00000367603.2_Silent_p.S1431S			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	1431					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.S1431S(1)		NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GGGTGGCCACGCTGTCAGAGG	0.522													G|||	18	0.00359425	0.0121	0.0029	5008	,	,		19195	0.0		0.0	False		,,,				2504	0.0				p.S1431S	Esophageal Squamous(107;843 1510 13293 16805 42198)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4293T	6						.	G		41,3909		1,39,1935	82.0	82.0	82.0		4293	-6.2	0.0	6	dbSNP_126	82	0,8334		0,0,4167	no	coding-synonymous	HIVEP2	NM_006734.3		1,39,6102	AA,AG,GG		0.0,1.038,0.3338		1431/2447	143091583	41,12243	1975	4167	6142	143133276	SO:0001819	synonymous_variant	3097	exon5			M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"""Zinc fingers, C2H2-type"""	4921	protein-coding gene	gene with protein product	"""c-myc intron binding protein 1"""	143054	"""human immunodeficiency virus type I enhancer-binding protein 2"""			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.4293C>T	6.37:g.143091583G>A		Somatic		Capture	Illumina HiSeq	Phase_I	143133276	NM_006734	Q02646|Q5THT5|Q9NS05	Silent	SNP	ENST00000367604.1	37	CCDS43510.1																																																																																				0.522	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1		
UTRN	7402	broad.mit.edu	37	6	145157020	145157020	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:145157020G>T	ENST00000367545.3	+	69	9770	c.9770G>T	c.(9769-9771)aGg>aTg	p.R3257M	UTRN_ENST00000367526.4_Missense_Mutation_p.R812M	NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	3257					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.R3257M(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)		TCAGTAGAGAGGGAAGAACGT	0.532																																					p.R3257M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G9770T	6						.						113.0	109.0	111.0					6																	145157020		2203	4300	6503	145198713	SO:0001583	missense	7402	exon69			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.9770G>T	6.37:g.145157020G>T	ENSP00000356515:p.Arg3257Met	Somatic		Capture	Illumina HiSeq	Phase_I	145198713	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	g	15.49	2.847766	0.51164	.	.	ENSG00000152818	ENST00000367545;ENST00000367526;ENST00000455022	D;D;D	0.82619	-1.63;-1.63;-1.63	5.9	4.12	0.48240	.	0.323685	0.26623	N	0.023347	T	0.63153	0.2487	L	0.36672	1.1	0.25121	N	0.990641	P	0.40250	0.709	B	0.42087	0.375	T	0.57929	-0.7726	10	0.54805	T	0.06	.	7.5642	0.27868	0.3498:0.0:0.6502:0.0	.	3257	P46939	UTRO_HUMAN	M	3257;812;169	ENSP00000356515:R3257M;ENSP00000356496:R812M;ENSP00000387927:R169M	ENSP00000356496:R812M	R	+	2	0	UTRN	145198713	1.000000	0.71417	0.996000	0.52242	0.663000	0.39108	1.919000	0.40015	0.838000	0.34948	-0.127000	0.14921	AGG		0.532	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
PPIL4	85313	broad.mit.edu	37	6	149856807	149856807	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:149856807G>A	ENST00000253329.2	-	5	421	c.389C>T	c.(388-390)aCa>aTa	p.T130I		NM_139126.3	NP_624311.1	Q8WUA2	PPIL4_HUMAN	peptidylprolyl isomerase (cyclophilin)-like 4	130	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)	p.T130I(1)		endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	13		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.11e-11)|GBM - Glioblastoma multiforme(68;0.0885)		CATGCCTTCTGTCACCTCACC	0.348																																					p.T130I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C389T	6						.						138.0	124.0	129.0					6																	149856807		2203	4299	6502	149898500	SO:0001583	missense	85313	exon5				CCDS34550.1	6q25.1	2013-02-12			ENSG00000131013	ENSG00000131013		"""RNA binding motif (RRM) containing"""	15702	protein-coding gene	gene with protein product		607609					Standard	NM_139126		Approved		uc003qmo.2	Q8WUA2	OTTHUMG00000015788	ENST00000253329.2:c.389C>T	6.37:g.149856807G>A	ENSP00000253329:p.Thr130Ile	Somatic		Capture	Illumina HiSeq	Phase_I	149898500	NM_139126	B2RD34|Q7Z3Q5	Missense_Mutation	SNP	ENST00000253329.2	37	CCDS34550.1	.	.	.	.	.	.	.	.	.	.	G	18.89	3.719834	0.68844	.	.	ENSG00000131013	ENST00000253329	T	0.19532	2.14	4.86	4.86	0.63082	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (4);Cyclophilin-like (1);	0.046019	0.85682	D	0.000000	T	0.12305	0.0299	N	0.11427	0.14	0.80722	D	1	P;P	0.49559	0.481;0.925	B;P	0.52514	0.291;0.701	T	0.17471	-1.0368	10	0.30078	T	0.28	.	18.3534	0.90345	0.0:0.0:1.0:0.0	.	130;130	B3KRR4;Q8WUA2	.;PPIL4_HUMAN	I	130	ENSP00000253329:T130I	ENSP00000253329:T130I	T	-	2	0	PPIL4	149898500	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.540000	0.82074	2.395000	0.81488	0.650000	0.86243	ACA		0.348	PPIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042642.1		
MTHFD1L	25902	broad.mit.edu	37	6	151265685	151265685	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:151265685G>A	ENST00000367321.3	+	14	1778	c.1504G>A	c.(1504-1506)Gcc>Acc	p.A502T		NM_001242767.1|NM_001242768.1|NM_015440.4	NP_001229696.1|NP_001229697.1|NP_056255.2	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	502	Formyltetrahydrofolate synthetase.				folic acid-containing compound biosynthetic process (GO:0009396)|folic acid-containing compound metabolic process (GO:0006760)|formate metabolic process (GO:0015942)|one-carbon metabolic process (GO:0006730)|oxidation-reduction process (GO:0055114)|tetrahydrofolate interconversion (GO:0035999)|tetrahydrofolate metabolic process (GO:0046653)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|protein homodimerization activity (GO:0042803)	p.A502T(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	29		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		GCTGGCTGCCGCCATCGACAC	0.428																																					p.A502T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1504A	6						.						50.0	47.0	48.0					6																	151265685		2203	4300	6503	151307378	SO:0001583	missense	25902	exon14			BC017477	CCDS5228.1, CCDS56457.1, CCDS75535.1, CCDS75536.1	6q25.1	2010-07-19	2004-12-13	2004-12-14	ENSG00000120254	ENSG00000120254	6.3.4.3		21055	protein-coding gene	gene with protein product	"""10-formyl-THF synthetase"", ""mitochondrial C1-tetrahydrofolate synthase"", ""monofunctional C1-tetrahydrofolate synthase, mitochondrial"""	611427	"""formyltetrahydrofolate synthetase domain containing 1"""	FTHFSDC1		18804703	Standard	NM_015440		Approved	DKFZP586G1517, FLJ21145	uc021zgs.1	Q6UB35	OTTHUMG00000015828	ENST00000367321.3:c.1504G>A	6.37:g.151265685G>A	ENSP00000356290:p.Ala502Thr	Somatic		Capture	Illumina HiSeq	Phase_I	151307378	NM_015440	Q2TBF3|Q8WVW0|Q96HG8|Q9H789|Q9UFU8	Missense_Mutation	SNP	ENST00000367321.3	37	CCDS5228.1	.	.	.	.	.	.	.	.	.	.	G	33	5.262782	0.95399	.	.	ENSG00000120254	ENST00000367321	T	0.24723	1.84	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.58509	0.2127	M	0.93375	3.41	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.995;0.999	T	0.69083	-0.5239	10	0.59425	D	0.04	.	19.4315	0.94772	0.0:0.0:1.0:0.0	.	503;257;502	B7ZM99;B2RD24;Q6UB35	.;.;C1TM_HUMAN	T	502	ENSP00000356290:A502T	ENSP00000356290:A502T	A	+	1	0	MTHFD1L	151307378	1.000000	0.71417	0.310000	0.25168	0.882000	0.50991	9.749000	0.98871	2.600000	0.87896	0.655000	0.94253	GCC		0.428	MTHFD1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042699.1	NM_015440	
AKAP12	9590	broad.mit.edu	37	6	151669975	151669975	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:151669975C>A	ENST00000253332.1	+	3	638	c.449C>A	c.(448-450)cCt>cAt	p.P150H	snoU13_ENST00000458767.1_RNA|AKAP12_ENST00000359755.5_Missense_Mutation_p.P45H|AKAP12_ENST00000354675.6_Missense_Mutation_p.P52H|AKAP12_ENST00000402676.2_Missense_Mutation_p.P150H|AKAP12_ENST00000490177.1_3'UTR			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	150					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.P150H(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)		GAACAGATTCCTTCTTCAGAA	0.413																																					p.P150H	Melanoma(141;1616 1805 10049 24534 51979)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C449A	6						.						121.0	110.0	114.0					6																	151669975		2203	4300	6503	151711668	SO:0001583	missense	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.449C>A	6.37:g.151669975C>A	ENSP00000253332:p.Pro150His	Somatic		Capture	Illumina HiSeq	Phase_I	151711668	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.429722	0.83776	.	.	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.14144	2.53;2.53;2.7;2.55	5.55	5.55	0.83447	.	0.192741	0.25909	N	0.027513	T	0.28830	0.0715	L	0.59436	1.845	0.44402	D	0.997311	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72338	0.977;0.977;0.95	T	0.01096	-1.1453	10	0.72032	D	0.01	.	19.8621	0.96787	0.0:1.0:0.0:0.0	.	45;52;150	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	H	150;150;52;45	ENSP00000384537:P150H;ENSP00000253332:P150H;ENSP00000346702:P52H;ENSP00000352794:P45H	ENSP00000253332:P150H	P	+	2	0	AKAP12	151711668	0.146000	0.22672	0.702000	0.30337	0.531000	0.34715	3.117000	0.50407	2.770000	0.95276	0.563000	0.77884	CCT		0.413	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
AKAP12	9590	broad.mit.edu	37	6	151671679	151671679	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:151671679G>A	ENST00000253332.1	+	3	2342	c.2153G>A	c.(2152-2154)gGa>gAa	p.G718E	AKAP12_ENST00000359755.5_Missense_Mutation_p.G613E|AKAP12_ENST00000354675.6_Missense_Mutation_p.G620E|AKAP12_ENST00000402676.2_Missense_Mutation_p.G718E			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	718					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.G718E(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)		GATGAGGCCGGAAAAGACAAA	0.557																																					p.G718E	Melanoma(141;1616 1805 10049 24534 51979)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2153A	6						.						98.0	108.0	105.0					6																	151671679		2203	4300	6503	151713372	SO:0001583	missense	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.2153G>A	6.37:g.151671679G>A	ENSP00000253332:p.Gly718Glu	Somatic		Capture	Illumina HiSeq	Phase_I	151713372	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	G	10.95	1.496155	0.26774	.	.	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.06933	3.24;3.24;3.24;3.24	5.52	3.68	0.42216	.	0.395578	0.18765	N	0.131771	T	0.03564	0.0102	M	0.70595	2.14	0.22531	N	0.999014	P;P;P	0.48503	0.897;0.897;0.911	P;P;B	0.45558	0.485;0.485;0.291	T	0.19943	-1.0290	10	0.02654	T	1	.	9.8726	0.41185	0.0712:0.4074:0.5213:0.0	.	613;620;718	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	E	718;718;620;613	ENSP00000384537:G718E;ENSP00000253332:G718E;ENSP00000346702:G620E;ENSP00000352794:G613E	ENSP00000253332:G718E	G	+	2	0	AKAP12	151713372	0.953000	0.32496	0.004000	0.12327	0.034000	0.12701	1.544000	0.36158	0.645000	0.30675	0.655000	0.94253	GGA		0.557	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
ZBTB2	57621	broad.mit.edu	37	6	151694692	151694692	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:151694692C>T	ENST00000325144.4	-	2	221	c.81G>A	c.(79-81)acG>acA	p.T27T		NM_020861.1	NP_065912.1	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	27	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				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.T27T(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(6)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.63e-11)		CGATTGCAACCGTGCAGTCAC	0.403																																					p.T27T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G81A	6						.						137.0	129.0	132.0					6																	151694692		2203	4300	6503	151736385	SO:0001819	synonymous_variant	57621	exon2			BC020172	CCDS5231.1	6q25.1	2013-01-09			ENSG00000181472	ENSG00000181472		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	20868	protein-coding gene	gene with protein product						10819331	Standard	NM_020861		Approved	KIAA1483, ZNF437, bA351K16.2	uc003qoh.3	Q8N680	OTTHUMG00000015834	ENST00000325144.4:c.81G>A	6.37:g.151694692C>T		Somatic		Capture	Illumina HiSeq	Phase_I	151736385	NM_020861	A8K7C7|Q5SZ81|Q9P245	Silent	SNP	ENST00000325144.4	37	CCDS5231.1																																																																																				0.403	ZBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042715.1	NM_020861	
CCDC170	80129	broad.mit.edu	37	6	151936595	151936595	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:151936595G>T	ENST00000239374.7	+	10	1827	c.1728G>T	c.(1726-1728)caG>caT	p.Q576H	CCDC170_ENST00000367290.5_Missense_Mutation_p.Q583H|RNU6-813P_ENST00000384691.1_RNA	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	576								p.Q576H(1)									CTTTGGAACAGACTAAAGCCA	0.358																																					p.Q576H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1728T	6						.						128.0	127.0	127.0					6																	151936595		1840	4085	5925	151978288	SO:0001583	missense	80129	exon10			AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1728G>T	6.37:g.151936595G>T	ENSP00000239374:p.Gln576His	Somatic		Capture	Illumina HiSeq	Phase_I	151978288	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.122525	0.77436	.	.	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.77229	2.3;-1.08	5.86	5.0	0.66597	.	0.000000	0.85682	D	0.000000	D	0.85309	0.5667	M	0.80616	2.505	0.58432	D	0.999995	D	0.89917	1.0	D	0.80764	0.994	D	0.87056	0.2150	10	0.52906	T	0.07	-19.739	15.0674	0.72008	0.0677:0.0:0.9323:0.0	.	576	Q8IYT3	CF097_HUMAN	H	576;583	ENSP00000239374:Q576H;ENSP00000356259:Q583H	ENSP00000239374:Q576H	Q	+	3	2	C6orf97	151978288	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.005000	0.57075	1.626000	0.50381	0.650000	0.86243	CAG		0.358	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059	
SYNE1	23345	broad.mit.edu	37	6	152614840	152614840	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:152614840C>T	ENST00000367255.5	-	95	18496	c.17895G>A	c.(17893-17895)caG>caA	p.Q5965Q	SYNE1_ENST00000265368.4_Silent_p.Q5965Q|SYNE1_ENST00000448038.1_Silent_p.Q5894Q|SYNE1_ENST00000356820.4_Silent_p.Q489Q|SYNE1_ENST00000423061.1_Silent_p.Q5894Q|SYNE1_ENST00000341594.5_Silent_p.Q5577Q	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5965					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.Q5965Q(2)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GGTACTTCTGCTGGCGTTCCA	0.507										HNSCC(10;0.0054)																											p.Q489Q												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1467A	6						.						120.0	113.0	115.0					6																	152614840		2203	4300	6503	152656533	SO:0001819	synonymous_variant	23345	exon10			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.17895G>A	6.37:g.152614840C>T		Somatic		Capture	Illumina HiSeq	Phase_I	152656533	NM_015293	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																				0.507	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
SCAF8	22828	broad.mit.edu	37	6	155126566	155126566	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:155126566G>A	ENST00000367178.3	+	9	1503	c.927G>A	c.(925-927)caG>caA	p.Q309Q	SCAF8_ENST00000417268.1_Silent_p.Q309Q|SCAF8_ENST00000367186.4_Silent_p.Q375Q	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	309	Gln-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)	p.Q309Q(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						AACTACAACAGCAAAACCTAG	0.363																																					p.Q309Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G927A	6						.						83.0	80.0	81.0					6																	155126566		2203	4300	6503	155168258	SO:0001819	synonymous_variant	22828	exon9			AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"""RNA binding motif (RRM) containing"""	20959	protein-coding gene	gene with protein product			"""RNA binding motif protein 16"""	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.927G>A	6.37:g.155126566G>A		Somatic		Capture	Illumina HiSeq	Phase_I	155168258	NM_014892	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Silent	SNP	ENST00000367178.3	37	CCDS5247.1																																																																																				0.363	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892	
ARID1B	57492	broad.mit.edu	37	6	157488298	157488298	+	Missense_Mutation	SNP	G	G	A	rs527731946		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:157488298G>A	ENST00000350026.5	+	9	2966	c.2965G>A	c.(2965-2967)Gcc>Acc	p.A989T	ARID1B_ENST00000275248.4_Missense_Mutation_p.A931T|ARID1B_ENST00000478761.2_3'UTR|ARID1B_ENST00000367148.1_Missense_Mutation_p.A989T|ARID1B_ENST00000346085.5_Missense_Mutation_p.A1002T	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	989					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.A931T(1)		NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		CATGGCGCCCGCCATGGTGAA	0.607													G|||	1	0.000199681	0.0	0.0014	5008	,	,		15184	0.0		0.0	False		,,,				2504	0.0				p.A989T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2965A	6						.						74.0	84.0	81.0					6																	157488298		2203	4296	6499	157529990	SO:0001583	missense	57492	exon9			AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.2965G>A	6.37:g.157488298G>A	ENSP00000055163:p.Ala989Thr	Somatic		Capture	Illumina HiSeq	Phase_I	157529990	NM_017519	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	37	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	G	3.820	-0.037851	0.07497	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000354354;ENST00000414678;ENST00000319584;ENST00000400790	T;T;T;T;T;T;T	0.23754	4.83;4.83;4.88;4.83;4.55;2.33;1.89	5.75	1.8	0.24995	.	0.521534	0.21912	N	0.067298	T	0.01730	0.0055	N	0.03608	-0.345	0.19575	N	0.999966	B;B;B;B	0.22541	0.0;0.071;0.043;0.0	B;B;B;B	0.10450	0.001;0.005;0.003;0.0	T	0.44967	-0.9293	10	0.02654	T	1	.	4.1027	0.10020	0.6645:0.0:0.1785:0.157	.	239;989;1002;931	Q8NFD5-4;Q8NFD5;Q8NFD5-2;G3XAA0	.;ARI1B_HUMAN;.;.	T	1002;989;989;931;406;458;411;56	ENSP00000344546:A1002T;ENSP00000055163:A989T;ENSP00000356116:A989T;ENSP00000275248:A931T;ENSP00000412835:A458T;ENSP00000313006:A411T;ENSP00000383596:A56T	ENSP00000275248:A931T	A	+	1	0	ARID1B	157529990	0.917000	0.31117	0.375000	0.26029	0.878000	0.50629	0.821000	0.27338	0.051000	0.15978	-0.345000	0.07892	GCC		0.607	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
ARID1B	57492	broad.mit.edu	37	6	157525060	157525060	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:157525060C>T	ENST00000350026.5	+	18	4917	c.4916C>T	c.(4915-4917)aCg>aTg	p.T1639M	ARID1B_ENST00000275248.4_Missense_Mutation_p.T1634M|ARID1B_ENST00000367148.1_Missense_Mutation_p.T1692M|ARID1B_ENST00000346085.5_Missense_Mutation_p.T1652M	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1639					chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.T1634M(1)		NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		GCTGAGAGTACGTGGGCTTTG	0.438																																					p.T1639M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4916T	6						.						515.0	511.0	512.0					6																	157525060		2203	4296	6499	157566752	SO:0001583	missense	57492	exon18			AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.4916C>T	6.37:g.157525060C>T	ENSP00000055163:p.Thr1639Met	Somatic		Capture	Illumina HiSeq	Phase_I	157566752	NM_017519	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Missense_Mutation	SNP	ENST00000350026.5	37	CCDS5251.2	.	.	.	.	.	.	.	.	.	.	C	17.03	3.283465	0.59867	.	.	ENSG00000049618	ENST00000346085;ENST00000350026;ENST00000367148;ENST00000275248;ENST00000414678	T;T;T;T;T	0.03920	4.14;4.14;4.11;4.15;3.76	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.19685	0.0473	M	0.82517	2.595	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.992;0.996;0.996	T	0.01140	-1.1439	10	0.87932	D	0	.	19.7096	0.96089	0.0:1.0:0.0:0.0	.	1639;1652;1634	Q8NFD5;Q8NFD5-2;G3XAA0	ARI1B_HUMAN;.;.	M	1652;1639;1692;1634;1161	ENSP00000344546:T1652M;ENSP00000055163:T1639M;ENSP00000356116:T1692M;ENSP00000275248:T1634M;ENSP00000412835:T1161M	ENSP00000275248:T1634M	T	+	2	0	ARID1B	157566752	1.000000	0.71417	0.926000	0.36857	0.530000	0.34684	7.818000	0.86416	2.652000	0.90054	0.655000	0.94253	ACG		0.438	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
SNX9	51429	broad.mit.edu	37	6	158363839	158363839	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:158363839G>T	ENST00000392185.3	+	18	1928	c.1757G>T	c.(1756-1758)aGg>aTg	p.R586M		NM_016224.3	NP_057308.1	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	586	BAR.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|lipid tube assembly (GO:0060988)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein oligomerization (GO:0032461)|receptor-mediated endocytosis (GO:0006898)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	1-phosphatidylinositol binding (GO:0005545)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)	p.R586M(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		GAAAAGCTGAGGCAGGCCCTC	0.463																																					p.R586M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1757T	6						.						59.0	64.0	63.0					6																	158363839		2203	4300	6503	158283827	SO:0001583	missense	51429	exon18			AF121859	CCDS5253.1	6q25.1-q26	2008-05-22			ENSG00000130340	ENSG00000130340		"""Sorting nexins"""	14973	protein-coding gene	gene with protein product		605952				10531379, 17609109	Standard	NM_016224		Approved	SH3PX1, SDP1, SH3PXD3A	uc003qqv.1	Q9Y5X1	OTTHUMG00000015903	ENST00000392185.3:c.1757G>T	6.37:g.158363839G>T	ENSP00000376024:p.Arg586Met	Somatic		Capture	Illumina HiSeq	Phase_I	158283827	NM_016224	Q9BSI7|Q9BVM1|Q9UJH6|Q9UP20	Missense_Mutation	SNP	ENST00000392185.3	37	CCDS5253.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.840719	0.91197	.	.	ENSG00000130340	ENST00000539592;ENST00000392185;ENST00000252631	T	0.44083	0.93	5.68	5.68	0.88126	Sorting nexin protein, WASP-binding domain (1);	0.130005	0.64402	D	0.000001	T	0.44582	0.1300	L	0.43152	1.355	0.80722	D	1	D	0.63880	0.993	P	0.61275	0.886	T	0.39981	-0.9587	10	0.72032	D	0.01	-12.0675	13.3664	0.60687	0.0724:0.0:0.9276:0.0	.	586	Q9Y5X1	SNX9_HUMAN	M	586;586;386	ENSP00000376024:R586M	ENSP00000252631:R386M	R	+	2	0	SNX9	158283827	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.071000	0.71229	2.839000	0.97877	0.650000	0.86243	AGG		0.463	SNX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042856.1		
TULP4	56995	broad.mit.edu	37	6	158924442	158924442	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:158924442G>A	ENST00000367097.3	+	13	5104	c.3747G>A	c.(3745-3747)acG>acA	p.T1249T	TULP4_ENST00000367094.2_Intron	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	1249					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.T1249T(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)		GAAGCAGCACGTGCTCTAGTT	0.622																																					p.T1249T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3747A	6						.						66.0	66.0	66.0					6																	158924442		2203	4300	6503	158844430	SO:0001819	synonymous_variant	56995	exon13				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.3747G>A	6.37:g.158924442G>A		Somatic		Capture	Illumina HiSeq	Phase_I	158844430	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Silent	SNP	ENST00000367097.3	37	CCDS34561.1																																																																																				0.622	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
FNDC1	84624	broad.mit.edu	37	6	159653262	159653262	+	Missense_Mutation	SNP	G	G	A	rs552629097		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:159653262G>A	ENST00000297267.9	+	11	1918	c.1718G>A	c.(1717-1719)gGc>gAc	p.G573D	FNDC1_ENST00000340366.6_Missense_Mutation_p.G510D	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	573					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.G573D(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AGTAGACACGGCCACTCGGTG	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		13024	0.001		0.0	False		,,,				2504	0.0				p.G573D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1718A	6						.						22.0	30.0	27.0					6																	159653262		2048	4185	6233	159573252	SO:0001583	missense	84624	exon11			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.1718G>A	6.37:g.159653262G>A	ENSP00000297267:p.Gly573Asp	Somatic		Capture	Illumina HiSeq	Phase_I	159573252	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	G	10.17	1.276334	0.23307	.	.	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.07800	3.16;3.95	5.23	4.19	0.49359	.	0.844568	0.10538	N	0.663058	T	0.03136	0.0092	N	0.24115	0.695	0.09310	N	1	D;P	0.54964	0.969;0.855	P;B	0.51016	0.656;0.36	T	0.40384	-0.9566	10	0.26408	T	0.33	-1.4737	6.0673	0.19870	0.0:0.102:0.2808:0.6172	.	510;573	Q4ZHG4-2;Q4ZHG4	.;FNDC1_HUMAN	D	573;510	ENSP00000297267:G573D;ENSP00000342460:G510D	ENSP00000297267:G573D	G	+	2	0	FNDC1	159573252	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.884000	0.28214	1.005000	0.39183	0.655000	0.94253	GGC		0.652	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
IGF2R	3482	broad.mit.edu	37	6	160490974	160490974	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:160490974G>A	ENST00000356956.1	+	31	4475	c.4327G>A	c.(4327-4329)Gga>Aga	p.G1443R		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1443					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.G1443R(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)	GGTAAGGGACGGACCTCAGTG	0.552																																					p.G1443R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4327A	6						.						88.0	68.0	75.0					6																	160490974		2203	4300	6503	160410964	SO:0001583	missense	3482	exon31			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.4327G>A	6.37:g.160490974G>A	ENSP00000349437:p.Gly1443Arg	Somatic		Capture	Illumina HiSeq	Phase_I	160410964	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	G	13.95	2.388830	0.42308	.	.	ENSG00000197081	ENST00000356956	T	0.15256	2.44	5.62	0.682	0.17992	Mannose-6-phosphate receptor, binding (1);	0.272691	0.41712	D	0.000833	T	0.23054	0.0557	M	0.80847	2.515	0.27122	N	0.962126	D	0.67145	0.996	D	0.69307	0.963	T	0.06625	-1.0816	10	0.66056	D	0.02	-20.9313	9.2587	0.37599	0.4343:0.0:0.5657:0.0	.	1443	P11717	MPRI_HUMAN	R	1443	ENSP00000349437:G1443R	ENSP00000349437:G1443R	G	+	1	0	IGF2R	160410964	0.978000	0.34361	0.012000	0.15200	0.240000	0.25518	1.778000	0.38614	-0.173000	0.10761	0.561000	0.74099	GGA		0.552	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
MAP3K4	4216	broad.mit.edu	37	6	161530874	161530874	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:161530874C>T	ENST00000392142.4	+	23	4472	c.4324C>T	c.(4324-4326)Ctg>Ttg	p.L1442L	MAP3K4_ENST00000366919.2_Silent_p.L1392L|MAP3K4_ENST00000366920.2_Silent_p.L1438L|MAP3K4_ENST00000348824.7_Silent_p.L1388L	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1442	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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.L1441L(1)|p.L1442L(1)		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)		TGTGATTAGGCTGTATTCAAA	0.493																																					p.L1392L												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C4174T	6						.						178.0	150.0	159.0					6																	161530874		2203	4300	6503	161450864	SO:0001819	synonymous_variant	4216	exon22			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.4324C>T	6.37:g.161530874C>T		Somatic		Capture	Illumina HiSeq	Phase_I	161450864	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Silent	SNP	ENST00000392142.4	37	CCDS34565.1																																																																																				0.493	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3		
AGPAT4	56895	broad.mit.edu	37	6	161574408	161574408	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:161574408C>T	ENST00000320285.4	-	5	846	c.634G>A	c.(634-636)Gcc>Acc	p.A212T	AGPAT4_ENST00000457520.2_Intron|AGPAT4_ENST00000366908.5_3'UTR|AGPAT4_ENST00000366911.5_3'UTR	NM_020133.2	NP_064518.1	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	212					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.A212T(2)		endometrium(1)|large_intestine(10)|lung(10)|ovary(2)|skin(2)	25		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		ACGGTGATGGCGAAGCCCTTG	0.622											OREG0017775	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A212T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G634A	6						.						94.0	69.0	77.0					6																	161574408		2203	4300	6503	161494398	SO:0001583	missense	56895	exon5			AF156776	CCDS5280.1	6q25.3	2013-02-05	2013-02-05		ENSG00000026652	ENSG00000026652	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	20885	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, delta"""	614795	"""1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)"""				Standard	XM_005267052		Approved	LPAAT-delta, dJ473J16.2	uc003qtr.1	Q9NRZ5	OTTHUMG00000015966	ENST00000320285.4:c.634G>A	6.37:g.161574408C>T	ENSP00000314036:p.Ala212Thr	Somatic	1817	Capture	Illumina HiSeq	Phase_I	161494398	NM_020133	B4DSF9|Q5TEF0	Missense_Mutation	SNP	ENST00000320285.4	37	CCDS5280.1	.	.	.	.	.	.	.	.	.	.	C	5.808	0.333347	0.11013	.	.	ENSG00000026652	ENST00000320285	D	0.93426	-3.22	4.82	3.96	0.45880	Phospholipid/glycerol acyltransferase (2);	0.316586	0.34676	N	0.003763	T	0.65144	0.2663	N	0.01219	-0.95	0.80722	D	1	P	0.51653	0.947	B	0.42030	0.373	T	0.78677	-0.2111	10	0.02654	T	1	-15.6488	13.2004	0.59765	0.0:0.923:0.0:0.077	.	212	Q9NRZ5	PLCD_HUMAN	T	212	ENSP00000314036:A212T	ENSP00000314036:A212T	A	-	1	0	AGPAT4	161494398	0.999000	0.42202	0.338000	0.25549	0.901000	0.52897	3.935000	0.56560	1.273000	0.44346	0.555000	0.69702	GCC		0.622	AGPAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042983.1	NM_020133	
PDE10A	10846	broad.mit.edu	37	6	165862423	165862423	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:165862423C>T	ENST00000366882.1	-	6	513	c.359G>A	c.(358-360)tGc>tAc	p.C120Y	PDE10A_ENST00000539869.2_Missense_Mutation_p.C130Y|PDE10A_ENST00000354448.4_Missense_Mutation_p.C120Y			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	120	GAF 1.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|metal ion binding (GO:0046872)	p.C120Y(1)		breast(4)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(39)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	71		Breast(66;0.000425)|Prostate(117;0.104)|Ovarian(120;0.221)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-17)|BRCA - Breast invasive adenocarcinoma(81;1.8e-06)|GBM - Glioblastoma multiforme(31;1.92e-05)	Caffeine(DB00201)|Dipyridamole(DB00975)|Papaverine(DB01113)|Tofisopam(DB08811)|Triflusal(DB08814)	TACATTATTGCACTCTCCAAG	0.333																																					p.C120Y	Esophageal Squamous(22;308 615 5753 12038 40624)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G359A	6						.						74.0	78.0	77.0					6																	165862423		2203	4300	6503	165782413	SO:0001583	missense	10846	exon6			AB020593	CCDS47513.1	6q26	2008-03-18			ENSG00000112541	ENSG00000112541	3.1.4.17	"""Phosphodiesterases"""	8772	protein-coding gene	gene with protein product		610652				10373451	Standard	NM_001130690		Approved		uc003quo.3	Q9Y233	OTTHUMG00000015986	ENST00000366882.1:c.359G>A	6.37:g.165862423C>T	ENSP00000355847:p.Cys120Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	165782413	NM_006661	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	37		.	.	.	.	.	.	.	.	.	.	C	18.85	3.712256	0.68730	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.68765	-0.35;-0.35	5.88	5.88	0.94601	GAF (1);	0.042249	0.85682	D	0.000000	T	0.72867	0.3514	L	0.47716	1.5	0.80722	D	1	D;B	0.65815	0.995;0.22	D;B	0.63283	0.913;0.197	T	0.72909	-0.4149	10	0.59425	D	0.04	.	20.2441	0.98394	0.0:1.0:0.0:0.0	.	130;120	Q9ULW9;Q9Y233	.;PDE10_HUMAN	Y	120;148;130;120;119	ENSP00000355847:C120Y;ENSP00000346435:C120Y	ENSP00000341187:C130Y	C	-	2	0	PDE10A	165782413	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.305000	0.78891	2.774000	0.95407	0.655000	0.94253	TGC		0.333	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1		
RPS6KA2	6196	broad.mit.edu	37	6	166826324	166826324	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:166826324G>A	ENST00000265678.4	-	21	2351	c.2128C>T	c.(2128-2130)Cgg>Tgg	p.R710W	RPS6KA2_ENST00000405189.3_Missense_Mutation_p.R621W|RPS6KA2_ENST00000481261.2_Missense_Mutation_p.R621W|RPS6KA2_ENST00000510118.1_Missense_Mutation_p.R735W|RPS6KA2_ENST00000509742.1_5'UTR|RPS6KA2_ENST00000503859.1_Missense_Mutation_p.R718W	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	710					axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|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)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)	p.R718W(1)|p.R710W(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		GGCTCCAGCCGCGGGGCCTGA	0.657																																					p.R710W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2128T	6						.						28.0	29.0	28.0					6																	166826324		2192	4289	6481	166746314	SO:0001583	missense	6196	exon21			L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"""ribosomal protein S6 kinase, 90kD, polypeptide 2"""			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.2128C>T	6.37:g.166826324G>A	ENSP00000265678:p.Arg710Trp	Somatic		Capture	Illumina HiSeq	Phase_I	166746314	NM_021135	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Missense_Mutation	SNP	ENST00000265678.4	37	CCDS5294.1	.	.	.	.	.	.	.	.	.	.	G	13.84	2.358356	0.41801	.	.	ENSG00000071242	ENST00000265678;ENST00000510118;ENST00000503859;ENST00000481261;ENST00000405189	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	4.38	1.08	0.20341	Protein kinase-like domain (1);	0.340768	0.27759	N	0.017980	T	0.15652	0.0377	N	0.08118	0	0.34150	D	0.667417	P;P;D	0.60575	0.919;0.917;0.988	P;B;B	0.48677	0.586;0.279;0.265	T	0.11155	-1.0599	10	0.62326	D	0.03	.	12.5909	0.56443	0.0:0.0:0.3838:0.6162	.	735;718;710	F2Z2J1;Q15349-3;Q15349	.;.;KS6A2_HUMAN	W	710;735;718;621;621	ENSP00000265678:R710W;ENSP00000422435:R735W;ENSP00000427015:R718W;ENSP00000422484:R621W;ENSP00000386050:R621W	ENSP00000265678:R710W	R	-	1	2	RPS6KA2	166746314	0.009000	0.17119	0.927000	0.36925	0.971000	0.66376	0.694000	0.25512	0.007000	0.14760	-0.269000	0.10298	CGG		0.657	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135	
RNASET2	8635	broad.mit.edu	37	6	167352449	167352449	+	Missense_Mutation	SNP	G	G	A	rs117003826		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	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	
TUBB2B	347733	broad.mit.edu	37	6	3225760	3225760	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:3225760G>A	ENST00000259818.7	-	4	754	c.563C>T	c.(562-564)tCg>tTg	p.S188L	TUBB2B_ENST00000473006.1_5'UTR	NM_178012.4	NP_821080.1	Q9BVA1	TBB2B_HUMAN	tubulin, beta 2B class IIb	188					'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.S188L(1)		kidney(2)|large_intestine(5)|lung(1)|prostate(1)|skin(1)	10	Ovarian(93;0.0386)	all_hematologic(90;0.108)				CTGGTGGACCGAGAGGGTGGC	0.577																																					p.S188L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C563T	6						.						31.0	31.0	31.0					6																	3225760		1647	3414	5061	3170759	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.563C>T	6.37:g.3225760G>A	ENSP00000259818:p.Ser188Leu	Somatic		Capture	Illumina HiSeq	Phase_I	3170759	NM_178012	A8K068	Missense_Mutation	SNP	ENST00000259818.7	37	CCDS4485.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.801688	0.50315	.	.	ENSG00000137285	ENST00000259818	T	0.72282	-0.64	5.21	5.21	0.72293	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.64402	D	0.000006	D	0.91085	0.7194	H	0.99565	4.63	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.987	D;D;D	0.85130	0.997;0.997;0.96	D	0.95051	0.8187	10	0.87932	D	0	.	18.7626	0.91858	0.0:0.0:1.0:0.0	.	188;188;188	Q8IZ29;Q8IWP6;Q9BVA1	.;.;TBB2B_HUMAN	L	188	ENSP00000259818:S188L	ENSP00000259818:S188L	S	-	2	0	TUBB2B	3170759	1.000000	0.71417	0.139000	0.22197	0.819000	0.46315	9.673000	0.98631	2.420000	0.82092	0.514000	0.50259	TCG		0.577	TUBB2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039680.2	NM_178012	
CDYL	9425	broad.mit.edu	37	6	4937849	4937849	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:4937849C>A	ENST00000328908.5	+	6	1292	c.1161C>A	c.(1159-1161)agC>agA	p.S387R	CDYL_ENST00000449732.2_Missense_Mutation_p.S201R|CDYL_ENST00000472453.1_3'UTR|CDYL_ENST00000343762.5_Missense_Mutation_p.S201R|CDYL_ENST00000397588.3_Missense_Mutation_p.S333R			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	387					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.S387R(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)		CCGATGACAGCAAGCTGGTAC	0.453																																					p.S201R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C603A	6						.						74.0	72.0	73.0					6																	4937849		2203	4300	6503	4882848	SO:0001583	missense	9425	exon4			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.1161C>A	6.37:g.4937849C>A	ENSP00000330512:p.Ser387Arg	Somatic		Capture	Illumina HiSeq	Phase_I	4882848	NM_001143970	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Missense_Mutation	SNP	ENST00000328908.5	37		.	.	.	.	.	.	.	.	.	.	C	15.97	2.990720	0.54041	.	.	ENSG00000153046	ENST00000328908;ENST00000440139;ENST00000397588;ENST00000449732;ENST00000343762	T;T;T;T;T	0.68624	0.87;-0.34;0.87;0.87;0.87	5.67	4.57	0.56435	Crotonase, core (1);	0.000000	0.85682	D	0.000000	T	0.79569	0.4468	M	0.90198	3.095	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.81805	-0.0764	10	0.87932	D	0	.	8.3543	0.32321	0.0:0.8439:0.0:0.1561	.	333;387	Q9Y232-2;Q9Y232	.;CDYL1_HUMAN	R	387;113;333;201;201	ENSP00000330512:S387R;ENSP00000394740:S113R;ENSP00000380718:S333R;ENSP00000394076:S201R;ENSP00000340908:S201R	ENSP00000330512:S387R	S	+	3	2	CDYL	4882848	1.000000	0.71417	1.000000	0.80357	0.302000	0.27658	0.706000	0.25690	2.832000	0.97577	0.585000	0.79938	AGC		0.453	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824	
F13A1	2162	broad.mit.edu	37	6	6266931	6266931	+	Missense_Mutation	SNP	C	C	T	rs142954620		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:6266931C>T	ENST00000264870.3	-	4	696	c.431G>A	c.(430-432)cGg>cAg	p.R144Q		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	144					blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.R144Q(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	GATGGACAGCCGCACAGACCT	0.512													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17742	0.0		0.0	False		,,,				2504	0.0				p.R144Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G431A	6						.						131.0	120.0	124.0					6																	6266931		2203	4300	6503	6211930	SO:0001583	missense	2162	exon4			M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"""Transglutaminases"""	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.431G>A	6.37:g.6266931C>T	ENSP00000264870:p.Arg144Gln	Somatic		Capture	Illumina HiSeq	Phase_I	6211930	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	37	CCDS4496.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	19.23	3.787880	0.70337	.	.	ENSG00000124491	ENST00000264870;ENST00000441301	D	0.84660	-1.88	5.65	4.79	0.61399	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	0.158566	0.48767	N	0.000174	T	0.80768	0.4686	L	0.47190	1.495	0.37891	D	0.930707	D;D	0.65815	0.992;0.995	P;P	0.54965	0.759;0.765	T	0.78922	-0.2013	10	0.22109	T	0.4	.	13.3447	0.60566	0.0:0.9249:0.0:0.0751	.	81;144	F5H080;P00488	.;F13A_HUMAN	Q	144;81	ENSP00000264870:R144Q	ENSP00000264870:R144Q	R	-	2	0	F13A1	6211930	0.412000	0.25392	0.996000	0.52242	0.610000	0.37248	0.950000	0.29122	1.389000	0.46526	0.655000	0.94253	CGG		0.512	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129	
CAGE1	285782	broad.mit.edu	37	6	7374236	7374236	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:7374236G>A	ENST00000512086.1	-	5	1018	c.816C>T	c.(814-816)ggC>ggT	p.G272G	CAGE1_ENST00000338150.4_Silent_p.G272G|CAGE1_ENST00000502583.1_Silent_p.G272G|CAGE1_ENST00000296742.7_Silent_p.G136G|CAGE1_ENST00000509324.1_5'UTR|CAGE1_ENST00000379918.4_Silent_p.G272G			Q8TC20	CAGE1_HUMAN	cancer antigen 1	272								p.G272G(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					TCCAGGAAATGCCTGCCGAAG	0.483																																					p.G136G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C408T	6						.						96.0	97.0	96.0					6																	7374236		1977	4149	6126	7319235	SO:0001819	synonymous_variant	285782	exon4			BC026194	CCDS47367.1, CCDS54964.1, CCDS54965.1	6p24.3	2009-08-06	2005-01-26	2005-01-27	ENSG00000164304	ENSG00000164304			21622	protein-coding gene	gene with protein product	"""cancer/testis antigen 95"""	608304	"""cancer/testis antigen 3"""	CTAG3		12531476	Standard	NM_205864		Approved	bA69L16.7, CT95	uc003mxl.2	Q8TC20	OTTHUMG00000014200	ENST00000512086.1:c.816C>T	6.37:g.7374236G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7319235	NM_205864	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Silent	SNP	ENST00000512086.1	37																																																																																					0.483	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745	
DSP	1832	broad.mit.edu	37	6	7556050	7556050	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:7556050G>A	ENST00000379802.3	+	2	611	c.270G>A	c.(268-270)caG>caA	p.Q90Q	DSP_ENST00000418664.2_Silent_p.Q90Q	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	90	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.Q90Q(1)		biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		TCATCGTGCAGCCTGTAAGCT	0.582																																					p.Q90Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G270A	6						.						75.0	60.0	65.0					6																	7556050		2203	4300	6503	7501049	SO:0001819	synonymous_variant	1832	exon2			J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.270G>A	6.37:g.7556050G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7501049	NM_001008844	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	37	CCDS4501.1																																																																																				0.582	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
CAP2	10486	broad.mit.edu	37	6	17426902	17426902	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:17426902C>T	ENST00000229922.2	+	3	735	c.203C>T	c.(202-204)gCt>gTt	p.A68V	CAP2_ENST00000489374.1_Missense_Mutation_p.A68V|CAP2_ENST00000493172.1_Missense_Mutation_p.A68V|CAP2_ENST00000378990.2_Missense_Mutation_p.A68V|CAP2_ENST00000465994.1_Missense_Mutation_p.A68V	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	68					activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)		p.A68V(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			AGGATCCTTGCTGGGGACGTG	0.517																																					p.A68V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C203T	6						.						116.0	103.0	107.0					6																	17426902		2203	4300	6503	17534881	SO:0001583	missense	10486	exon3			BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.203C>T	6.37:g.17426902C>T	ENSP00000229922:p.Ala68Val	Somatic		Capture	Illumina HiSeq	Phase_I	17534881	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Missense_Mutation	SNP	ENST00000229922.2	37	CCDS4539.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.053764	0.55218	.	.	ENSG00000112186	ENST00000229922;ENST00000378994;ENST00000489374;ENST00000378990;ENST00000493172;ENST00000465994	T;T;T;T;T	0.30981	1.51;1.51;1.51;2.62;1.51	5.57	5.57	0.84162	Adenylate cyclase-associated CAP, N-terminal (2);	0.230585	0.44688	D	0.000431	T	0.41419	0.1158	M	0.71581	2.175	0.23468	N	0.997618	D;D;P;B;P	0.71674	0.991;0.998;0.924;0.254;0.571	P;D;P;B;B	0.69654	0.864;0.965;0.784;0.284;0.312	T	0.36040	-0.9764	10	0.87932	D	0	-17.0359	12.0662	0.53590	0.1719:0.8281:0.0:0.0	.	68;68;68;68;68	B7Z214;B7Z385;B7Z1C4;E9PDI2;P40123	.;.;.;.;CAP2_HUMAN	V	68	ENSP00000229922:A68V;ENSP00000417705:A68V;ENSP00000368275:A68V;ENSP00000417208:A68V;ENSP00000418604:A68V	ENSP00000229922:A68V	A	+	2	0	CAP2	17534881	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	2.707000	0.47143	2.626000	0.88956	0.591000	0.81541	GCT		0.517	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2		
SLC17A3	10786	broad.mit.edu	37	6	25855390	25855390	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:25855390A>C	ENST00000360657.3	-	5	745	c.460T>G	c.(460-462)Ttt>Gtt	p.F154V	SLC17A3_ENST00000361703.6_Missense_Mutation_p.F154V|SLC17A3_ENST00000397060.4_Missense_Mutation_p.F232V			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3	154					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|glucose-6-phosphate transport (GO:0015760)|ion transmembrane transport (GO:0034220)|organic acid transport (GO:0015849)|organic anion transport (GO:0015711)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|regulation of anion transport (GO:0044070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|efflux transmembrane transporter activity (GO:0015562)|organic anion transmembrane transporter activity (GO:0008514)|sodium:phosphate symporter activity (GO:0005436)|toxin transporter activity (GO:0019534)|urate transmembrane transporter activity (GO:0015143)|voltage-gated anion channel activity (GO:0008308)	p.F154V(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)	20						TAGAAGACAAAGGGCCACCCA	0.418																																					p.F232V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T694G	6						.						72.0	68.0	69.0					6																	25855390		2203	4300	6503	25963369	SO:0001583	missense	10786	exon6			U90545	CCDS4566.2, CCDS47385.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124564	ENSG00000124564		"""Solute carriers"""	10931	protein-coding gene	gene with protein product		611034	"""solute carrier family 17 (sodium phosphate), member 3"""			9149941	Standard	NM_006632		Approved	NPT4	uc003nfk.4	O00476	OTTHUMG00000014412	ENST00000360657.3:c.460T>G	6.37:g.25855390A>C	ENSP00000353873:p.Phe154Val	Somatic		Capture	Illumina HiSeq	Phase_I	25963369	NM_001098486	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Missense_Mutation	SNP	ENST00000360657.3	37	CCDS4566.2	.	.	.	.	.	.	.	.	.	.	A	14.41	2.526726	0.44969	.	.	ENSG00000124564	ENST00000397060;ENST00000360657;ENST00000361703	T;T;T	0.55588	0.51;0.51;0.51	4.05	4.05	0.47172	Major facilitator superfamily domain, general substrate transporter (1);	0.150329	0.31312	N	0.007862	T	0.41558	0.1164	L	0.46670	1.46	0.33838	D	0.631101	B;P;B;P	0.46064	0.071;0.872;0.295;0.872	B;P;B;P	0.51582	0.18;0.474;0.27;0.674	T	0.43605	-0.9381	10	0.45353	T	0.12	.	9.9616	0.41699	1.0:0.0:0.0:0.0	.	154;213;232;154	B7Z531;B7Z3L7;B7Z511;O00476	.;.;.;NPT4_HUMAN	V	232;154;154	ENSP00000380250:F232V;ENSP00000353873:F154V;ENSP00000355307:F154V	ENSP00000353873:F154V	F	-	1	0	SLC17A3	25963369	0.022000	0.18835	0.999000	0.59377	0.617000	0.37484	1.972000	0.40540	1.754000	0.51921	0.528000	0.53228	TTT		0.418	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2		
SLC17A2	10246	broad.mit.edu	37	6	25913553	25913553	+	3'UTR	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:25913553G>A	ENST00000265425.3	-	0	1484				SLC17A2_ENST00000377850.3_Missense_Mutation_p.R477C|SLC17A2_ENST00000360488.3_Silent_p.P427P			O00624	NPT3_HUMAN	solute carrier family 17, member 2						phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)	p.P427P(2)		endometrium(3)|kidney(1)|large_intestine(9)|lung(12)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	31						CCTCAGAGGCGGGTAAGGGTC	0.428																																					p.P427P												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C1281T	6						.						141.0	132.0	135.0					6																	25913553		2203	4300	6503	26021532	SO:0001624	3_prime_UTR_variant	10246	exon11			U90544	CCDS4567.1, CCDS69060.1	6p22.2	2013-07-18	2013-07-18		ENSG00000112337	ENSG00000112337		"""Solute carriers"""	10930	protein-coding gene	gene with protein product		611049	"""solute carrier family 17 (sodium phosphate), member 2"""			9149941	Standard	NM_001286123		Approved	NPT3	uc003nfl.3	O00624	OTTHUMG00000014413	ENST00000265425.3:c.*144C>T	6.37:g.25913553G>A		Somatic		Capture	Illumina HiSeq	Phase_I	26021532	NM_005835	A6NK81|A6NLD6|Q5TB84|Q76P85	Silent	SNP	ENST00000265425.3	37		.	.	.	.	.	.	.	.	.	.	G	14.06	2.423718	0.43020	.	.	ENSG00000112337	ENST00000377850	T	0.65178	-0.14	4.65	4.65	0.58169	.	0.097554	0.46442	D	0.000281	T	0.63129	0.2485	.	.	.	0.19300	N	0.999971	D	0.76494	0.999	P	0.57244	0.816	T	0.57429	-0.7813	9	0.87932	D	0	.	13.4126	0.60952	0.0:0.0:1.0:0.0	.	477	A6NK81	.	C	477	ENSP00000367081:R477C	ENSP00000367081:R477C	R	-	1	0	SLC17A2	26021532	0.950000	0.32346	0.686000	0.30086	0.001000	0.01503	2.888000	0.48594	2.890000	0.99128	0.650000	0.86243	CGC		0.428	SLC17A2-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040075.1		
HIST1H3D	8351	broad.mit.edu	37	6	26197280	26197280	+	Missense_Mutation	SNP	G	G	A	rs188573880		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:26197280G>A	ENST00000356476.2	-	1	198	c.199C>T	c.(199-201)Cca>Tca	p.P67S	HIST1H2BF_ENST00000359985.1_5'Flank|HIST1H3D_ENST00000377831.5_Missense_Mutation_p.P67S			P68431	H31_HUMAN	histone cluster 1, H3d	67					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.P67S(1)		NS(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)	14		all_hematologic(11;0.196)				CGCTGGAATGGCAGTTTGCGA	0.637																																					p.P67S	GBM(108;3816 4467)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C199T	6						.						73.0	73.0	73.0					6																	26197280		2203	4300	6503	26305259	SO:0001583	missense	8351	exon2			Z80784	CCDS4590.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197409	ENSG00000197409		"""Histones / Replication-dependent"""	4767	protein-coding gene	gene with protein product		602811	"""H3 histone family, member B"", ""histone 1, H3d"""	H3FB		9119399, 12408966	Standard	NM_003530		Approved	H3/b	uc003ngv.4	P68431	OTTHUMG00000014433	ENST00000356476.2:c.199C>T	6.37:g.26197280G>A	ENSP00000366999:p.Pro67Ser	Somatic		Capture	Illumina HiSeq	Phase_I	26305259	NM_003530	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000356476.2	37	CCDS4590.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	.	17.06	3.293734	0.60086	.	.	ENSG00000197409	ENST00000356476;ENST00000377831	T;T	0.74002	-0.8;-0.8	4.29	4.29	0.51040	.	.	.	.	.	T	0.80171	0.4574	.	.	.	0.46396	D	0.99902	.	.	.	.	.	.	T	0.83318	-0.0019	6	0.66056	D	0.02	.	16.087	0.81065	0.0:0.0:1.0:0.0	.	.	.	.	S	67	ENSP00000366999:P67S;ENSP00000367062:P67S	ENSP00000366999:P67S	P	-	1	0	HIST1H3D	26305259	1.000000	0.71417	0.991000	0.47740	0.402000	0.30811	9.276000	0.95745	2.085000	0.62840	0.655000	0.94253	CCA		0.637	HIST1H3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040096.1	NM_003530	
BTN2A3P	54718	broad.mit.edu	37	6	26431386	26431386	+	RNA	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:26431386G>A	ENST00000466808.2	+	0	1447							Q96KV6	BT2A3_HUMAN	butyrophilin, subfamily 2, member A3, pseudogene							integral component of membrane (GO:0016021)		p.R435K(1)									TACAACATGAGGGACAGATCA	0.502																																					.												.	.	1	Substitution - Missense(1)	large_intestine(1)	.	6						.						116.0	109.0	111.0					6																	26431386		2203	4300	6503	26539365			54718	.			AL021917		6p22.1	2014-01-14	2011-09-06	2011-09-06	ENSG00000124549	ENSG00000124549		"""Butyrophilins"""	13229	pseudogene	pseudogene		613592	"""butyrophilin, subfamily 2, member A3"""	BTN2A3			Standard	NR_027795		Approved	BTN2.3	uc011dkl.1	Q96KV6	OTTHUMG00000014453		6.37:g.26431386G>A		Somatic		Capture	Illumina HiSeq	Phase_I	26539365	.	A6NEF4	Missense_Mutation	SNP	ENST00000466808.2	37																																																																																					0.502	BTN2A3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000040118.4	NR_027795	
OR2B6	26212	broad.mit.edu	37	6	27925452	27925452	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:27925452C>T	ENST00000244623.1	+	1	434	c.434C>T	c.(433-435)gCa>gTa	p.A145V		NM_012367.1	NP_036499.1	P58173	OR2B6_HUMAN	olfactory receptor, family 2, subfamily B, member 6	145						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A145V(1)		endometrium(1)|large_intestine(3)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CTCCAGTTGGCAGCTGCATCC	0.488																																					p.A145V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C434T	6						.						102.0	104.0	104.0					6																	27925452		2203	4300	6503	28033431	SO:0001583	missense	26212	exon1			U86275	CCDS4642.1	6p22.1	2012-08-09			ENSG00000124657	ENSG00000124657		"""GPCR / Class A : Olfactory receptors"""	8241	protein-coding gene	gene with protein product				OR2B6P, OR2B1, OR2B1P, OR2B5		9500546	Standard	NM_012367		Approved	OR6-31, dJ408B20.2, OR5-40, OR5-41	uc011dkx.2	P58173	OTTHUMG00000014497	ENST00000244623.1:c.434C>T	6.37:g.27925452C>T	ENSP00000244623:p.Ala145Val	Somatic		Capture	Illumina HiSeq	Phase_I	28033431	NM_012367	O43883|Q6IF89|Q9H5B0	Missense_Mutation	SNP	ENST00000244623.1	37	CCDS4642.1	.	.	.	.	.	.	.	.	.	.	c	7.382	0.629024	0.14257	.	.	ENSG00000124657	ENST00000244623	T	0.34472	1.36	3.68	3.68	0.42216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33515	U	0.004825	T	0.12092	0.0294	L	0.31065	0.9	0.27319	N	0.957083	B	0.30664	0.289	B	0.37888	0.26	T	0.14727	-1.0462	10	0.19590	T	0.45	.	7.7199	0.28725	0.0:0.8776:0.0:0.1223	.	145	P58173	OR2B6_HUMAN	V	145	ENSP00000244623:A145V	ENSP00000244623:A145V	A	+	2	0	OR2B6	28033431	0.007000	0.16637	0.996000	0.52242	0.766000	0.43426	0.268000	0.18571	1.964000	0.57103	0.563000	0.77884	GCA		0.488	OR2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040165.1		
NKAPL	222698	broad.mit.edu	37	6	28227199	28227199	+	Missense_Mutation	SNP	G	G	A	rs570929796		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:28227199G>A	ENST00000343684.3	+	1	102	c.50G>A	c.(49-51)cGg>cAg	p.R17Q	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	17								p.R17Q(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						GTGGGCTCTCGGAGAAGGCGA	0.667													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17056	0.0		0.0	False		,,,				2504	0.0				p.R17Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G50A	6						.						33.0	31.0	31.0					6																	28227199		2202	4297	6499	28335178	SO:0001583	missense	222698	exon1			BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 194"""	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.50G>A	6.37:g.28227199G>A	ENSP00000345716:p.Arg17Gln	Somatic		Capture	Illumina HiSeq	Phase_I	28335178	NM_001007531	Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	ENST00000343684.3	37	CCDS34353.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.408575	0.25378	.	.	ENSG00000189134	ENST00000343684	T	0.15487	2.42	3.47	1.64	0.23874	.	1.562420	0.03950	N	0.288416	T	0.05410	0.0143	L	0.58669	1.825	0.09310	N	1	B	0.28470	0.213	B	0.15870	0.014	T	0.34254	-0.9836	10	0.22109	T	0.4	-3.6857	5.4803	0.16719	0.2439:0.0:0.7561:0.0	.	17	Q5M9Q1	NKAPL_HUMAN	Q	17	ENSP00000345716:R17Q	ENSP00000345716:R17Q	R	+	2	0	NKAPL	28335178	0.004000	0.15560	0.001000	0.08648	0.002000	0.02628	0.450000	0.21762	0.462000	0.27095	0.655000	0.94253	CGG		0.667	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1		
NKAPL	222698	broad.mit.edu	37	6	28227442	28227442	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:28227442G>A	ENST00000343684.3	+	1	345	c.293G>A	c.(292-294)cGt>cAt	p.R98H	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	98								p.R98H(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						CGCTACCATCGTCACTGCTAT	0.572																																					p.R98H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G293A	6						.						62.0	62.0	62.0					6																	28227442		2203	4300	6503	28335421	SO:0001583	missense	222698	exon1			BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 194"""	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.293G>A	6.37:g.28227442G>A	ENSP00000345716:p.Arg98His	Somatic		Capture	Illumina HiSeq	Phase_I	28335421	NM_001007531	Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	ENST00000343684.3	37	CCDS34353.1	.	.	.	.	.	.	.	.	.	.	G	5.124	0.208527	0.09757	.	.	ENSG00000189134	ENST00000343684	T	0.14893	2.47	4.13	1.63	0.23807	.	0.822182	0.10356	N	0.684591	T	0.01592	0.0051	N	0.02315	-0.6	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47837	-0.9086	10	0.27082	T	0.32	-2.1284	4.4533	0.11631	0.6962:0.1979:0.1059:0.0	.	98	Q5M9Q1	NKAPL_HUMAN	H	98	ENSP00000345716:R98H	ENSP00000345716:R98H	R	+	2	0	NKAPL	28335421	0.000000	0.05858	0.241000	0.24154	0.017000	0.09413	0.251000	0.18257	0.231000	0.21079	-0.294000	0.09567	CGT		0.572	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1		
NKAPL	222698	broad.mit.edu	37	6	28228189	28228189	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:28228189G>A	ENST00000343684.3	+	1	1092	c.1040G>A	c.(1039-1041)cGc>cAc	p.R347H	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	347								p.R347H(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						AGCAGGCATCGCAGAATGGAG	0.473																																					p.R347H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1040A	6						.						167.0	158.0	161.0					6																	28228189		2203	4300	6503	28336168	SO:0001583	missense	222698	exon1			BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 194"""	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.1040G>A	6.37:g.28228189G>A	ENSP00000345716:p.Arg347His	Somatic		Capture	Illumina HiSeq	Phase_I	28336168	NM_001007531	Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	ENST00000343684.3	37	CCDS34353.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.898467	0.91962	.	.	ENSG00000189134	ENST00000343684	T	0.19669	2.13	4.63	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.40322	0.1112	M	0.83692	2.655	0.80722	D	1	D	0.61080	0.989	D	0.65140	0.932	T	0.41893	-0.9483	10	0.87932	D	0	-3.1482	15.3885	0.74723	0.0:0.0:1.0:0.0	.	347	Q5M9Q1	NKAPL_HUMAN	H	347	ENSP00000345716:R347H	ENSP00000345716:R347H	R	+	2	0	NKAPL	28336168	1.000000	0.71417	0.994000	0.49952	0.989000	0.77384	6.461000	0.73522	2.563000	0.86464	0.655000	0.94253	CGC		0.473	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1		
ABCF1	23	broad.mit.edu	37	6	30554261	30554261	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:30554261C>T	ENST00000326195.8	+	19	2008	c.1896C>T	c.(1894-1896)ttC>ttT	p.F632F	MIR877_ENST00000401282.1_RNA|ABCF1_ENST00000376545.3_Silent_p.F594F|ABCF1_ENST00000396515.4_Intron	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	632	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)	p.F632F(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						GTGTGACATTCGGCTACCAGG	0.483																																					p.F632F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1896T	6						.						201.0	210.0	207.0					6																	30554261		1511	2709	4220	30662240	SO:0001819	synonymous_variant	23	exon19			AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"""ATP binding cassette transporters / subfamily F"""	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.1896C>T	6.37:g.30554261C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30662240	NM_001025091	A2BF75|O14897|Q69YP6	Silent	SNP	ENST00000326195.8	37	CCDS34380.1																																																																																				0.483	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3		
DDR1	780	broad.mit.edu	37	6	30857173	30857173	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:30857173G>A	ENST00000324771.8	+	6	931	c.383G>A	c.(382-384)cGc>cAc	p.R128H	DDR1_ENST00000418800.2_Missense_Mutation_p.R128H|DDR1_ENST00000376567.2_Missense_Mutation_p.R128H|DDR1_ENST00000376570.4_Missense_Mutation_p.R128H|DDR1_ENST00000454612.2_Missense_Mutation_p.R128H|DDR1_ENST00000376569.3_Missense_Mutation_p.R128H|DDR1_ENST00000513240.1_Missense_Mutation_p.R128H|DDR1_ENST00000446312.1_Missense_Mutation_p.R128H|DDR1_ENST00000508312.1_Missense_Mutation_p.R146H|DDR1_ENST00000361741.4_5'Flank|DDR1_ENST00000376575.3_Missense_Mutation_p.R128H|MIR4640_ENST00000581824.1_RNA|DDR1_ENST00000452441.1_Missense_Mutation_p.R128H|DDR1_ENST00000376568.3_Missense_Mutation_p.R128H			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	128	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R128H(2)		central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	GATGGTCGCCGCTGGATGGGC	0.657																																					p.R128H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G383A	6						.						21.0	19.0	19.0					6																	30857173		1506	2705	4211	30965152	SO:0001583	missense	780	exon5			X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.383G>A	6.37:g.30857173G>A	ENSP00000318217:p.Arg128His	Somatic		Capture	Illumina HiSeq	Phase_I	30965152	NM_013993	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	37	CCDS34385.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.053243	0.75960	.	.	ENSG00000204580	ENST00000505066;ENST00000460944;ENST00000324771;ENST00000418800;ENST00000454612;ENST00000437124;ENST00000396342;ENST00000512694;ENST00000515233;ENST00000376569;ENST00000511510;ENST00000376575;ENST00000376570;ENST00000446312;ENST00000504927;ENST00000428153;ENST00000376568;ENST00000452441;ENST00000508312;ENST00000421124;ENST00000512725;ENST00000503495;ENST00000376567;ENST00000513240	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98192	-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78;-4.78	4.54	3.67	0.42095	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.176042	0.38436	N	0.001681	D	0.90964	0.7159	L	0.35341	1.055	0.80722	D	1	B;B;P;B;B	0.39071	0.327;0.378;0.658;0.225;0.019	B;B;B;B;B	0.22880	0.025;0.042;0.032;0.019;0.003	D	0.90752	0.4658	10	0.46703	T	0.11	.	10.0885	0.42432	0.0989:0.0:0.9011:0.0	.	128;154;146;128;128	Q08345-4;B7Z3A2;B7Z2K0;Q08345-5;Q08345	.;.;.;.;DDR1_HUMAN	H	128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;128;146;128;128;154;128;128	ENSP00000421189:R128H;ENSP00000426420:R128H;ENSP00000318217:R128H;ENSP00000407699:R128H;ENSP00000406091:R128H;ENSP00000394273:R128H;ENSP00000379631:R128H;ENSP00000426229:R128H;ENSP00000422467:R128H;ENSP00000365753:R128H;ENSP00000425113:R128H;ENSP00000365759:R128H;ENSP00000365754:R128H;ENSP00000405998:R128H;ENSP00000427597:R128H;ENSP00000390593:R128H;ENSP00000365752:R128H;ENSP00000405039:R128H;ENSP00000422442:R146H;ENSP00000409682:R128H;ENSP00000422108:R128H;ENSP00000423749:R154H;ENSP00000365751:R128H;ENSP00000427552:R128H	ENSP00000318217:R128H	R	+	2	0	DDR1	30965152	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	3.073000	0.50057	1.103000	0.41568	0.313000	0.20887	CGC		0.657	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
PSORS1C1	170679	broad.mit.edu	37	6	31085254	31085254	+	Intron	SNP	C	C	T	rs553582464		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:31085254C>T	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Silent_p.T46T|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1									p.T46T(1)		kidney(1)|ovary(2)|prostate(1)|skin(1)	5						AGGTGATACGCGTGGGGTCCT	0.572													C|||	0	0.0	0.0	0.0	5008	,	,		18235	0.0		0.0	False		,,,				2504	0.0				p.T46T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G138A	6						.						16.0	9.0	12.0					6																	31085254		1773	3470	5243	31193233	SO:0001627	intron_variant	1041	exon2			AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+2586C>T	6.37:g.31085254C>T		Somatic		Capture	Illumina HiSeq	Phase_I	31193233	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Silent	SNP	ENST00000259881.9	37	CCDS34390.1																																																																																				0.572	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
TCF19	6941	broad.mit.edu	37	6	31130320	31130320	+	Silent	SNP	C	C	T	rs369152415		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:31130320C>T	ENST00000376257.3	+	4	1618	c.864C>T	c.(862-864)ggC>ggT	p.G288G	TCF19_ENST00000376255.4_Silent_p.G288G|TCF19_ENST00000496421.1_3'UTR	NM_007109.2	NP_009040.2	Q9Y242	TCF19_HUMAN	transcription factor 19	288	Pro-rich.				cell proliferation (GO:0008283)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.G288G(1)		kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						CAGTTGGGGGCGGGGAGCCCT	0.622																																					p.G288G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C864T	6						.	C	,	0,2582		0,0,1291	58.0	67.0	64.0		864,864	-6.8	0.4	6		64	2,5114		0,2,2556	no	coding-synonymous,coding-synonymous	TCF19	NM_001077511.1,NM_007109.2	,	0,2,3847	TT,TC,CC		0.0391,0.0,0.026	,	288/346,288/346	31130320	2,7696	1291	2558	3849	31238299	SO:0001819	synonymous_variant	6941	exon4			U25826	CCDS43446.1	6p21.3	2013-01-28	2009-02-05		ENSG00000137310	ENSG00000137310		"""Zinc fingers, PHD-type"""	11629	protein-coding gene	gene with protein product		600912				1868030, 8595903	Standard	NM_001077511		Approved	SC1	uc003nss.3	Q9Y242	OTTHUMG00000031274	ENST00000376257.3:c.864C>T	6.37:g.31130320C>T		Somatic		Capture	Illumina HiSeq	Phase_I	31238299	NM_001077511	A6NCT8|B0UY11|Q0EFA8|Q13176|Q15967|Q5SQ89|Q5STD6|Q5STF5|Q9BUM2|Q9UBH7	Silent	SNP	ENST00000376257.3	37	CCDS43446.1																																																																																				0.622	TCF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076595.2	NM_007109	
NCR3	259197	broad.mit.edu	37	6	31557750	31557750	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:31557750A>G	ENST00000340027.5	-	2	460	c.197T>C	c.(196-198)gTg>gCg	p.V66A	NCR3_ENST00000491161.1_5'UTR|NCR3_ENST00000376071.4_Splice_Site|NCR3_ENST00000376072.3_Missense_Mutation_p.V66A|NCR3_ENST00000376073.4_Missense_Mutation_p.V66A	NM_147130.2	NP_667341.1	O14931	NCTR3_HUMAN	natural cytotoxicity triggering receptor 3	66	Ig-like.				cell recognition (GO:0008037)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	integral component of plasma membrane (GO:0005887)		p.V66A(1)		cervix(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|skin(2)	9						TCCATTCCTCACCTCCTTCCC	0.617																																					p.V66A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T197C	6						.						126.0	119.0	122.0					6																	31557750		1511	2709	4220	31665729	SO:0001583	missense	259197	exon2			AB055881	CCDS34397.1, CCDS47401.1, CCDS47402.1	6p21.3	2013-01-11	2002-11-13	2002-11-15	ENSG00000204475	ENSG00000204475		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	19077	protein-coding gene	gene with protein product		611550	"""lymphocyte antigen 117"""	LY117		8824804, 11782277	Standard	NM_001145466		Approved	1C7, NKp30, CD337	uc003nuv.2	O14931	OTTHUMG00000031123	ENST00000340027.5:c.197T>C	6.37:g.31557750A>G	ENSP00000342156:p.Val66Ala	Somatic		Capture	Illumina HiSeq	Phase_I	31665729	NM_147130	B0S8F2|B0S8F4|B0S8F5|O14930|O14932|O95667|O95668|O95669|Q5ST89|Q5ST90|Q5ST91|Q5ST92|Q5STA3	Missense_Mutation	SNP	ENST00000340027.5	37	CCDS34397.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.98|13.98	2.400322|2.400322	0.42613|0.42613	.|.	.|.	ENSG00000204475|ENSG00000204475	ENST00000376071|ENST00000340027;ENST00000376073;ENST00000376072	.|T;T;T	.|0.64260	.|-0.09;-0.09;-0.09	4.1|4.1	4.1|4.1	0.47936|0.47936	.|Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.437537	.|0.18658	.|N	.|0.134804	.|T	.|0.53610	.|0.1807	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|P;P;D	.|0.56521	.|0.889;0.856;0.976	.|P;P;P	.|0.55222	.|0.611;0.731;0.771	.|T	.|0.53634	.|-0.8411	.|10	.|0.36615	.|T	.|0.2	.|-9.4374	9.6808|9.6808	0.40070|0.40070	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|66;66;66	.|O14931-2;Q05D23;O14931	.|.;.;NCTR3_HUMAN	.|A	-1|66	.|ENSP00000342156:V66A;ENSP00000365241:V66A;ENSP00000365240:V66A	.|ENSP00000342156:V66A	.|V	-|-	.|2	.|0	NCR3|NCR3	31665729|31665729	0.983000|0.983000	0.35010|0.35010	0.997000|0.997000	0.53966|0.53966	0.610000|0.610000	0.37248|0.37248	3.596000|3.596000	0.54024|0.54024	1.844000|1.844000	0.53588|0.53588	0.528000|0.528000	0.53228|0.53228	.|GTG		0.617	NCR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076210.2		
PRRC2A	7916	broad.mit.edu	37	6	31598451	31598451	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:31598451C>T	ENST00000376033.2	+	15	2572	c.2338C>T	c.(2338-2340)Cgg>Tgg	p.R780W	PRRC2A_ENST00000376007.4_Missense_Mutation_p.R780W	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	780	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R780W(1)		breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						GTTACGGGAACGGGGCACTCC	0.592																																					p.R780W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2338T	6						.						106.0	94.0	98.0					6																	31598451		2203	4300	6503	31706430	SO:0001583	missense	7916	exon15			M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.2338C>T	6.37:g.31598451C>T	ENSP00000365201:p.Arg780Trp	Somatic		Capture	Illumina HiSeq	Phase_I	31706430	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	C	14.68	2.608676	0.46527	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.16597	2.33;2.33	5.3	3.5	0.40072	.	0.000000	0.51477	D	0.000096	T	0.25306	0.0615	L	0.55990	1.75	0.58432	D	0.999993	D	0.89917	1.0	D	0.87578	0.998	T	0.03268	-1.1054	10	0.87932	D	0	-14.3345	13.7618	0.62971	0.2784:0.7216:0.0:0.0	.	780	P48634	PRC2A_HUMAN	W	780;769;780;780;5	ENSP00000365175:R780W;ENSP00000365201:R780W	ENSP00000365175:R780W	R	+	1	2	PRRC2A	31706430	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	3.506000	0.53364	0.788000	0.33755	0.655000	0.94253	CGG		0.592	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
PRRC2A	7916	broad.mit.edu	37	6	31599695	31599695	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:31599695G>A	ENST00000376033.2	+	16	3479	c.3245G>A	c.(3244-3246)cGc>cAc	p.R1082H	PRRC2A_ENST00000376007.4_Missense_Mutation_p.R1082H	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1082	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R1082H(1)		breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CCCCGAGGCCGCACTGCCAGC	0.642																																					p.R1082H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3245A	6						.						26.0	27.0	27.0					6																	31599695		1508	2707	4215	31707674	SO:0001583	missense	7916	exon16			M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3245G>A	6.37:g.31599695G>A	ENSP00000365201:p.Arg1082His	Somatic		Capture	Illumina HiSeq	Phase_I	31707674	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.46|14.46	2.543298|2.543298	0.45280|0.45280	.|.	.|.	ENSG00000204469|ENSG00000204469	ENST00000424184;ENST00000435052|ENST00000376007;ENST00000376033;ENST00000376010	.|T;T	.|0.02552	.|4.25;4.25	5.04|5.04	5.04|5.04	0.67666|0.67666	.|.	.|0.000000	.|0.49305	.|D	.|0.000150	T|T	0.08582|0.08582	0.0213|0.0213	L|L	0.59436|0.59436	1.845|1.845	0.51482|0.51482	D|D	0.999922|0.999922	.|D	.|0.89917	.|1.0	.|D	.|0.83275	.|0.996	T|T	0.03887|0.03887	-1.0995|-1.0995	6|10	0.87932|0.87932	D|D	0|0	-7.7335|-7.7335	17.3102|17.3102	0.87207|0.87207	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1082	.|P48634	.|PRC2A_HUMAN	T|H	1081;1070|1082;1082;307	.|ENSP00000365175:R1082H;ENSP00000365201:R1082H	ENSP00000407986:A1081T|ENSP00000365175:R1082H	A|R	+|+	1|2	0|0	PRRC2A|PRRC2A	31707674|31707674	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	8.811000|8.811000	0.91954|0.91954	2.640000|2.640000	0.89533|0.89533	0.655000|0.655000	0.94253|0.94253	GCA|CGC		0.642	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
PRRC2A	7916	broad.mit.edu	37	6	31603025	31603025	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:31603025A>G	ENST00000376033.2	+	22	5511	c.5277A>G	c.(5275-5277)ccA>ccG	p.P1759P	PRRC2A_ENST00000376007.4_Silent_p.P1759P	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1759	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.P1759P(1)		breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CTGGTCCCCCAGTCCAGTTTG	0.592																																					p.P1759P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A5277G	6						.						89.0	79.0	82.0					6																	31603025		2203	4300	6503	31711004	SO:0001819	synonymous_variant	7916	exon22			M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.5277A>G	6.37:g.31603025A>G		Somatic		Capture	Illumina HiSeq	Phase_I	31711004	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	37	CCDS4708.1																																																																																				0.592	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
GPANK1	7918	broad.mit.edu	37	6	31630285	31630285	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:31630285G>A	ENST00000375906.1	-	4	1513	c.829C>T	c.(829-831)Cgg>Tgg	p.R277W	C6orf47_ENST00000375911.1_5'Flank|CSNK2B_ENST00000375885.4_5'Flank|C6orf47-AS1_ENST00000422049.1_RNA|GPANK1_ENST00000375895.2_Missense_Mutation_p.R277W|GPANK1_ENST00000375893.2_Missense_Mutation_p.R277W|GPANK1_ENST00000375896.4_Missense_Mutation_p.R277W|GPANK1_ENST00000375900.4_Missense_Mutation_p.R277W|Y_RNA_ENST00000364337.1_RNA	NM_001199237.1	NP_001186166.1	O95872	GPAN1_HUMAN	G patch domain and ankyrin repeats 1	277	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.						nucleic acid binding (GO:0003676)	p.R277W(1)		central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(7)	12						CCCTCACCCCGGGGTCCCAGC	0.647																																					p.R277W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C829T	6						.						46.0	51.0	49.0					6																	31630285		1510	2709	4219	31738264	SO:0001583	missense	7918	exon4				CCDS4711.1	6p21.3	2013-01-28	2010-11-24	2010-11-24	ENSG00000204438	ENSG00000204438		"""Ankyrin repeat domain containing"", ""G patch domain containing"""	13920	protein-coding gene	gene with protein product	"""G patch domain containing 10"", ""ankyrin repeat domain 59"""	142610	"""HLA-B associated transcript 4"""	BAT4		2911734, 2813433	Standard	NM_001199237		Approved	G5, D6S54E, GPATCH10, ANKRD59	uc021yuu.1	O95872	OTTHUMG00000031174	ENST00000375906.1:c.829C>T	6.37:g.31630285G>A	ENSP00000365071:p.Arg277Trp	Somatic		Capture	Illumina HiSeq	Phase_I	31738264	NM_001199237	A6NG25|B0UXA2|Q5SQ49	Missense_Mutation	SNP	ENST00000375906.1	37	CCDS4711.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.564500	0.45694	.	.	ENSG00000204438	ENST00000375906;ENST00000375896;ENST00000375893;ENST00000375895;ENST00000375900	T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49	5.0	2.21	0.28008	D111/G-patch (3);	0.340710	0.27206	N	0.020422	T	0.14184	0.0343	M	0.73962	2.25	0.37595	D	0.920325	B	0.19073	0.033	B	0.15484	0.013	T	0.03863	-1.0997	10	0.66056	D	0.02	-6.9137	3.2562	0.06832	0.0848:0.1523:0.4491:0.3138	.	277	O95872	GPAN1_HUMAN	W	277	ENSP00000365071:R277W;ENSP00000365060:R277W;ENSP00000365057:R277W;ENSP00000365059:R277W;ENSP00000365065:R277W	ENSP00000365057:R277W	R	-	1	2	GPANK1	31738264	0.995000	0.38212	0.977000	0.42913	0.984000	0.73092	1.345000	0.33953	0.278000	0.22164	-0.169000	0.13324	CGG		0.647	GPANK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144445.2	NM_033177	
VWA7	80737	broad.mit.edu	37	6	31744345	31744345	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:31744345G>A	ENST00000375688.4	-	2	412	c.212C>T	c.(211-213)cCt>cTt	p.P71L	VWA7_ENST00000447450.1_Missense_Mutation_p.P71L|VWA7_ENST00000467576.1_5'UTR|VWA7_ENST00000375686.3_Missense_Mutation_p.P71L|Y_RNA_ENST00000364685.1_RNA			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	71						extracellular region (GO:0005576)		p.P71L(1)									AAGACGAAGAGGGGGGCGGCC	0.637																																					p.P71L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C212T	6						.						11.0	6.0	8.0					6																	31744345		1332	2410	3742	31852324	SO:0001583	missense	80737	exon2				CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"""chromosome 6 open reading frame 27"""	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.212C>T	6.37:g.31744345G>A	ENSP00000364840:p.Pro71Leu	Somatic		Capture	Illumina HiSeq	Phase_I	31852324	NM_025258	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	37	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	G	14.14	2.446717	0.43429	.	.	ENSG00000204396	ENST00000375688;ENST00000375686;ENST00000447450	T;T;T	0.14022	2.54;2.54;2.54	5.05	2.27	0.28462	.	0.463445	0.21276	N	0.077228	T	0.02970	0.0088	L	0.36672	1.1	0.09310	N	1	B	0.33238	0.403	B	0.28232	0.087	T	0.36553	-0.9743	10	0.56958	D	0.05	-7.3295	5.0822	0.14663	0.0825:0.1448:0.623:0.1497	.	71	Q9Y334	G7C_HUMAN	L	71	ENSP00000364840:P71L;ENSP00000364838:P71L;ENSP00000390554:P71L	ENSP00000364838:P71L	P	-	2	0	C6orf27	31852324	0.455000	0.25736	0.000000	0.03702	0.006000	0.05464	1.769000	0.38522	0.302000	0.22762	-0.157000	0.13467	CCT		0.637	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258	
TNXB	7148	broad.mit.edu	37	6	32012951	32012951	+	Missense_Mutation	SNP	C	C	T	rs560288296		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:32012951C>T	ENST00000375244.3	-	32	10960	c.10759G>A	c.(10759-10761)Gtg>Atg	p.V3587M	TNXB_ENST00000375247.2_Missense_Mutation_p.V3585M|TNXB_ENST00000451343.1_Missense_Mutation_p.V16M			P22105	TENX_HUMAN	tenascin XB	3632	Fibronectin type-III 27. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.V16M(1)|p.V3652M(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						TACTGGACCACGAAGGAATCA	0.642													C|||	1	0.000199681	0.0	0.0	5008	,	,		28581	0.0		0.0	False		,,,				2504	0.001				p.V16M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G46A	6						.						50.0	44.0	46.0					6																	32012951		1507	2706	4213	32120929	SO:0001583	missense	7148	exon1			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.10759G>A	6.37:g.32012951C>T	ENSP00000364393:p.Val3587Met	Somatic		Capture	Illumina HiSeq	Phase_I	32120929	NM_032470	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	c	19.07	3.756516	0.69648	.	.	ENSG00000168477	ENST00000375244;ENST00000451343;ENST00000375247	T;T;T	0.57595	0.39;0.39;0.39	4.85	4.85	0.62838	.	0.000000	0.48286	D	0.000185	T	0.55689	0.1936	M	0.72894	2.215	0.25859	N	0.98384	D	0.69078	0.997	D	0.63877	0.919	T	0.49322	-0.8952	10	0.34782	T	0.22	.	11.7463	0.51821	0.0:0.7057:0.2943:0.0	.	3585	P22105-3	.	M	3587;16;3585	ENSP00000364393:V3587M;ENSP00000407685:V16M;ENSP00000364396:V3585M	ENSP00000364393:V3587M	V	-	1	0	TNXB	32120929	0.946000	0.32159	0.997000	0.53966	0.984000	0.73092	0.609000	0.24238	2.526000	0.85167	0.651000	0.88453	GTG		0.642	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
TNXB	7148	broad.mit.edu	37	6	32056606	32056606	+	Missense_Mutation	SNP	C	C	T	rs374779610		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:32056606C>T	ENST00000375244.3	-	6	2936	c.2735G>A	c.(2734-2736)cGg>cAg	p.R912Q	TNXB_ENST00000375247.2_Missense_Mutation_p.R912Q			P22105	TENX_HUMAN	tenascin XB	1014					actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.R864Q(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						TGCCCGGCCCCGCTCCGCTGT	0.617																																					p.R912Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2735A	6						.	C	GLN/ARG	1,4085		0,1,2042	26.0	31.0	29.0		2735	4.5	0.9	6		29	0,8394		0,0,4197	no	missense	TNXB	NM_019105.6	43	0,1,6239	TT,TC,CC		0.0,0.0245,0.0080	probably-damaging	912/4243	32056606	1,12479	2043	4197	6240	32164584	SO:0001583	missense	7148	exon6			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.2735G>A	6.37:g.32056606C>T	ENSP00000364393:p.Arg912Gln	Somatic		Capture	Illumina HiSeq	Phase_I	32164584	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	C	23.6	4.434333	0.83776	2.45E-4	0.0	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.56941	0.43;0.43	5.39	4.53	0.55603	.	0.000000	0.48286	D	0.000199	T	0.55784	0.1942	M	0.62016	1.91	0.21950	N	0.999454	D	0.89917	1.0	D	0.91635	0.999	T	0.52403	-0.8580	10	0.44086	T	0.13	.	12.0005	0.53228	0.0:0.915:0.0:0.085	.	912	P22105-3	.	Q	912	ENSP00000364393:R912Q;ENSP00000364396:R912Q	ENSP00000364393:R912Q	R	-	2	0	TNXB	32164584	0.071000	0.21146	0.940000	0.37924	0.978000	0.69477	1.159000	0.31749	1.289000	0.44618	0.561000	0.74099	CGG		0.617	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
TNXB	7148	broad.mit.edu	37	6	32056710	32056710	+	Silent	SNP	G	G	A	rs374167680		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:32056710G>A	ENST00000375244.3	-	6	2832	c.2631C>T	c.(2629-2631)gcC>gcT	p.A877A	TNXB_ENST00000375247.2_Silent_p.A877A			P22105	TENX_HUMAN	tenascin XB	829	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.A829A(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						TCTGGTTGCCGGCACTGACGT	0.617																																					p.A877A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2631T	6						.	G		3,4305		0,3,2151	35.0	42.0	39.0		2631	-7.7	0.9	6		39	0,8502		0,0,4251	no	coding-synonymous	TNXB	NM_019105.6		0,3,6402	AA,AG,GG		0.0,0.0696,0.0234		877/4243	32056710	3,12807	2154	4251	6405	32164688	SO:0001819	synonymous_variant	7148	exon6			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.2631C>T	6.37:g.32056710G>A		Somatic		Capture	Illumina HiSeq	Phase_I	32164688	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																					0.617	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
TNXB	7148	broad.mit.edu	37	6	32064657	32064657	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:32064657G>A	ENST00000479795.1	-	3	1113	c.973C>T	c.(973-975)Cgc>Tgc	p.R325C	TNXB_ENST00000375247.2_Missense_Mutation_p.R325C|TNXB_ENST00000375244.3_Missense_Mutation_p.R325C			P22105	TENX_HUMAN	tenascin XB	325	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.R325C(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CACACGCAGCGCCCGTCCTTG	0.716																																					p.R325C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C973T	6						.						20.0	24.0	23.0					6																	32064657		2164	4247	6411	32172635	SO:0001583	missense	7148	exon3			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000479795.1:c.973C>T	6.37:g.32064657G>A	ENSP00000418248:p.Arg325Cys	Somatic		Capture	Illumina HiSeq	Phase_I	32172635	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000479795.1	37		.	.	.	.	.	.	.	.	.	.	G	17.30	3.355078	0.61293	.	.	ENSG00000168477	ENST00000375244;ENST00000375247;ENST00000479795	T;T;T	0.07800	3.79;3.79;3.16	4.5	2.49	0.30216	.	0.345581	0.21517	N	0.073290	T	0.20088	0.0483	M	0.91818	3.245	0.34578	D	0.714143	D	0.89917	1.0	D	0.74674	0.984	T	0.05194	-1.0900	10	0.59425	D	0.04	.	8.2076	0.31465	0.0:0.1723:0.6503:0.1774	.	325	P22105-3	.	C	325	ENSP00000364393:R325C;ENSP00000364396:R325C;ENSP00000418248:R325C	ENSP00000364393:R325C	R	-	1	0	TNXB	32172635	0.000000	0.05858	0.993000	0.49108	0.981000	0.71138	-0.453000	0.06778	0.826000	0.34661	0.467000	0.42956	CGC		0.716	TNXB-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000357059.1	NM_019105	
AGPAT1	10554	broad.mit.edu	37	6	32137758	32137758	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:32137758G>A	ENST00000395499.1	-	6	1243	c.664C>T	c.(664-666)Cgt>Tgt	p.R222C	PPT2-EGFL8_ENST00000422437.1_3'UTR|AGPAT1_ENST00000375104.2_Missense_Mutation_p.R222C|AGPAT1_ENST00000395496.1_Missense_Mutation_p.R222C|AGPAT1_ENST00000336984.6_Missense_Mutation_p.R222C|AGPAT1_ENST00000395497.1_Missense_Mutation_p.R222C|AGPAT1_ENST00000375107.3_Missense_Mutation_p.R222C|AGPAT1_ENST00000412465.2_Missense_Mutation_p.R110C|AGPAT1_ENST00000490711.1_5'UTR			Q99943	PLCA_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 1	222					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|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)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.R222C(1)		central_nervous_system(1)|large_intestine(3)|lung(6)|ovary(2)	12						GTGAAGCGACGCTCCTTCTTG	0.562																																					p.R222C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C664T	6						.						90.0	77.0	82.0					6																	32137758		1511	2709	4220	32245736	SO:0001583	missense	10554	exon6			U56417	CCDS4744.1	6p21.3	2013-02-05	2013-02-05		ENSG00000204310	ENSG00000204310	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	324	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, alpha"""	603099	"""1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)"""			9461603, 9291118	Standard	NM_032741		Approved	LPAAT-alpha	uc003oae.3	Q99943	OTTHUMG00000031210	ENST00000395499.1:c.664C>T	6.37:g.32137758G>A	ENSP00000378877:p.Arg222Cys	Somatic		Capture	Illumina HiSeq	Phase_I	32245736	NM_032741	A2BFI5|Q5BL03	Missense_Mutation	SNP	ENST00000395499.1	37	CCDS4744.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.3|23.3	4.398642|4.398642	0.83120|0.83120	.|.	.|.	ENSG00000204310|ENSG00000204310	ENST00000538952|ENST00000395496;ENST00000375107;ENST00000395499;ENST00000375104;ENST00000395497;ENST00000336984;ENST00000412465	.|D;D;D;D;D;D;D	.|0.94497	.|-3.44;-3.44;-3.44;-3.44;-3.44;-3.44;-3.44	5.99|5.99	5.12|5.12	0.69794|0.69794	.|.	.|0.211240	.|0.43747	.|D	.|0.000532	D|D	0.95046|0.95046	0.8396|0.8396	L|L	0.60455|0.60455	1.87|1.87	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D;D	.|0.89917	.|1.0;0.999;0.999	.|P;D;P	.|0.68765	.|0.872;0.96;0.786	D|D	0.95454|0.95454	0.8537|0.8537	6|10	0.87932|0.62326	D|D	0|0.03	-13.3857|-13.3857	12.3675|12.3675	0.55236|0.55236	0.0:0.0:0.6955:0.3045|0.0:0.0:0.6955:0.3045	.|.	.|186;112;222	.|B4DRH1;B3KPH3;Q99943	.|.;.;PLCA_HUMAN	V|C	86|222;222;222;222;222;222;110	.|ENSP00000378874:R222C;ENSP00000364248:R222C;ENSP00000378877:R222C;ENSP00000364245:R222C;ENSP00000378875:R222C;ENSP00000337463:R222C;ENSP00000410473:R110C	ENSP00000446173:A86V|ENSP00000337463:R222C	A|R	-|-	2|1	0|0	AGPAT1|AGPAT1	32245736|32245736	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	2.648000|2.648000	0.46647|0.46647	1.513000|1.513000	0.48852|0.48852	0.655000|0.655000	0.94253|0.94253	GCG|CGT		0.562	AGPAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268941.1	NM_006411	
HLA-DRA	3122	broad.mit.edu	37	6	32411018	32411018	+	Missense_Mutation	SNP	G	G	A	rs61117681	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:32411018G>A	ENST00000395388.2	+	3	494	c.385G>A	c.(385-387)Gtc>Atc	p.V129I	HLA-DRA_ENST00000374982.5_Intron	NM_019111.4	NP_061984.2	P01903	DRA_HUMAN	major histocompatibility complex, class II, DR alpha	129	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002504)|cognition (GO:0050890)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|polysaccharide assembly with MHC class II protein complex (GO:0002506)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)	p.V129I(1)		NS(1)|breast(1)|large_intestine(6)|lung(5)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19						AGAGCCCAACGTCCTCATCTG	0.507									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Kaposi Sarcoma, Familial Clustering of																												p.V129I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G385A	6						.						133.0	100.0	112.0					6																	32411018		1511	2709	4220	32518996	SO:0001583	missense	3122	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;		CCDS4750.1	6p21.3	2013-01-11			ENSG00000204287	ENSG00000204287		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4947	protein-coding gene	gene with protein product		142860		HLA-DRA1			Standard	NM_019111		Approved		uc003obh.3	P01903	OTTHUMG00000031269	ENST00000395388.2:c.385G>A	6.37:g.32411018G>A	ENSP00000378786:p.Val129Ile	Somatic		Capture	Illumina HiSeq	Phase_I	32518996	NM_019111	A2BET4|Q30160|Q6IAZ1|Q861I2|Q9TP70	Missense_Mutation	SNP	ENST00000395388.2	37	CCDS4750.1	.	.	.	.	.	.	.	.	.	.	.	8.459	0.854772	0.17106	.	.	ENSG00000204287	ENST00000395388	T	0.00614	6.21	5.59	-6.87	0.01671	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.688144	0.15056	N	0.283037	T	0.00178	0.0005	N	0.12443	0.215	0.27988	N	0.935773	B	0.06786	0.001	B	0.09377	0.004	T	0.39603	-0.9606	10	0.19147	T	0.46	.	17.4709	0.87646	0.8229:0.0:0.1771:0.0	.	129	P01903	DRA_HUMAN	I	129	ENSP00000378786:V129I	ENSP00000378786:V129I	V	+	1	0	HLA-DRA	32518996	0.000000	0.05858	0.100000	0.21137	0.885000	0.51271	-2.154000	0.01285	-1.369000	0.02147	-0.136000	0.14681	GTC		0.507	HLA-DRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076586.2	NM_019111	
WDR46	9277	broad.mit.edu	37	6	33248687	33248687	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:33248687C>T	ENST00000374617.4	-	11	1549	c.1193G>A	c.(1192-1194)cGg>cAg	p.R398Q	B3GALT4_ENST00000606990.1_Intron	NM_001164267.1|NM_005452.5	NP_001157739.1|NP_005443.3	O15213	WDR46_HUMAN	WD repeat domain 46	398							poly(A) RNA binding (GO:0044822)	p.R398Q(1)		NS(1)|breast(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	20						GGGCAGGGTCCGAGTGCTCAG	0.607																																					p.R344Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1031A	6						.						74.0	79.0	77.0					6																	33248687		2203	4300	6503	33356665	SO:0001583	missense	9277	exon11			Z97184	CCDS4772.1	6p21.3	2013-01-09	2005-05-31	2005-05-31	ENSG00000227057	ENSG00000227057		"""WD repeat domain containing"""	13923	protein-coding gene	gene with protein product		611440	"""chromosome 6 open reading frame 11"""	C6orf11		9545376, 9521053	Standard	NM_005452		Approved	BING4, UTP7	uc003ods.3	O15213	OTTHUMG00000031192	ENST00000374617.4:c.1193G>A	6.37:g.33248687C>T	ENSP00000363746:p.Arg398Gln	Somatic		Capture	Illumina HiSeq	Phase_I	33356665	NM_001164267	A6NDP5|Q5HYZ0|Q5STK5|Q5STR3	Missense_Mutation	SNP	ENST00000374617.4	37	CCDS4772.1	.	.	.	.	.	.	.	.	.	.	C	13.68	2.310829	0.40895	.	.	ENSG00000227057	ENST00000374617	T	0.01295	5.04	5.39	4.52	0.55395	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.256685	0.41097	N	0.000948	T	0.00784	0.0026	L	0.54323	1.7	0.33859	D	0.633514	B;B	0.16396	0.013;0.017	B;B	0.08055	0.003;0.003	T	0.48281	-0.9049	10	0.32370	T	0.25	-18.8604	11.6462	0.51263	0.0:0.9152:0.0:0.0848	.	344;398	B4DP15;O15213	.;WDR46_HUMAN	Q	398	ENSP00000363746:R398Q	ENSP00000363746:R398Q	R	-	2	0	WDR46	33356665	1.000000	0.71417	1.000000	0.80357	0.704000	0.40688	2.080000	0.41586	1.514000	0.48869	0.549000	0.68633	CGG		0.607	WDR46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076382.2	NM_005452	
WDR46	9277	broad.mit.edu	37	6	33248757	33248757	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:33248757C>T	ENST00000374617.4	-	11	1479	c.1123G>A	c.(1123-1125)Gcc>Acc	p.A375T	B3GALT4_ENST00000606990.1_Intron	NM_001164267.1|NM_005452.5	NP_001157739.1|NP_005443.3	O15213	WDR46_HUMAN	WD repeat domain 46	375							poly(A) RNA binding (GO:0044822)	p.A375T(1)		NS(1)|breast(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	20						CCAGAGGTGGCCATGTACCTG	0.557																																					p.A321T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G961A	6						.						77.0	80.0	79.0					6																	33248757		2203	4300	6503	33356735	SO:0001583	missense	9277	exon11			Z97184	CCDS4772.1	6p21.3	2013-01-09	2005-05-31	2005-05-31	ENSG00000227057	ENSG00000227057		"""WD repeat domain containing"""	13923	protein-coding gene	gene with protein product		611440	"""chromosome 6 open reading frame 11"""	C6orf11		9545376, 9521053	Standard	NM_005452		Approved	BING4, UTP7	uc003ods.3	O15213	OTTHUMG00000031192	ENST00000374617.4:c.1123G>A	6.37:g.33248757C>T	ENSP00000363746:p.Ala375Thr	Somatic		Capture	Illumina HiSeq	Phase_I	33356735	NM_001164267	A6NDP5|Q5HYZ0|Q5STK5|Q5STR3	Missense_Mutation	SNP	ENST00000374617.4	37	CCDS4772.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.019723	0.93462	.	.	ENSG00000227057	ENST00000374617;ENST00000444176	T;T	0.70282	-0.47;-0.47	5.39	5.39	0.77823	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.051805	0.85682	D	0.000000	D	0.86188	0.5873	M	0.92880	3.355	0.80722	D	1	D;D	0.89917	0.993;1.0	P;D	0.80764	0.863;0.994	D	0.88489	0.3074	10	0.72032	D	0.01	-24.018	16.6862	0.85309	0.0:1.0:0.0:0.0	.	321;375	B4DP15;O15213	.;WDR46_HUMAN	T	375;302	ENSP00000363746:A375T;ENSP00000405568:A302T	ENSP00000363746:A375T	A	-	1	0	WDR46	33356735	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.774000	0.55341	2.806000	0.96561	0.549000	0.68633	GCC		0.557	WDR46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076382.2	NM_005452	
SYNGAP1	8831	broad.mit.edu	37	6	33419664	33419664	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:33419664G>A	ENST00000418600.2	+	19	4114	c.4013G>A	c.(4012-4014)cGa>cAa	p.R1338Q	ZBTB9_ENST00000395064.2_5'Flank|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.R1279Q|SYNGAP1_ENST00000496374.1_3'UTR	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	1338					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)	p.R1323Q(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						GGCGAGTTCCGAAACACCGCA	0.627																																					p.R1338Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4013A	6						.						33.0	36.0	35.0					6																	33419664		2198	4296	6494	33527642	SO:0001583	missense	8831	exon19			AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.4013G>A	6.37:g.33419664G>A	ENSP00000403636:p.Arg1338Gln	Somatic		Capture	Illumina HiSeq	Phase_I	33527642	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	G	13.47	2.245737	0.39697	.	.	ENSG00000197283	ENST00000418600;ENST00000428982	T;T	0.20598	2.07;2.06	2.97	2.97	0.34412	.	.	.	.	.	T	0.04770	0.0129	N	0.19112	0.55	0.80722	D	1	P	0.47484	0.896	B	0.35039	0.194	T	0.21449	-1.0245	9	0.72032	D	0.01	.	7.423	0.27083	0.0:0.0:0.7411:0.2589	.	1338	Q96PV0	SYGP1_HUMAN	Q	1338;1279	ENSP00000403636:R1338Q;ENSP00000412475:R1279Q	ENSP00000403636:R1338Q	R	+	2	0	SYNGAP1	33527642	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.734000	0.55037	1.676000	0.50930	0.400000	0.26472	CGA		0.627	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
GGNBP1	449520	broad.mit.edu	37	6	33555553	33555553	+	Intron	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:33555553G>A	ENST00000374458.1	+	5	846				LINC00336_ENST00000477984.1_RNA			Q5YKI7	GGNB1_HUMAN	gametogenetin binding protein 1 (pseudogene)						cell differentiation (GO:0030154)|mitochondrial fission (GO:0000266)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)		p.G145G(1)									agtggctcacgcctataatcc	0.542																																					.												.	.	1	Substitution - coding silent(1)	large_intestine(1)	.	6						.						32.0	30.0	31.0					6																	33555553		2203	4299	6502	33663531	SO:0001627	intron_variant	401253	.					6p21	2012-04-19	2012-04-19		ENSG00000204188	ENSG00000204188			19427	pseudogene	pseudogene		609495	"""gametogenetin binding protein 1"""			15642376	Standard	NR_028361		Approved		uc021ywq.1	Q5YKI7		ENST00000374458.1:c.216+988G>A	6.37:g.33555553G>A		Somatic		Capture	Illumina HiSeq	Phase_I	33663531	.	Q5YKI8	Silent	SNP	ENST00000374458.1	37																																																																																					0.542	GGNBP1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
ITPR3	3710	broad.mit.edu	37	6	33648413	33648413	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:33648413G>A	ENST00000374316.5	+	34	5492	c.4432G>A	c.(4432-4434)Gcc>Acc	p.A1478T	ITPR3_ENST00000605930.1_Missense_Mutation_p.A1478T			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1478					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|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)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.A1478T(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	CACCATCAACGCCTTCTTCAG	0.592																																					p.A1478T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4432A	6						.						118.0	100.0	106.0					6																	33648413		2203	4300	6503	33756391	SO:0001583	missense	3710	exon33			D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.4432G>A	6.37:g.33648413G>A	ENSP00000363435:p.Ala1478Thr	Somatic		Capture	Illumina HiSeq	Phase_I	33756391	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	G	8.559	0.877277	0.17395	.	.	ENSG00000096433	ENST00000374316	T	0.60171	0.21	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.12518	0.0304	N	0.05177	-0.1	0.51767	D	0.999938	P	0.40230	0.708	B	0.31101	0.124	T	0.34950	-0.9808	10	0.02654	T	1	-31.1811	12.5287	0.56102	0.0763:0.0:0.9237:0.0	.	1478	Q14573	ITPR3_HUMAN	T	1478	ENSP00000363435:A1478T	ENSP00000363435:A1478T	A	+	1	0	ITPR3	33756391	1.000000	0.71417	0.951000	0.38953	0.729000	0.41735	4.870000	0.63035	2.515000	0.84797	0.655000	0.94253	GCC		0.592	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
ITPR3	3710	broad.mit.edu	37	6	33656100	33656100	+	Missense_Mutation	SNP	C	C	T	rs142820127		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:33656100C>T	ENST00000374316.5	+	49	7520	c.6460C>T	c.(6460-6462)Cgg>Tgg	p.R2154W	ITPR3_ENST00000605930.1_Missense_Mutation_p.R2154W			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2154					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|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)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)	p.R2154W(1)		NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	AACCAAGCACCGGCTCTTCAC	0.592																																					p.R2154W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6460T	6						.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	112.0	94.0	100.0		6460	3.7	1.0	6	dbSNP_134	100	0,8600		0,0,4300	no	missense	ITPR3	NM_002224.3	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	2154/2672	33656100	1,13005	2203	4300	6503	33764078	SO:0001583	missense	3710	exon48			D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.6460C>T	6.37:g.33656100C>T	ENSP00000363435:p.Arg2154Trp	Somatic		Capture	Illumina HiSeq	Phase_I	33764078	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.175783	0.78564	2.27E-4	0.0	ENSG00000096433	ENST00000374316	D	0.92397	-3.03	5.53	3.68	0.42216	.	0.066724	0.64402	D	0.000012	D	0.93976	0.8071	M	0.72353	2.195	0.54753	D	0.999988	D;D	0.89917	1.0;0.998	D;P	0.78314	0.991;0.803	D	0.94227	0.7473	10	0.87932	D	0	-37.1723	13.8106	0.63262	0.3954:0.6046:0.0:0.0	.	2154;1824	Q14573;Q59ES2	ITPR3_HUMAN;.	W	2154	ENSP00000363435:R2154W	ENSP00000363435:R2154W	R	+	1	2	ITPR3	33764078	0.961000	0.32948	1.000000	0.80357	0.975000	0.68041	0.721000	0.25911	0.622000	0.30249	0.650000	0.86243	CGG		0.592	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
GRM4	2914	broad.mit.edu	37	6	34100925	34100925	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:34100925C>T	ENST00000538487.2	-	2	792	c.349G>A	c.(349-351)Gag>Aag	p.E117K	GRM4_ENST00000374177.3_Intron|GRM4_ENST00000374181.4_Missense_Mutation_p.E117K	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	117					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)	p.E117K(2)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						AGCGACTGCTCGAGGGCATGG	0.627																																					p.E117K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G349A	6						.						60.0	52.0	55.0					6																	34100925		2203	4300	6503	34208903	SO:0001583	missense	2914	exon1			U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.349G>A	6.37:g.34100925C>T	ENSP00000440556:p.Glu117Lys	Somatic		Capture	Illumina HiSeq	Phase_I	34208903	NM_000841	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Missense_Mutation	SNP	ENST00000538487.2	37	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.176846	0.78564	.	.	ENSG00000124493	ENST00000374181;ENST00000538487	D;D	0.85411	-1.98;-1.98	3.99	3.99	0.46301	Extracellular ligand-binding receptor (1);	0.000000	0.64402	D	0.000001	D	0.90304	0.6967	M	0.74258	2.255	0.80722	D	1	P;D;D	0.76494	0.902;0.999;0.999	P;D;D	0.79784	0.701;0.993;0.993	D	0.91141	0.4945	10	0.59425	D	0.04	.	16.2077	0.82141	0.0:1.0:0.0:0.0	.	117;117;117	B7ZLU9;A1L4F9;Q14833	.;.;GRM4_HUMAN	K	117	ENSP00000363296:E117K;ENSP00000440556:E117K	ENSP00000363296:E117K	E	-	1	0	GRM4	34208903	1.000000	0.71417	0.990000	0.47175	0.989000	0.77384	7.512000	0.81728	2.230000	0.72887	0.467000	0.42956	GAG		0.627	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2		
ANKS1A	23294	broad.mit.edu	37	6	35047672	35047672	+	Silent	SNP	G	G	A	rs565747592		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:35047672G>A	ENST00000360359.3	+	16	2649	c.2511G>A	c.(2509-2511)ccG>ccA	p.P837P	ANKS1A_ENST00000535627.1_Intron|ANKS1A_ENST00000470698.1_3'UTR	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	837	SAM 2. {ECO:0000255|PROSITE- ProRule:PRU00184}.				ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)		p.P837P(1)		cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						ACGAGGAGCCGCCCCAGAAGC	0.572													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16753	0.0		0.0	False		,,,				2504	0.0				p.P837P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2511A	6						.						18.0	20.0	19.0					6																	35047672		2180	4278	6458	35155650	SO:0001819	synonymous_variant	23294	exon16			D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	20961	protein-coding gene	gene with protein product		608994	"""ankyrin repeat and SAM domain containing 1"", ""ankyrin repeat and sterile alpha motif domain containing 1"""	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.2511G>A	6.37:g.35047672G>A		Somatic		Capture	Illumina HiSeq	Phase_I	35155650	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Silent	SNP	ENST00000360359.3	37	CCDS4798.1																																																																																				0.572	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478	
SCUBE3	222663	broad.mit.edu	37	6	35210038	35210038	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:35210038G>A	ENST00000274938.7	+	13	1475	c.1475G>A	c.(1474-1476)tGc>tAc	p.C492Y	SCUBE3_ENST00000394681.1_Missense_Mutation_p.C508Y	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3									p.C492Y(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						GATGCCAAATGCCGTTTGCAC	0.542																																					p.C492Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1475A	6						.						131.0	127.0	129.0					6																	35210038		2203	4300	6503	35318016	SO:0001583	missense	222663	exon13			AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"""CUB domain and EGF-like repeat containing 3"""	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.1475G>A	6.37:g.35210038G>A	ENSP00000274938:p.Cys492Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	35318016	NM_152753		Missense_Mutation	SNP	ENST00000274938.7	37	CCDS4800.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.780808	0.70222	.	.	ENSG00000146197	ENST00000394681;ENST00000274938	D;D	0.85258	-1.61;-1.96	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	D	0.91327	0.7265	M	0.73962	2.25	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.991	D	0.92196	0.5764	10	0.87932	D	0	.	18.6036	0.91257	0.0:0.0:1.0:0.0	.	508;492	Q8IX30-2;Q8IX30	.;SCUB3_HUMAN	Y	508;492	ENSP00000378174:C508Y;ENSP00000274938:C492Y	ENSP00000274938:C492Y	C	+	2	0	SCUBE3	35318016	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.325000	0.79124	2.466000	0.83321	0.650000	0.86243	TGC		0.542	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040275.1	NM_152753	
SCUBE3	222663	broad.mit.edu	37	6	35211800	35211800	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:35211800G>A	ENST00000274938.7	+	17	2132	c.2132G>A	c.(2131-2133)cGt>cAt	p.R711H	SCUBE3_ENST00000394681.1_Missense_Mutation_p.R727H	NM_152753.2	NP_689966.2			signal peptide, CUB domain, EGF-like 3									p.R711H(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(12)|lung(11)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	37						CCATGCCCACGTGGCACCTAC	0.582																																					p.R711H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2132A	6						.						141.0	114.0	123.0					6																	35211800		2203	4300	6503	35319778	SO:0001583	missense	222663	exon17			AF452494.1	CCDS4800.1	6p21.3	2008-02-05	2004-05-19	2004-05-21		ENSG00000146197			13655	protein-coding gene	gene with protein product		614708	"""CUB domain and EGF-like repeat containing 3"""	CEGF3		12270931	Standard	NM_152753		Approved	FLJ34743	uc003okf.1	Q8IX30		ENST00000274938.7:c.2132G>A	6.37:g.35211800G>A	ENSP00000274938:p.Arg711His	Somatic		Capture	Illumina HiSeq	Phase_I	35319778	NM_152753		Missense_Mutation	SNP	ENST00000274938.7	37	CCDS4800.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.708516	0.48517	.	.	ENSG00000146197	ENST00000394681;ENST00000274938	T;T	0.17528	2.27;2.27	5.75	5.75	0.90469	Tyrosine-protein kinase ephrin type A/B receptor-like (1);Growth factor, receptor (1);	0.176759	0.52532	D	0.000080	T	0.20170	0.0485	M	0.67625	2.065	0.48087	D	0.999589	D;D	0.59767	0.983;0.986	P;P	0.55667	0.674;0.781	T	0.02751	-1.1115	10	0.15952	T	0.53	.	14.7486	0.69508	0.0:0.0:0.8554:0.1446	.	727;711	Q8IX30-2;Q8IX30	.;SCUB3_HUMAN	H	727;711	ENSP00000378174:R727H;ENSP00000274938:R711H	ENSP00000274938:R711H	R	+	2	0	SCUBE3	35319778	0.952000	0.32445	0.975000	0.42487	0.995000	0.86356	1.886000	0.39688	2.719000	0.93026	0.655000	0.94253	CGT		0.582	SCUBE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040275.1	NM_152753	
SRPK1	6732	broad.mit.edu	37	6	35842021	35842021	+	Frame_Shift_Del	DEL	T	T	-	rs34144793		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:35842021delT	ENST00000373825.2	-	7	859	c.574delA	c.(574-576)attfs	p.I193fs	SRPK1_ENST00000373821.2_5'UTR|SRPK1_ENST00000423325.2_Frame_Shift_Del_p.I177fs|SRPK1_ENST00000373822.1_Frame_Shift_Del_p.I86fs					SRSF protein kinase 1									p.I192fs*32(1)		endometrium(2)|large_intestine(10)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21						TGCTGAATAATTTTTTTGACA	0.353																																					p.I192fs	NSCLC(31;67 978 16289 24856 26454)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.574delA	6						.						89.0	83.0	85.0					6																	35842021		1843	4098	5941	35949999	SO:0001589	frameshift_variant	6732	exon7			U09564	CCDS47415.1	6p21.31	2010-06-23	2010-06-23		ENSG00000096063	ENSG00000096063			11305	protein-coding gene	gene with protein product	"""SR protein kinase 1"", ""serine/arginine-rich splicing factor kinase 1"""	601939	"""SFRS protein kinase 1"""			8208298, 10198174	Standard	NM_003137		Approved	SFRSK1	uc003olj.3	Q96SB4	OTTHUMG00000014583	ENST00000373825.2:c.574delA	6.37:g.35842021delT	ENSP00000362931:p.Ile193fs	Somatic		Capture	Illumina HiSeq	Phase_I	35949999	NM_003137		Frame_Shift_Del	DEL	ENST00000373825.2	37	CCDS47415.1																																																																																				0.353	SRPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040319.3	NM_003137	
PIM1	5292	broad.mit.edu	37	6	37140804	37140804	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:37140804C>T	ENST00000373509.5	+	5	1013	c.640C>T	c.(640-642)Cgc>Tgc	p.R214C	PIM1_ENST00000468243.1_3'UTR	NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	305	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|hyaluronan metabolic process (GO:0030212)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|ribosomal small subunit binding (GO:0043024)|transcription factor binding (GO:0008134)	p.R214C(2)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(17)|large_intestine(4)|lung(3)|prostate(2)|skin(2)	30			OV - Ovarian serous cystadenocarcinoma(102;0.241)		Adenosine monophosphate(DB00131)	AGAGTGGATCCGCTACCATCG	0.517			T	BCL6	NHL																																p.R214C			Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C640T	6						.						103.0	96.0	99.0					6																	37140804		2203	4300	6503	37248782	SO:0001583	missense	5292	exon5				CCDS4830.1	6p21	2014-06-25	2014-06-25		ENSG00000137193	ENSG00000137193			8986	protein-coding gene	gene with protein product		164960	"""pim-1 oncogene"""	PIM			Standard	NM_002648		Approved		uc003onk.3	P11309	OTTHUMG00000016426	ENST00000373509.5:c.640C>T	6.37:g.37140804C>T	ENSP00000362608:p.Arg214Cys	Somatic		Capture	Illumina HiSeq	Phase_I	37248782	NM_002648	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.172932	0.78452	.	.	ENSG00000137193	ENST00000373509	T	0.67523	-0.27	5.35	5.35	0.76521	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.205047	0.42548	N	0.000698	T	0.70360	0.3215	M	0.67953	2.075	0.48632	D	0.999685	D	0.76494	0.999	P	0.61722	0.893	T	0.68561	-0.5376	10	0.33940	T	0.23	.	13.195	0.59732	0.1597:0.8403:0.0:0.0	.	305	P11309	PIM1_HUMAN	C	214	ENSP00000362608:R214C	ENSP00000362608:R214C	R	+	1	0	PIM1	37248782	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.035000	0.49759	2.660000	0.90430	0.591000	0.81541	CGC		0.517	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		
TBC1D22B	55633	broad.mit.edu	37	6	37284922	37284922	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:37284922C>T	ENST00000373491.3	+	12	1475	c.1329C>T	c.(1327-1329)taC>taT	p.Y443Y		NM_017772.2	NP_060242.2	Q9NU19	TB22B_HUMAN	TBC1 domain family, member 22B	443							Rab GTPase activator activity (GO:0005097)	p.Y443Y(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(10)|prostate(1)	15			OV - Ovarian serous cystadenocarcinoma(102;0.241)			TTCATCTCTACGTGTGTGCAG	0.488																																					p.Y443Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1329T	6						.						108.0	88.0	95.0					6																	37284922		2202	4299	6501	37392900	SO:0001819	synonymous_variant	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.1329C>T	6.37:g.37284922C>T		Somatic		Capture	Illumina HiSeq	Phase_I	37392900	NM_017772	A8KA28|Q32MQ8|Q5VUK9|Q6P4C3|Q7Z6P7|Q9BPV6|Q9BUT5|Q9NXB6	Silent	SNP	ENST00000373491.3	37	CCDS4832.1																																																																																				0.488	TBC1D22B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040402.1	NM_017772	
MDGA1	266727	broad.mit.edu	37	6	37623625	37623625	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:37623625G>A	ENST00000434837.3	-	4	1608	c.430C>T	c.(430-432)Cga>Tga	p.R144*	MDGA1_ENST00000505425.1_Nonsense_Mutation_p.R144*|MDGA1_ENST00000297153.7_Nonsense_Mutation_p.R144*	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	144	Ig-like 2.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)		p.R144*(1)		central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						AAGTTGCCTCGCACATCGCTC	0.607																																					p.R144X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C430T	6						.						46.0	48.0	47.0					6																	37623625		2125	4222	6347	37731603	SO:0001587	stop_gained	266727	exon4			AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.430C>T	6.37:g.37623625G>A	ENSP00000402584:p.Arg144*	Somatic		Capture	Illumina HiSeq	Phase_I	37731603	NM_153487	A6NHG0|Q8NBE3	Nonsense_Mutation	SNP	ENST00000434837.3	37	CCDS47417.1	.	.	.	.	.	.	.	.	.	.	G	46	12.517085	0.99674	.	.	ENSG00000112139	ENST00000434837;ENST00000297153;ENST00000505425;ENST00000515437	.	.	.	5.8	4.92	0.64577	.	0.000000	0.42821	D	0.000658	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	15.3632	0.74499	0.0:0.0:0.8595:0.1405	.	.	.	.	X	144;144;144;88	.	ENSP00000297153:R144X	R	-	1	2	MDGA1	37731603	0.964000	0.33143	0.708000	0.30435	0.691000	0.40173	2.602000	0.46257	1.443000	0.47586	0.655000	0.94253	CGA		0.607	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		
MDGA1	266727	broad.mit.edu	37	6	37626132	37626132	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:37626132C>T	ENST00000434837.3	-	3	1449	c.271G>A	c.(271-273)Gag>Aag	p.E91K	MDGA1_ENST00000505425.1_Missense_Mutation_p.E91K|MDGA1_ENST00000297153.7_Missense_Mutation_p.E91K	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	91	Ig-like 1.				brain development (GO:0007420)|cerebral cortex radially oriented cell migration (GO:0021799)|neuron migration (GO:0001764)|spinal cord association neuron differentiation (GO:0021527)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)		p.E91K(1)		central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	38						CGCAGCGTCTCGTTGAACACC	0.647																																					p.E91K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G271A	6						.						82.0	91.0	88.0					6																	37626132		2128	4224	6352	37734110	SO:0001583	missense	266727	exon3			AF478693	CCDS47417.1	6p21	2013-01-29			ENSG00000112139	ENSG00000112139		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19267	protein-coding gene	gene with protein product		609626				15922729, 15019943	Standard	NM_153487		Approved	GPIM, MAMDC3	uc003onu.1	Q8NFP4	OTTHUMG00000014626	ENST00000434837.3:c.271G>A	6.37:g.37626132C>T	ENSP00000402584:p.Glu91Lys	Somatic		Capture	Illumina HiSeq	Phase_I	37734110	NM_153487	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	37	CCDS47417.1	.	.	.	.	.	.	.	.	.	.	C	36	5.972529	0.97162	.	.	ENSG00000112139	ENST00000434837;ENST00000297153;ENST00000505425;ENST00000515437;ENST00000508399	T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22	5.07	5.07	0.68467	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.49916	D	0.000134	T	0.64649	0.2617	N	0.20986	0.625	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.64076	-0.6492	10	0.32370	T	0.25	.	17.8109	0.88616	0.0:1.0:0.0:0.0	.	91	Q8NFP4	MDGA1_HUMAN	K	91;91;91;35;35	ENSP00000402584:E91K;ENSP00000297153:E91K;ENSP00000422042:E91K;ENSP00000421510:E35K;ENSP00000427645:E35K	ENSP00000297153:E91K	E	-	1	0	MDGA1	37734110	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	6.090000	0.71397	2.515000	0.84797	0.655000	0.94253	GAG		0.647	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3		
DNAH8	1769	broad.mit.edu	37	6	38879249	38879249	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:38879249G>A	ENST00000359357.3	+	64	9349	c.9095G>A	c.(9094-9096)cGc>cAc	p.R3032H	DNAH8_ENST00000441566.1_Missense_Mutation_p.R2996H|DNAH8_ENST00000449981.2_Missense_Mutation_p.R3249H			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3032	AAA 4. {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.R3032H(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						TTCAGATACCGCCGAAGAGCA	0.378																																					p.R3032H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G9095A	6						.						85.0	81.0	82.0					6																	38879249		2203	4300	6503	38987227	SO:0001583	missense	1769	exon64			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.9095G>A	6.37:g.38879249G>A	ENSP00000352312:p.Arg3032His	Somatic		Capture	Illumina HiSeq	Phase_I	38987227	NM_001371	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		.	.	.	.	.	.	.	.	.	.	G	33	5.215243	0.95104	.	.	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.51071	0.72;0.72;0.72	5.65	5.65	0.86999	Dynein heavy chain, P-loop containing D4 domain (1);	0.000000	0.85682	D	0.000000	T	0.75079	0.3801	M	0.93507	3.425	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81540	-0.0886	10	0.87932	D	0	.	19.3425	0.94349	0.0:0.0:1.0:0.0	.	3032	Q96JB1	DYH8_HUMAN	H	3237;3237;3032;2996	ENSP00000333363:R3237H;ENSP00000352312:R3032H;ENSP00000402294:R2996H	ENSP00000333363:R3237H	R	+	2	0	DNAH8	38987227	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.166000	0.94766	2.680000	0.91292	0.467000	0.42956	CGC		0.378	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
KCNK5	8645	broad.mit.edu	37	6	39158873	39158873	+	Silent	SNP	G	G	A	rs144931567		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:39158873G>A	ENST00000359534.3	-	5	1631	c.1293C>T	c.(1291-1293)gaC>gaT	p.D431D		NM_003740.3	NP_003731.1	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	431					excretion (GO:0007588)|potassium ion transport (GO:0006813)	integral component of plasma membrane (GO:0005887)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.D431D(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(4)|skin(3)	19						AGGTCTCCTCGTCTGAGAGGC	0.632																																					p.D431D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1293T	6						.	G		1,4405	2.1+/-5.4	0,1,2202	56.0	54.0	55.0		1293	-9.9	0.0	6	dbSNP_134	55	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KCNK5	NM_003740.3		0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231		431/500	39158873	3,13003	2203	4300	6503	39266851	SO:0001819	synonymous_variant	8645	exon5			AF084830	CCDS4841.1	6p21	2012-03-07			ENSG00000164626	ENSG00000164626		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6280	protein-coding gene	gene with protein product		603493				9812978, 16382106	Standard	XM_005249456		Approved	K2p5.1, TASK-2	uc003oon.3	O95279	OTTHUMG00000014642	ENST00000359534.3:c.1293C>T	6.37:g.39158873G>A		Somatic		Capture	Illumina HiSeq	Phase_I	39266851	NM_003740	B2RAQ6|B5TJL2|Q5VV76	Silent	SNP	ENST00000359534.3	37	CCDS4841.1																																																																																				0.632	KCNK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040449.1	NM_003740	
KCNK5	8645	broad.mit.edu	37	6	39159217	39159217	+	Missense_Mutation	SNP	C	C	T	rs142417837		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:39159217C>T	ENST00000359534.3	-	5	1287	c.949G>A	c.(949-951)Ggg>Agg	p.G317R		NM_003740.3	NP_003731.1	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	317					excretion (GO:0007588)|potassium ion transport (GO:0006813)	integral component of plasma membrane (GO:0005887)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.G317W(1)|p.G317R(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(4)|skin(3)	19						TCCCCACCCCCGCTTGTCTTC	0.607																																					p.G317R												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G949A	6						.	C	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	82.0	87.0	85.0		949	3.0	0.0	6	dbSNP_134	85	0,8600		0,0,4300	no	missense	KCNK5	NM_003740.3	125	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	317/500	39159217	1,13005	2203	4300	6503	39267195	SO:0001583	missense	8645	exon5			AF084830	CCDS4841.1	6p21	2012-03-07			ENSG00000164626	ENSG00000164626		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6280	protein-coding gene	gene with protein product		603493				9812978, 16382106	Standard	XM_005249456		Approved	K2p5.1, TASK-2	uc003oon.3	O95279	OTTHUMG00000014642	ENST00000359534.3:c.949G>A	6.37:g.39159217C>T	ENSP00000352527:p.Gly317Arg	Somatic		Capture	Illumina HiSeq	Phase_I	39267195	NM_003740	B2RAQ6|B5TJL2|Q5VV76	Missense_Mutation	SNP	ENST00000359534.3	37	CCDS4841.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.671061	0.29693	2.27E-4	0.0	ENSG00000164626	ENST00000359534	T	0.20069	2.1	5.8	3.05	0.35203	.	3.767860	0.00357	N	0.000031	T	0.04861	0.0131	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24119	-1.0169	10	0.23891	T	0.37	.	4.9749	0.14135	0.0:0.4987:0.1438:0.3575	.	317	O95279	KCNK5_HUMAN	R	317	ENSP00000352527:G317R	ENSP00000352527:G317R	G	-	1	0	KCNK5	39267195	0.008000	0.16893	0.001000	0.08648	0.892000	0.51952	1.291000	0.33330	0.370000	0.24538	-0.140000	0.14226	GGG		0.607	KCNK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040449.1	NM_003740	
DAAM2	23500	broad.mit.edu	37	6	39846264	39846264	+	Missense_Mutation	SNP	C	C	T	rs192352327		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:39846264C>T	ENST00000398904.2	+	13	1627	c.1445C>T	c.(1444-1446)aCg>aTg	p.T482M	DAAM2_ENST00000538976.1_Missense_Mutation_p.T482M|DAAM2_ENST00000274867.4_Missense_Mutation_p.T482M			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	482					actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)			p.T482M(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)					ATGATGCGGACGCTGAACAAA	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		20037	0.001		0.0	False		,,,				2504	0.0				p.T482M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1445T	6						.	C	MET/THR,MET/THR	0,4076		0,0,2038	43.0	50.0	48.0		1445,1445	5.6	1.0	6		48	1,8385		0,1,4192	no	missense,missense	DAAM2	NM_001201427.1,NM_015345.3	81,81	0,1,6230	TT,TC,CC		0.0119,0.0,0.0080	probably-damaging,probably-damaging	482/1069,482/1068	39846264	1,12461	2038	4193	6231	39954242	SO:0001583	missense	23500	exon13			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.1445C>T	6.37:g.39846264C>T	ENSP00000381876:p.Thr482Met	Somatic		Capture	Illumina HiSeq	Phase_I	39954242	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	32	5.125941	0.94429	0.0	1.19E-4	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	D;D;D	0.90676	-2.71;-2.71;-2.71	5.59	5.59	0.84812	.	0.108387	0.64402	D	0.000007	D	0.92639	0.7661	M	0.62723	1.935	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.58077	0.832;0.683	D	0.92360	0.5896	10	0.54805	T	0.06	.	19.1807	0.93622	0.0:1.0:0.0:0.0	.	482;482	G5EA45;Q86T65	.;DAAM2_HUMAN	M	482	ENSP00000274867:T482M;ENSP00000381876:T482M;ENSP00000437808:T482M	ENSP00000274867:T482M	T	+	2	0	DAAM2	39954242	1.000000	0.71417	0.970000	0.41538	0.980000	0.70556	7.776000	0.85560	2.621000	0.88768	0.650000	0.86243	ACG		0.582	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
DAAM2	23500	broad.mit.edu	37	6	39859183	39859183	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:39859183C>T	ENST00000398904.2	+	18	2394	c.2212C>T	c.(2212-2214)Cgg>Tgg	p.R738W	RP11-61I13.3_ENST00000420293.1_RNA|RP11-61I13.3_ENST00000606829.1_RNA|DAAM2_ENST00000538976.1_Missense_Mutation_p.R738W|RP11-61I13.3_ENST00000607675.1_RNA|RP11-61I13.3_ENST00000430595.1_RNA|DAAM2_ENST00000274867.4_Missense_Mutation_p.R738W			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	738	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)			p.R738W(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)					TGAAATTGAGCGGATGGCCCG	0.562																																					p.R738W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2212T	6						.						49.0	48.0	48.0					6																	39859183		2030	4184	6214	39967161	SO:0001583	missense	23500	exon18			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.2212C>T	6.37:g.39859183C>T	ENSP00000381876:p.Arg738Trp	Somatic		Capture	Illumina HiSeq	Phase_I	39967161	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.146644	0.77888	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.18174	2.23;2.23;2.23	5.41	3.57	0.40892	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.000000	0.85682	D	0.000000	T	0.34745	0.0908	M	0.85373	2.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.985;0.996	T	0.41070	-0.9529	10	0.72032	D	0.01	.	13.6394	0.62241	0.2808:0.7192:0.0:0.0	.	738;738	G5EA45;Q86T65	.;DAAM2_HUMAN	W	738	ENSP00000274867:R738W;ENSP00000381876:R738W;ENSP00000437808:R738W	ENSP00000274867:R738W	R	+	1	2	DAAM2	39967161	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	2.395000	0.44459	0.777000	0.33496	0.563000	0.77884	CGG		0.562	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
TFEB	7942	broad.mit.edu	37	6	41658482	41658482	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:41658482G>A	ENST00000230323.4	-	4	688	c.387C>T	c.(385-387)caC>caT	p.H129H	TFEB_ENST00000373033.1_Silent_p.H129H|TFEB_ENST00000358871.2_Silent_p.H143H|TFEB_ENST00000394283.1_Silent_p.H129H|TFEB_ENST00000403298.4_Silent_p.H129H|TFEB_ENST00000420312.1_Intron	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB	129				GSPKPPPAASPGVRAGHVLSSSAGNSAPN -> ALRNPHQP PPQGCELDTCCPPPLATVLPI (in Ref. 1; AAA36730). {ECO:0000305}.	autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.H129H(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			AGGACAGCACGTGTCCAGCTC	0.637			T	ALPHA	renal (childhood epithelioid)																																p.H129H			Dom	yes		6	6p21	7942	transcription factor EB		"""E,M"""	.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C387T	6						.						48.0	49.0	48.0					6																	41658482		2203	4300	6503	41766460	SO:0001819	synonymous_variant	7942	exon4			M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"""Basic helix-loop-helix proteins"""	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.387C>T	6.37:g.41658482G>A		Somatic		Capture	Illumina HiSeq	Phase_I	41766460	NM_007162	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Missense_Mutation	SNP	ENST00000230323.4	37	CCDS4858.1																																																																																				0.637	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3		
UBR2	23304	broad.mit.edu	37	6	42582835	42582835	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:42582835G>T	ENST00000372899.1	+	9	1270	c.1012G>T	c.(1012-1014)Gtt>Ttt	p.V338F	UBR2_ENST00000372903.2_Missense_Mutation_p.V338F|UBR2_ENST00000372901.1_Missense_Mutation_p.V338F|UBR2_ENST00000372883.3_5'Flank	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	338					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.V338F(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TTTATGTCAAGTTGGTTTACA	0.358																																					p.V338F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1012T	6						.						134.0	136.0	135.0					6																	42582835		2203	4300	6503	42690813	SO:0001583	missense	23304	exon9			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.1012G>T	6.37:g.42582835G>T	ENSP00000361990:p.Val338Phe	Somatic		Capture	Illumina HiSeq	Phase_I	42690813	NM_001184801	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	.	.	.	.	.	.	.	.	.	.	G	33	5.248891	0.95305	.	.	ENSG00000024048	ENST00000372903;ENST00000372899;ENST00000372901	T;T;T	0.73469	-0.75;0.26;0.26	5.81	5.81	0.92471	.	0.062472	0.64402	D	0.000006	D	0.83101	0.5181	M	0.66939	2.045	0.80722	D	1	D;D	0.65815	0.992;0.995	D;D	0.69654	0.923;0.965	T	0.82045	-0.0652	10	0.51188	T	0.08	0.1583	20.0804	0.97772	0.0:0.0:1.0:0.0	.	338;338	Q8IWV8;Q8IWV8-2	UBR2_HUMAN;.	F	338	ENSP00000361994:V338F;ENSP00000361990:V338F;ENSP00000361992:V338F	ENSP00000361990:V338F	V	+	1	0	UBR2	42690813	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.357000	0.97099	2.738000	0.93877	0.655000	0.94253	GTT		0.358	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
KLC4	89953	broad.mit.edu	37	6	43039985	43039985	+	Missense_Mutation	SNP	C	C	T	rs368025562		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:43039985C>T	ENST00000394056.2	+	13	1975	c.1480C>T	c.(1480-1482)Cgg>Tgg	p.R494W	KLC4_ENST00000259708.3_Missense_Mutation_p.R512W|KLC4_ENST00000453940.2_Missense_Mutation_p.R417W|RP11-387M24.5_ENST00000606123.1_RNA|KLC4_ENST00000394058.1_Missense_Mutation_p.R494W|KLC4_ENST00000347162.5_Missense_Mutation_p.R494W|KLC4_ENST00000479388.1_Missense_Mutation_p.R494W			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	494						cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)	p.R494W(1)		endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			CCTGCGGTCCCGGAGACAGGT	0.592													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17352	0.0		0.0	False		,,,				2504	0.0				p.R494W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1480T	6						.	C	TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	47.0	52.0	50.0		1480,1480,1534	3.1	1.0	6		50	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	KLC4	NM_201521.1,NM_201522.1,NM_201523.1	101,101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	494/620,494/620,512/638	43039985	1,13005	2203	4300	6503	43147963	SO:0001583	missense	89953	exon12			AK055293	CCDS4882.1, CCDS4883.1, CCDS47429.1, CCDS75459.1	6p21.1	2013-01-10	2005-09-13	2005-09-13	ENSG00000137171	ENSG00000137171		"""Tetratricopeptide (TTC) repeat domain containing"""	21624	protein-coding gene	gene with protein product			"""kinesin-like 8"""	KNSL8			Standard	NM_001289034		Approved	bA387M24.3	uc003otw.1	Q9NSK0	OTTHUMG00000014720	ENST00000394056.2:c.1480C>T	6.37:g.43039985C>T	ENSP00000377620:p.Arg494Trp	Somatic		Capture	Illumina HiSeq	Phase_I	43147963	NM_201521	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Missense_Mutation	SNP	ENST00000394056.2	37	CCDS4883.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.064817	0.76187	0.0	1.16E-4	ENSG00000137171	ENST00000347162;ENST00000453940;ENST00000259708;ENST00000479388;ENST00000394056;ENST00000394058	T;T;T;T;T;T	0.79940	-1.3;-1.32;-1.32;-1.3;-1.3;-1.3	6.04	3.07	0.35406	.	0.231402	0.30714	N	0.009023	D	0.84220	0.5424	M	0.77103	2.36	0.58432	D	0.999994	D;B;B	0.89917	1.0;0.021;0.026	D;B;B	0.91635	0.999;0.007;0.013	D	0.84659	0.0705	10	0.59425	D	0.04	-19.7747	9.1552	0.36988	0.3588:0.5729:0.0:0.0683	.	417;512;494	B4DME9;Q9NSK0-3;Q9NSK0	.;.;KLC4_HUMAN	W	494;417;512;494;494;494	ENSP00000340221:R494W;ENSP00000395806:R417W;ENSP00000259708:R512W;ENSP00000418031:R494W;ENSP00000377620:R494W;ENSP00000377622:R494W	ENSP00000259708:R512W	R	+	1	2	KLC4	43147963	1.000000	0.71417	1.000000	0.80357	0.720000	0.41350	1.197000	0.32211	0.794000	0.33899	-0.367000	0.07326	CGG		0.592	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343	
PTK7	5754	broad.mit.edu	37	6	43127543	43127543	+	Missense_Mutation	SNP	G	G	A	rs146766128		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:43127543G>A	ENST00000230419.4	+	19	3112	c.2891G>A	c.(2890-2892)cGc>cAc	p.R964H	PTK7_ENST00000349241.2_Missense_Mutation_p.R834H|PTK7_ENST00000481273.1_Missense_Mutation_p.R972H|PTK7_ENST00000352931.2_Missense_Mutation_p.R908H|PTK7_ENST00000345201.2_Missense_Mutation_p.R924H	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	964	Interaction with CTNNB1.|Protein kinase; inactive. {ECO:0000255|PROSITE-ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.R964H(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			TACCACTTCCGCCAGGCCTGG	0.637																																					p.R924H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2771A	6						.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	71.0	59.0	63.0		2891,2771,2501,2723	4.7	1.0	6	dbSNP_134	63	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense,missense	PTK7	NM_002821.3,NM_152880.2,NM_152881.2,NM_152882.2	29,29,29,29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	964/1071,924/1031,834/941,908/1015	43127543	2,13004	2203	4300	6503	43235521	SO:0001583	missense	5754	exon18			AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9618	protein-coding gene	gene with protein product		601890	"""PTK7 protein tyrosine kinase 7"""			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.2891G>A	6.37:g.43127543G>A	ENSP00000230419:p.Arg964His	Somatic		Capture	Illumina HiSeq	Phase_I	43235521	NM_152880	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Missense_Mutation	SNP	ENST00000230419.4	37	CCDS4884.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.16|17.16	3.317746|3.317746	0.60524|0.60524	0.0|0.0	2.33E-4|2.33E-4	ENSG00000112655|ENSG00000112655	ENST00000489707|ENST00000230419;ENST00000325774;ENST00000349241;ENST00000352931;ENST00000345201;ENST00000481273;ENST00000473339	.|D;D;D;D;D;D	.|0.82893	.|-1.66;-1.66;-1.66;-1.66;-1.66;-1.66	5.59|5.59	4.72|4.72	0.59763|0.59763	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.77315|0.77315	0.4112|0.4112	L|L	0.48174|0.48174	1.505|1.505	0.80722|0.80722	D|D	1|1	.|B;B;D;B;B;B;B	.|0.61697	.|0.123;0.219;0.99;0.183;0.029;0.122;0.1	.|B;B;P;B;B;B;B	.|0.54629	.|0.052;0.034;0.757;0.096;0.014;0.032;0.024	T|T	0.76558|0.76558	-0.2915|-0.2915	5|10	.|0.31617	.|T	.|0.26	.|.	10.4693|10.4693	0.44626|0.44626	0.0694:0.0:0.7953:0.1353|0.0694:0.0:0.7953:0.1353	.|.	.|972;290;309;834;924;908;964	.|E9PFZ5;F8W9X8;B3KP36;Q13308-3;Q13308-2;Q13308-4;Q13308	.|.;.;.;.;.;.;PTK7_HUMAN	T|H	259|964;290;834;908;924;972;232	.|ENSP00000230419:R964H;ENSP00000325462:R834H;ENSP00000326029:R908H;ENSP00000325992:R924H;ENSP00000418754:R972H;ENSP00000420186:R232H	.|ENSP00000230419:R964H	A|R	+|+	1|2	0|0	PTK7|PTK7	43235521|43235521	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.770000|7.770000	0.85390|0.85390	1.479000|1.479000	0.48272|0.48272	0.591000|0.591000	0.81541|0.81541	GCC|CGC		0.637	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2		
ZNF318	24149	broad.mit.edu	37	6	43323232	43323232	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:43323232G>A	ENST00000361428.2	-	4	1917	c.1840C>T	c.(1840-1842)Cgc>Tgc	p.R614C	ZNF318_ENST00000318149.3_Missense_Mutation_p.R614C	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	614					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R614C(1)		autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			TCCTGGGTGCGTGCAGCCAAT	0.488																																					p.R614C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1840T	6						.						155.0	144.0	148.0					6																	43323232		2203	4300	6503	43431210	SO:0001583	missense	24149	exon4			AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"""Zinc fingers, C2H2-type"""	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.1840C>T	6.37:g.43323232G>A	ENSP00000354964:p.Arg614Cys	Somatic		Capture	Illumina HiSeq	Phase_I	43431210	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Missense_Mutation	SNP	ENST00000361428.2	37	CCDS4895.2	.	.	.	.	.	.	.	.	.	.	G	17.62	3.434680	0.62955	.	.	ENSG00000171467	ENST00000318149;ENST00000361428	T;T	0.03441	3.93;3.93	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.08802	0.0218	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.22800	-1.0206	10	0.87932	D	0	-8.3234	20.8794	0.99867	0.0:0.0:1.0:0.0	.	614	Q5VUA4	ZN318_HUMAN	C	614	ENSP00000323032:R614C;ENSP00000354964:R614C	ENSP00000323032:R614C	R	-	1	0	ZNF318	43431210	1.000000	0.71417	0.681000	0.30009	0.965000	0.64279	5.505000	0.66981	2.941000	0.99782	0.655000	0.94253	CGC		0.488	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	
ABCC10	89845	broad.mit.edu	37	6	43399923	43399923	+	Nonsense_Mutation	SNP	C	C	T	rs142310490	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:43399923C>T	ENST00000372530.4	+	3	420	c.205C>T	c.(205-207)Cga>Tga	p.R69*	ABCC10_ENST00000244533.3_Nonsense_Mutation_p.R26*|ABCC10_ENST00000443426.2_Intron	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	69					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.R26*(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	ATGGCGCCTCCGACTTGCAGC	0.592																																					p.R69X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C205T	6						.	C	stop/ARG,stop/ARG	2,4404	4.2+/-10.8	0,2,2201	130.0	111.0	117.0		205,76	3.9	1.0	6	dbSNP_134	117	0,8600		0,0,4300	no	stop-gained,stop-gained	ABCC10	NM_001198934.1,NM_033450.2	,	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	,	69/1493,26/1465	43399923	2,13004	2203	4300	6503	43507901	SO:0001587	stop_gained	89845	exon3			U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"""ATP binding cassette transporters / subfamily C"""	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.205C>T	6.37:g.43399923C>T	ENSP00000361608:p.Arg69*	Somatic		Capture	Illumina HiSeq	Phase_I	43507901	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Nonsense_Mutation	SNP	ENST00000372530.4	37	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.913859	0.92178	4.54E-4	0.0	ENSG00000124574	ENST00000372530;ENST00000244533	.	.	.	5.79	3.87	0.44632	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-32.8736	12.5822	0.56397	0.5186:0.4814:0.0:0.0	.	.	.	.	X	69;26	.	ENSP00000244533:R26X	R	+	1	2	ABCC10	43507901	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	2.606000	0.46291	1.419000	0.47118	0.561000	0.74099	CGA		0.592	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
GTPBP2	54676	broad.mit.edu	37	6	43592282	43592282	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:43592282G>A	ENST00000307126.5	-	7	1064	c.1065C>T	c.(1063-1065)gcC>gcT	p.A355A	GTPBP2_ENST00000307114.7_Silent_p.A267A|GTPBP2_ENST00000476510.1_5'UTR	NM_019096.3	NP_061969.3			GTP binding protein 2									p.A355A(2)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000501)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			CAGCAGTGACGGCATCATCCT	0.602																																					p.A355A	GBM(116;405 1620 28302 32150 44768)											.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C1065T	6						.						63.0	51.0	55.0					6																	43592282		2203	4300	6503	43700260	SO:0001819	synonymous_variant	54676	exon7			AB024574	CCDS4903.1, CCDS69124.1	6p21	2008-07-28			ENSG00000172432	ENSG00000172432			4670	protein-coding gene	gene with protein product		607434				10833435, 11054535	Standard	NM_019096		Approved		uc003ovs.3	Q9BX10	OTTHUMG00000014744	ENST00000307126.5:c.1065C>T	6.37:g.43592282G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43700260	NM_019096		Silent	SNP	ENST00000307126.5	37	CCDS4903.1																																																																																				0.602	GTPBP2-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040679.1		
RSPH9	221421	broad.mit.edu	37	6	43613043	43613043	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:43613043C>T	ENST00000372163.4	+	1	261	c.208C>T	c.(208-210)Ccg>Tcg	p.P70S	RSPH9_ENST00000372165.4_Missense_Mutation_p.P70S	NM_152732.4	NP_689945.2	Q9H1X1	RSPH9_HUMAN	radial spoke head 9 homolog (Chlamydomonas)	70					axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)		p.P70S(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						CCAGCTCGCACCGCGCAAGAC	0.662									Kartagener syndrome																												p.P70S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C208T	6						.						31.0	32.0	31.0					6																	43613043		2194	4274	6468	43721021	SO:0001583	missense	221421	exon1	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AK055407	CCDS4905.1, CCDS55005.1	6p21.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000172426	ENSG00000172426			21057	protein-coding gene	gene with protein product		612648	"""mitochondrial ribosomal protein S18A-like 1"", ""chromosome 6 open reading frame 206"""	MRPS18AL1, C6orf206		19200523	Standard	NM_152732		Approved	FLJ30845, CILD12	uc003ovx.2	Q9H1X1	OTTHUMG00000014746	ENST00000372163.4:c.208C>T	6.37:g.43613043C>T	ENSP00000361236:p.Pro70Ser	Somatic		Capture	Illumina HiSeq	Phase_I	43721021	NM_001193341	A8K5T4|Q96NH9	Missense_Mutation	SNP	ENST00000372163.4	37	CCDS4905.1	.	.	.	.	.	.	.	.	.	.	c	10.45	1.354481	0.24512	.	.	ENSG00000172426	ENST00000372165;ENST00000372163;ENST00000372154	T	0.44482	0.92	4.94	4.05	0.47172	.	0.722014	0.13277	N	0.400030	T	0.13927	0.0337	L	0.32530	0.975	0.34587	D	0.715096	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.001	T	0.05550	-1.0878	10	0.13108	T	0.6	.	9.8597	0.41107	0.0:0.7246:0.2754:0.0	.	70;70	Q96NH9;Q9H1X1	.;RSPH9_HUMAN	S	70;70;38	ENSP00000361236:P70S	ENSP00000361227:P38S	P	+	1	0	RSPH9	43721021	0.812000	0.29077	1.000000	0.80357	0.618000	0.37518	2.718000	0.47236	2.269000	0.75478	0.558000	0.71614	CCG		0.662	RSPH9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040690.1	NM_152732	
TCTE1	202500	broad.mit.edu	37	6	44248038	44248038	+	Silent	SNP	G	G	A	rs149052184		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:44248038G>A	ENST00000371505.4	-	5	1508	c.1386C>T	c.(1384-1386)agC>agT	p.S462S	TMEM151B_ENST00000438774.2_Intron|TCTE1_ENST00000371504.1_Silent_p.S159S|TCTE1_ENST00000371503.3_Silent_p.S159S|RP11-444E17.6_ENST00000505802.1_Intron	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	462								p.S462S(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGAGGTACTCGCTTTCCTGGG	0.587																																					p.S462S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1386T	6						.	G		1,4405	2.1+/-5.4	0,1,2202	103.0	100.0	101.0		1386	2.5	1.0	6	dbSNP_134	101	0,8600		0,0,4300	no	coding-synonymous	TCTE1	NM_182539.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		462/502	44248038	1,13005	2203	4300	6503	44356016	SO:0001819	synonymous_variant	202500	exon5			BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.1386C>T	6.37:g.44248038G>A		Somatic		Capture	Illumina HiSeq	Phase_I	44356016	NM_182539	B4DX59|Q8IYS6	Silent	SNP	ENST00000371505.4	37	CCDS4910.1																																																																																				0.587	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539	
AARS2	57505	broad.mit.edu	37	6	44270584	44270584	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:44270584C>A	ENST00000244571.4	-	17	2321	c.2319G>T	c.(2317-2319)aaG>aaT	p.K773N	TMEM151B_ENST00000438774.2_Intron|RP11-444E17.6_ENST00000505802.1_Intron|AARS2_ENST00000491573.1_5'Flank	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial									p.K773N(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GGGTAGTGCCCTTGGAAAGCT	0.622																																					p.K773N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2319T	6						.						50.0	47.0	48.0					6																	44270584		2203	4300	6503	44378562	SO:0001583	missense	57505	exon17			AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	21022	protein-coding gene	gene with protein product	"""alanine tRNA ligase 2, mitochondrial"""	612035	"""alanyl-tRNA synthetase like"", ""alanyl-tRNA synthetase 2, mitochondrial (putative)"""	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.2319G>T	6.37:g.44270584C>A	ENSP00000244571:p.Lys773Asn	Somatic		Capture	Illumina HiSeq	Phase_I	44378562	NM_020745		Missense_Mutation	SNP	ENST00000244571.4	37	CCDS34464.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.525016	0.64747	.	.	ENSG00000124608	ENST00000244571	T	0.67171	-0.25	5.79	2.01	0.26516	Threonyl/alanyl tRNA synthetase, SAD (2);Alanyl-tRNA synthetase, class IIc, core domain (1);Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain (1);	0.268415	0.42294	D	0.000732	T	0.66479	0.2793	L	0.54863	1.705	0.51233	D	0.999913	D	0.76494	0.999	D	0.72982	0.979	T	0.68941	-0.5276	10	0.72032	D	0.01	-23.7522	9.9083	0.41390	0.0:0.6532:0.0:0.3468	.	773	Q5JTZ9	SYAM_HUMAN	N	773	ENSP00000244571:K773N	ENSP00000244571:K773N	K	-	3	2	AARS2	44378562	1.000000	0.71417	0.996000	0.52242	0.921000	0.55340	0.682000	0.25335	0.366000	0.24427	-0.137000	0.14449	AAG		0.622	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745	
RUNX2	860	broad.mit.edu	37	6	45515008	45515008	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:45515008G>A	ENST00000371438.1	+	8	1890	c.1532G>A	c.(1531-1533)gGc>gAc	p.G511D	RUNX2_ENST00000359524.5_Missense_Mutation_p.G497D|RUNX2_ENST00000576263.1_Intron|RUNX2_ENST00000541979.1_Missense_Mutation_p.G557D|RUNX2_ENST00000371432.3_Missense_Mutation_p.G475D|RUNX2_ENST00000352853.5_Missense_Mutation_p.G579D|RUNX2_ENST00000371436.6_Missense_Mutation_p.G489D|RUNX2_ENST00000465038.2_Missense_Mutation_p.G511D	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	511	Pro/Ser/Thr-rich.		G -> S (in CLCD; unknown pathological significance; dbSNP:rs11498198). {ECO:0000269|PubMed:10521292}.		BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.G579D(1)|p.G511D(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						AATTCTAGTGGCAGAATGGAT	0.448																																					p.G497D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1490A	6						.						86.0	90.0	89.0					6																	45515008		2203	4300	6503	45622986	SO:0001583	missense	860	exon7			AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.1532G>A	6.37:g.45515008G>A	ENSP00000360493:p.Gly511Asp	Somatic		Capture	Illumina HiSeq	Phase_I	45622986	NM_004348	O14614|O14615|O95181	Missense_Mutation	SNP	ENST00000371438.1	37	CCDS43467.2	.	.	.	.	.	.	.	.	.	.	G	19.39	3.818218	0.71028	.	.	ENSG00000124813	ENST00000465038;ENST00000352853;ENST00000541979;ENST00000371438;ENST00000371436;ENST00000359524;ENST00000371432	T;T;T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46;1.46;1.46	5.77	5.77	0.91146	Runx inhibition (1);	0.000000	0.85682	D	0.000000	T	0.49745	0.1575	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.995	T	0.29243	-1.0018	9	.	.	.	-8.7419	20.3626	0.98863	0.0:0.0:1.0:0.0	.	557;511;497	F6RGB9;Q13950;Q13950-2	.;RUNX2_HUMAN;.	D	511;579;557;511;489;497;475	ENSP00000420707:G511D;ENSP00000319087:G579D;ENSP00000446290:G557D;ENSP00000360493:G511D;ENSP00000360491:G489D;ENSP00000352514:G497D;ENSP00000360486:G475D	.	G	+	2	0	RUNX2	45622986	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.420000	0.97426	2.885000	0.99019	0.655000	0.94253	GGC		0.448	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348	
GPR116	221395	broad.mit.edu	37	6	46830761	46830761	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:46830761C>T	ENST00000283296.7	-	15	2351	c.2063G>A	c.(2062-2064)cGg>cAg	p.R688Q	GPR116_ENST00000265417.7_Missense_Mutation_p.R688Q|GPR116_ENST00000545669.1_Missense_Mutation_p.R117Q|GPR116_ENST00000362015.4_Missense_Mutation_p.R688Q|GPR116_ENST00000456426.2_Missense_Mutation_p.R546Q	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	688					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R688Q(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			GTTTGAGAACCGGCATAGCTT	0.512																																					p.R688Q	NSCLC(59;410 1274 8751 36715 50546)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2063A	6						.						103.0	98.0	100.0					6																	46830761		2203	4300	6503	46938720	SO:0001583	missense	221395	exon15			AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.2063G>A	6.37:g.46830761C>T	ENSP00000283296:p.Arg688Gln	Somatic		Capture	Illumina HiSeq	Phase_I	46938720	NM_001098518	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	C	6.926	0.540532	0.13250	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000545557;ENST00000265417;ENST00000545669	T;T;T;T;T	0.25912	1.83;2.22;1.82;1.83;1.77	5.33	-5.52	0.02560	.	1.071200	0.07239	N	0.863949	T	0.02156	0.0067	N	0.02315	-0.6	0.09310	N	0.999996	B;B;B;B;B	0.11235	0.0;0.0;0.002;0.004;0.002	B;B;B;B;B	0.12837	0.001;0.001;0.001;0.008;0.001	T	0.44452	-0.9327	10	0.13853	T	0.58	-0.1635	8.1152	0.30940	0.0:0.4763:0.1815:0.3423	.	117;243;688;546;688	F5GWK9;B4DTV3;E9PBS6;Q8IZF2-3;Q8IZF2	.;.;.;.;GP116_HUMAN	Q	688;688;688;546;59;688;117	ENSP00000283296:R688Q;ENSP00000354563:R688Q;ENSP00000412866:R546Q;ENSP00000265417:R688Q;ENSP00000441581:R117Q	ENSP00000265417:R688Q	R	-	2	0	GPR116	46938720	0.000000	0.05858	0.240000	0.24138	0.701000	0.40568	-2.059000	0.01393	-0.697000	0.05092	-0.290000	0.09829	CGG		0.512	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
GPR115	221393	broad.mit.edu	37	6	47680212	47680212	+	Silent	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:47680212C>A	ENST00000283303.2	+	5	678	c.420C>A	c.(418-420)ccC>ccA	p.P140P	GPR115_ENST00000371220.1_Silent_p.P197P|RN7SKP116_ENST00000516902.1_RNA|GPR115_ENST00000327753.3_Silent_p.P140P	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	140					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P140P(1)		NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						AGAACTGCCCCTTTGATTATG	0.398																																					p.P140P	GBM(22;431 510 9010 26644 32828)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C420A	6						.						153.0	144.0	147.0					6																	47680212		2203	4300	6503	47788171	SO:0001819	synonymous_variant	221393	exon5			AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"""-"", ""GPCR / Class B : Orphans"""	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.420C>A	6.37:g.47680212C>A		Somatic		Capture	Illumina HiSeq	Phase_I	47788171	NM_153838	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Silent	SNP	ENST00000283303.2	37	CCDS4922.2																																																																																				0.398	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838	
PKHD1	5314	broad.mit.edu	37	6	51524374	51524374	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:51524374G>T	ENST00000371117.3	-	61	10825	c.10550C>A	c.(10549-10551)cCc>cAc	p.P3517H		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3517					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.P3517H(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)					AACCAGAGTGGGTGGAATAAA	0.438																																					p.P3517H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C10550A	6						.						72.0	70.0	71.0					6																	51524374		2203	4300	6503	51632333	SO:0001583	missense	5314	exon61			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.10550C>A	6.37:g.51524374G>T	ENSP00000360158:p.Pro3517His	Somatic		Capture	Illumina HiSeq	Phase_I	51632333	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.261756	0.59431	.	.	ENSG00000170927	ENST00000371117	D	0.88896	-2.44	5.72	5.72	0.89469	.	0.077976	0.56097	D	0.000039	D	0.89283	0.6671	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.90661	0.4590	10	0.72032	D	0.01	.	14.0999	0.65049	0.074:0.0:0.926:0.0	.	3517	P08F94	PKHD1_HUMAN	H	3517	ENSP00000360158:P3517H	ENSP00000360158:P3517H	P	-	2	0	PKHD1	51632333	0.998000	0.40836	0.964000	0.40570	0.741000	0.42261	2.993000	0.49425	2.695000	0.91970	0.655000	0.94253	CCC		0.438	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
PKHD1	5314	broad.mit.edu	37	6	51524673	51524673	+	Silent	SNP	G	G	A	rs372394177		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:51524673G>A	ENST00000371117.3	-	61	10526	c.10251C>T	c.(10249-10251)agC>agT	p.S3417S		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3417					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.S3417S(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)					TGGCATCAGCGCTATCAAGAA	0.383																																					p.S3417S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C10251T	6						.	G		0,4406		0,0,2203	79.0	70.0	73.0		10251	3.7	0.0	6		73	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PKHD1	NM_138694.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		3417/4075	51524673	1,13005	2203	4300	6503	51632632	SO:0001819	synonymous_variant	5314	exon61			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.10251C>T	6.37:g.51524673G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51632632	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																				0.383	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
GSTA3	2940	broad.mit.edu	37	6	52767271	52767271	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:52767271T>G	ENST00000211122.3	-	4	210	c.145A>C	c.(145-147)Agt>Cgt	p.S49R	GSTA3_ENST00000370968.1_5'UTR	NM_000847.4	NP_000838.3	Q16772	GSTA3_HUMAN	glutathione S-transferase alpha 3	49	GST N-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)	p.S49R(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(2)	10	Lung NSC(77;0.0912)				Glutathione(DB00143)	AACATCAAACTCCCATCTTTA	0.368																																					p.S49R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A145C	6						.						112.0	110.0	111.0					6																	52767271		2203	4300	6503	52875230	SO:0001583	missense	2940	exon4			AF020919	CCDS4947.1	6p12.2	2012-06-21	2008-11-26		ENSG00000174156	ENSG00000174156	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4628	protein-coding gene	gene with protein product		605449	"""glutathione S-transferase A3"""			8307579, 9480897	Standard	NM_000847		Approved		uc003pbb.3	Q16772	OTTHUMG00000014865	ENST00000211122.3:c.145A>C	6.37:g.52767271T>G	ENSP00000211122:p.Ser49Arg	Somatic		Capture	Illumina HiSeq	Phase_I	52875230	NM_000847	O43468|Q068V6|Q8WWA8|Q9H415	Missense_Mutation	SNP	ENST00000211122.3	37	CCDS4947.1	.	.	.	.	.	.	.	.	.	.	T	6.097	0.386140	0.11524	.	.	ENSG00000174156	ENST00000211122	T	0.13420	2.59	4.16	-1.86	0.07760	Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (2);	0.545864	0.20028	N	0.100774	T	0.06781	0.0173	L	0.38953	1.18	0.80722	D	1	P	0.46784	0.884	P	0.55055	0.767	T	0.33523	-0.9865	10	0.22706	T	0.39	.	6.3667	0.21459	0.3564:0.0:0.3647:0.2789	.	49	Q16772	GSTA3_HUMAN	R	49	ENSP00000211122:S49R	ENSP00000211122:S49R	S	-	1	0	GSTA3	52875230	0.000000	0.05858	0.016000	0.15963	0.006000	0.05464	-3.318000	0.00514	-0.396000	0.07703	-1.511000	0.00944	AGT		0.368	GSTA3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040933.1		
LGSN	51557	broad.mit.edu	37	6	63990451	63990451	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:63990451C>T	ENST00000370657.4	-	4	1038	c.1005G>A	c.(1003-1005)gaG>gaA	p.E335E	LGSN_ENST00000370658.5_Missense_Mutation_p.S195N			Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase domain	335					glutamine biosynthetic process (GO:0006542)	plasma membrane (GO:0005886)	glutamate-ammonia ligase activity (GO:0004356)	p.E335E(1)		NS(1)|endometrium(2)|large_intestine(5)|lung(16)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TCGTGAGCTGCTCAGTTCCAG	0.483																																					p.S195N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G584A	6						.						91.0	92.0	92.0					6																	63990451		2202	4300	6502	64048410	SO:0001819	synonymous_variant	51557	exon5			AF242388	CCDS4964.1, CCDS55027.1	6q12	2013-09-19	2008-09-19	2008-09-19	ENSG00000146166	ENSG00000146166			21016	protein-coding gene	gene with protein product		611470	"""glutamate-ammonia ligase (glutamine synthetase) domain containing 1"""	GLULD1		12107412	Standard	NM_016571		Approved	LGS	uc003peh.3	Q5TDP6	OTTHUMG00000014946	ENST00000370657.4:c.1005G>A	6.37:g.63990451C>T		Somatic		Capture	Illumina HiSeq	Phase_I	64048410	NM_001143940	A1L421|Q0PVN9|Q0PVP0|Q9NYJ0	Missense_Mutation	SNP	ENST00000370657.4	37	CCDS4964.1	.	.	.	.	.	.	.	.	.	.	C	5.451	0.268316	0.10349	.	.	ENSG00000146166	ENST00000370658	T	0.23552	1.9	5.77	0.457	0.16661	.	.	.	.	.	T	0.05456	0.0144	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.42865	-0.9426	8	0.23891	T	0.37	-10.0288	10.4765	0.44667	0.0:0.5299:0.0:0.4701	.	195	Q5TDP6-2	.	N	195	ENSP00000359692:S195N	ENSP00000359692:S195N	S	-	2	0	LGSN	64048410	0.052000	0.20516	0.003000	0.11579	0.040000	0.13550	0.037000	0.13840	0.015000	0.14971	0.655000	0.94253	AGC		0.483	LGSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041076.2	NM_016571	
FAM135A	57579	broad.mit.edu	37	6	71235933	71235933	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:71235933C>T	ENST00000418814.2	+	15	3760	c.3146C>T	c.(3145-3147)aCg>aTg	p.T1049M	FAM135A_ENST00000361499.3_Missense_Mutation_p.T853M|FAM135A_ENST00000457062.2_Missense_Mutation_p.T836M|FAM135A_ENST00000505868.1_Missense_Mutation_p.T1049M|FAM135A_ENST00000370479.3_Missense_Mutation_p.T836M|FAM135A_ENST00000505769.1_Missense_Mutation_p.T629M	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1049								p.T836M(1)		breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						CAAAGCAGTACGGATATTTCT	0.393																																					p.T1049M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3146T	6						.						60.0	59.0	59.0					6																	71235933		2203	4297	6500	71292654	SO:0001583	missense	57579	exon13			AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"""KIAA1411"""	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.3146C>T	6.37:g.71235933C>T	ENSP00000410768:p.Thr1049Met	Somatic		Capture	Illumina HiSeq	Phase_I	71292654	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.455360	0.43634	.	.	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T;T	0.34275	1.63;1.62;1.37;1.62;1.6;1.57	5.85	4.98	0.66077	.	0.045950	0.85682	D	0.000000	T	0.47581	0.1453	L	0.61218	1.895	0.58432	D	0.999994	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.71870	0.975;0.944;0.944;0.975	T	0.54221	-0.8326	10	0.72032	D	0.01	.	15.1276	0.72494	0.0:0.932:0.0:0.068	.	1049;1049;853;836	Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;F135A_HUMAN;.;.	M	1049;836;629;836;853;1049	ENSP00000410768:T1049M;ENSP00000359510:T836M;ENSP00000423785:T629M;ENSP00000409201:T836M;ENSP00000354913:T853M;ENSP00000423307:T1049M	ENSP00000354913:T853M	T	+	2	0	FAM135A	71292654	0.994000	0.37717	0.667000	0.29798	0.020000	0.10135	3.186000	0.50942	1.468000	0.48064	-0.150000	0.13652	ACG		0.393	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
RIMS1	22999	broad.mit.edu	37	6	72806813	72806813	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:72806813G>A	ENST00000521978.1	+	3	407	c.407G>A	c.(406-408)cGc>cAc	p.R136H	RIMS1_ENST00000522291.1_Missense_Mutation_p.R136H|RIMS1_ENST00000517960.1_Missense_Mutation_p.R136H|RIMS1_ENST00000518273.1_Missense_Mutation_p.R136H|RIMS1_ENST00000520567.1_Missense_Mutation_p.R136H|RIMS1_ENST00000348717.5_Missense_Mutation_p.R136H|RIMS1_ENST00000264839.7_Missense_Mutation_p.R136H|RIMS1_ENST00000491071.2_Missense_Mutation_p.R136H	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	136	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.R136H(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)				TCCTATTGTCGCACTAAGTTC	0.507																																					p.R136H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G407A	6						.						85.0	88.0	87.0					6																	72806813		2088	4236	6324	72863534	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.407G>A	6.37:g.72806813G>A	ENSP00000428417:p.Arg136His	Somatic		Capture	Illumina HiSeq	Phase_I	72863534	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	.	.	.	.	.	.	.	.	.	.	G	29.3	4.990869	0.93106	.	.	ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978	T;T;T;T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06	5.81	5.81	0.92471	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	0.000011	T	0.63236	0.2494	L	0.32530	0.975	0.80722	D	1	P	0.46064	0.872	B	0.38683	0.279	T	0.70920	-0.4741	10	0.66056	D	0.02	-8.618	20.0804	0.97772	0.0:0.0:1.0:0.0	.	136	Q86UR5	RIMS1_HUMAN	H	136	ENSP00000430101:R136H;ENSP00000275037:R136H;ENSP00000264839:R136H;ENSP00000429959:R136H;ENSP00000430408:R136H;ENSP00000430502:R136H;ENSP00000430932:R136H;ENSP00000428417:R136H	ENSP00000264839:R136H	R	+	2	0	RIMS1	72863534	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.297000	0.78799	2.738000	0.93877	0.655000	0.94253	CGC		0.507	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
RIMS1	22999	broad.mit.edu	37	6	72947556	72947556	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:72947556C>T	ENST00000521978.1	+	9	1888	c.1888C>T	c.(1888-1890)Cga>Tga	p.R630*	RIMS1_ENST00000401910.3_Nonsense_Mutation_p.R104*|RIMS1_ENST00000522291.1_Nonsense_Mutation_p.R630*|RIMS1_ENST00000517960.1_Nonsense_Mutation_p.R630*|RIMS1_ENST00000518273.1_Nonsense_Mutation_p.R630*|RIMS1_ENST00000520567.1_Nonsense_Mutation_p.R630*|RIMS1_ENST00000425662.2_Nonsense_Mutation_p.R23*|RIMS1_ENST00000517827.1_Nonsense_Mutation_p.R89*|RIMS1_ENST00000348717.5_Nonsense_Mutation_p.R630*|RIMS1_ENST00000264839.7_Nonsense_Mutation_p.R630*|RIMS1_ENST00000491071.2_Nonsense_Mutation_p.R630*|RIMS1_ENST00000523963.1_Nonsense_Mutation_p.R104*	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	630	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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.R630*(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)				TGACTTAGGACGACTTGGTGC	0.338																																					p.R23X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C67T	6						.						103.0	99.0	100.0					6																	72947556		1849	4088	5937	73004277	SO:0001587	stop_gained	22999	exon4			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.1888C>T	6.37:g.72947556C>T	ENSP00000428417:p.Arg630*	Somatic		Capture	Illumina HiSeq	Phase_I	73004277	NM_001168409	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Nonsense_Mutation	SNP	ENST00000521978.1	37	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	42|42	9.191080|9.191080	0.99094|0.99094	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827|ENST00000517433	.|.	.|.	.|.	4.94|4.94	4.94|4.94	0.65067|0.65067	.|.	0.000000|.	0.64402|.	D|.	0.000006|.	.|T	.|0.67776	.|0.2929	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.67401	.|-0.5680	.|4	0.02654|.	T|.	1|.	-11.8349|-11.8349	18.1582|18.1582	0.89700|0.89700	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|M	630;630;630;630;630;630;630;630;630;630;630;630;104;104;23;23;89|203	.|.	ENSP00000264839:R630X|.	R|T	+|+	1|2	2|0	RIMS1|RIMS1	73004277|73004277	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	3.928000|3.928000	0.56506|0.56506	2.294000|2.294000	0.77228|0.77228	0.491000|0.491000	0.48974|0.48974	CGA|ACG		0.338	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
MB21D1	115004	broad.mit.edu	37	6	74138522	74138522	+	Missense_Mutation	SNP	C	C	T	rs531954415		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:74138522C>T	ENST00000370315.3	-	4	1221	c.1127G>A	c.(1126-1128)cGg>cAg	p.R376Q	MB21D1_ENST00000370318.1_Missense_Mutation_p.R376Q	NM_138441.2	NP_612450.2	Q8N884	CGAS_HUMAN	Mab-21 domain containing 1	376					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|cyclic nucleotide biosynthetic process (GO:0009190)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of type I interferon production (GO:0032481)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cyclic-GMP-AMP synthase activity (GO:0061501)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.R376Q(1)		central_nervous_system(1)|large_intestine(4)|lung(1)	6						GAAGGATAGCCGCCATGTTTC	0.338																																					p.R376Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1127A	6						.						83.0	79.0	81.0					6																	74138522		2203	4300	6503	74195243	SO:0001583	missense	115004	exon4			BC012928	CCDS4978.1	6q13	2011-02-23	2011-02-23	2011-02-23	ENSG00000164430	ENSG00000164430			21367	protein-coding gene	gene with protein product		613973	"""chromosome 6 open reading frame 150"""	C6orf150			Standard	NM_138441		Approved		uc003pgx.1	Q8N884	OTTHUMG00000015034	ENST00000370315.3:c.1127G>A	6.37:g.74138522C>T	ENSP00000359339:p.Arg376Gln	Somatic		Capture	Illumina HiSeq	Phase_I	74195243	NM_138441	L0L2J9|Q14CV6|Q32NC9|Q5SWL0|Q5SWL1|Q96E45	Missense_Mutation	SNP	ENST00000370315.3	37	CCDS4978.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.281505	0.59758	.	.	ENSG00000164430	ENST00000370318;ENST00000370315;ENST00000296913	T;T	0.14516	2.5;2.5	5.14	4.27	0.50696	.	0.000000	0.64402	D	0.000015	T	0.25082	0.0609	M	0.83483	2.645	0.31829	N	0.625032	D	0.89917	1.0	D	0.91635	0.999	T	0.11641	-1.0579	10	0.32370	T	0.25	-18.5478	12.4134	0.55480	0.0:0.9207:0.0:0.0793	.	376	Q8N884	M21D1_HUMAN	Q	376	ENSP00000359342:R376Q;ENSP00000359339:R376Q	ENSP00000296913:R376Q	R	-	2	0	MB21D1	74195243	1.000000	0.71417	0.852000	0.33557	0.166000	0.22503	5.545000	0.67237	1.291000	0.44653	-0.150000	0.13652	CGG		0.338	MB21D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041221.5	NM_138441	
MTO1	25821	broad.mit.edu	37	6	74176064	74176064	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:74176064G>A	ENST00000370300.4	+	2	440	c.350G>A	c.(349-351)cGt>cAt	p.R117H	MTO1_ENST00000415954.2_Missense_Mutation_p.R117H|MTO1_ENST00000370305.1_Missense_Mutation_p.R43H|MTO1_ENST00000498286.1_Missense_Mutation_p.R117H|MTO1_ENST00000518210.1_3'UTR|RNU6-975P_ENST00000384296.1_RNA	NM_012123.3|NM_133645.2	NP_036255.2|NP_598400.1	Q9Y2Z2	MTO1_HUMAN	mitochondrial tRNA translation optimization 1	117					mitochondrial tRNA wobble uridine modification (GO:0070899)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|poly(A) RNA binding (GO:0044822)	p.R117H(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)	27						TTAAACCGGCGTAAGGGACCA	0.448																																					p.R117H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G350A	6						.						110.0	105.0	107.0					6																	74176064		2203	4300	6503	74232785	SO:0001583	missense	25821	exon2			AF132937	CCDS4979.1, CCDS34485.1, CCDS47452.1	6q14.1	2013-05-07	2013-05-07		ENSG00000135297	ENSG00000135297			19261	protein-coding gene	gene with protein product		614667	"""mitochondrial translation optimization 1 homolog (S. cerevisiae)"""			12011058, 22608499	Standard	NM_012123		Approved		uc003pgy.4	Q9Y2Z2	OTTHUMG00000015032	ENST00000370300.4:c.350G>A	6.37:g.74176064G>A	ENSP00000359323:p.Arg117His	Somatic		Capture	Illumina HiSeq	Phase_I	74232785	NM_001123226	B3KQB5|Q5SWL2|Q5SWL3|Q5SWL4|Q8NDN7|Q8WZ57|Q96FE6|Q9BS06	Missense_Mutation	SNP	ENST00000370300.4	37	CCDS4979.1	.	.	.	.	.	.	.	.	.	.	G	32	5.186454	0.94885	.	.	ENSG00000135297	ENST00000415954;ENST00000498286;ENST00000357845;ENST00000370305;ENST00000370300	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	5.99	5.99	0.97316	.	0.206561	0.51477	D	0.000100	T	0.81749	0.4888	L	0.55743	1.74	0.47737	D	0.999509	D;D;D	0.65815	0.993;0.976;0.995	P;P;P	0.61070	0.88;0.693;0.883	T	0.80214	-0.1475	10	0.46703	T	0.11	-8.2115	18.638	0.91385	0.0:0.0:1.0:0.0	.	117;117;117	Q9Y2Z2-6;Q9Y2Z2-4;Q9Y2Z2	.;.;MTO1_HUMAN	H	117;117;117;43;117	ENSP00000402038:R117H;ENSP00000419561:R117H;ENSP00000359328:R43H;ENSP00000359323:R117H	ENSP00000350506:R117H	R	+	2	0	MTO1	74232785	1.000000	0.71417	0.967000	0.41034	0.924000	0.55760	8.631000	0.90991	2.843000	0.97960	0.591000	0.81541	CGT		0.448	MTO1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041215.2	NM_012123	
MTO1	25821	broad.mit.edu	37	6	74190430	74190430	+	Missense_Mutation	SNP	C	C	T	rs539835237		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:74190430C>T	ENST00000370300.4	+	8	1327	c.1237C>T	c.(1237-1239)Cgt>Tgt	p.R413C	MTO1_ENST00000415954.2_Missense_Mutation_p.R388C|MTO1_ENST00000370305.1_Missense_Mutation_p.R339C|MTO1_ENST00000498286.1_Missense_Mutation_p.R388C	NM_012123.3|NM_133645.2	NP_036255.2|NP_598400.1	Q9Y2Z2	MTO1_HUMAN	mitochondrial tRNA translation optimization 1	413					mitochondrial tRNA wobble uridine modification (GO:0070899)|oxidation-reduction process (GO:0055114)	mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|poly(A) RNA binding (GO:0044822)	p.R413S(1)|p.R413C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)	27						CTTAGATCCCCGTCAGATCAC	0.443													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19110	0.0		0.0	False		,,,				2504	0.0				p.R388C												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C1162T	6						.						202.0	183.0	189.0					6																	74190430		2203	4300	6503	74247151	SO:0001583	missense	25821	exon7			AF132937	CCDS4979.1, CCDS34485.1, CCDS47452.1	6q14.1	2013-05-07	2013-05-07		ENSG00000135297	ENSG00000135297			19261	protein-coding gene	gene with protein product		614667	"""mitochondrial translation optimization 1 homolog (S. cerevisiae)"""			12011058, 22608499	Standard	NM_012123		Approved		uc003pgy.4	Q9Y2Z2	OTTHUMG00000015032	ENST00000370300.4:c.1237C>T	6.37:g.74190430C>T	ENSP00000359323:p.Arg413Cys	Somatic		Capture	Illumina HiSeq	Phase_I	74247151	NM_001123226	B3KQB5|Q5SWL2|Q5SWL3|Q5SWL4|Q8NDN7|Q8WZ57|Q96FE6|Q9BS06	Missense_Mutation	SNP	ENST00000370300.4	37	CCDS4979.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.415804	0.83449	.	.	ENSG00000135297	ENST00000415954;ENST00000498286;ENST00000357845;ENST00000370305;ENST00000370300	T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17	5.15	5.15	0.70609	.	0.095205	0.64402	D	0.000004	D	0.89051	0.6605	M	0.88704	2.975	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.996;0.977;0.996;0.998	D	0.91047	0.4875	10	0.87932	D	0	-11.4318	18.617	0.91306	0.0:1.0:0.0:0.0	.	388;291;388;413	Q9Y2Z2-6;Q9Y2Z2-2;Q9Y2Z2-4;Q9Y2Z2	.;.;.;MTO1_HUMAN	C	388;388;291;339;413	ENSP00000402038:R388C;ENSP00000419561:R388C;ENSP00000359328:R339C;ENSP00000359323:R413C	ENSP00000350506:R291C	R	+	1	0	MTO1	74247151	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	5.444000	0.66587	2.392000	0.81423	0.591000	0.81541	CGT		0.443	MTO1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041215.2	NM_012123	
COL12A1	1303	broad.mit.edu	37	6	75866088	75866088	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:75866088delG	ENST00000322507.8	-	15	3444	c.3135delC	c.(3133-3135)cccfs	p.P1045fs	COL12A1_ENST00000483888.2_Frame_Shift_Del_p.P1045fs|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Frame_Shift_Del_p.P1045fs	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1045	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.T1046fs*7(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						AAGTGACTGTGGGGGGCACCT	0.488																																					p.P1045fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3135delC	6						.						219.0	203.0	208.0					6																	75866088		1963	4153	6116	75922808	SO:0001589	frameshift_variant	1303	exon15			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.3135delC	6.37:g.75866088delG	ENSP00000325146:p.Pro1045fs	Somatic		Capture	Illumina HiSeq	Phase_I	75922808	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Frame_Shift_Del	DEL	ENST00000322507.8	37	CCDS43482.1																																																																																				0.488	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
FILIP1	27145	broad.mit.edu	37	6	76063328	76063328	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:76063328C>T	ENST00000237172.7	-	4	886	c.556G>A	c.(556-558)Gag>Aag	p.E186K	FILIP1_ENST00000393004.2_Missense_Mutation_p.E186K|FILIP1_ENST00000370020.1_Missense_Mutation_p.E87K	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	186								p.E186K(1)		breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						TTATGCTTCTCGTTCTCTAAC	0.517																																					p.E186K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G556A	6						.						249.0	220.0	230.0					6																	76063328		2203	4300	6503	76120048	SO:0001583	missense	27145	exon4			AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.556G>A	6.37:g.76063328C>T	ENSP00000237172:p.Glu186Lys	Somatic		Capture	Illumina HiSeq	Phase_I	76120048	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	37	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	C	37	6.015552	0.97205	.	.	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.54279	0.58;0.58;0.58	5.79	5.79	0.91817	Cortactin-binding protein-2, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.75576	0.3868	M	0.88775	2.98	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	T	0.78836	-0.2047	10	0.66056	D	0.02	-26.9377	20.0366	0.97561	0.0:1.0:0.0:0.0	.	186;186;186	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	K	186;186;87	ENSP00000376728:E186K;ENSP00000237172:E186K;ENSP00000359037:E87K	ENSP00000237172:E186K	E	-	1	0	FILIP1	76120048	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.601000	0.82783	2.736000	0.93811	0.561000	0.74099	GAG		0.517	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179	
FILIP1	27145	broad.mit.edu	37	6	76072565	76072565	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:76072565G>A	ENST00000237172.7	-	3	675	c.345C>T	c.(343-345)taC>taT	p.Y115Y	FILIP1_ENST00000393004.2_Silent_p.Y115Y|RP11-415D17.3_ENST00000440220.1_RNA|RP11-415D17.3_ENST00000415457.2_RNA|RP11-415D17.3_ENST00000609544.1_RNA|RP11-415D17.3_ENST00000419709.1_RNA|RP11-415D17.3_ENST00000588761.1_RNA|RP11-415D17.3_ENST00000591821.2_RNA|FILIP1_ENST00000370020.1_Silent_p.Y16Y	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	115								p.Y115Y(1)		breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						CCGCAGACCCGTAATGAGCCT	0.502																																					p.Y115Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C345T	6						.						130.0	130.0	130.0					6																	76072565		2203	4300	6503	76129285	SO:0001819	synonymous_variant	27145	exon3			AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.345C>T	6.37:g.76072565G>A		Somatic		Capture	Illumina HiSeq	Phase_I	76129285	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Silent	SNP	ENST00000237172.7	37	CCDS4984.1																																																																																				0.502	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179	
IRAK1BP1	134728	broad.mit.edu	37	6	79607782	79607782	+	Splice_Site	SNP	C	C	T	rs140101604		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:79607782C>T	ENST00000369940.2	+	4	619	c.514C>T	c.(514-516)Cgg>Tgg	p.R172W	IRAK1BP1_ENST00000607739.1_Splice_Site_p.R85W	NM_001010844.2	NP_001010844.1	Q5VVH5	IKBP1_HUMAN	interleukin-1 receptor-associated kinase 1 binding protein 1	172					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R172W(1)		endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(3)	12		all_cancers(76;0.0398)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)		BRCA - Breast invasive adenocarcinoma(397;0.21)		ATTCCTAAGACGGCAAGCCTG	0.363																																					p.R172W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C514T	6						.						78.0	78.0	78.0					6																	79607782		2203	4300	6503	79664501	SO:0001630	splice_region_variant	134728	exon4			AI478629	CCDS34488.1	6q14-q15	2006-04-12				ENSG00000146243			17368	protein-coding gene	gene with protein product		615375				11096118	Standard	XM_005248654		Approved	AIP70, SIMPL	uc003pim.4	Q5VVH5		ENST00000369940.2:c.513-1C>T	6.37:g.79607782C>T		Somatic		Capture	Illumina HiSeq	Phase_I	79664501	NM_001010844		Missense_Mutation	SNP	ENST00000369940.2	37	CCDS34488.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.385028	0.61956	.	.	ENSG00000146243	ENST00000369940	.	.	.	4.95	2.15	0.27550	.	0.139086	0.48767	D	0.000167	T	0.59321	0.2185	M	0.72118	2.19	0.45662	D	0.998584	D	0.89917	1.0	D	0.91635	0.999	T	0.59606	-0.7423	8	.	.	.	-7.2186	6.7604	0.23538	0.1423:0.7015:0.0:0.1562	.	172	Q5VVH5	IKBP1_HUMAN	W	172	.	.	R	+	1	2	IRAK1BP1	79664501	0.997000	0.39634	0.991000	0.47740	0.929000	0.56500	1.755000	0.38379	0.252000	0.21531	0.655000	0.94253	CGG		0.363	IRAK1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041296.2	XM_059729	Missense_Mutation
PHIP	55023	broad.mit.edu	37	6	79656492	79656492	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:79656492T>C	ENST00000275034.4	-	37	4473	c.4306A>G	c.(4306-4308)Acc>Gcc	p.T1436A	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1436					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.T1436A(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TTGGTTATGGTATTTCTTTTA	0.348																																					p.T1436A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4306G	6						.						95.0	98.0	97.0					6																	79656492		2203	4300	6503	79713211	SO:0001583	missense	55023	exon37			AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.4306A>G	6.37:g.79656492T>C	ENSP00000275034:p.Thr1436Ala	Somatic		Capture	Illumina HiSeq	Phase_I	79713211	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	T	8.571	0.880001	0.17467	.	.	ENSG00000146247	ENST00000275034;ENST00000355098	T	0.39406	1.08	5.76	4.6	0.57074	Bromodomain (1);	0.225130	0.38959	N	0.001516	T	0.12220	0.0297	N	0.19112	0.55	0.46564	D	0.999105	B;B	0.14438	0.01;0.01	B;B	0.12156	0.007;0.007	T	0.07751	-1.0756	9	.	.	.	-6.86	11.1629	0.48526	0.0:0.072:0.0:0.928	.	1436;1436	A7J992;Q8WWQ0	.;PHIP_HUMAN	A	1436;162	ENSP00000275034:T1436A	.	T	-	1	0	PHIP	79713211	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.788000	0.47806	1.111000	0.41721	0.528000	0.53228	ACC		0.348	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
FAM46A	55603	broad.mit.edu	37	6	82459454	82459454	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:82459454C>T	ENST00000320172.6	-	3	1601	c.1287G>A	c.(1285-1287)acG>acA	p.T429T	FAM46A_ENST00000369754.3_Silent_p.T448T|FAM46A_ENST00000369756.3_Silent_p.T510T	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	429					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)	p.T429T(2)		endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		GTTGCTGGCACGTGAATACTG	0.443																																					p.T429T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1287A	6						.						131.0	118.0	123.0					6																	82459454		2203	4300	6503	82516173	SO:0001819	synonymous_variant	55603	exon3			AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"""chromosome 6 open reading frame 37"""	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.1287G>A	6.37:g.82459454C>T		Somatic		Capture	Illumina HiSeq	Phase_I	82516173	NM_017633	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Silent	SNP	ENST00000320172.6	37	CCDS34489.1																																																																																				0.443	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1		
DOPEY1	23033	broad.mit.edu	37	6	83869564	83869564	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:83869564A>G	ENST00000349129.2	+	37	7107	c.6847A>G	c.(6847-6849)Aat>Gat	p.N2283D	DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000369739.3_Missense_Mutation_p.N2274D|DOPEY1_ENST00000237163.5_Missense_Mutation_p.N2167D	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	2283					protein transport (GO:0015031)			p.N2283D(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)		CACAGGAGGTAATGGCTTCTC	0.498																																					p.N2283D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A6847G	6						.						84.0	86.0	85.0					6																	83869564		2203	4300	6503	83926283	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.6847A>G	6.37:g.83869564A>G	ENSP00000195654:p.Asn2283Asp	Somatic		Capture	Illumina HiSeq	Phase_I	83926283	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	A	17.22	3.334856	0.60853	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.45276	0.9;0.9	5.55	5.55	0.83447	.	0.094982	0.64402	D	0.000001	T	0.51975	0.1706	M	0.64170	1.965	0.80722	D	1	P;D;D	0.71674	0.647;0.998;0.998	B;D;D	0.75484	0.341;0.986;0.986	T	0.49597	-0.8923	10	0.33940	T	0.23	-19.0418	15.6839	0.77393	1.0:0.0:0.0:0.0	.	2174;2274;2283	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	D	2283;2167;2167	ENSP00000195654:N2283D;ENSP00000237163:N2167D	ENSP00000237163:N2167D	N	+	1	0	DOPEY1	83926283	1.000000	0.71417	0.996000	0.52242	0.479000	0.33129	8.923000	0.92808	2.106000	0.64143	0.533000	0.62120	AAT		0.498	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
NT5E	4907	broad.mit.edu	37	6	86201805	86201805	+	Missense_Mutation	SNP	G	G	A	rs143859595		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:86201805G>A	ENST00000257770.3	+	8	1520	c.1471G>A	c.(1471-1473)Gag>Aag	p.E491K	NT5E_ENST00000369651.3_Missense_Mutation_p.E441K	NM_002526.3	NP_002517.1	P21589	5NTD_HUMAN	5'-nucleotidase, ecto (CD73)	491					adenosine biosynthetic process (GO:0046086)|AMP catabolic process (GO:0006196)|dephosphorylation (GO:0016311)|DNA metabolic process (GO:0006259)|negative regulation of inflammatory response (GO:0050728)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.E491K(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;0.000215)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0427)		BRCA - Breast invasive adenocarcinoma(108;0.0417)	Cytarabine(DB00987)|Pentoxifylline(DB00806)	CAAAATGGACGAGGTATATAA	0.433													G|||	1	0.000199681	0.0	0.0014	5008	,	,		20763	0.0		0.0	False		,,,				2504	0.0				p.E491K	Melanoma(140;797 1765 2035 2752 18208)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1471A	6						.	G	LYS/GLU,LYS/GLU	0,4406		0,0,2203	158.0	148.0	151.0		1321,1471	0.8	0.0	6	dbSNP_134	151	2,8598	3.0+/-9.4	0,2,4298	no	missense,missense	NT5E	NM_001204813.1,NM_002526.3	56,56	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	441/525,491/575	86201805	2,13004	2203	4300	6503	86258524	SO:0001583	missense	4907	exon8			X55740	CCDS5002.1, CCDS56439.1	6q14-q21	2013-08-28	2002-04-18	2002-04-19	ENSG00000135318	ENSG00000135318	3.1.3.5	"""CD molecules"""	8021	protein-coding gene	gene with protein product		129190	"""5' nucleotidase (CD73)"""	NT5			Standard	NM_002526		Approved	CD73, eN, eNT, CALJA	uc003pko.4	P21589	OTTHUMG00000015139	ENST00000257770.3:c.1471G>A	6.37:g.86201805G>A	ENSP00000257770:p.Glu491Lys	Somatic		Capture	Illumina HiSeq	Phase_I	86258524	NM_002526	B3KQI8|O75520|Q5W116	Missense_Mutation	SNP	ENST00000257770.3	37	CCDS5002.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.664454	0.00765	0.0	2.33E-4	ENSG00000135318	ENST00000257770;ENST00000369651	T;T	0.48522	0.81;0.81	5.66	0.832	0.18867	5&apos (3);-Nucleotidase, C-terminal (3);	0.782008	0.13049	N	0.417828	T	0.03827	0.0108	N	0.00859	-1.14	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.46527	-0.9185	10	0.02654	T	1	-0.7262	9.8447	0.41019	0.4877:0.0:0.5123:0.0	.	441;491	B3KQI8;P21589	.;5NTD_HUMAN	K	491;441	ENSP00000257770:E491K;ENSP00000358665:E441K	ENSP00000257770:E491K	E	+	1	0	NT5E	86258524	0.000000	0.05858	0.040000	0.18447	0.043000	0.13939	0.259000	0.18405	-0.064000	0.13043	0.655000	0.94253	GAG		0.433	NT5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041388.1		
ZNF292	23036	broad.mit.edu	37	6	87970987	87970987	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:87970987T>C	ENST00000369577.3	+	8	7683	c.7640T>C	c.(7639-7641)gTt>gCt	p.V2547A	ZNF292_ENST00000339907.4_Missense_Mutation_p.V2542A	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	2547						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.V2402A(1)|p.V2547A(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		AAAAGGAAAGTTGAAAAAGCT	0.378																																					p.V2547A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T7640C	6						.						45.0	44.0	44.0					6																	87970987		1848	4089	5937	88027706	SO:0001583	missense	23036	exon8			AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"""Zinc fingers, C2H2-type"""	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.7640T>C	6.37:g.87970987T>C	ENSP00000358590:p.Val2547Ala	Somatic		Capture	Illumina HiSeq	Phase_I	88027706	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	T	0.876	-0.730465	0.03135	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.06849	3.25;3.26	5.74	3.35	0.38373	.	0.785759	0.11749	N	0.533183	T	0.02012	0.0063	L	0.27053	0.805	0.23076	N	0.998334	B	0.06786	0.001	B	0.04013	0.001	T	0.45991	-0.9223	10	0.38643	T	0.18	.	9.0018	0.36085	0.0:0.2276:0.0:0.7724	.	2547	O60281	ZN292_HUMAN	A	2547;2542	ENSP00000358590:V2547A;ENSP00000342847:V2542A	ENSP00000342847:V2542A	V	+	2	0	ZNF292	88027706	0.952000	0.32445	0.980000	0.43619	0.443000	0.32047	0.607000	0.24209	0.444000	0.26612	-0.290000	0.09829	GTT		0.378	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021	
CASP8AP2	9994	broad.mit.edu	37	6	90572449	90572449	+	RNA	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:90572449delA	ENST00000551025.1	+	0	2458									caspase 8 associated protein 2									p.K342fs*2(1)		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)		TCAAAGTGACAAAAAACTAGA	0.348																																					p.K341fs	Colon(187;1656 2025 17045 31481 39901)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1021delA	6						.						64.0	65.0	64.0					6																	90572449		1811	4070	5881	90629170			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.90572449delA		Somatic		Capture	Illumina HiSeq	Phase_I	90629170	NM_001137667		Frame_Shift_Del	DEL	ENST00000551025.1	37																																																																																					0.348	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
CASP8AP2	9994	broad.mit.edu	37	6	90573251	90573251	+	RNA	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:90573251C>T	ENST00000551025.1	+	0	3260									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)		TATGTTCCCTCCATAAGTGAA	0.428																																					p.S608F	Colon(187;1656 2025 17045 31481 39901)											.	.	0			c.C1823T	6						.						41.0	41.0	41.0					6																	90573251		1937	4130	6067	90629972			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.90573251C>T		Somatic		Capture	Illumina HiSeq	Phase_I	90629972	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																					0.428	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
CASP8AP2	9994	broad.mit.edu	37	6	90578659	90578659	+	RNA	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:90578659G>A	ENST00000551025.1	+	0	7087									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)		TAAGAAGAAGGCCCCTCCTGT	0.413																																					p.A1884T	Colon(187;1656 2025 17045 31481 39901)											.	.	0			c.G5650A	6						.						41.0	39.0	39.0					6																	90578659		1848	4095	5943	90635380			9994	exon8			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.90578659G>A		Somatic		Capture	Illumina HiSeq	Phase_I	90635380	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																					0.413	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
AGPAT4	56895	broad.mit.edu	37	6	161560589	161560589	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:161560589delG	ENST00000320285.4	-	8	1119	c.907delC	c.(907-909)cggfs	p.R304fs	AGPAT4_ENST00000457520.2_Frame_Shift_Del_p.R142fs|AGPAT4_ENST00000366911.5_3'UTR	NM_020133.2	NP_064518.1	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	304					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.R303fs*7(2)|p.R303fs*60(1)		endometrium(1)|large_intestine(10)|lung(10)|ovary(2)|skin(2)	25		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		CAGGGCCGCCGGGGGGGCACC	0.627																																					p.R303fs												.	.	3	Deletion - Frameshift(2)|Insertion - Frameshift(1)	large_intestine(2)|ovary(1)	c.907delC	6						.						60.0	70.0	66.0					6																	161560589		2203	4300	6503	161480579	SO:0001589	frameshift_variant	56895	exon8			AF156776	CCDS5280.1	6q25.3	2013-02-05	2013-02-05		ENSG00000026652	ENSG00000026652	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	20885	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, delta"""	614795	"""1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)"""				Standard	XM_005267052		Approved	LPAAT-delta, dJ473J16.2	uc003qtr.1	Q9NRZ5	OTTHUMG00000015966	ENST00000320285.4:c.907delC	6.37:g.161560589delG	ENSP00000314036:p.Arg304fs	Somatic		Capture	Illumina HiSeq	Phase_I	161480579	NM_020133	B4DSF9|Q5TEF0	Frame_Shift_Del	DEL	ENST00000320285.4	37	CCDS5280.1																																																																																				0.627	AGPAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042983.1	NM_020133	
FAM120B	84498	broad.mit.edu	37	6	170700183	170700183	+	Missense_Mutation	SNP	G	G	A	rs544872777	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr6:170700183G>A	ENST00000476287.1	+	8	2681	c.2573G>A	c.(2572-2574)cGa>cAa	p.R858Q	FAM120B_ENST00000252510.9_Missense_Mutation_p.R190Q|FAM120B_ENST00000537664.1_Missense_Mutation_p.R881Q|FAM120B_ENST00000540480.1_Missense_Mutation_p.R870Q	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	858					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.R858Q(1)		endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		ATCACTGGCCGAGCCCACTGG	0.552													G|||	5	0.000998403	0.0	0.0	5008	,	,		16723	0.002		0.0	False		,,,				2504	0.0031				p.R858Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2573A	6						.						60.0	53.0	55.0					6																	170700183		2203	4300	6503	170542108	SO:0001583	missense	84498	exon8			AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.2573G>A	6.37:g.170700183G>A	ENSP00000417970:p.Arg858Gln	Somatic		Capture	Illumina HiSeq	Phase_I	170542108	NM_032448	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	.	.	.	.	.	.	.	.	.	.	G	11.30	1.598709	0.28445	.	.	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287;ENST00000252510	T;T;T	0.10288	2.9;2.89;2.91	5.5	3.73	0.42828	.	0.000000	0.64402	D	0.000001	T	0.02533	0.0077	L	0.27053	0.805	0.26385	N	0.976664	B;B	0.32203	0.36;0.36	B;B	0.24155	0.051;0.028	T	0.33471	-0.9867	10	0.72032	D	0.01	-13.023	10.3121	0.43714	0.1545:0.0:0.8455:0.0	.	858;858	Q96EK7;F2Z2E1	F120B_HUMAN;.	Q	870;881;858;190	ENSP00000444125:R870Q;ENSP00000440125:R881Q;ENSP00000417970:R858Q	ENSP00000252510:R190Q	R	+	2	0	FAM120B	170542108	0.865000	0.29922	0.016000	0.15963	0.012000	0.07955	1.987000	0.40687	0.818000	0.34468	-0.136000	0.14681	CGA		0.552	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
IRF5	3663	broad.mit.edu	37	7	128586562	128586563	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:128586562_128586563insC	ENST00000402030.2	+	4	465_466	c.393_394insC	c.(394-396)cccfs	p.P132fs	IRF5_ENST00000249375.4_Frame_Shift_Ins_p.P132fs|IRF5_ENST00000357234.5_Frame_Shift_Ins_p.P132fs|IRF5_ENST00000477535.1_Frame_Shift_Ins_p.P132fs|IRF5_ENST00000473745.1_Frame_Shift_Ins_p.P132fs	NM_001098629.1|NM_001098630.1	NP_001092099.1|NP_001092100.1	Q13568	IRF5_HUMAN	interferon regulatory factor 5	132					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E134fs*1(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|prostate(1)	15						CAGACTCCCAGCCCCCTGAGGA	0.569																																					p.Q131fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.393_394insC	7						.																																			128373799	SO:0001589	frameshift_variant	3663	exon4				CCDS5808.1, CCDS43645.1, CCDS56512.1	7q32	2008-07-18			ENSG00000128604	ENSG00000128604			6120	protein-coding gene	gene with protein product		607218					Standard	XM_005250317		Approved		uc003vog.3	Q13568	OTTHUMG00000158410	ENST00000402030.2:c.398dupC	7.37:g.128586567_128586567dupC	ENSP00000385352:p.Pro132fs	Somatic		Capture	Illumina HiSeq	Phase_I	128373798	NM_001098627	A4D1J8|A8DUA8|A8DUA9|E7EQ16|E7EW54|Q1A7B4|Q64GA9|Q64GB1|Q64GB2|Q6RCM8|Q9BQF0	Frame_Shift_Ins	INS	ENST00000402030.2	37	CCDS5808.1																																																																																				0.569	IRF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350934.1	NM_001098627	
LRCH4	4034	broad.mit.edu	37	7	100174587	100174587	+	Missense_Mutation	SNP	G	G	A	rs375173199	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:100174587G>A	ENST00000310300.6	-	13	1458	c.1406C>T	c.(1405-1407)gCg>gTg	p.A469V	LRCH4_ENST00000497245.1_Missense_Mutation_p.A17V	NM_002319.3	NP_002310.2	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 4	469				AAAGQGA -> GCSGAGS (in Ref. 1; AAC78793). {ECO:0000305}.	nervous system development (GO:0007399)	PML body (GO:0016605)		p.A469V(1)		NS(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	23	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TCCCTGCCCCGCTGCAGCCCC	0.642													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		14647	0.0		0.0	False		,,,				2504	0.0				p.A469V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1406T	7						.	G	VAL/ALA	1,4405		0,1,2202	26.0	27.0	26.0		1406	-0.5	0.0	7		26	0,8596		0,0,4298	no	missense	LRCH4	NM_002319.3	64	0,1,6500	AA,AG,GG		0.0,0.0227,0.0077	benign	469/684	100174587	1,13001	2203	4298	6501	100012523	SO:0001583	missense	4034	exon13			AF053356	CCDS34706.1	7q22	2008-05-20	2004-05-27	2004-05-28	ENSG00000077454	ENSG00000077454			6691	protein-coding gene	gene with protein product				LRN, LRRN1		9799793	Standard	XM_005250346		Approved		uc003uvj.3	O75427	OTTHUMG00000159544	ENST00000310300.6:c.1406C>T	7.37:g.100174587G>A	ENSP00000309689:p.Ala469Val	Somatic		Capture	Illumina HiSeq	Phase_I	100012523	NM_002319	A4D2D5|Q8WV85|Q96ID0	Missense_Mutation	SNP	ENST00000310300.6	37	CCDS34706.1	.	.	.	.	.	.	.	.	.	.	G	7.201	0.593433	0.13875	2.27E-4	0.0	ENSG00000077454	ENST00000310300;ENST00000497245	T;T	0.49432	1.51;0.78	3.51	-0.528	0.11905	.	1.397130	0.04581	N	0.394877	T	0.24431	0.0592	N	0.08118	0	0.09310	N	1	B	0.31241	0.315	B	0.23852	0.049	T	0.12502	-1.0545	10	0.22109	T	0.4	-2.374	7.163	0.25675	0.4216:0.2409:0.3375:0.0	.	469	O75427	LRCH4_HUMAN	V	469;17	ENSP00000309689:A469V;ENSP00000419870:A17V	ENSP00000309689:A469V	A	-	2	0	LRCH4	100012523	0.000000	0.05858	0.003000	0.11579	0.009000	0.06853	-0.364000	0.07583	-0.156000	0.11079	-1.874000	0.00550	GCG		0.642	LRCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356110.1	NM_002319	
PCOLCE	5118	broad.mit.edu	37	7	100203329	100203329	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:100203329C>T	ENST00000223061.5	+	5	899	c.619C>T	c.(619-621)Ctg>Ttg	p.L207L	PCOLCE-AS1_ENST00000446022.1_RNA|PCOLCE-AS1_ENST00000442166.2_RNA|PCOLCE-AS1_ENST00000544873.1_RNA	NM_002593.3	NP_002584.2	Q15113	PCOC1_HUMAN	procollagen C-endopeptidase enhancer	207	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				multicellular organismal development (GO:0007275)|positive regulation of peptidase activity (GO:0010952)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)	p.L207L(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					GAAGTTTGACCTGGAGCCGGA	0.677																																					p.L207L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C619T	7						.						22.0	22.0	22.0					7																	100203329		2197	4290	6487	100041265	SO:0001819	synonymous_variant	5118	exon5			L33799	CCDS5700.1	7q22	2008-07-18			ENSG00000106333	ENSG00000106333			8738	protein-coding gene	gene with protein product	"""procollagen, type 1, COOH-terminal proteinase enhancer"", ""procollagen C-proteinase enhancer 1"""	600270				8824813, 9799793	Standard	NM_002593		Approved	PCPE, PCPE1	uc003uvo.3	Q15113	OTTHUMG00000156675	ENST00000223061.5:c.619C>T	7.37:g.100203329C>T		Somatic		Capture	Illumina HiSeq	Phase_I	100041265	NM_002593	B2R9E1|O14550	Silent	SNP	ENST00000223061.5	37	CCDS5700.1																																																																																				0.677	PCOLCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345285.1	NM_002593	
MOSPD3	64598	broad.mit.edu	37	7	100210606	100210606	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:100210606G>A	ENST00000393950.2	+	1	474	c.192G>A	c.(190-192)gcG>gcA	p.A64A	MOSPD3_ENST00000379527.2_Silent_p.A64A|MOSPD3_ENST00000424091.2_Silent_p.A64A|MOSPD3_ENST00000223054.4_Silent_p.A64A	NM_023948.4	NP_076438.1	O75425	MSPD3_HUMAN	motile sperm domain containing 3	64	MSP. {ECO:0000255|PROSITE- ProRule:PRU00132}.				heart development (GO:0007507)	integral component of membrane (GO:0016021)	structural molecule activity (GO:0005198)	p.A64A(1)		breast(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					CAGGAACTGCGCTTCGCTTCC	0.637																																					p.A64A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G192A	7						.						54.0	61.0	59.0					7																	100210606		2202	4300	6502	100048542	SO:0001819	synonymous_variant	64598	exon2			BC011653	CCDS5701.1, CCDS47662.1	7q22	2009-11-06			ENSG00000106330	ENSG00000106330			25078	protein-coding gene	gene with protein product		609125				15533722	Standard	XM_005250531		Approved	CDS3, NET30	uc003uvs.3	O75425	OTTHUMG00000159599	ENST00000393950.2:c.192G>A	7.37:g.100210606G>A		Somatic		Capture	Illumina HiSeq	Phase_I	100048542	NM_001040098	A4D2D1|A6NG17|C9JE89|D6W5W1|O75423|O75424	Silent	SNP	ENST00000393950.2	37	CCDS5701.1																																																																																				0.637	MOSPD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356395.1	NM_023948	
SLC12A9	56996	broad.mit.edu	37	7	100464108	100464108	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:100464108C>T	ENST00000354161.3	+	14	2751	c.2626C>T	c.(2626-2628)Ccg>Tcg	p.P876S	TRIP6_ENST00000200457.4_5'Flank	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	876					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)	p.P876S(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					CTTGCCTCGGCCGCCAGCCGA	0.701																																					p.P876S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2626T	7						.						12.0	10.0	11.0					7																	100464108		2148	4238	6386	100302044	SO:0001583	missense	56996	exon14			AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"""Solute carriers"""	17435	protein-coding gene	gene with protein product	"""cation-chloride cotransporter-interacting protein"""					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.2626C>T	7.37:g.100464108C>T	ENSP00000275730:p.Pro876Ser	Somatic		Capture	Illumina HiSeq	Phase_I	100302044	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Missense_Mutation	SNP	ENST00000354161.3	37	CCDS5707.1	.	.	.	.	.	.	.	.	.	.	C	19.18	3.778676	0.70107	.	.	ENSG00000146828	ENST00000354161	D	0.95342	-3.68	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	D	0.97126	0.9061	M	0.82823	2.61	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.97623	1.0137	10	0.72032	D	0.01	.	15.1532	0.72717	0.0:1.0:0.0:0.0	.	876	Q9BXP2	S12A9_HUMAN	S	876	ENSP00000275730:P876S	ENSP00000275730:P876S	P	+	1	0	SLC12A9	100302044	1.000000	0.71417	0.984000	0.44739	0.373000	0.29922	7.576000	0.82467	2.425000	0.82216	0.555000	0.69702	CCG		0.701	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
SRRT	51593	broad.mit.edu	37	7	100479772	100479772	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:100479772C>T	ENST00000347433.4	+	5	655	c.497C>T	c.(496-498)aCg>aTg	p.T166M	SRRT_ENST00000432932.1_Missense_Mutation_p.T166M|SRRT_ENST00000457580.2_Missense_Mutation_p.T166M|SRRT_ENST00000388793.4_Missense_Mutation_p.T166M			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	166					cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.T166M(1)		breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						GTGGATGAGACGGAGGCCGTC	0.562																																					p.T166M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C497T	7						.						129.0	113.0	119.0					7																	100479772		2203	4300	6503	100317708	SO:0001583	missense	51593	exon5				CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"""arsenite resistance protein"""	614469	"""serrate RNA effector molecule homolog (Arabidopsis)"""			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.497C>T	7.37:g.100479772C>T	ENSP00000314491:p.Thr166Met	Somatic		Capture	Illumina HiSeq	Phase_I	100317708	NM_001128852	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Missense_Mutation	SNP	ENST00000347433.4	37	CCDS34709.1	.	.	.	.	.	.	.	.	.	.	C	13.47	2.246053	0.39697	.	.	ENSG00000087087	ENST00000457580;ENST00000388793;ENST00000539682;ENST00000432932;ENST00000347433	.	.	.	4.46	4.46	0.54185	.	0.000000	0.85682	D	0.000000	T	0.69869	0.3159	L	0.49350	1.555	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.996;0.996;0.996;0.998	T	0.71167	-0.4672	9	0.51188	T	0.08	.	14.602	0.68447	0.0:1.0:0.0:0.0	.	166;166;166;166	Q9BXP5-3;Q9BXP5-4;Q9BXP5-2;Q9BXP5	.;.;.;SRRT_HUMAN	M	166;166;81;166;166	.	ENSP00000314491:T166M	T	+	2	0	SRRT	100317708	1.000000	0.71417	0.935000	0.37517	0.010000	0.07245	7.427000	0.80284	2.281000	0.76405	0.462000	0.41574	ACG		0.562	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908	
SRRT	51593	broad.mit.edu	37	7	100484479	100484479	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:100484479G>A	ENST00000347433.4	+	14	1869	c.1711G>A	c.(1711-1713)Gcc>Acc	p.A571T	SRRT_ENST00000432932.1_Missense_Mutation_p.A570T|SRRT_ENST00000457580.2_Missense_Mutation_p.A571T|SRRT_ENST00000388793.4_Missense_Mutation_p.A570T			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	571					cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.A571T(1)		breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						GGAAGTAAGCGCCGAGGAGGA	0.582																																					p.A570T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1708A	7						.						40.0	46.0	44.0					7																	100484479		2203	4300	6503	100322415	SO:0001583	missense	51593	exon14				CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"""arsenite resistance protein"""	614469	"""serrate RNA effector molecule homolog (Arabidopsis)"""			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.1711G>A	7.37:g.100484479G>A	ENSP00000314491:p.Ala571Thr	Somatic		Capture	Illumina HiSeq	Phase_I	100322415	NM_001128852	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Missense_Mutation	SNP	ENST00000347433.4	37	CCDS34709.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.469258	0.63625	.	.	ENSG00000087087	ENST00000457580;ENST00000388793;ENST00000432932;ENST00000347433;ENST00000448764	.	.	.	5.63	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.76140	0.3946	M	0.65498	2.005	0.80722	D	1	D;D;D;P	0.76494	0.982;0.999;0.999;0.867	P;D;D;B	0.80764	0.617;0.994;0.994;0.221	T	0.76658	-0.2878	9	0.45353	T	0.12	.	14.0793	0.64909	0.0:0.1522:0.8478:0.0	.	570;570;571;571	Q9BXP5-3;Q9BXP5-4;Q9BXP5-2;Q9BXP5	.;.;.;SRRT_HUMAN	T	571;570;570;571;201	.	ENSP00000314491:A571T	A	+	1	0	SRRT	100322415	1.000000	0.71417	0.963000	0.40424	0.778000	0.44026	9.000000	0.93564	1.308000	0.44962	0.561000	0.74099	GCC		0.582	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908	
ACHE	43	broad.mit.edu	37	7	100491167	100491167	+	Silent	SNP	C	C	T	rs151335006	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:100491167C>T	ENST00000412389.1	-	1	842	c.687G>A	c.(685-687)acG>acA	p.T229T	ACHE_ENST00000241069.5_Silent_p.T229T|ACHE_ENST00000419336.2_Silent_p.T229T|ACHE_ENST00000411582.1_Silent_p.T229T|ACHE_ENST00000497647.1_5'Flank|ACHE_ENST00000428317.1_Silent_p.T229T|ACHE_ENST00000302913.4_Silent_p.T229T			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)	229					acetylcholine catabolic process (GO:0006581)|acetylcholine catabolic process in synaptic cleft (GO:0001507)|amyloid precursor protein metabolic process (GO:0042982)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|choline metabolic process (GO:0019695)|DNA replication (GO:0006260)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|negative regulation of synaptic transmission, cholinergic (GO:0032223)|nervous system development (GO:0007399)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter receptor biosynthetic process (GO:0045212)|osteoblast development (GO:0002076)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of protein secretion (GO:0050714)|protein tetramerization (GO:0051262)|receptor internalization (GO:0031623)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of receptor recycling (GO:0001919)|response to wounding (GO:0009611)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|cholinesterase activity (GO:0004104)|collagen binding (GO:0005518)|hydrolase activity (GO:0016787)|laminin binding (GO:0043236)|protein homodimerization activity (GO:0042803)|serine hydrolase activity (GO:0017171)	p.T229T(1)		large_intestine(3)|lung(7)|skin(3)|urinary_tract(3)	16	Lung NSC(181;0.041)|all_lung(186;0.0581)				Ambenonium(DB01122)|Choline(DB00122)|Decamethonium(DB01245)|Demecarium(DB00944)|Dipivefrin(DB00449)|Donepezil(DB00843)|Edrophonium(DB01010)|Ephedrine(DB01364)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Isoflurophate(DB00677)|Mefloquine(DB00358)|Minaprine(DB00805)|Neostigmine(DB01400)|Physostigmine(DB00981)|Pralidoxime(DB00733)|Pyridostigmine(DB00545)|Rivastigmine(DB00989)|Tubocurarine(DB01199)	CCCCAAACAGCGTCACTGATG	0.701													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		16025	0.0		0.0	False		,,,				2504	0.0				p.T229T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G687A	7						.	C	,	13,4393		0,13,2190	40.0	42.0	42.0		687,687	-10.1	0.4	7	dbSNP_134	42	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous	ACHE	NM_000665.3,NM_015831.2	,	0,13,6487	TT,TC,CC		0.0,0.2951,0.1	,	229/615,229/618	100491167	13,12987	2203	4297	6500	100329103	SO:0001819	synonymous_variant	43	exon2				CCDS5709.1, CCDS5710.1, CCDS64736.1	7q22	2014-07-19	2014-01-02		ENSG00000087085	ENSG00000087085	3.1.1.7	"""Blood group antigens"""	108	protein-coding gene	gene with protein product	"""Yt blood group"""	100740	"""acetylcholinesterase (YT blood group)"", ""acetylcholinesterase (Yt blood group)"", ""acetylcholinesterase"""	YT		1380483	Standard	XM_005250357		Approved		uc003uxe.3	P22303	OTTHUMG00000157033	ENST00000412389.1:c.687G>A	7.37:g.100491167C>T		Somatic		Capture	Illumina HiSeq	Phase_I	100329103	NM_000665	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Silent	SNP	ENST00000412389.1	37	CCDS5709.1																																																																																				0.701	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831	
MUC17	140453	broad.mit.edu	37	7	100681721	100681721	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:100681721C>T	ENST00000306151.4	+	3	7088	c.7024C>T	c.(7024-7026)Cgt>Tgt	p.R2342C		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2342	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.R2342C(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCCATTAACACGTATGCCTGT	0.478																																					p.R2342C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C7024T	7						.						253.0	247.0	249.0					7																	100681721		2203	4300	6503	100468441	SO:0001583	missense	140453	exon3			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.7024C>T	7.37:g.100681721C>T	ENSP00000302716:p.Arg2342Cys	Somatic		Capture	Illumina HiSeq	Phase_I	100468441	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	10.59	1.393818	0.25205	.	.	ENSG00000169876	ENST00000306151	T	0.02944	4.1	1.23	-2.46	0.06461	.	.	.	.	.	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	P	0.46952	0.887	B	0.23419	0.046	T	0.44467	-0.9326	9	0.62326	D	0.03	.	5.6705	0.17719	0.4272:0.5728:0.0:0.0	.	2342	Q685J3	MUC17_HUMAN	C	2342	ENSP00000302716:R2342C	ENSP00000302716:R2342C	R	+	1	0	MUC17	100468441	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.518000	0.02246	-2.687000	0.00405	-2.210000	0.00300	CGT		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CUX1	1523	broad.mit.edu	37	7	101813827	101813827	+	Silent	SNP	C	C	T	rs143307709	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:101813827C>T	ENST00000292535.7	+	10	863	c.825C>T	c.(823-825)gaC>gaT	p.D275D	CUX1_ENST00000393824.3_Silent_p.D249D|CUX1_ENST00000437600.4_Silent_p.D286D|CUX1_ENST00000360264.3_Silent_p.D286D|CUX1_ENST00000549414.2_Silent_p.D275D|CUX1_ENST00000546411.2_Silent_p.D275D|CUX1_ENST00000550008.2_Silent_p.D275D|CUX1_ENST00000560541.1_3'UTR|CUX1_ENST00000425244.2_Silent_p.D240D|CUX1_ENST00000556210.1_Silent_p.D275D|CUX1_ENST00000547394.2_Silent_p.D270D|CUX1_ENST00000292538.4_Silent_p.D286D	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	275					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)	p.D286D(1)|p.D275D(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						AGGCACCAGACGTGGTGGGTA	0.607																																					p.D275D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C825T	7						.	C	,,,,,,	1,4399		0,1,2199	31.0	22.0	25.0		858,810,720,747,858,858,825	-3.9	1.0	7	dbSNP_134	25	2,8592		0,2,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CUX1	NM_001202543.1,NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2,NM_181552.3	,,,,,,	0,3,6494	TT,TC,CC		0.0233,0.0227,0.0231	,,,,,,	286/1517,270/663,240/633,249/640,286/679,286/677,275/1506	101813827	3,12991	2200	4297	6497	101600547	SO:0001819	synonymous_variant	1523	exon10			M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.825C>T	7.37:g.101813827C>T		Somatic		Capture	Illumina HiSeq	Phase_I	101600547	NM_181552	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000292535.7	37	CCDS5721.1																																																																																				0.607	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913	
KMT2E	55904	broad.mit.edu	37	7	104702621	104702621	+	Missense_Mutation	SNP	G	G	A	rs367956492		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:104702621G>A	ENST00000311117.3	+	4	627	c.82G>A	c.(82-84)Gta>Ata	p.V28I	KMT2E_ENST00000476671.1_Missense_Mutation_p.V28I|KMT2E_ENST00000334914.7_5'UTR|KMT2E_ENST00000257745.4_Missense_Mutation_p.V28I|KMT2E_ENST00000334877.4_Missense_Mutation_p.V28I	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	28					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.V28I(1)									ACCAGAATCCGTAGAAGCTAG	0.378																																					p.V28I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G82A	7						.						160.0	157.0	158.0					7																	104702621		2203	4300	6503	104489857	SO:0001583	missense	55904	exon4			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	18541	protein-coding gene	gene with protein product		608444	"""myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"""	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.82G>A	7.37:g.104702621G>A	ENSP00000312379:p.Val28Ile	Somatic		Capture	Illumina HiSeq	Phase_I	104489857	NM_182931	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	.	.	.	.	.	.	.	.	.	.	G	33	5.272088	0.95429	.	.	ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000495267;ENST00000476671;ENST00000474203	D;D;D;T;D	0.96300	-3.75;-3.12;-3.75;0.88;-3.97	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.97417	0.9155	L	0.52573	1.65	0.80722	D	1	D;D	0.76494	0.999;0.992	D;D	0.71184	0.972;0.952	D	0.97462	1.0035	10	0.54805	T	0.06	.	19.994	0.97377	0.0:0.0:1.0:0.0	.	28;28	Q8IZD2;Q8IZD2-3	MLL5_HUMAN;.	I	28	ENSP00000312379:V28I;ENSP00000335599:V28I;ENSP00000257745:V28I;ENSP00000420415:V28I;ENSP00000417888:V28I	ENSP00000257745:V28I	V	+	1	0	MLL5	104489857	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.781000	0.99029	2.730000	0.93505	0.557000	0.71058	GTA		0.378	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1		
PIK3CG	5294	broad.mit.edu	37	7	106508151	106508151	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:106508151C>T	ENST00000359195.3	+	2	455	c.145C>T	c.(145-147)Cgc>Tgc	p.R49C	PIK3CG_ENST00000440650.2_Missense_Mutation_p.R49C|PIK3CG_ENST00000496166.1_Missense_Mutation_p.R49C	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	49	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R49C(1)		breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						CACCAGCCAGCGCAAATGCAA	0.672																																					p.R49C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C145T	7						.						32.0	37.0	35.0					7																	106508151		2202	4299	6501	106295387	SO:0001583	missense	5294	exon2				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"""phosphoinositide-3-kinase, catalytic, gamma polypeptide"""				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.145C>T	7.37:g.106508151C>T	ENSP00000352121:p.Arg49Cys	Somatic		Capture	Illumina HiSeq	Phase_I	106295387	NM_002649	A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	C	12.83	2.054882	0.36277	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.71698	-0.59;-0.59;-0.59	5.64	5.64	0.86602	.	2.908750	0.00973	N	0.003270	T	0.71169	0.3308	L	0.47716	1.5	0.42414	D	0.992612	D	0.61697	0.99	B	0.43623	0.425	T	0.62358	-0.6871	10	0.39692	T	0.17	-17.0655	12.6616	0.56817	0.257:0.743:0.0:0.0	.	49	P48736	PK3CG_HUMAN	C	49	ENSP00000392258:R49C;ENSP00000419260:R49C;ENSP00000352121:R49C	ENSP00000352121:R49C	R	+	1	0	PIK3CG	106295387	0.979000	0.34478	1.000000	0.80357	0.899000	0.52679	4.223000	0.58587	2.816000	0.96949	0.563000	0.77884	CGC		0.672	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1		
LAMB1	3912	broad.mit.edu	37	7	107600244	107600244	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:107600244C>T	ENST00000222399.6	-	19	2580	c.2350G>A	c.(2350-2352)Gtg>Atg	p.V784M	LAMB1_ENST00000393561.1_Missense_Mutation_p.V808M|LAMB1_ENST00000393560.1_Missense_Mutation_p.V784M	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	784	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)	p.V784M(1)		NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						GGATCACACACGGAACTTAAC	0.577																																					p.V784M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2350A	7						.						51.0	44.0	47.0					7																	107600244		2203	4300	6503	107387480	SO:0001583	missense	3912	exon19			M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"""Laminins"""	6486	protein-coding gene	gene with protein product		150240	"""cutis laxa with marfanoid phenotype"""	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.2350G>A	7.37:g.107600244C>T	ENSP00000222399:p.Val784Met	Somatic		Capture	Illumina HiSeq	Phase_I	107387480	NM_002291	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	37	CCDS5750.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.547434	0.65311	.	.	ENSG00000091136	ENST00000393561;ENST00000222399;ENST00000393560	T;T;T	0.61742	0.08;0.08;0.08	5.31	5.31	0.75309	EGF-like, laminin (3);	.	.	.	.	T	0.75496	0.3857	M	0.72118	2.19	0.80722	D	1	P;D;D	0.89917	0.857;0.981;1.0	B;P;D	0.71414	0.349;0.658;0.973	T	0.75039	-0.3458	9	0.48119	T	0.1	.	19.1741	0.93597	0.0:1.0:0.0:0.0	.	784;784;808	E7EPA6;P07942;G3XAI2	.;LAMB1_HUMAN;.	M	808;784;784	ENSP00000377191:V808M;ENSP00000222399:V784M;ENSP00000377190:V784M	ENSP00000222399:V784M	V	-	1	0	LAMB1	107387480	0.991000	0.36638	0.964000	0.40570	0.191000	0.23601	2.945000	0.49043	2.759000	0.94783	0.563000	0.77884	GTG		0.577	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291	
LAMB1	3912	broad.mit.edu	37	7	107603377	107603377	+	Silent	SNP	G	G	A	rs141175689		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:107603377G>A	ENST00000222399.6	-	15	2060	c.1830C>T	c.(1828-1830)taC>taT	p.Y610Y	LAMB1_ENST00000393561.1_Silent_p.Y634Y|LAMB1_ENST00000393560.1_Silent_p.Y610Y	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	610	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)	p.Y610Y(1)		NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						TTAGGATGTCGTACTCCATGG	0.488													G|||	1	0.000199681	0.0	0.0014	5008	,	,		14393	0.0		0.0	False		,,,				2504	0.0				p.Y610Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1830T	7						.	G		1,4405	2.1+/-5.4	0,1,2202	98.0	96.0	97.0		1830	-4.8	1.0	7	dbSNP_134	97	0,8600		0,0,4300	no	coding-synonymous	LAMB1	NM_002291.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		610/1787	107603377	1,13005	2203	4300	6503	107390613	SO:0001819	synonymous_variant	3912	exon15			M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"""Laminins"""	6486	protein-coding gene	gene with protein product		150240	"""cutis laxa with marfanoid phenotype"""	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.1830C>T	7.37:g.107603377G>A		Somatic		Capture	Illumina HiSeq	Phase_I	107390613	NM_002291	Q14D91	Silent	SNP	ENST00000222399.6	37	CCDS5750.1																																																																																				0.488	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291	
LAMB4	22798	broad.mit.edu	37	7	107708517	107708517	+	Missense_Mutation	SNP	C	C	A	rs151119551		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:107708517C>A	ENST00000388781.3	-	19	2473	c.2390G>T	c.(2389-2391)cGc>cTc	p.R797L	LAMB4_ENST00000205386.4_Missense_Mutation_p.R797L|LAMB4_ENST00000388780.3_Missense_Mutation_p.R797L	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	797	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.R797L(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						GTCACAGCAGCGCCCGACCAC	0.562																																					p.R797L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2390T	7						.						182.0	170.0	174.0					7																	107708517		2203	4300	6503	107495753	SO:0001583	missense	22798	exon19			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.2390G>T	7.37:g.107708517C>A	ENSP00000373433:p.Arg797Leu	Somatic		Capture	Illumina HiSeq	Phase_I	107495753	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.369598	0.61624	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780	T;T;T	0.63096	-0.02;-0.02;-0.02	4.78	0.985	0.19779	EGF-like, laminin (4);EGF-like region, conserved site (1);	0.111749	0.40640	N	0.001049	T	0.53449	0.1797	L	0.41027	1.25	0.80722	D	1	P	0.40578	0.722	B	0.43103	0.408	T	0.52616	-0.8552	10	0.87932	D	0	.	9.572	0.39433	0.0:0.7137:0.0:0.2863	.	797	A4D0S4	LAMB4_HUMAN	L	797	ENSP00000205386:R797L;ENSP00000373433:R797L;ENSP00000373432:R797L	ENSP00000205386:R797L	R	-	2	0	LAMB4	107495753	0.986000	0.35501	0.684000	0.30055	0.584000	0.36387	1.666000	0.37460	0.068000	0.16574	-0.137000	0.14449	CGC		0.562	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
LAMB4	22798	broad.mit.edu	37	7	107738990	107738990	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:107738990G>A	ENST00000388781.3	-	11	1301	c.1218C>T	c.(1216-1218)ggC>ggT	p.G406G	LAMB4_ENST00000205386.4_Silent_p.G406G|LAMB4_ENST00000418464.1_Silent_p.G406G|LAMB4_ENST00000414450.2_Silent_p.G406G|LAMB4_ENST00000388780.3_Silent_p.G406G	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	406	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.G406G(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						TCACACAAATGCCACCAGATA	0.493																																					p.G406G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1218T	7						.						118.0	105.0	110.0					7																	107738990		2203	4300	6503	107526226	SO:0001819	synonymous_variant	22798	exon11			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.1218C>T	7.37:g.107738990G>A		Somatic		Capture	Illumina HiSeq	Phase_I	107526226	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																				0.493	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
TES	26136	broad.mit.edu	37	7	115891940	115891940	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:115891940G>A	ENST00000358204.4	+	5	1044	c.829G>A	c.(829-831)Gac>Aac	p.D277N	AC073130.3_ENST00000444244.1_RNA|TES_ENST00000537767.1_Missense_Mutation_p.D35N|AC002066.1_ENST00000446355.2_RNA|TES_ENST00000393481.2_Missense_Mutation_p.D268N	NM_015641.3	NP_056456.1	Q9UGI8	TES_HUMAN	testis derived transcript (3 LIM domains)	277	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|protein complex (GO:0043234)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.D277N(1)		endometrium(4)|large_intestine(4)|lung(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	12	Lung NSC(10;0.0137)|all_lung(10;0.0148)	Breast(660;0.0602)	STAD - Stomach adenocarcinoma(10;0.00878)			ACTCCTGGTTGACATGATTTA	0.478																																					p.D277N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G829A	7						.						99.0	96.0	97.0					7																	115891940		2203	4300	6503	115679176	SO:0001583	missense	26136	exon5			AJ250865	CCDS5763.1, CCDS5764.1	7q31.2	2004-04-20			ENSG00000135269	ENSG00000135269			14620	protein-coding gene	gene with protein product		606085				10950921	Standard	NM_015641		Approved	DKFZP586B2022, TESS-2, TESTIN	uc003vho.3	Q9UGI8	OTTHUMG00000023092	ENST00000358204.4:c.829G>A	7.37:g.115891940G>A	ENSP00000350937:p.Asp277Asn	Somatic		Capture	Illumina HiSeq	Phase_I	115679176	NM_015641	A4D0U6|Q9GZQ1|Q9HAJ9	Missense_Mutation	SNP	ENST00000358204.4	37	CCDS5763.1	.	.	.	.	.	.	.	.	.	.	G	35	5.474609	0.96291	.	.	ENSG00000135269	ENST00000358204;ENST00000537767;ENST00000257721;ENST00000393481	D;D;D	0.87334	-2.24;-2.24;-2.24	5.61	5.61	0.85477	Zinc finger, LIM-type (4);	0.000000	0.85682	D	0.000000	D	0.90714	0.7086	L	0.46819	1.47	0.80722	D	1	D	0.59767	0.986	P	0.59357	0.856	D	0.90728	0.4640	10	0.62326	D	0.03	-20.3082	20.0016	0.97412	0.0:0.0:1.0:0.0	.	277	Q9UGI8	TES_HUMAN	N	277;35;277;268	ENSP00000350937:D277N;ENSP00000441607:D35N;ENSP00000377121:D268N	ENSP00000257721:D277N	D	+	1	0	TES	115679176	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	9.792000	0.99085	2.802000	0.96397	0.655000	0.94253	GAC		0.478	TES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059413.2	NM_015641	
CAPZA2	830	broad.mit.edu	37	7	116528208	116528208	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:116528208C>T	ENST00000361183.3	+	2	206	c.67C>T	c.(67-69)Cat>Tat	p.H23Y	CAPZA2_ENST00000458284.2_Missense_Mutation_p.H23Y|CAPZA2_ENST00000490693.1_Missense_Mutation_p.H23Y	NM_006136.2	NP_006127.1	P47755	CAZA2_HUMAN	capping protein (actin filament) muscle Z-line, alpha 2	23					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|WASH complex (GO:0071203)		p.H23Y(1)		endometrium(2)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	13	all_cancers(3;8.53e-08)|all_epithelial(6;7.79e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)		GBM - Glioblastoma multiforme(2;5.01e-06)|STAD - Stomach adenocarcinoma(10;0.000512)|all cancers(2;0.00326)			ATTCATCATTCATGCCCCTCC	0.343																																					p.H23Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C67T	7						.						101.0	102.0	102.0					7																	116528208		2203	4300	6503	116315444	SO:0001583	missense	830	exon2				CCDS5768.1	7q31.2-q31.3	2008-07-18			ENSG00000198898	ENSG00000198898			1490	protein-coding gene	gene with protein product	"""F-actin capping protein alpha-2 subunit"""	601571					Standard	NM_006136		Approved	CAPZ, CAPPA2	uc003vil.3	P47755	OTTHUMG00000023185	ENST00000361183.3:c.67C>T	7.37:g.116528208C>T	ENSP00000354947:p.His23Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	116315444	NM_006136	B4DG50	Missense_Mutation	SNP	ENST00000361183.3	37	CCDS5768.1	.	.	.	.	.	.	.	.	.	.	c	27.2	4.810761	0.90707	.	.	ENSG00000198898	ENST00000361183;ENST00000458284;ENST00000490693	.	.	.	5.86	5.86	0.93980	.	0.104498	0.64402	D	0.000004	T	0.72614	0.3482	M	0.67953	2.075	0.58432	D	0.999998	P	0.47191	0.891	P	0.51055	0.657	T	0.74542	-0.3631	9	0.72032	D	0.01	-11.3277	18.9609	0.92677	0.0:1.0:0.0:0.0	.	23	P47755	CAZA2_HUMAN	Y	23	.	ENSP00000354947:H23Y	H	+	1	0	CAPZA2	116315444	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.941000	0.70195	2.776000	0.95493	0.586000	0.80456	CAT		0.343	CAPZA2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059506.4	NM_006136	
PTPRZ1	5803	broad.mit.edu	37	7	121624143	121624143	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:121624143C>T	ENST00000393386.2	+	8	1311	c.900C>T	c.(898-900)taC>taT	p.Y300Y	PTPRZ1_ENST00000449182.1_Silent_p.Y300Y	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	300	Alpha-carbonic anhydrase.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.Y300Y(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						TTTCCTCATACACTGGAAAGG	0.353																																					p.Y300Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C900T	7						.						124.0	121.0	122.0					7																	121624143		2203	4300	6503	121411379	SO:0001819	synonymous_variant	5803	exon8			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.900C>T	7.37:g.121624143C>T		Somatic		Capture	Illumina HiSeq	Phase_I	121411379	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																				0.353	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
AASS	10157	broad.mit.edu	37	7	121718988	121718988	+	Missense_Mutation	SNP	C	C	T	rs372473763		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:121718988C>T	ENST00000393376.1	-	21	2508	c.2413G>A	c.(2413-2415)Gat>Aat	p.D805N	AASS_ENST00000473553.1_5'UTR|RNU7-154P_ENST00000516194.1_RNA|AASS_ENST00000417368.2_Missense_Mutation_p.D805N			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	805	Saccharopine dehydrogenase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)	p.D805N(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						ACTTGTTCATCCCCAAGTAAG	0.438																																					p.D805N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2413A	7						.						117.0	109.0	112.0					7																	121718988		2203	4300	6503	121506224	SO:0001583	missense	10157	exon22			AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.2413G>A	7.37:g.121718988C>T	ENSP00000377040:p.Asp805Asn	Somatic		Capture	Illumina HiSeq	Phase_I	121506224	NM_005763	O95462	Missense_Mutation	SNP	ENST00000393376.1	37	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	C	17.29	3.352794	0.61293	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	.	.	.	5.44	3.64	0.41730	.	0.173904	0.56097	D	0.000033	T	0.66616	0.2807	L	0.58669	1.825	0.48762	D	0.999708	P	0.49447	0.924	P	0.60886	0.88	T	0.63395	-0.6647	9	0.40728	T	0.16	-14.947	10.1289	0.42667	0.0:0.8443:0.0:0.1557	.	805	Q9UDR5	AASS_HUMAN	N	805	.	ENSP00000377040:D805N	D	-	1	0	AASS	121506224	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	3.577000	0.53885	0.672000	0.31204	0.650000	0.86243	GAT		0.438	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763	
TMEM106B	54664	broad.mit.edu	37	7	12271508	12271508	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:12271508C>T	ENST00000396667.3	+	9	1054	c.732C>T	c.(730-732)tcC>tcT	p.S244S	TMEM106B_ENST00000396668.3_Silent_p.S244S	NM_018374.3	NP_060844.2	Q9NUM4	T106B_HUMAN	transmembrane protein 106B	244					cell death (GO:0008219)|dendrite morphogenesis (GO:0048813)|lysosome localization (GO:0032418)|transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)		p.S244S(1)		NS(1)|endometrium(8)|large_intestine(2)|lung(7)	18				UCEC - Uterine corpus endometrioid carcinoma (126;0.185)		AACAGATATCCCAGGAGAGGT	0.368																																					p.S244S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C732T	7						.						89.0	82.0	85.0					7																	12271508		2203	4299	6502	12238033	SO:0001819	synonymous_variant	54664	exon8			BC033901	CCDS5358.1	7p21.3	2012-06-06			ENSG00000106460	ENSG00000106460			22407	protein-coding gene	gene with protein product		613413				20154673, 22511793	Standard	NM_018374		Approved	MGC33727, FLJ11273	uc003ssh.3	Q9NUM4	OTTHUMG00000125537	ENST00000396667.3:c.732C>T	7.37:g.12271508C>T		Somatic		Capture	Illumina HiSeq	Phase_I	12238033	NM_001134232	A4D108|Q53FL9|Q8N4L0	Silent	SNP	ENST00000396667.3	37	CCDS5358.1																																																																																				0.368	TMEM106B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246870.3	NM_018374	
CADPS2	93664	broad.mit.edu	37	7	122261711	122261711	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:122261711G>A	ENST00000449022.2	-	5	947	c.928C>T	c.(928-930)Cgg>Tgg	p.R310W	CADPS2_ENST00000412584.2_Missense_Mutation_p.R310W|CADPS2_ENST00000313070.7_Missense_Mutation_p.R310W|CADPS2_ENST00000334010.7_Missense_Mutation_p.R310W	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	310					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)	p.R310W(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						ACTGAAGACCGCAACTCTTCT	0.308																																					p.R310W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C928T	7						.						73.0	72.0	72.0					7																	122261711		1792	4065	5857	122048947	SO:0001583	missense	93664	exon5				CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"""Pleckstrin homology (PH) domain containing"""	16018	protein-coding gene	gene with protein product		609978	"""Ca++-dependent activator protein for secretion 2"""				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.928C>T	7.37:g.122261711G>A	ENSP00000398481:p.Arg310Trp	Somatic		Capture	Illumina HiSeq	Phase_I	122048947	NM_001167940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Missense_Mutation	SNP	ENST00000449022.2	37	CCDS55158.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.461437	0.63513	.	.	ENSG00000081803	ENST00000313070;ENST00000334010;ENST00000420900;ENST00000545465;ENST00000412584;ENST00000449022	T;T;T;T	0.49432	0.78;0.78;0.78;0.79	5.6	1.32	0.21799	.	0.056380	0.64402	D	0.000003	T	0.62889	0.2465	L	0.61387	1.9	0.50813	D	0.99989	D;D;D	0.89917	1.0;0.999;0.998	D;P;P	0.71870	0.975;0.857;0.859	T	0.64487	-0.6396	10	0.49607	T	0.09	-13.3148	15.1829	0.72975	0.0:0.0:0.3855:0.6145	.	310;310;310	Q86UW7-2;Q86UW7;Q86UW7-3	.;CAPS2_HUMAN;.	W	310;310;310;277;310;310	ENSP00000325581:R310W;ENSP00000333940:R310W;ENSP00000400401:R310W;ENSP00000398481:R310W	ENSP00000325581:R310W	R	-	1	2	CADPS2	122048947	0.784000	0.28713	1.000000	0.80357	0.981000	0.71138	1.034000	0.30204	0.241000	0.21283	0.467000	0.42956	CGG		0.308	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954	
LMOD2	442721	broad.mit.edu	37	7	123296084	123296084	+	Missense_Mutation	SNP	G	G	A	rs143098443	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:123296084G>A	ENST00000458573.2	+	1	224	c.67G>A	c.(67-69)Gcc>Acc	p.A23T	LMOD2_ENST00000456238.2_Missense_Mutation_p.A23T	NM_207163.1	NP_997046.1	Q6P5Q4	LMOD2_HUMAN	leiomodin 2 (cardiac)	23	Glu-rich.|Tropomyosin-binding. {ECO:0000250}.					cytoskeleton (GO:0005856)		p.A23T(1)									TGAACTCCTCGCCTCCCTGTC	0.537													G|||	7	0.00139776	0.0038	0.0014	5008	,	,		19998	0.0		0.001	False		,,,				2504	0.0				p.A23T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G67A	7						.	G	THR/ALA	26,3914		0,26,1944	43.0	46.0	45.0		67	5.9	1.0	7	dbSNP_134	45	0,8312		0,0,4156	yes	missense	LMOD2	NM_207163.1	58	0,26,6100	AA,AG,GG		0.0,0.6599,0.2122	probably-damaging	23/548	123296084	26,12226	1970	4156	6126	123083320	SO:0001583	missense	442721	exon1			AC006333	CCDS47693.1	7q31.32	2008-08-08			ENSG00000170807	ENSG00000170807			6648	protein-coding gene	gene with protein product		608006					Standard	NM_207163		Approved		uc003vky.2	Q6P5Q4	OTTHUMG00000157149	ENST00000458573.2:c.67G>A	7.37:g.123296084G>A	ENSP00000411932:p.Ala23Thr	Somatic		Capture	Illumina HiSeq	Phase_I	123083320	NM_207163	A4D0W9|A4D0Y2|Q8WVJ8	Missense_Mutation	SNP	ENST00000458573.2	37	CCDS47693.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	35	5.491149	0.96339	0.006599	0.0	ENSG00000170807	ENST00000458573;ENST00000444702;ENST00000332074;ENST00000456238	T;T	0.29655	1.56;1.56	5.91	5.91	0.95273	.	0.000000	0.36591	N	0.002513	T	0.48095	0.1481	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.43766	-0.9371	10	0.46703	T	0.11	-10.4682	20.2985	0.98592	0.0:0.0:1.0:0.0	.	23	Q6P5Q4	LMOD2_HUMAN	T	23	ENSP00000411932:A23T;ENSP00000398975:A23T	ENSP00000405123:A23T	A	+	1	0	LMOD2	123083320	1.000000	0.71417	0.962000	0.40283	0.858000	0.48976	9.869000	0.99810	2.793000	0.96121	0.655000	0.94253	GCC		0.537	LMOD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348525.1		
SCIN	85477	broad.mit.edu	37	7	12683794	12683794	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:12683794A>C	ENST00000297029.5	+	12	1714	c.1613A>C	c.(1612-1614)aAc>aCc	p.N538T	SCIN_ENST00000519209.1_Missense_Mutation_p.N291T|SCIN_ENST00000445618.2_Missense_Mutation_p.N291T	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	538	Ca(2+)-dependent actin binding.				actin filament capping (GO:0051693)|actin filament severing (GO:0051014)|actin nucleation (GO:0045010)|calcium ion-dependent exocytosis (GO:0017156)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of secretion (GO:0051047)|regulation of chondrocyte differentiation (GO:0032330)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	1-phosphatidylinositol binding (GO:0005545)|actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)	p.N538T(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	17				UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		CTGAATTCTAACGATGTTTTT	0.398																																					p.N538T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1613C	7						.						50.0	50.0	50.0					7																	12683794		1886	4131	6017	12650319	SO:0001583	missense	85477	exon12			AF276507	CCDS47545.1, CCDS47546.1	7p21.3	2006-04-25			ENSG00000006747	ENSG00000006747			21695	protein-coding gene	gene with protein product		613416					Standard	NM_033128		Approved	adseverin, KIAA1905	uc003ssn.4	Q9Y6U3	OTTHUMG00000152385	ENST00000297029.5:c.1613A>C	7.37:g.12683794A>C	ENSP00000297029:p.Asn538Thr	Somatic		Capture	Illumina HiSeq	Phase_I	12650319	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	37	CCDS47545.1	.	.	.	.	.	.	.	.	.	.	A	19.03	3.747552	0.69533	.	.	ENSG00000006747	ENST00000297029;ENST00000519209;ENST00000445618	T;T;T	0.40476	1.03;1.03;1.03	5.22	5.22	0.72569	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	T	0.62221	0.2410	M	0.65320	2	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.66114	-0.6004	10	0.87932	D	0	-27.0827	15.1035	0.72303	1.0:0.0:0.0:0.0	.	538	Q9Y6U3	ADSV_HUMAN	T	538;291;291	ENSP00000297029:N538T;ENSP00000430997:N291T;ENSP00000390189:N291T	ENSP00000297029:N538T	N	+	2	0	SCIN	12650319	1.000000	0.71417	0.997000	0.53966	0.602000	0.36980	6.869000	0.75521	1.978000	0.57642	0.460000	0.39030	AAC		0.398	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128	
WASL	8976	broad.mit.edu	37	7	123332424	123332424	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:123332424G>A	ENST00000223023.4	-	9	1656	c.1324C>T	c.(1324-1326)Cga>Tga	p.R442*		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	442	WH2 2. {ECO:0000255|PROSITE- ProRule:PRU00406}.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cellular protein complex localization (GO:0034629)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane budding (GO:0006900)|mitotic nuclear division (GO:0007067)|nitric oxide metabolic process (GO:0046209)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of filopodium assembly (GO:0051491)|protein complex assembly (GO:0006461)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|response to bacterium (GO:0009617)|small molecule metabolic process (GO:0044281)|spindle localization (GO:0051653)|transcription, DNA-templated (GO:0006351)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	small GTPase regulator activity (GO:0005083)	p.R442*(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ATACCCTGTCGTATCTGGTCT	0.348																																					p.R442X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1324T	7						.						65.0	63.0	63.0					7																	123332424		2203	4300	6503	123119660	SO:0001587	stop_gained	8976	exon9			D88460	CCDS34743.1	7q31.3	2008-02-01			ENSG00000106299	ENSG00000106299			12735	protein-coding gene	gene with protein product		605056				9422512, 9322739	Standard	NM_003941		Approved	N-WASP, NWASP	uc003vkz.3	O00401	OTTHUMG00000157346	ENST00000223023.4:c.1324C>T	7.37:g.123332424G>A	ENSP00000223023:p.Arg442*	Somatic		Capture	Illumina HiSeq	Phase_I	123119660	NM_003941	A1JUI9|Q7Z746	Nonsense_Mutation	SNP	ENST00000223023.4	37	CCDS34743.1	.	.	.	.	.	.	.	.	.	.	G	40	8.102322	0.98654	.	.	ENSG00000106299	ENST00000223023	.	.	.	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.0687	19.6847	0.95976	0.0:0.0:1.0:0.0	.	.	.	.	X	442	.	ENSP00000223023:R442X	R	-	1	2	WASL	123119660	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.348000	0.66004	2.651000	0.90000	0.650000	0.86243	CGA		0.348	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941	
FSCN3	29999	broad.mit.edu	37	7	127238546	127238546	+	Nonsense_Mutation	SNP	C	C	T	rs146611259	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:127238546C>T	ENST00000265825.5	+	4	1237	c.1018C>T	c.(1018-1020)Cga>Tga	p.R340*	FSCN3_ENST00000420086.2_Nonsense_Mutation_p.R206*	NM_020369.2	NP_065102.1	Q9NQT6	FSCN3_HUMAN	fascin actin-bundling protein 3, testicular	340						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R340*(1)		endometrium(2)|large_intestine(3)|liver(2)|lung(17)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30						CACGTTCTTCCGAATGCACTG	0.567																																					p.R340X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1018T	7						.	C	stop/ARG	2,4404	4.2+/-10.8	0,2,2201	108.0	102.0	104.0		1018	3.9	0.9	7	dbSNP_134	104	0,8600		0,0,4300	yes	stop-gained	FSCN3	NM_020369.2		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		340/499	127238546	2,13004	2203	4300	6503	127025782	SO:0001587	stop_gained	29999	exon4				CCDS34746.1	7q31.3	2014-02-03	2014-02-03		ENSG00000106328	ENSG00000106328		"""Fascins"""	3961	protein-coding gene	gene with protein product		615800	"""fascin (Strongylocentrotus purpuratus) homolog 3 (actin-bundling protein, testicular)"", ""fascin homolog 3, actin-bundling protein, testicular (Strongylocentrotus purpuratus)"""			11925108	Standard	NM_020369		Approved		uc003vmd.2	Q9NQT6	OTTHUMG00000022935	ENST00000265825.5:c.1018C>T	7.37:g.127238546C>T	ENSP00000265825:p.Arg340*	Somatic		Capture	Illumina HiSeq	Phase_I	127025782	NM_020369	A4D0Z2|A6NLL7|B2RA62|B4DU68	Nonsense_Mutation	SNP	ENST00000265825.5	37	CCDS34746.1	.	.	.	.	.	.	.	.	.	.	C	40	8.051237	0.98629	4.54E-4	0.0	ENSG00000106328	ENST00000265825;ENST00000420086	.	.	.	5.94	3.91	0.45181	.	0.421997	0.23008	N	0.052987	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-28.9189	5.8783	0.18842	0.0:0.7445:0.0:0.2554	.	.	.	.	X	340;206	.	ENSP00000265825:R340X	R	+	1	2	FSCN3	127025782	0.885000	0.30320	0.899000	0.35326	0.361000	0.29550	1.136000	0.31467	1.521000	0.48983	0.561000	0.74099	CGA		0.567	FSCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059256.2	NM_020369	
PAX4	5078	broad.mit.edu	37	7	127251219	127251219	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:127251219G>T	ENST00000341640.2	-	9	1136	c.931C>A	c.(931-933)Ctt>Att	p.L311I	PAX4_ENST00000463946.1_Missense_Mutation_p.L309I|PAX4_ENST00000378740.2_Intron|PAX4_ENST00000338516.3_3'UTR	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	324	Transcription repression.				cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|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)	p.L311I(1)		cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						GGAAGGCAAAGCAGTCCTGAG	0.582																																					p.L311I	Ovarian(113;737 1605 7858 27720 34092)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C931A	7						.						63.0	57.0	59.0					7																	127251219		2203	4300	6503	127038455	SO:0001583	missense	5078	exon9				CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"""Paired boxes"", ""Homeoboxes / PRD class"""	8618	protein-coding gene	gene with protein product		167413	"""paired box gene 4"""				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.931C>A	7.37:g.127251219G>T	ENSP00000339906:p.Leu311Ile	Somatic		Capture	Illumina HiSeq	Phase_I	127038455	NM_006193	O95161|Q6B0H0	Missense_Mutation	SNP	ENST00000341640.2	37	CCDS5797.1	.	.	.	.	.	.	.	.	.	.	G	12.59	1.982945	0.34942	.	.	ENSG00000106331	ENST00000341640;ENST00000463946	D;D	0.93811	-3.29;-3.15	5.3	3.24	0.37175	.	3.296890	0.01020	N	0.003974	D	0.90967	0.7160	L	0.46157	1.445	0.09310	N	0.999999	B;B	0.26809	0.16;0.16	B;B	0.31337	0.082;0.128	T	0.76836	-0.2812	10	0.22706	T	0.39	.	6.0013	0.19521	0.2687:0.0:0.7313:0.0	.	311;309	O43316-4;G3V4Q1	.;.	I	311;309	ENSP00000339906:L311I;ENSP00000451923:L309I	ENSP00000339906:L311I	L	-	1	0	PAX4	127038455	0.000000	0.05858	0.005000	0.12908	0.015000	0.08874	0.605000	0.24179	1.153000	0.42468	0.655000	0.94253	CTT		0.582	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1		
SND1	27044	broad.mit.edu	37	7	127724857	127724857	+	Missense_Mutation	SNP	G	G	A	rs552426263		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:127724857G>A	ENST00000354725.3	+	19	2386	c.2192G>A	c.(2191-2193)cGc>cAc	p.R731H	MIR593_ENST00000384856.1_RNA	NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	731	Tudor. {ECO:0000255|PROSITE- ProRule:PRU00211}.				gene silencing by RNA (GO:0031047)|osteoblast differentiation (GO:0001649)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dense body (GO:0097433)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|RISC complex (GO:0016442)	nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|transcription cofactor activity (GO:0003712)	p.R731H(1)		central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						TATGCCCCCCGCAGGGGAGAG	0.552													G|||	1	0.000199681	0.0	0.0	5008	,	,		19288	0.001		0.0	False		,,,				2504	0.0				p.R731H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2192A	7						.						61.0	59.0	60.0					7																	127724857		2203	4300	6503	127512093	SO:0001583	missense	27044	exon19				CCDS34747.1	7q31.3	2014-03-24			ENSG00000197157	ENSG00000197157		"""Tudor domain containing"""	30646	protein-coding gene	gene with protein product	"""p100 EBNA2 co-activator"", ""Tudor-SN"""	602181				7651391, 9003410, 12819296	Standard	NM_014390		Approved	TDRD11, p100	uc003vmi.3	Q7KZF4	OTTHUMG00000157560	ENST00000354725.3:c.2192G>A	7.37:g.127724857G>A	ENSP00000346762:p.Arg731His	Somatic		Capture	Illumina HiSeq	Phase_I	127512093	NM_014390	Q13122|Q96AG0	Missense_Mutation	SNP	ENST00000354725.3	37	CCDS34747.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.643086	0.87859	.	.	ENSG00000197157	ENST00000354725;ENST00000438400;ENST00000486037	T;T	0.09538	2.97;2.97	5.42	5.42	0.78866	Tudor subgroup (1);Maternal tudor protein (1);Tudor domain (1);	0.000000	0.85682	D	0.000000	T	0.32010	0.0815	M	0.71206	2.165	0.80722	D	1	D	0.89917	1.0	D	0.65573	0.936	T	0.01608	-1.1313	10	0.66056	D	0.02	-13.713	16.714	0.85393	0.0:0.0:1.0:0.0	.	731	Q7KZF4	SND1_HUMAN	H	731;721;217	ENSP00000346762:R731H;ENSP00000419327:R217H	ENSP00000346762:R731H	R	+	2	0	SND1	127512093	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.179000	0.71974	2.529000	0.85273	0.561000	0.74099	CGC		0.552	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390	
FLNC	2318	broad.mit.edu	37	7	128484814	128484814	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:128484814G>A	ENST00000325888.8	+	21	3556	c.3295G>A	c.(3295-3297)Gta>Ata	p.V1099I	FLNC_ENST00000346177.6_Missense_Mutation_p.V1099I	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1099					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)	p.V1099I(1)		biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						GGGGCTGACCGTAGAGGGCCC	0.637																																					p.V1099I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3295A	7						.						56.0	65.0	62.0					7																	128484814		2067	4220	6287	128272050	SO:0001583	missense	2318	exon21			AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.3295G>A	7.37:g.128484814G>A	ENSP00000327145:p.Val1099Ile	Somatic		Capture	Illumina HiSeq	Phase_I	128272050	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	g	21.4	4.144121	0.77888	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.92699	-3.09;-3.09	5.54	5.54	0.83059	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.87985	0.6316	N	0.13371	0.34	0.49051	D	0.999749	D;P	0.53151	0.958;0.84	P;P	0.47118	0.527;0.538	D	0.86635	0.1888	10	0.23891	T	0.37	.	19.5124	0.95148	0.0:0.0:1.0:0.0	.	1099;1099	Q14315-2;Q14315	.;FLNC_HUMAN	I	1099	ENSP00000327145:V1099I;ENSP00000344002:V1099I	ENSP00000327145:V1099I	V	+	1	0	FLNC	128272050	1.000000	0.71417	0.971000	0.41717	0.913000	0.54294	9.869000	0.99810	2.611000	0.88343	0.550000	0.68814	GTA		0.637	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
AHCYL2	23382	broad.mit.edu	37	7	129028934	129028934	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:129028934G>A	ENST00000325006.3	+	3	567	c.513G>A	c.(511-513)tcG>tcA	p.S171S	AHCYL2_ENST00000446212.1_Silent_p.S69S|AHCYL2_ENST00000446544.2_Silent_p.S170S|AHCYL2_ENST00000472554.1_3'UTR|AHCYL2_ENST00000490911.1_Silent_p.S68S|AHCYL2_ENST00000531335.2_Silent_p.S90S|AHCYL2_ENST00000474594.1_Silent_p.S68S	NM_001130720.2|NM_015328.3	NP_001124192.1|NP_056143.1	Q96HN2	SAHH3_HUMAN	adenosylhomocysteinase-like 2	171					one-carbon metabolic process (GO:0006730)		adenosylhomocysteinase activity (GO:0004013)	p.S171S(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	22						ATGAGACATCGCCCAGGGACA	0.403																																					p.S171S	Pancreas(160;1736 1964 29875 40941 45605)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G513A	7						.						102.0	95.0	98.0					7																	129028934		2203	4300	6503	128816170	SO:0001819	synonymous_variant	23382	exon3			AB020635	CCDS5812.1, CCDS47706.1, CCDS47707.1, CCDS47708.1, CCDS47707.2	7q32.1	2009-06-12	2009-06-12		ENSG00000158467	ENSG00000158467			22204	protein-coding gene	gene with protein product			"""S-adenosylhomocysteine hydrolase-like 2"""				Standard	NM_001130720		Approved	KIAA0828	uc011kov.2	Q96HN2	OTTHUMG00000157677	ENST00000325006.3:c.513G>A	7.37:g.129028934G>A		Somatic		Capture	Illumina HiSeq	Phase_I	128816170	NM_015328	B4DIZ5|D9N155|O94917	Silent	SNP	ENST00000325006.3	37	CCDS5812.1	.	.	.	.	.	.	.	.	.	.	G	7.591	0.670710	0.14776	.	.	ENSG00000158467	ENST00000466924	.	.	.	5.62	-4.9	0.03094	.	.	.	.	.	T	0.37972	0.1023	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38373	-0.9664	4	.	.	.	-15.2176	2.0358	0.03539	0.1899:0.3884:0.0941:0.3276	.	.	.	.	H	78	.	.	R	+	2	0	AHCYL2	128816170	0.003000	0.15002	0.939000	0.37840	0.987000	0.75469	-1.134000	0.03228	-0.823000	0.04301	-0.738000	0.03535	CGC		0.403	AHCYL2-012	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354065.1		
AHCYL2	23382	broad.mit.edu	37	7	129053527	129053527	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:129053527G>A	ENST00000325006.3	+	12	1513	c.1459G>A	c.(1459-1461)Gtg>Atg	p.V487M	AHCYL2_ENST00000446212.1_Missense_Mutation_p.V385M|AHCYL2_ENST00000446544.2_Missense_Mutation_p.V486M|AHCYL2_ENST00000490911.1_Missense_Mutation_p.V384M|AHCYL2_ENST00000531335.2_Missense_Mutation_p.V406M|AHCYL2_ENST00000474594.1_Missense_Mutation_p.V384M	NM_001130720.2|NM_015328.3	NP_001124192.1|NP_056143.1	Q96HN2	SAHH3_HUMAN	adenosylhomocysteinase-like 2	487					one-carbon metabolic process (GO:0006730)		adenosylhomocysteinase activity (GO:0004013)	p.V487M(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	22						AGAGATTGACGTGGTAAGATC	0.423																																					p.V487M	Pancreas(160;1736 1964 29875 40941 45605)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1459A	7						.						144.0	121.0	129.0					7																	129053527		2203	4300	6503	128840763	SO:0001583	missense	23382	exon12			AB020635	CCDS5812.1, CCDS47706.1, CCDS47707.1, CCDS47708.1, CCDS47707.2	7q32.1	2009-06-12	2009-06-12		ENSG00000158467	ENSG00000158467			22204	protein-coding gene	gene with protein product			"""S-adenosylhomocysteine hydrolase-like 2"""				Standard	NM_001130720		Approved	KIAA0828	uc011kov.2	Q96HN2	OTTHUMG00000157677	ENST00000325006.3:c.1459G>A	7.37:g.129053527G>A	ENSP00000315931:p.Val487Met	Somatic		Capture	Illumina HiSeq	Phase_I	128840763	NM_015328	B4DIZ5|D9N155|O94917	Missense_Mutation	SNP	ENST00000325006.3	37	CCDS5812.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.728171	0.89390	.	.	ENSG00000158467	ENST00000325006;ENST00000446544;ENST00000531335;ENST00000474594;ENST00000446212;ENST00000490911	T;T;T;T;T;T	0.79749	-1.3;-1.3;-1.28;-1.27;-1.27;-1.26	5.6	5.6	0.85130	S-adenosyl-L-homocysteine hydrolase, NAD binding (1);	0.000000	0.85682	D	0.000000	D	0.87521	0.6198	L	0.53561	1.675	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.999;1.0;0.999;1.0	D;D;D;D;D	0.70016	0.922;0.922;0.967;0.922;0.944	D	0.87315	0.2314	10	0.52906	T	0.07	-18.1885	18.1784	0.89769	0.0:0.0:1.0:0.0	.	384;385;487;384;486	B4DIZ5;D7UEQ7;Q96HN2;D9N155;Q96HN2-2	.;.;SAHH3_HUMAN;.;.	M	487;486;406;384;385;384	ENSP00000315931:V487M;ENSP00000413639:V486M;ENSP00000431787:V406M;ENSP00000420459:V384M;ENSP00000405267:V385M;ENSP00000420801:V384M	ENSP00000315931:V487M	V	+	1	0	AHCYL2	128840763	1.000000	0.71417	0.996000	0.52242	0.986000	0.74619	9.433000	0.97501	2.625000	0.88918	0.650000	0.86243	GTG		0.423	AHCYL2-012	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354065.1		
STRIP2	57464	broad.mit.edu	37	7	129125498	129125498	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:129125498G>A	ENST00000249344.2	+	21	2373	c.2333G>A	c.(2332-2334)cGc>cAc	p.R778H	RNU1-72P_ENST00000362976.1_RNA	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	778					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)		p.R778H(2)									AACAGCCGTCGCTATGACAGA	0.498																																					p.R778H												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G2333A	7						.						102.0	92.0	95.0					7																	129125498		2203	4300	6503	128912734	SO:0001583	missense	57464	exon21			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.2333G>A	7.37:g.129125498G>A	ENSP00000249344:p.Arg778His	Somatic		Capture	Illumina HiSeq	Phase_I	128912734	NM_020704	Q8WUZ4	Missense_Mutation	SNP	ENST00000249344.2	37	CCDS34752.1	.	.	.	.	.	.	.	.	.	.	G	34	5.375033	0.95923	.	.	ENSG00000128578	ENST00000249344	T	0.49139	0.79	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.69504	0.3118	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.63932	-0.6525	10	0.28530	T	0.3	-20.8352	19.2409	0.93883	0.0:0.0:1.0:0.0	.	778	Q9ULQ0	FA40B_HUMAN	H	778	ENSP00000249344:R778H	ENSP00000249344:R778H	R	+	2	0	FAM40B	128912734	1.000000	0.71417	0.993000	0.49108	0.949000	0.60115	9.813000	0.99286	2.788000	0.95919	0.557000	0.71058	CGC		0.498	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336	
ZC3HC1	51530	broad.mit.edu	37	7	129662246	129662246	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:129662246G>A	ENST00000358303.4	-	9	1437	c.1353C>T	c.(1351-1353)agC>agT	p.S451S	ZC3HC1_ENST00000360708.5_Silent_p.S380S|RP11-306G20.1_ENST00000480018.1_RNA|ZC3HC1_ENST00000481503.1_Silent_p.S408S|ZC3HC1_ENST00000311873.5_Silent_p.S430S|RP11-306G20.1_ENST00000587038.1_RNA	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	451					mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)	p.S451S(1)		endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					CTGCTGGGGCGCTGGCATCTG	0.547																																					p.S451S	Melanoma(115;540 1606 16325 28853 48167)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1353T	7						.						112.0	96.0	102.0					7																	129662246		2203	4300	6503	129449482	SO:0001819	synonymous_variant	51530	exon9			AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"""Zinc fingers, C3HC-type"""	29913	protein-coding gene	gene with protein product	"""nuclear interaction partner of ALK"""					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.1353C>T	7.37:g.129662246G>A		Somatic		Capture	Illumina HiSeq	Phase_I	129449482	NM_016478	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Silent	SNP	ENST00000358303.4	37	CCDS34753.1																																																																																				0.547	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478	
CPA5	93979	broad.mit.edu	37	7	130008324	130008324	+	Silent	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:130008324G>T	ENST00000485477.1	+	12	2326	c.1197G>T	c.(1195-1197)cgG>cgT	p.R399R	CPA5_ENST00000355388.3_Silent_p.R399R|CPA5_ENST00000461828.1_Silent_p.R399R|CPA5_ENST00000393213.3_Silent_p.R399R|CPA5_ENST00000466363.2_Silent_p.R399R|CPA5_ENST00000474905.1_Silent_p.R399R|CPA5_ENST00000431780.2_Missense_Mutation_p.G371V			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	399						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.R399R(1)		NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					TTGAGCTCCGGGACACTGGGC	0.577																																					p.G371V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1112T	7						.						148.0	129.0	135.0					7																	130008324		2203	4300	6503	129795560	SO:0001819	synonymous_variant	93979	exon11			AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.1197G>T	7.37:g.130008324G>T		Somatic		Capture	Illumina HiSeq	Phase_I	129795560	NM_001127442	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Missense_Mutation	SNP	ENST00000485477.1	37	CCDS5819.1	.	.	.	.	.	.	.	.	.	.	G	12.96	2.093270	0.36952	.	.	ENSG00000158525	ENST00000431780;ENST00000479492	T	0.12147	2.71	5.85	2.04	0.26737	.	.	.	.	.	T	0.07503	0.0189	.	.	.	0.80722	D	1	B	0.20550	0.046	B	0.19946	0.027	T	0.32903	-0.9889	7	.	.	.	.	2.7787	0.05355	0.1366:0.1252:0.4793:0.259	.	371	G3V0G8	.	V	371;48	ENSP00000393045:G371V	.	G	+	2	0	CPA5	129795560	0.686000	0.27661	0.999000	0.59377	0.010000	0.07245	-0.162000	0.10012	0.100000	0.17581	-0.136000	0.14681	GGG		0.577	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441	
MKLN1	4289	broad.mit.edu	37	7	131096100	131096100	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:131096100T>C	ENST00000352689.6	+	7	779	c.739T>C	c.(739-741)Tat>Cat	p.Y247H	MKLN1_ENST00000421797.2_Missense_Mutation_p.Y155H	NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	247	CTLH. {ECO:0000255|PROSITE- ProRule:PRU00058}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)		p.Y247H(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					TCAACAGGAATATAAGCCACG	0.318																																					p.Y247H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T739C	7						.						103.0	90.0	94.0					7																	131096100		2203	4300	6503	130746640	SO:0001583	missense	4289	exon7			AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585			7109	protein-coding gene	gene with protein product		605623				10640805	Standard	NM_001145354		Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.739T>C	7.37:g.131096100T>C	ENSP00000323527:p.Tyr247His	Somatic		Capture	Illumina HiSeq	Phase_I	130746640	NM_013255	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	Missense_Mutation	SNP	ENST00000352689.6	37	CCDS34754.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.508017	0.85282	.	.	ENSG00000128585	ENST00000421797;ENST00000352689	T;T	0.48522	1.81;0.81	5.7	5.7	0.88788	CTLH, C-terminal LisH motif (1);	0.000000	0.85682	D	0.000000	T	0.65709	0.2717	M	0.68317	2.08	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.78314	0.969;0.991;0.991	T	0.66862	-0.5816	10	0.49607	T	0.09	-15.0941	13.3424	0.60553	0.0:0.0:0.0:1.0	.	247;224;155	Q9UL63;B4DG30;C9J7E8	MKLN1_HUMAN;.;.	H	155;247	ENSP00000398094:Y155H;ENSP00000323527:Y247H	ENSP00000323527:Y247H	Y	+	1	0	MKLN1	130746640	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	6.252000	0.72447	2.162000	0.67917	0.528000	0.53228	TAT		0.318	MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337473.4	NM_013255	
PLXNA4	91584	broad.mit.edu	37	7	131864608	131864608	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:131864608C>T	ENST00000359827.3	-	20	4674	c.3712G>A	c.(3712-3714)Gcc>Acc	p.A1238T	PLXNA4_ENST00000321063.4_Missense_Mutation_p.A1238T			Q9HCM2	PLXA4_HUMAN	plexin A4	1238					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.A1238T(1)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CTGACGATGGCGGGCAGGCTG	0.632																																					p.A1238T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3712A	7						.						18.0	22.0	20.0					7																	131864608		2181	4274	6455	131515148	SO:0001583	missense	91584	exon20			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.3712G>A	7.37:g.131864608C>T	ENSP00000352882:p.Ala1238Thr	Somatic		Capture	Illumina HiSeq	Phase_I	131515148	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	34	5.368570	0.95900	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.01106	5.33;5.33	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	T	0.05640	0.0148	L	0.60904	1.88	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	T	0.47018	-0.9149	10	0.42905	T	0.14	.	18.3041	0.90175	0.0:1.0:0.0:0.0	.	1238	Q9HCM2	PLXA4_HUMAN	T	1238	ENSP00000323194:A1238T;ENSP00000352882:A1238T	ENSP00000323194:A1238T	A	-	1	0	PLXNA4	131515148	1.000000	0.71417	0.997000	0.53966	0.912000	0.54170	5.907000	0.69908	2.582000	0.87167	0.484000	0.47621	GCC		0.632	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
PLXNA4	91584	broad.mit.edu	37	7	131913125	131913125	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:131913125C>T	ENST00000359827.3	-	6	2670	c.1708G>A	c.(1708-1710)Gtc>Atc	p.V570I	PLXNA4_ENST00000321063.4_Missense_Mutation_p.V570I			Q9HCM2	PLXA4_HUMAN	plexin A4	570					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.V570I(1)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						TACTGAGAGACGGAGATATTG	0.592																																					p.V570I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1708A	7						.						75.0	78.0	77.0					7																	131913125		1980	4160	6140	131563665	SO:0001583	missense	91584	exon6			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.1708G>A	7.37:g.131913125C>T	ENSP00000352882:p.Val570Ile	Somatic		Capture	Illumina HiSeq	Phase_I	131563665	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	C	16.49	3.138614	0.56936	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.00922	5.54;5.54	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.01523	0.0049	L	0.45228	1.405	0.58432	D	0.999999	D	0.58268	0.982	B	0.41946	0.371	T	0.77918	-0.2408	10	0.20046	T	0.44	.	20.2985	0.98592	0.0:1.0:0.0:0.0	.	570	Q9HCM2	PLXA4_HUMAN	I	570	ENSP00000323194:V570I;ENSP00000352882:V570I	ENSP00000323194:V570I	V	-	1	0	PLXNA4	131563665	1.000000	0.71417	0.994000	0.49952	0.992000	0.81027	5.965000	0.70387	2.793000	0.96121	0.655000	0.94253	GTC		0.592	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
EXOC4	60412	broad.mit.edu	37	7	132959871	132959871	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:132959871G>A	ENST00000253861.4	+	2	250	c.221G>A	c.(220-222)cGc>cAc	p.R74H	EXOC4_ENST00000393161.2_Missense_Mutation_p.R74H|EXOC4_ENST00000539845.1_5'UTR	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	74					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)	p.R74H(2)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				ACAGCCATTCGCACATACCAG	0.463																																					p.R74H												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G221A	7						.						130.0	114.0	120.0					7																	132959871		2203	4300	6503	132610411	SO:0001583	missense	60412	exon2			AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"""SEC8-like 1 (S. cerevisiae)"""	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.221G>A	7.37:g.132959871G>A	ENSP00000253861:p.Arg74His	Somatic		Capture	Illumina HiSeq	Phase_I	132610411	NM_001037126	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	G	32	5.180782	0.94846	.	.	ENSG00000131558	ENST00000253861;ENST00000393161	.	.	.	5.49	5.49	0.81192	Sec8 exocyst complex component specific domain (1);	0.000000	0.85682	D	0.000000	T	0.72843	0.3511	L	0.43152	1.355	0.80722	D	1	D;D	0.89917	1.0;0.998	D;P	0.66602	0.945;0.903	T	0.70680	-0.4805	9	0.39692	T	0.17	.	19.3733	0.94498	0.0:0.0:1.0:0.0	.	74;74	Q96A65;Q8TAR2	EXOC4_HUMAN;.	H	74	.	ENSP00000253861:R74H	R	+	2	0	EXOC4	132610411	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.539000	0.82063	2.579000	0.87056	0.650000	0.86243	CGC		0.463	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	
AKR1B1	231	broad.mit.edu	37	7	134132069	134132069	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:134132069C>T	ENST00000285930.4	-	8	885	c.806G>A	c.(805-807)cGc>cAc	p.R269H	AKR1B1_ENST00000489022.1_5'Flank	NM_001628.2	NP_001619.1	P15121	ALDR_HUMAN	aldo-keto reductase family 1, member B1 (aldose reductase)	269					C21-steroid hormone biosynthetic process (GO:0006700)|carbohydrate metabolic process (GO:0005975)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)|glyceraldehyde oxidoreductase activity (GO:0043795)	p.R269H(1)		kidney(1)|large_intestine(5)|lung(2)|ovary(3)|prostate(1)|skin(2)	14					Sulindac(DB00605)	CTCAGCAATGCGTTCTGGTGT	0.557																																					p.R269H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G806A	7						.						166.0	120.0	135.0					7																	134132069		2203	4300	6503	133782609	SO:0001583	missense	231	exon8			J04795	CCDS5831.1	7q35	2010-04-08			ENSG00000085662	ENSG00000085662	1.1.1.21	"""Aldo-keto reductases"""	381	protein-coding gene	gene with protein product		103880		ALDR1		1901827	Standard	NM_001628		Approved	AR	uc003vrp.1	P15121	OTTHUMG00000155322	ENST00000285930.4:c.806G>A	7.37:g.134132069C>T	ENSP00000285930:p.Arg269His	Somatic		Capture	Illumina HiSeq	Phase_I	133782609	NM_001628	B2R8N3|Q5U031|Q6FGA4|Q6ICP2|Q9BS21|Q9UCI9	Missense_Mutation	SNP	ENST00000285930.4	37	CCDS5831.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.447949	0.63178	.	.	ENSG00000085662	ENST00000285930	T	0.23552	1.9	5.12	5.12	0.69794	Aldo/keto reductase, conserved site (1);NADP-dependent oxidoreductase domain (3);	0.044768	0.85682	D	0.000000	T	0.29817	0.0745	L	0.60067	1.865	0.80722	D	1	B	0.17268	0.021	B	0.17433	0.018	T	0.08046	-1.0741	10	0.72032	D	0.01	.	16.0955	0.81117	0.0:1.0:0.0:0.0	.	269	P15121	ALDR_HUMAN	H	269	ENSP00000285930:R269H	ENSP00000285930:R269H	R	-	2	0	AKR1B1	133782609	1.000000	0.71417	0.996000	0.52242	0.962000	0.63368	3.381000	0.52455	2.551000	0.86045	0.561000	0.74099	CGC		0.557	AKR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339448.2	NM_001628	
CNOT4	4850	broad.mit.edu	37	7	135047844	135047844	+	Silent	SNP	G	G	A	rs372251198		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:135047844G>A	ENST00000451834.1	-	12	2209	c.1926C>T	c.(1924-1926)gaC>gaT	p.D642D	CNOT4_ENST00000423368.2_Silent_p.D574D|CNOT4_ENST00000473470.1_5'UTR|CNOT4_ENST00000541284.1_Silent_p.D645D|CNOT4_ENST00000361528.4_Silent_p.D571D			O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	0					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D571D(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						CGCTGGGGCCGTCCATCTCTG	0.552																																					p.D645D	Ovarian(51;766 1130 5502 35047 50875)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1935T	7						.	G	,,,	0,4078		0,0,2039	129.0	139.0	136.0		1722,1926,1935,1713	5.0	1.0	7		136	1,8379		0,1,4189	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CNOT4	NM_001190847.1,NM_001190849.1,NM_001190850.1,NM_013316.3	,,,	0,1,6228	AA,AG,GG		0.0119,0.0,0.0080	,,,	574/643,642/711,645/714,571/640	135047844	1,12457	2039	4190	6229	134698384	SO:0001819	synonymous_variant	4850	exon12			AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"""RNA binding motif (RRM) containing"""	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000451834.1:c.1926C>T	7.37:g.135047844G>A		Somatic		Capture	Illumina HiSeq	Phase_I	134698384	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Silent	SNP	ENST00000451834.1	37	CCDS55167.1																																																																																				0.552	CNOT4-003	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340670.1	NM_013316	
KIAA1549	57670	broad.mit.edu	37	7	138554474	138554474	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:138554474C>T	ENST00000422774.1	-	14	4633	c.4585G>A	c.(4585-4587)Gag>Aag	p.E1529K	KIAA1549_ENST00000242365.4_Missense_Mutation_p.E1479K|KIAA1549_ENST00000440172.1_Missense_Mutation_p.E1529K			Q9HCM3	K1549_HUMAN	KIAA1549	1529						integral component of membrane (GO:0016021)		p.E1479K(2)|p.E1529K(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CGATGGTGCTCGATCTCAGAC	0.612			O	BRAF	pilocytic astrocytoma																																p.E1529K	NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G4585A	7						.						31.0	38.0	35.0					7																	138554474		2016	4186	6202	138205014	SO:0001583	missense	57670	exon14				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.4585G>A	7.37:g.138554474C>T	ENSP00000416040:p.Glu1529Lys	Somatic		Capture	Illumina HiSeq	Phase_I	138205014	NM_001164665	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	C	36	5.698942	0.96802	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.72051	-0.61;-0.59;-0.62	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.85182	0.5638	M	0.80422	2.495	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;0.997;0.998;0.994	D	0.87279	0.2291	10	0.87932	D	0	.	17.8016	0.88589	0.0:1.0:0.0:0.0	.	1529;313;1529;313	Q9HCM3;Q9HCM3-4;Q9HCM3-2;Q9HCM3-3	K1549_HUMAN;.;.;.	K	1529;1479;1529	ENSP00000406661:E1529K;ENSP00000242365:E1479K;ENSP00000416040:E1529K	ENSP00000242365:E1479K	E	-	1	0	KIAA1549	138205014	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.487000	0.81328	2.431000	0.82371	0.655000	0.94253	GAG		0.612	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
KIAA1549	57670	broad.mit.edu	37	7	138602190	138602190	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:138602190C>T	ENST00000422774.1	-	2	2230	c.2182G>A	c.(2182-2184)Gag>Aag	p.E728K	KIAA1549_ENST00000242365.4_Missense_Mutation_p.E678K|KIAA1549_ENST00000440172.1_Missense_Mutation_p.E728K			Q9HCM3	K1549_HUMAN	KIAA1549	728	Ser-rich.					integral component of membrane (GO:0016021)		p.E728K(1)|p.E678K(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						TCAACAAACTCGAGAGAATCA	0.468			O	BRAF	pilocytic astrocytoma																																p.E728K	NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2182A	7						.						72.0	68.0	69.0					7																	138602190		1958	4159	6117	138252730	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.2182G>A	7.37:g.138602190C>T	ENSP00000416040:p.Glu728Lys	Somatic		Capture	Illumina HiSeq	Phase_I	138252730	NM_001164665	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	C	0.028	-1.353619	0.01256	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.21191	2.02;2.02;2.02	4.25	-8.5	0.00927	.	2.235860	0.01635	N	0.023729	T	0.06872	0.0175	N	0.04880	-0.145	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.25293	-1.0136	10	0.06236	T	0.91	.	3.6663	0.08257	0.0944:0.3612:0.2867:0.2578	.	728;728	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	K	728;678;728	ENSP00000406661:E728K;ENSP00000242365:E678K;ENSP00000416040:E728K	ENSP00000242365:E678K	E	-	1	0	KIAA1549	138252730	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.827000	0.01704	-3.291000	0.00194	-3.489000	0.00034	GAG		0.468	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
UBN2	254048	broad.mit.edu	37	7	138946196	138946196	+	Silent	SNP	C	C	T	rs371716160		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:138946196C>T	ENST00000473989.3	+	6	1104	c.1104C>T	c.(1102-1104)gaC>gaT	p.D368D	UBN2_ENST00000288561.8_Silent_p.D285D	NM_173569.3	NP_775840.3	Q6ZU65	UBN2_HUMAN	ubinuclein 2	368						extracellular space (GO:0005615)|nucleus (GO:0005634)		p.D285D(2)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	42						TGGGGAATGACGTCCCGGACT	0.483																																					p.D368D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1104T	7						.	C		0,3790		0,0,1895	83.0	82.0	82.0		1104	-12.2	0.0	7		82	1,8223		0,1,4111	no	coding-synonymous	UBN2	NM_173569.3		0,1,6006	TT,TC,CC		0.0122,0.0,0.0083		368/1348	138946196	1,12013	1895	4112	6007	138596736	SO:0001819	synonymous_variant	254048	exon6			AK098644	CCDS43655.1, CCDS43655.2	7q34	2008-12-08			ENSG00000157741	ENSG00000157741			21931	protein-coding gene	gene with protein product		613841				19029251	Standard	NM_173569		Approved	FLJ25778, KIAA2030	uc011kqr.2	Q6ZU65	OTTHUMG00000157623	ENST00000473989.3:c.1104C>T	7.37:g.138946196C>T		Somatic		Capture	Illumina HiSeq	Phase_I	138596736	NM_173569	A4D1S2|Q2YDY4|Q6P1K0|Q86XN9|Q8N7D1	Silent	SNP	ENST00000473989.3	37	CCDS43655.2	.	.	.	.	.	.	.	.	.	.	C	0.362	-0.938861	0.02340	0.0	1.22E-4	ENSG00000157741	ENST00000483726	.	.	.	6.08	-12.2	0.00006	.	.	.	.	.	T	0.39937	0.1097	.	.	.	0.45129	D	0.998146	.	.	.	.	.	.	T	0.49331	-0.8951	4	.	.	.	-6.5709	5.5729	0.17206	0.1582:0.4179:0.0749:0.3489	.	.	.	.	M	137	.	.	T	+	2	0	UBN2	138596736	0.000000	0.05858	0.022000	0.16811	0.217000	0.24651	-0.818000	0.04467	-2.078000	0.00872	-1.152000	0.01820	ACG		0.483	UBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349272.3	NM_173569	
SLC37A3	84255	broad.mit.edu	37	7	140080089	140080089	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:140080089G>A	ENST00000326232.9	-	3	394	c.191C>T	c.(190-192)cCt>cTt	p.P64L	SLC37A3_ENST00000340308.3_Missense_Mutation_p.P64L|SLC37A3_ENST00000461089.1_Intron|SLC37A3_ENST00000429996.2_Missense_Mutation_p.P64L|SLC37A3_ENST00000447932.2_Missense_Mutation_p.P64L	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	64					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.P64L(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					TACCTCCACAGGCAGCTCAAC	0.463																																					p.P64L	Esophageal Squamous(133;211 1716 4665 11387 37873)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C191T	7						.						123.0	99.0	107.0					7																	140080089		2203	4300	6503	139726558	SO:0001583	missense	84255	exon3			AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"""Solute carriers"""	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.191C>T	7.37:g.140080089G>A	ENSP00000321498:p.Pro64Leu	Somatic		Capture	Illumina HiSeq	Phase_I	139726558	NM_032295	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	37	CCDS5859.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.100941	0.76983	.	.	ENSG00000157800	ENST00000340308;ENST00000447932;ENST00000326232;ENST00000429996;ENST00000539816;ENST00000469193	T;T;T;T;T	0.47528	2.15;2.46;2.44;0.84;0.84	4.93	4.93	0.64822	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.631105	0.16606	N	0.207111	T	0.60077	0.2241	L	0.41027	1.25	0.80722	D	1	D;D;D;D;D	0.89917	0.995;0.997;0.976;1.0;1.0	D;D;P;D;D	0.83275	0.943;0.931;0.693;0.994;0.996	T	0.60234	-0.7303	10	0.59425	D	0.04	-22.5683	13.6671	0.62403	0.0:0.0:1.0:0.0	.	64;64;64;64;64	B4DKF5;F5H743;Q8NCC5-2;Q8NCC5-3;Q8NCC5	.;.;.;.;SPX3_HUMAN	L	64	ENSP00000343358:P64L;ENSP00000397481:P64L;ENSP00000321498:P64L;ENSP00000412208:P64L;ENSP00000419024:P64L	ENSP00000321498:P64L	P	-	2	0	SLC37A3	139726558	0.999000	0.42202	0.949000	0.38748	0.784000	0.44337	3.598000	0.54038	2.282000	0.76494	0.313000	0.20887	CCT		0.463	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295	
MKRN1	23608	broad.mit.edu	37	7	140179117	140179117	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:140179117T>G	ENST00000255977.2	-	1	252	c.28A>C	c.(28-30)Aca>Cca	p.T10P	MKRN1_ENST00000480552.1_5'Flank|MKRN1_ENST00000443720.2_Missense_Mutation_p.T10P|MKRN1_ENST00000437223.2_5'UTR|MKRN1_ENST00000474576.1_5'Flank|MKRN1_ENST00000481705.1_5'UTR	NM_013446.3	NP_038474.2	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1	10					protein polyubiquitination (GO:0000209)		chromatin binding (GO:0003682)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	16	Melanoma(164;0.00956)					gttgtggctgttgttccggga	0.677																																					p.T10P												.	.	0			c.A28C	7						.																																			139825586	SO:0001583	missense	23608	exon1			AF192784	CCDS5860.1, CCDS47725.1	7q34	2013-01-09	2008-08-13		ENSG00000133606	ENSG00000133606		"""RING-type (C3HC4) zinc fingers"""	7112	protein-coding gene	gene with protein product		607754				10843807	Standard	NM_013446		Approved	RNF61	uc003vvt.2	Q9UHC7	OTTHUMG00000157412	ENST00000255977.2:c.28A>C	7.37:g.140179117T>G	ENSP00000255977:p.Thr10Pro	None		Capture	Illumina HiSeq	Phase_I	139825586	NM_001145125	A4D1T7|B3KXB4|Q256Y7|Q59G11|Q6GSF1|Q9H0G0|Q9UEZ7|Q9UHW2	Missense_Mutation	SNP	ENST00000255977.2	37	CCDS5860.1	.	.	.	.	.	.	.	.	.	.	T	16.27	3.075296	0.55646	.	.	ENSG00000133606	ENST00000255977;ENST00000443720;ENST00000481705	T;T	0.15139	2.82;2.45	4.76	0.722	0.18225	.	0.153339	0.41938	U	0.000781	T	0.06781	0.0173	N	0.19112	0.55	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.36601	-0.9741	10	0.02654	T	1	.	4.2988	0.10915	0.0:0.1899:0.1715:0.6386	.	10	Q9UHC7	MKRN1_HUMAN	P	10	ENSP00000255977:T10P;ENSP00000416369:T10P	ENSP00000255977:T10P	T	-	1	0	MKRN1	139825586	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.092000	0.30927	0.192000	0.20272	0.439000	0.28862	ACA		0.677	MKRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348752.1	NM_013446	
MGAM	8972	broad.mit.edu	37	7	141795484	141795484	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:141795484C>T	ENST00000549489.2	+	41	4985	c.4890C>T	c.(4888-4890)ggC>ggT	p.G1630G	MGAM_ENST00000475668.2_Silent_p.G2526G	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1630	Glucoamylase.				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.G1630G(1)		cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	ACACGGAGGGCGTCACTGTTG	0.483																																					p.G1630G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4890T	7						.						200.0	183.0	189.0					7																	141795484		1968	4147	6115	141441953	SO:0001819	synonymous_variant	8972	exon41			AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.4890C>T	7.37:g.141795484C>T		Somatic		Capture	Illumina HiSeq	Phase_I	141441953	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																				0.483	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
EPHB6	2051	broad.mit.edu	37	7	142561932	142561932	+	Missense_Mutation	SNP	G	G	A	rs201326184		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:142561932G>A	ENST00000392957.2	+	7	1161	c.374G>A	c.(373-375)cGg>cAg	p.R125Q	EPHB6_ENST00000411471.2_Intron|EPHB6_ENST00000442129.1_Missense_Mutation_p.R125Q	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	125	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)	p.R110Q(1)		NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					GGCACCTGCCGGGAGACCTTC	0.632																																					p.R125Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G374A	7						.						56.0	62.0	60.0					7																	142561932		2203	4300	6503	142272054	SO:0001583	missense	2051	exon7			D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3396	protein-coding gene	gene with protein product		602757	"""EphB6"""				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.374G>A	7.37:g.142561932G>A	ENSP00000376684:p.Arg125Gln	Somatic		Capture	Illumina HiSeq	Phase_I	142272054	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	37	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	G	29.9	5.044467	0.93685	.	.	ENSG00000106123	ENST00000392957;ENST00000442129	T;T	0.03951	3.75;3.75	5.6	5.6	0.85130	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.40064	N	0.001181	T	0.17109	0.0411	M	0.69823	2.125	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.00069	-1.2136	10	0.87932	D	0	.	8.2191	0.31530	0.1691:0.0:0.8309:0.0	.	125	O15197	EPHB6_HUMAN	Q	125	ENSP00000376684:R125Q;ENSP00000410789:R125Q	ENSP00000376684:R125Q	R	+	2	0	EPHB6	142272054	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.589000	0.82641	2.640000	0.89533	0.655000	0.94253	CGG		0.632	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1		
TRPV6	55503	broad.mit.edu	37	7	142570171	142570171	+	Missense_Mutation	SNP	C	C	T	rs576385529		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:142570171C>T	ENST00000359396.3	-	14	2094	c.1849G>A	c.(1849-1851)Ggg>Agg	p.G617R		NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	617					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)	p.G617R(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					CCGCAGATCCCGGAGCGAGGC	0.617													C|||	1	0.000199681	0.0	0.0	5008	,	,		18018	0.0		0.0	False		,,,				2504	0.001				p.G617R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1849A	7						.						58.0	53.0	55.0					7																	142570171		2203	4300	6503	142280293	SO:0001583	missense	55503	exon14			AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	14006	protein-coding gene	gene with protein product		606680	"""epithelial calcium channel 2"""	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.1849G>A	7.37:g.142570171C>T	ENSP00000352358:p.Gly617Arg	Somatic		Capture	Illumina HiSeq	Phase_I	142280293	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	ENST00000359396.3	37	CCDS5874.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906837	0.92107	.	.	ENSG00000165125	ENST00000359396;ENST00000311470	T	0.78364	-1.17	5.38	4.49	0.54785	.	0.111729	0.64402	D	0.000009	D	0.88325	0.6406	M	0.84948	2.725	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88495	0.3078	10	0.38643	T	0.18	-32.9065	14.5599	0.68128	0.1473:0.8527:0.0:0.0	.	617	Q9H1D0	TRPV6_HUMAN	R	617;449	ENSP00000352358:G617R	ENSP00000310825:G449R	G	-	1	0	TRPV6	142280293	1.000000	0.71417	0.748000	0.31131	0.958000	0.62258	7.423000	0.80229	1.476000	0.48215	0.655000	0.94253	GGG		0.617	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274	
TRPV5	56302	broad.mit.edu	37	7	142626551	142626551	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:142626551G>A	ENST00000265310.1	-	4	807	c.459C>T	c.(457-459)cgC>cgT	p.R153R	TRPV5_ENST00000442623.1_Silent_p.R153R	NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	153					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.R153R(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)					GGGGACTACGGCGGAAGGCAG	0.617																																					p.R153R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C459T	7						.						82.0	71.0	75.0					7																	142626551		2203	4300	6503	142336673	SO:0001819	synonymous_variant	56302	exon4			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.459C>T	7.37:g.142626551G>A		Somatic		Capture	Illumina HiSeq	Phase_I	142336673	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Silent	SNP	ENST00000265310.1	37	CCDS5875.1																																																																																				0.617	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841	
CASP2	835	broad.mit.edu	37	7	142997327	142997327	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:142997327G>A	ENST00000310447.5	+	8	1148	c.907G>A	c.(907-909)Gcc>Acc	p.A303T	RN7SL481P_ENST00000477764.2_RNA|CASP2_ENST00000493642.1_3'UTR	NM_032982.3|NM_032983.3	NP_116764.2|NP_116765.2	P42575	CASP2_HUMAN	caspase 2, apoptosis-related cysteine peptidase	303					aging (GO:0007568)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|cellular response to mechanical stimulus (GO:0071260)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|ectopic germ cell programmed cell death (GO:0035234)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|luteolysis (GO:0001554)|neural retina development (GO:0003407)|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 neuron apoptotic process (GO:0043525)|protein processing (GO:0016485)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)	p.A303T(1)		endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(164;0.059)					CTTTGACAACGCCAACTGCCC	0.522																																					p.A303T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G907A	7						.						83.0	75.0	77.0					7																	142997327		2203	4300	6503	142707449	SO:0001583	missense	835	exon8			AK096245, BC002427, BM998653, BX537669, CB988674, U13021	CCDS5879.1, CCDS47733.1	7q34-q35	2014-01-20	2008-08-01		ENSG00000106144	ENSG00000106144		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1503	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 57"""	600639	"""neural precursor cell expressed, developmentally down-regulated 2"""	NEDD2		7789948, 8780721	Standard	NM_032982		Approved	ICH1, PPP1R57, MGC2181	uc003wco.3	P42575	OTTHUMG00000023641	ENST00000310447.5:c.907G>A	7.37:g.142997327G>A	ENSP00000312664:p.Ala303Thr	Somatic		Capture	Illumina HiSeq	Phase_I	142707449	NM_032982	A8K5F9|D3DXD6|E9PDN0|P42576|Q59F21|Q7KZL6|Q86UJ3|Q9BUP7|Q9BZK9|Q9BZL0	Missense_Mutation	SNP	ENST00000310447.5	37	CCDS5879.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.989340	0.93106	.	.	ENSG00000106144	ENST00000310447;ENST00000392923	T	0.20200	2.09	5.52	5.52	0.82312	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);Peptidase C14, ICE, catalytic subunit p20 (1);	0.000000	0.85682	D	0.000000	T	0.37517	0.1006	L	0.33245	0.995	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.03166	-1.1065	10	0.39692	T	0.17	.	19.5137	0.95154	0.0:0.0:1.0:0.0	.	303	P42575	CASP2_HUMAN	T	303;272	ENSP00000312664:A303T	ENSP00000312664:A303T	A	+	1	0	CASP2	142707449	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.196000	0.94978	2.612000	0.88384	0.644000	0.83932	GCC		0.522	CASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059962.3	NM_032982	
OR2A25	392138	broad.mit.edu	37	7	143772073	143772073	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:143772073C>T	ENST00000408898.2	+	1	799	c.761C>T	c.(760-762)gCc>gTc	p.A254V		NM_001004488.1	NP_001004488.1	A4D2G3	O2A25_HUMAN	olfactory receptor, family 2, subfamily A, member 25	254						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A254V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(16)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	24	Melanoma(164;0.0783)					TATGGCACAGCCATCATCATG	0.498																																					p.A254V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C761T	7						.						130.0	141.0	137.0					7																	143772073		2199	4299	6498	143403006	SO:0001583	missense	392138	exon1				CCDS43669.1	7q35	2012-08-09		2004-03-10	ENSG00000221933	ENSG00000221933		"""GPCR / Class A : Olfactory receptors"""	19562	protein-coding gene	gene with protein product				OR2A25P, OR2A27			Standard	NM_001004488		Approved		uc011ktx.2	A4D2G3	OTTHUMG00000158013	ENST00000408898.2:c.761C>T	7.37:g.143772073C>T	ENSP00000386167:p.Ala254Val	Somatic		Capture	Illumina HiSeq	Phase_I	143403006	NM_001004488	B2RNC9	Missense_Mutation	SNP	ENST00000408898.2	37	CCDS43669.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957135	0.53293	.	.	ENSG00000221933	ENST00000408898	T	0.00123	8.7	4.69	4.69	0.59074	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00328	0.0010	L	0.46885	1.475	0.32602	N	0.525788	D	0.89917	1.0	D	0.87578	0.998	T	0.69676	-0.5081	9	0.52906	T	0.07	-10.0815	8.6906	0.34264	0.0:0.8987:0.0:0.1013	.	254	A4D2G3	O2A25_HUMAN	V	254	ENSP00000386167:A254V	ENSP00000386167:A254V	A	+	2	0	OR2A25	143403006	0.000000	0.05858	1.000000	0.80357	0.782000	0.44232	-0.171000	0.09883	2.435000	0.82474	0.563000	0.77884	GCC		0.498	OR2A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350000.1		
EZH2	2146	broad.mit.edu	37	7	148506454	148506454	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:148506454A>G	ENST00000460911.1	-	18	2131	c.2043T>C	c.(2041-2043)ggT>ggC	p.G681G	EZH2_ENST00000541220.1_Silent_p.G630G|EZH2_ENST00000483967.1_Silent_p.G672G|EZH2_ENST00000478654.1_Silent_p.G630G|EZH2_ENST00000320356.2_Silent_p.G686G|EZH2_ENST00000476773.1_Silent_p.G630G|EZH2_ENST00000350995.2_Silent_p.G642G			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	681	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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.G686G(1)|p.G642G(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)			GAATTTTGTTACCCTTGCGGG	0.368			Mis		DLBCL																																p.G642G			Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T1926C	7						.						109.0	109.0	109.0					7																	148506454		2203	4300	6503	148137387	SO:0001819	synonymous_variant	2146	exon17				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.2043T>C	7.37:g.148506454A>G		Somatic		Capture	Illumina HiSeq	Phase_I	148137387	NM_152998	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Silent	SNP	ENST00000460911.1	37	CCDS56516.1																																																																																				0.368	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456	
PDIA4	9601	broad.mit.edu	37	7	148701043	148701043	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:148701043C>T	ENST00000286091.4	-	10	2013	c.1781G>A	c.(1780-1782)cGc>cAc	p.R594H		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	594	Thioredoxin 3. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein secretion (GO:0009306)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)	p.R594H(1)		large_intestine(6)|lung(15)|ovary(2)|prostate(1)	24	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			CACCTTATAGCGGTCGCTGGG	0.562																																					p.R594H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1781A	7						.						94.0	95.0	95.0					7																	148701043		2203	4300	6503	148331976	SO:0001583	missense	9601	exon10			BC001928	CCDS5893.1	7q35	2009-11-20	2005-06-29		ENSG00000155660	ENSG00000155660	5.3.4.1	"""Protein disulfide isomerases"""	30167	protein-coding gene	gene with protein product			"""protein disulfide isomerase-associated 4"""			2549034, 2002068	Standard	NM_004911		Approved	ERP70, ERP72	uc003wff.2	P13667	OTTHUMG00000150248	ENST00000286091.4:c.1781G>A	7.37:g.148701043C>T	ENSP00000286091:p.Arg594His	Somatic		Capture	Illumina HiSeq	Phase_I	148331976	NM_004911	A8K4K6|Q549T6	Missense_Mutation	SNP	ENST00000286091.4	37	CCDS5893.1	.	.	.	.	.	.	.	.	.	.	C	5.977	0.364305	0.11296	.	.	ENSG00000155660	ENST00000286091	T	0.25085	1.82	5.81	1.41	0.22369	Thioredoxin domain (1);Thioredoxin-like fold (3);Disulphide isomerase (1);	0.524458	0.22280	N	0.062140	T	0.16727	0.0402	L	0.28649	0.875	0.24018	N	0.996157	B	0.10296	0.003	B	0.10450	0.005	T	0.18116	-1.0347	10	0.44086	T	0.13	.	8.3558	0.32329	0.0:0.5044:0.0:0.4956	.	594	P13667	PDIA4_HUMAN	H	594	ENSP00000286091:R594H	ENSP00000286091:R594H	R	-	2	0	PDIA4	148331976	0.239000	0.23836	1.000000	0.80357	0.758000	0.43043	-0.383000	0.07398	0.364000	0.24374	0.555000	0.69702	CGC		0.562	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911	
ZNF425	155054	broad.mit.edu	37	7	148801797	148801797	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:148801797C>T	ENST00000378061.2	-	4	1298	c.1166G>A	c.(1165-1167)gGt>gAt	p.G389D		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	389					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.G389D(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)			GCCACATTCACCACAAGAAAA	0.542																																					p.G389D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1166A	7						.						105.0	114.0	111.0					7																	148801797		2203	4300	6503	148432730	SO:0001583	missense	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.1166G>A	7.37:g.148801797C>T	ENSP00000367300:p.Gly389Asp	Somatic		Capture	Illumina HiSeq	Phase_I	148432730	NM_001001661	B3KPM1|Q08AG3	Missense_Mutation	SNP	ENST00000378061.2	37	CCDS34773.1	.	.	.	.	.	.	.	.	.	.	C	1.875	-0.459343	0.04508	.	.	ENSG00000204947	ENST00000378061	T	0.07216	3.21	3.43	-6.86	0.01676	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03477	0.0100	N	0.05510	-0.035	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45469	-0.9259	9	0.33141	T	0.24	.	8.4071	0.32621	0.0:0.4932:0.3462:0.1606	.	389	Q6IV72	ZN425_HUMAN	D	389	ENSP00000367300:G389D	ENSP00000367300:G389D	G	-	2	0	ZNF425	148432730	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-2.310000	0.01129	-1.244000	0.02516	-1.267000	0.01435	GGT		0.542	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140	
ZNF777	27153	broad.mit.edu	37	7	149153084	149153084	+	Silent	SNP	C	C	T	rs376056761	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:149153084C>T	ENST00000247930.4	-	2	353	c.30G>A	c.(28-30)tcG>tcA	p.S10S		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	10					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.S10S(1)		large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CACTGGGGAACGACAGAGGTG	0.512													C|||	10	0.00199681	0.0076	0.0	5008	,	,		16812	0.0		0.0	False		,,,				2504	0.0				p.S10S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G30A	7						.	C		16,3880		0,16,1932	57.0	60.0	59.0		30	-2.2	1.0	7		59	0,8270		0,0,4135	no	coding-synonymous	ZNF777	NM_015694.2		0,16,6067	TT,TC,CC		0.0,0.4107,0.1315		10/832	149153084	16,12150	1948	4135	6083	148784017	SO:0001819	synonymous_variant	27153	exon2			AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"""Zinc fingers, C2H2-type"", ""-"""	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.30G>A	7.37:g.149153084C>T		Somatic		Capture	Illumina HiSeq	Phase_I	148784017	NM_015694	Q8N2R2|Q8N659	Silent	SNP	ENST00000247930.4	37	CCDS43675.1																																																																																				0.512	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694	
KRBA1	84626	broad.mit.edu	37	7	149419995	149419995	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:149419995C>T	ENST00000485033.2	+	6	720	c.720C>T	c.(718-720)ggC>ggT	p.G240G	KRBA1_ENST00000479560.1_3'UTR|KRBA1_ENST00000255992.10_Silent_p.G240G|KRBA1_ENST00000319551.8_Silent_p.G240G			A5PL33	KRBA1_HUMAN	KRAB-A domain containing 1	240								p.G240G(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)			CTAGCCTGGGCACGTCCAGGC	0.622																																					p.G240G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C720T	7						.						33.0	36.0	35.0					7																	149419995		1884	4100	5984	149050928	SO:0001819	synonymous_variant	84626	exon7			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.720C>T	7.37:g.149419995C>T		Somatic		Capture	Illumina HiSeq	Phase_I	149050928	NM_032534	A7E2F5|E7ENE9|Q8N4X0|Q96JG5	Silent	SNP	ENST00000485033.2	37																																																																																					0.622	KRBA1-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000349841.3	NM_032534	
ZNF862	643641	broad.mit.edu	37	7	149547368	149547368	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:149547368G>A	ENST00000223210.4	+	5	1303	c.1058G>A	c.(1057-1059)cGg>cAg	p.R353Q		NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	353	KRAB 2. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.R353Q(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						CTAGACAAGCGGCAGAAGGAG	0.562																																					p.R353Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1058A	7						.						94.0	106.0	102.0					7																	149547368		2178	4280	6458	149178301	SO:0001583	missense	643641	exon5			AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"""Zinc fingers, C2H2-type"", ""-"""	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.1058G>A	7.37:g.149547368G>A	ENSP00000223210:p.Arg353Gln	Somatic		Capture	Illumina HiSeq	Phase_I	149178301	NM_001099220	A0AUL8	Missense_Mutation	SNP	ENST00000223210.4	37	CCDS47741.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.249486	0.39797	.	.	ENSG00000106479	ENST00000223210	T	0.01647	4.71	5.03	1.17	0.20885	Krueppel-associated box (4);	0.767059	0.11487	N	0.559133	T	0.00875	0.0029	N	0.03071	-0.42	0.25315	N	0.989164	B	0.19706	0.038	B	0.17979	0.02	T	0.48980	-0.8986	10	0.22706	T	0.39	-3.2493	4.551	0.12112	0.271:0.1626:0.5664:0.0	.	353	O60290	ZN862_HUMAN	Q	353	ENSP00000223210:R353Q	ENSP00000223210:R353Q	R	+	2	0	ZNF862	149178301	0.040000	0.19996	0.961000	0.40146	0.983000	0.72400	0.085000	0.14912	-0.061000	0.13110	-0.150000	0.13652	CGG		0.562	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
GIMAP1	170575	broad.mit.edu	37	7	150417468	150417468	+	Missense_Mutation	SNP	G	G	A	rs374968861		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:150417468G>A	ENST00000307194.5	+	3	516	c.376G>A	c.(376-378)Gcc>Acc	p.A126T		NM_130759.3	NP_570115.1	Q8WWP7	GIMA1_HUMAN	GTPase, IMAP family member 1	126	AIG1-type G.				B cell differentiation (GO:0030183)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)	p.A126T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCGGTTCACCGCCCAGGACCA	0.637																																					p.A126T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G376A	7						.	G	THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	46.0	45.0	45.0		376,376	-4.7	0.0	7		45	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GIMAP1,GIMAP1-GIMAP5	NM_001199577.1,NM_130759.3	58,58	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign,benign	126/512,126/307	150417468	2,13004	2203	4300	6503	150048401	SO:0001583	missense	170575	exon3			AJ306287	CCDS5906.1	7q36.1	2014-04-04			ENSG00000213203	ENSG00000213203		"""GTPases, IMAP"""	23237	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 2"""	608084				15474311, 18701445	Standard	NM_130759		Approved	HIMAP1, IMAP38, IMAP1, IAN2		Q8WWP7	OTTHUMG00000157489	ENST00000307194.5:c.376G>A	7.37:g.150417468G>A	ENSP00000302833:p.Ala126Thr	Somatic		Capture	Illumina HiSeq	Phase_I	150048401	NM_130759	B2RCI3|Q8NAZ0	Missense_Mutation	SNP	ENST00000307194.5	37	CCDS5906.1	.	.	.	.	.	.	.	.	.	.	G	9.811	1.183215	0.21870	2.27E-4	1.16E-4	ENSG00000213203	ENST00000307194	T	0.61742	0.08	4.72	-4.65	0.03339	AIG1 (1);	3.346840	0.01980	U	0.044724	T	0.37237	0.0996	N	0.16266	0.395	0.09310	N	1	B	0.15473	0.013	B	0.12156	0.007	T	0.13176	-1.0519	10	0.24483	T	0.36	.	6.2026	0.20585	0.5487:0.2703:0.1809:0.0	.	126	Q8WWP7	GIMA1_HUMAN	T	126	ENSP00000302833:A126T	ENSP00000302833:A126T	A	+	1	0	GIMAP1	150048401	0.000000	0.05858	0.001000	0.08648	0.627000	0.37826	-0.026000	0.12392	-0.826000	0.04284	-0.751000	0.03497	GCC		0.637	GIMAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348951.2	NM_130759	
SMARCD3	6604	broad.mit.edu	37	7	150937304	150937304	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:150937304G>A	ENST00000262188.8	-	10	1477	c.1067C>T	c.(1066-1068)gCg>gTg	p.A356V	RP4-548D19.3_ENST00000607902.1_RNA|MIR671_ENST00000390183.1_RNA|SMARCD3_ENST00000477169.1_5'Flank|SMARCD3_ENST00000356800.2_Missense_Mutation_p.A343V|SMARCD3_ENST00000392811.2_Missense_Mutation_p.A343V	NM_001003801.1	NP_001003801.1	Q6STE5	SMRD3_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3	356					cardiac right ventricle formation (GO:0003219)|cellular lipid metabolic process (GO:0044255)|chromatin remodeling (GO:0006338)|muscle cell differentiation (GO:0042692)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of protein binding (GO:0043393)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|secondary heart field specification (GO:0003139)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|receptor binding (GO:0005102)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.A343V(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(6)|ovary(2)	15			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTCATAGCACGCCGTCTTCTT	0.627																																					p.A343V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1028T	7						.						132.0	100.0	111.0					7																	150937304		2203	4300	6503	150568237	SO:0001583	missense	6604	exon11			U66619	CCDS5924.1, CCDS34780.1	7q35-q36	2008-07-18			ENSG00000082014	ENSG00000082014			11108	protein-coding gene	gene with protein product	"""mammalian chromatin remodeling complex BRG1-associated factor 60C"", ""Swp73-like protein"", ""SWI/SNF complex 60 kDa subunit C"", ""60kDa BRG-1/Brm associated factor subunit c"""	601737				8804307, 9693044	Standard	NM_001003801		Approved	BAF60C, Rsc6p, CRACD3	uc003wjs.3	Q6STE5	OTTHUMG00000157431	ENST00000262188.8:c.1067C>T	7.37:g.150937304G>A	ENSP00000262188:p.Ala356Val	Somatic		Capture	Illumina HiSeq	Phase_I	150568237	NM_003078	D3DX10|Q2YD86|Q75MJ2|Q75MR8|Q92926|Q9BUH1	Missense_Mutation	SNP	ENST00000262188.8	37	CCDS34780.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.957512	0.92726	.	.	ENSG00000082014	ENST00000262188;ENST00000392811;ENST00000356800;ENST00000347683	T;T;T	0.47177	0.85;0.85;0.85	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.73225	0.3560	M	0.88105	2.93	0.80722	D	1	D;D	0.76494	0.999;0.977	D;B	0.71184	0.972;0.434	T	0.78753	-0.2081	10	0.66056	D	0.02	-9.5223	16.4674	0.84083	0.0:0.0:1.0:0.0	.	343;356	Q6STE5-2;Q6STE5	.;SMRD3_HUMAN	V	356;343;343;308	ENSP00000262188:A356V;ENSP00000376558:A343V;ENSP00000349254:A343V	ENSP00000262188:A356V	A	-	2	0	SMARCD3	150568237	1.000000	0.71417	0.911000	0.35937	0.878000	0.50629	9.869000	0.99810	2.478000	0.83669	0.563000	0.77884	GCG		0.627	SMARCD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348825.1	NM_001003801	
TMEM184A	202915	broad.mit.edu	37	7	1589819	1589819	+	Silent	SNP	G	G	A	rs566323218	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:1589819G>A	ENST00000297477.5	-	5	808	c.492C>T	c.(490-492)taC>taT	p.Y164Y		NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	164					germ-line sex determination (GO:0018992)|regulation of protein localization (GO:0032880)|regulation of secretion (GO:0051046)	early endosome membrane (GO:0031901)|integral component of membrane (GO:0016021)		p.Y164Y(1)		endometrium(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	12		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;5.88e-15)		AGCAGGTGCCGTACAAGCAGC	0.711													G|||	2	0.000399361	0.0	0.0029	5008	,	,		12673	0.0		0.0	False		,,,				2504	0.0				p.Y164Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C492T	7						.						12.0	16.0	15.0					7																	1589819		2097	4238	6335	1556345	SO:0001819	synonymous_variant	202915	exon5				CCDS43537.1	7p22.3	2008-05-02			ENSG00000164855	ENSG00000164855			28797	protein-coding gene	gene with protein product						12477932	Standard	NM_001097620		Approved	MGC9712	uc003skv.4	Q6ZMB5	OTTHUMG00000119025	ENST00000297477.5:c.492C>T	7.37:g.1589819G>A		Somatic		Capture	Illumina HiSeq	Phase_I	1556345	NM_001097620	Q8TBQ6	De_novo_Start_InFrame	SNP	ENST00000297477.5	37	CCDS43537.1																																																																																				0.711	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689	
NUB1	51667	broad.mit.edu	37	7	151071275	151071275	+	Silent	SNP	C	C	T	rs567952492		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:151071275C>T	ENST00000355851.4	+	12	1418	c.1341C>T	c.(1339-1341)caC>caT	p.H447H	NUB1_ENST00000568733.1_Silent_p.H471H|NUB1_ENST00000566856.1_Silent_p.H447H|NUB1_ENST00000413040.2_Silent_p.H471H|WDR86_ENST00000463000.1_5'Flank	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	447	NEDD8-binding 1.|UBA 2. {ECO:0000255|PROSITE- ProRule:PRU00212}.				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.H447H(1)		endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		ACTCCACGCACGCGGCCCAGC	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		19509	0.001		0.0	False		,,,				2504	0.0				p.H447H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1341T	7						.						38.0	45.0	43.0					7																	151071275		2053	4173	6226	150702208	SO:0001819	synonymous_variant	51667	exon12			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.1341C>T	7.37:g.151071275C>T		Somatic		Capture	Illumina HiSeq	Phase_I	150702208	NM_016118	O95422|Q75MR9|Q8IX22|Q9BXR2	Silent	SNP	ENST00000355851.4	37		.	.	.	.	.	.	.	.	.	.	C	6.596	0.478370	0.12521	.	.	ENSG00000013374	ENST00000480714	.	.	.	5.09	-10.2	0.00374	.	.	.	.	.	T	0.32102	0.0818	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43925	-0.9361	4	.	.	.	-16.4843	1.0003	0.01475	0.3348:0.238:0.3056:0.1217	.	.	.	.	C	51	.	.	R	+	1	0	NUB1	150702208	0.000000	0.05858	0.000000	0.03702	0.809000	0.45718	-3.015000	0.00645	-3.314000	0.00189	-0.274000	0.10170	CGC		0.582	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118	
SNX8	29886	broad.mit.edu	37	7	2303988	2303988	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:2303988C>T	ENST00000222990.3	-	6	769	c.727G>A	c.(727-729)Gca>Aca	p.A243T		NM_013321.2	NP_037453.1	Q9Y5X2	SNX8_HUMAN	sorting nexin 8	243					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.A243T(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)		GCCCGCGATGCGATCCGCTCG	0.592																																					p.A243T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G727A	7						.						82.0	69.0	74.0					7																	2303988		2203	4300	6503	2270514	SO:0001583	missense	29886	exon6			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	ENST00000222990.3:c.727G>A	7.37:g.2303988C>T	ENSP00000222990:p.Ala243Thr	Somatic		Capture	Illumina HiSeq	Phase_I	2270514	NM_013321	A4D207|Q96I67	Missense_Mutation	SNP	ENST00000222990.3	37	CCDS5331.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.469620	0.43839	.	.	ENSG00000106266	ENST00000222990	.	.	.	5.19	5.19	0.71726	.	0.063758	0.64402	D	0.000007	T	0.54581	0.1867	L	0.43152	1.355	0.58432	D	0.999994	B	0.28783	0.222	B	0.17722	0.019	T	0.51317	-0.8721	9	0.27785	T	0.31	.	18.7147	0.91671	0.0:1.0:0.0:0.0	.	243	Q9Y5X2	SNX8_HUMAN	T	243	.	ENSP00000222990:A243T	A	-	1	0	SNX8	2270514	1.000000	0.71417	0.010000	0.14722	0.681000	0.39784	7.119000	0.77145	2.421000	0.82119	0.655000	0.94253	GCA		0.592	SNX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322949.2		
CHST12	55501	broad.mit.edu	37	7	2472318	2472318	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:2472318C>T	ENST00000258711.6	+	2	179	c.44C>T	c.(43-45)tCg>tTg	p.S15L		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	15					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)	p.S15L(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		GTGCTGGGGTCGGTGTTCATG	0.672																																					p.S15L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C44T	7						.						50.0	42.0	45.0					7																	2472318		2203	4300	6503	2438844	SO:0001583	missense	55501	exon2			AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"""Sulfotransferases, membrane-bound"""	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.44C>T	7.37:g.2472318C>T	ENSP00000258711:p.Ser15Leu	Somatic		Capture	Illumina HiSeq	Phase_I	2438844	NM_018641	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	37	CCDS5333.1	.	.	.	.	.	.	.	.	.	.	C	17.25	3.343056	0.61073	.	.	ENSG00000136213	ENST00000258711;ENST00000432336	T;T	0.69435	-0.4;0.37	5.05	4.17	0.49024	.	0.200912	0.44483	D	0.000445	T	0.68183	0.2973	M	0.70595	2.14	0.51767	D	0.999937	D	0.62365	0.991	P	0.45558	0.485	T	0.73116	-0.4084	10	0.72032	D	0.01	-4.7466	12.9888	0.58606	0.0:0.9215:0.0:0.0785	.	15	Q9NRB3	CHSTC_HUMAN	L	15	ENSP00000258711:S15L;ENSP00000411207:S15L	ENSP00000258711:S15L	S	+	2	0	CHST12	2438844	1.000000	0.71417	0.306000	0.25113	0.430000	0.31655	5.871000	0.69628	1.108000	0.41662	0.561000	0.74099	TCG		0.672	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641	
GNA12	2768	broad.mit.edu	37	7	2834753	2834753	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:2834753G>A	ENST00000275364.3	-	2	496	c.334C>T	c.(334-336)Cga>Tga	p.R112*	GNA12_ENST00000544127.1_Nonsense_Mutation_p.R36*|GNA12_ENST00000407904.3_Nonsense_Mutation_p.R53*	NM_007353.2	NP_031379.2	Q03113	GNA12_HUMAN	guanine nucleotide binding protein (G protein) alpha 12	112					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic digit morphogenesis (GO:0042733)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|platelet activation (GO:0030168)|regulation of cell shape (GO:0008360)|regulation of fibroblast migration (GO:0010762)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)|response to drug (GO:0042493)|Rho protein signal transduction (GO:0007266)	brush border membrane (GO:0031526)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)	p.R112*(1)		endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.02e-13)		AGCTTATCTCGTGCATCAACA	0.468																																					p.R112X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C334T	7						.						132.0	129.0	130.0					7																	2834753		2203	4300	6503	2801279	SO:0001587	stop_gained	2768	exon2			L01694	CCDS5335.1, CCDS64584.1, CCDS64583.1	7p22.3	2006-07-08			ENSG00000146535	ENSG00000146535			4380	protein-coding gene	gene with protein product		604394				8423800, 16247467	Standard	NM_007353		Approved	gep	uc003smu.3	Q03113	OTTHUMG00000023064	ENST00000275364.3:c.334C>T	7.37:g.2834753G>A	ENSP00000275364:p.Arg112*	Somatic		Capture	Illumina HiSeq	Phase_I	2801279	NM_007353	A4D204|B3KXS2|B7Z3F7|Q2T9L1|Q5PPR5|Q86UM8|Q8TD71|Q9UDU9	Nonsense_Mutation	SNP	ENST00000275364.3	37	CCDS5335.1	.	.	.	.	.	.	.	.	.	.	G	35	5.465874	0.96257	.	.	ENSG00000146535	ENST00000275364;ENST00000407904;ENST00000544127;ENST00000447791	.	.	.	5.58	4.71	0.59529	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	.	12.7454	0.57278	0.0757:0.0:0.9243:0.0	.	.	.	.	X	112;53;36;27	.	ENSP00000275364:R112X	R	-	1	2	GNA12	2801279	1.000000	0.71417	0.856000	0.33681	0.450000	0.32258	6.062000	0.71155	1.379000	0.46325	-0.251000	0.11542	CGA		0.468	GNA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241608.1	NM_007353	
CARD11	84433	broad.mit.edu	37	7	2959180	2959180	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:2959180C>T	ENST00000396946.4	-	18	2739	c.2336G>A	c.(2335-2337)cGg>cAg	p.R779Q		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	779					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)	p.R772Q(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CAGGTTCAGCCGGATGTAGAA	0.582			Mis		DLBCL																																p.R779Q			Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2336A	7						.						124.0	78.0	94.0					7																	2959180		2203	4300	6503	2925706	SO:0001583	missense	84433	exon18			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.2336G>A	7.37:g.2959180C>T	ENSP00000380150:p.Arg779Gln	Somatic		Capture	Illumina HiSeq	Phase_I	2925706	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	C	34	5.359684	0.95854	.	.	ENSG00000198286	ENST00000396946;ENST00000355508	T;T	0.61980	0.06;1.32	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.73289	0.3568	L	0.43923	1.385	0.80722	D	1	D	0.76494	0.999	D	0.67725	0.953	T	0.76214	-0.3041	10	0.87932	D	0	-39.3656	18.7247	0.91710	0.0:1.0:0.0:0.0	.	779	Q9BXL7	CAR11_HUMAN	Q	779;250	ENSP00000380150:R779Q;ENSP00000347695:R250Q	ENSP00000347695:R250Q	R	-	2	0	CARD11	2925706	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.743000	0.68655	2.503000	0.84419	0.561000	0.74099	CGG		0.582	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
FOXK1	221937	broad.mit.edu	37	7	4801817	4801817	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:4801817C>A	ENST00000328914.4	+	9	1924	c.1924C>A	c.(1924-1926)Ctc>Atc	p.L642I	FOXK1_ENST00000446823.1_Missense_Mutation_p.L479I	NM_001037165.1	NP_001032242.1			forkhead box K1									p.L642I(1)|p.L620I(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		CACTCCAGCCCTCACCAGCCC	0.622																																					p.L642I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1924A	7						.						46.0	29.0	35.0					7																	4801817		2137	4191	6328	4768343	SO:0001583	missense	221937	exon9			BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"""Forkhead boxes"""	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.1924C>A	7.37:g.4801817C>A	ENSP00000328720:p.Leu642Ile	Somatic		Capture	Illumina HiSeq	Phase_I	4768343	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	37	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	c	16.90	3.249000	0.59103	.	.	ENSG00000164916	ENST00000446823;ENST00000450194;ENST00000328914;ENST00000545598	D;D	0.96011	-3.53;-3.88	4.82	4.82	0.62117	.	0.371203	0.25200	N	0.032394	D	0.95639	0.8582	L	0.40543	1.245	0.44402	D	0.99731	P;D	0.71674	0.894;0.998	B;D	0.63488	0.437;0.915	D	0.94405	0.7626	10	0.29301	T	0.29	.	15.0709	0.72037	0.0:1.0:0.0:0.0	.	642;479	P85037;P85037-2	FOXK1_HUMAN;.	I	479;398;642;525	ENSP00000394442:L479I;ENSP00000328720:L642I	ENSP00000328720:L642I	L	+	1	0	FOXK1	4768343	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	2.455000	0.44988	2.232000	0.73038	0.556000	0.70494	CTC		0.622	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2		
RADIL	55698	broad.mit.edu	37	7	4917282	4917282	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:4917282C>T	ENST00000399583.3	-	2	676	c.489G>A	c.(487-489)tcG>tcA	p.S163S	RADIL_ENST00000536091.1_Silent_p.S163S	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	163	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)		p.S163S(1)		NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CCTCCACGTCCGACCTCTTCC	0.597																																					p.S163S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G489A	7						.						60.0	72.0	68.0					7																	4917282		2071	4197	6268	4883808	SO:0001819	synonymous_variant	55698	exon2			AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.489G>A	7.37:g.4917282C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4883808	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	37	CCDS43544.1																																																																																				0.597	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
PMS2	5395	broad.mit.edu	37	7	6027135	6027135	+	Nonsense_Mutation	SNP	G	G	A	rs587778617		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:6027135G>A	ENST00000265849.7	-	11	1366	c.1261C>T	c.(1261-1263)Cga>Tga	p.R421*	PMS2_ENST00000469652.1_Intron|PMS2_ENST00000441476.2_Nonsense_Mutation_p.R315*|PMS2_ENST00000406569.3_Nonsense_Mutation_p.R421*|PMS2_ENST00000382321.4_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	421					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.R421*(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)		AAGGCCTCTCGCAGTCTGGAA	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.R421X		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.C1261T	7						.						48.0	49.0	49.0					7																	6027135		2203	4300	6503	5993661	SO:0001587	stop_gained	5395	exon11	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.1261C>T	7.37:g.6027135G>A	ENSP00000265849:p.Arg421*	Somatic		Capture	Illumina HiSeq	Phase_I	5993661	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Nonsense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	.	.	.	.	.	.	.	.	.	.	g	34	5.402193	0.96030	.	.	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	.	.	.	5.84	-0.996	0.10218	.	0.863840	0.10001	N	0.728510	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.2058	18.4288	0.90618	0.0:0.0:0.5906:0.4094	.	.	.	.	X	421;374;315;421	.	ENSP00000265849:R421X	R	-	1	2	PMS2	5993661	1.000000	0.71417	0.993000	0.49108	0.604000	0.37047	1.203000	0.32284	-0.120000	0.11809	-0.271000	0.10264	CGA		0.483	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
ZDHHC4	55146	broad.mit.edu	37	7	6624666	6624666	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:6624666G>A	ENST00000396706.2	+	7	959	c.516G>A	c.(514-516)gtG>gtA	p.V172V	ZDHHC4_ENST00000335965.6_Silent_p.V172V|ZDHHC4_ENST00000396713.2_Silent_p.V172V|ZDHHC4_ENST00000396709.1_Silent_p.V172V|AC079742.4_ENST00000434951.1_RNA|ZDHHC4_ENST00000396707.2_Silent_p.V172V|ZDHHC4_ENST00000405731.3_Silent_p.V172V			Q9NPG8	ZDHC4_HUMAN	zinc finger, DHHC-type containing 4	172						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.V172V(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.1)		ACTGGTGTGTGCACCGTTTCG	0.537																																					p.V172V												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.G516A	7						.						167.0	105.0	126.0					7																	6624666		2203	4300	6503	6591191	SO:0001819	synonymous_variant	55146	exon7			AF201931	CCDS5352.1	7p22.1	2011-01-11			ENSG00000136247	ENSG00000136247		"""Zinc fingers, DHHC-type"""	18471	protein-coding gene	gene with protein product							Standard	NM_018106		Approved	FLJ10479, ZNF374	uc003sqj.3	Q9NPG8	OTTHUMG00000023579	ENST00000396706.2:c.516G>A	7.37:g.6624666G>A		Somatic		Capture	Illumina HiSeq	Phase_I	6591191	NM_018106	A4D2N9|Q53EV7|Q6FIB5|Q9H0R9	Silent	SNP	ENST00000396706.2	37	CCDS5352.1																																																																																				0.537	ZDHHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207477.3	NM_018106	
ANKMY2	57037	broad.mit.edu	37	7	16642068	16642068	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:16642068G>T	ENST00000306999.2	-	9	1321	c.1078C>A	c.(1078-1080)Ctg>Atg	p.L360M		NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	360						cilium (GO:0005929)	metal ion binding (GO:0046872)	p.L360M(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)		ATGTCCTTCAGATTCTTACAG	0.358																																					p.L360M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1078A	7						.						157.0	155.0	156.0					7																	16642068		2202	4300	6502	16608593	SO:0001583	missense	57037	exon9			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.1078C>A	7.37:g.16642068G>T	ENSP00000303570:p.Leu360Met	Somatic		Capture	Illumina HiSeq	Phase_I	16608593	NM_020319	A4D124|Q659G1|Q96BL3	Missense_Mutation	SNP	ENST00000306999.2	37	CCDS5361.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.325563	0.81580	.	.	ENSG00000106524	ENST00000306999	T	0.74947	-0.89	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.77974	0.4211	L	0.34521	1.04	0.58432	D	0.99999	D	0.63880	0.993	P	0.61397	0.888	T	0.79699	-0.1694	10	0.66056	D	0.02	-27.7096	14.7162	0.69272	0.0715:0.0:0.9285:0.0	.	360	Q8IV38	ANKY2_HUMAN	M	360	ENSP00000303570:L360M	ENSP00000303570:L360M	L	-	1	2	ANKMY2	16608593	1.000000	0.71417	0.993000	0.49108	0.969000	0.65631	6.408000	0.73285	2.607000	0.88179	0.563000	0.77884	CTG		0.358	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319	
HDAC9	9734	broad.mit.edu	37	7	18625136	18625136	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:18625136G>T	ENST00000432645.2	+	2	255	c.255G>T	c.(253-255)gaG>gaT	p.E85D	HDAC9_ENST00000406451.4_Missense_Mutation_p.E85D|HDAC9_ENST00000401921.1_Missense_Mutation_p.E85D|HDAC9_ENST00000405010.3_Missense_Mutation_p.E85D|HDAC9_ENST00000441542.2_Missense_Mutation_p.E85D|HDAC9_ENST00000428307.2_Missense_Mutation_p.E85D|HDAC9_ENST00000406072.1_Missense_Mutation_p.E113D|HDAC9_ENST00000456174.2_Missense_Mutation_p.E54D|HDAC9_ENST00000417496.2_Missense_Mutation_p.E127D|HDAC9_ENST00000476135.1_3'UTR|HDAC9_ENST00000524023.1_Missense_Mutation_p.E54D	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	85					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|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 deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.E85D(1)		breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	AGCTTCAGGAGCATATCAAGG	0.498																																					p.E85D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G255T	7						.						40.0	42.0	41.0					7																	18625136		2116	4234	6350	18591661	SO:0001583	missense	9734	exon3			AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.255G>T	7.37:g.18625136G>T	ENSP00000410337:p.Glu85Asp	Somatic		Capture	Illumina HiSeq	Phase_I	18591661	NM_178423	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Missense_Mutation	SNP	ENST00000432645.2	37	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.111234	0.77210	.	.	ENSG00000048052	ENST00000417496;ENST00000262069;ENST00000413509;ENST00000413380;ENST00000430454;ENST00000405010;ENST00000406451;ENST00000428307;ENST00000406072;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000441986;ENST00000456174;ENST00000524023;ENST00000341009	T;T;T;T;T;T;T;T;T;T;T;T;T	0.61510	0.63;0.7;0.68;0.6;0.1;0.64;0.69;0.13;0.1;0.13;0.68;0.67;0.68	5.71	2.86	0.33363	Histone deacetylase, glutamine rich N-terminal domain (1);	0.000000	0.56097	D	0.000021	T	0.70762	0.3261	M	0.65975	2.015	0.53688	D	0.999977	P;D;P;D;P;D;P;P;D;D;P;D;P	0.76494	0.788;0.999;0.884;0.999;0.788;0.992;0.884;0.884;0.999;0.997;0.884;0.998;0.905	P;D;B;D;P;D;B;B;D;D;B;D;P	0.87578	0.707;0.994;0.38;0.998;0.707;0.989;0.38;0.38;0.992;0.992;0.38;0.99;0.642	T	0.71708	-0.4511	10	0.87932	D	0	-2.9593	10.1911	0.43028	0.2214:0.0:0.7786:0.0	.	54;54;85;113;127;85;85;85;85;54;85;85;104	E7EX34;C9JS87;Q9UKV0-4;B5MCF1;B7Z917;Q68D71;Q9UKV0-6;Q9UKV0-7;Q9UKV0;B7Z928;Q9UKV0-5;Q9UKV0-3;Q8N879	.;.;.;.;.;.;.;.;HDAC9_HUMAN;.;.;.;.	D	127;130;85;85;54;85;85;85;113;85;85;85;54;54;54;85	ENSP00000401669:E127D;ENSP00000412497:E85D;ENSP00000392564:E85D;ENSP00000384382:E85D;ENSP00000384657:E85D;ENSP00000395655:E85D;ENSP00000384017:E113D;ENSP00000383912:E85D;ENSP00000410337:E85D;ENSP00000408617:E85D;ENSP00000404763:E54D;ENSP00000388568:E54D;ENSP00000430036:E54D	ENSP00000262069:E130D	E	+	3	2	HDAC9	18591661	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.584000	0.36589	0.716000	0.32124	-0.137000	0.14449	GAG		0.498	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		
SP8	221833	broad.mit.edu	37	7	20825354	20825354	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:20825354C>A	ENST00000361443.4	-	3	265	c.28G>T	c.(28-30)Ggc>Tgc	p.G10C	SP8_ENST00000418710.2_Missense_Mutation_p.G28C	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	10					dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|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.G28C(1)|p.G10C(1)		NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						CTGGGGCTGCCTATCTTATTA	0.612																																					p.G10C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G28T	7						.						37.0	40.0	39.0					7																	20825354		2203	4300	6503	20791879	SO:0001583	missense	221833	exon3				CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.28G>T	7.37:g.20825354C>A	ENSP00000354482:p.Gly10Cys	Somatic		Capture	Illumina HiSeq	Phase_I	20791879	NM_198956	Q7Z615|Q7Z616|Q96MJ1	Missense_Mutation	SNP	ENST00000361443.4	37	CCDS5372.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.646201	0.67358	.	.	ENSG00000164651	ENST00000297210;ENST00000418710;ENST00000361443	T;T	0.19669	2.13;2.3	3.67	3.67	0.42095	.	0.000000	0.85682	U	0.000000	T	0.38506	0.1043	L	0.49778	1.585	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.66602	0.945;0.945	T	0.35126	-0.9801	10	0.87932	D	0	.	15.1605	0.72782	0.0:1.0:0.0:0.0	.	10;10	Q7Z615;Q8IXZ3	.;SP8_HUMAN	C	28;28;10	ENSP00000408792:G28C;ENSP00000354482:G10C	ENSP00000297210:G28C	G	-	1	0	SP8	20791879	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	3.563000	0.53784	1.856000	0.53863	0.455000	0.32223	GGC		0.612	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2		
DNAH11	8701	broad.mit.edu	37	7	21657371	21657371	+	Nonsense_Mutation	SNP	G	G	A	rs367916239		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:21657371G>A	ENST00000409508.3	+	23	4261	c.4230G>A	c.(4228-4230)tgG>tgA	p.W1410*	DNAH11_ENST00000328843.6_Nonsense_Mutation_p.W1415*	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1415	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.W1415*(1)		NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						ACAGGCATTGGCACCAGCTGA	0.502									Kartagener syndrome																												p.W1415X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G4245A	7						.						54.0	55.0	55.0					7																	21657371		1953	4147	6100	21623896	SO:0001587	stop_gained	8701	exon23	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"""Axonemal dyneins"""	2942	protein-coding gene	gene with protein product	"""dynein, ciliary, heavy chain 11"", ""dynein, heavy chain beta-like"""	603339	"""dynein, axonemal, heavy polypeptide 11"""			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.4230G>A	7.37:g.21657371G>A	ENSP00000475939:p.Trp1410*	Somatic		Capture	Illumina HiSeq	Phase_I	21623896	NM_003777	Q9UJ82	Nonsense_Mutation	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	45	11.648683	0.99587	.	.	ENSG00000105877	ENST00000328843	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.3796	0.90445	0.0:0.0:1.0:0.0	.	.	.	.	X	1415	.	ENSP00000330671:W1415X	W	+	3	0	DNAH11	21623896	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	7.670000	0.83925	2.636000	0.89361	0.514000	0.50259	TGG		0.502	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777	
OSBPL3	26031	broad.mit.edu	37	7	24874220	24874220	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:24874220G>A	ENST00000313367.2	-	15	2082	c.1631C>T	c.(1630-1632)gCc>gTc	p.A544V	OSBPL3_ENST00000353930.1_Missense_Mutation_p.A508V|OSBPL3_ENST00000409069.1_Missense_Mutation_p.A477V|OSBPL3_ENST00000396429.1_Missense_Mutation_p.A508V|OSBPL3_ENST00000431825.2_Missense_Mutation_p.A477V|OSBPL3_ENST00000352860.1_Missense_Mutation_p.A513V|OSBPL3_ENST00000396431.1_Missense_Mutation_p.A513V	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	544					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)	p.A544V(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						CACCGGCATGGCCACCTTGGA	0.632																																					p.A508V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1523T	7						.						96.0	80.0	85.0					7																	24874220		2203	4300	6503	24840745	SO:0001583	missense	26031	exon14			AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.1631C>T	7.37:g.24874220G>A	ENSP00000315410:p.Ala544Val	Somatic		Capture	Illumina HiSeq	Phase_I	24840745	NM_145321	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Missense_Mutation	SNP	ENST00000313367.2	37	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	G	37	6.177929	0.97352	.	.	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069	T;T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6;1.6	5.85	5.85	0.93711	.	0.159881	0.56097	D	0.000038	T	0.53286	0.1787	L	0.58428	1.81	0.80722	D	1	P;D;P;D;P;D	0.60575	0.941;0.957;0.917;0.986;0.837;0.988	P;P;P;P;P;D	0.63703	0.571;0.772;0.772;0.864;0.617;0.917	T	0.50659	-0.8802	10	0.72032	D	0.01	-16.4906	20.1699	0.98157	0.0:0.0:1.0:0.0	.	477;508;477;513;508;544	Q9H4L5-8;Q9H4L5-7;Q9H4L5-4;Q9H4L5-2;Q9H4L5-3;Q9H4L5	.;.;.;.;.;OSBL3_HUMAN	V	544;513;508;477;513;508;477	ENSP00000315410:A544V;ENSP00000315331:A513V;ENSP00000315277:A508V;ENSP00000389779:A477V;ENSP00000379708:A513V;ENSP00000379706:A508V;ENSP00000386953:A477V	ENSP00000315410:A544V	A	-	2	0	OSBPL3	24840745	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.936000	0.87665	2.775000	0.95449	0.467000	0.42956	GCC		0.632	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		
HOXA4	3201	broad.mit.edu	37	7	27168882	27168882	+	Frame_Shift_Del	DEL	G	G	-	rs201659767		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:27168882delG	ENST00000360046.5	-	2	990	c.925delC	c.(925-927)cacfs	p.H309fs	HOXA4_ENST00000428284.2_Frame_Shift_Del_p.H309fs|HOXA-AS2_ENST00000517550.1_RNA|HOXA3_ENST00000317201.2_5'Flank|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS2_ENST00000521687.1_RNA|HOXA3_ENST00000521401.1_Intron|HOXA-AS3_ENST00000518848.1_RNA|HOXA-AS2_ENST00000521159.1_RNA	NM_002141.4	NP_002132.3	Q00056	HXA4_HUMAN	homeobox A4	309					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H309fs*>12(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(6)	12						gtgctcgggtgggggtgggga	0.557																																					p.H309fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.925delC	7						.						128.0	132.0	131.0					7																	27168882		2203	4300	6503	27135407	SO:0001589	frameshift_variant	3201	exon2				CCDS5405.1	7p15.2	2011-06-20	2005-12-22		ENSG00000197576	ENSG00000197576		"""Homeoboxes / ANTP class : HOXL subclass"""	5105	protein-coding gene	gene with protein product		142953	"""homeo box A4"""	HOX1D, HOX1		1973146, 1358459	Standard	NM_002141		Approved		uc003sym.4	Q00056	OTTHUMG00000023213	ENST00000360046.5:c.925delC	7.37:g.27168882delG	ENSP00000353151:p.His309fs	Somatic		Capture	Illumina HiSeq	Phase_I	27135407	NM_002141	A4D180|O43366	Frame_Shift_Del	DEL	ENST00000360046.5	37	CCDS5405.1																																																																																				0.557	HOXA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059534.4		
TAX1BP1	8887	broad.mit.edu	37	7	27856554	27856554	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:27856554C>A	ENST00000396319.2	+	15	2070	c.1982C>A	c.(1981-1983)cCt>cAt	p.P661H	TAX1BP1_ENST00000433216.2_Missense_Mutation_p.P462H|TAX1BP1_ENST00000543117.1_Missense_Mutation_p.P619H|TAX1BP1_ENST00000265393.6_Missense_Mutation_p.P619H|TAX1BP1_ENST00000409980.1_Missense_Mutation_p.P685H	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	661					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)	p.P661H(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			CAAAGGCCACCTGTCAGAGTC	0.458																																					p.P661H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1982A	7						.						62.0	64.0	64.0					7																	27856554		2203	4300	6503	27823079	SO:0001583	missense	8887	exon15			U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.1982C>A	7.37:g.27856554C>A	ENSP00000379612:p.Pro661His	Somatic		Capture	Illumina HiSeq	Phase_I	27823079	NM_006024	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Missense_Mutation	SNP	ENST00000396319.2	37	CCDS5415.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.696243	0.68386	.	.	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319;ENST00000457186	T;T;T;T;T	0.49432	2.07;2.07;2.01;0.78;1.81	5.67	4.78	0.61160	.	0.000000	0.53938	D	0.000059	T	0.66906	0.2837	M	0.64404	1.975	0.48452	D	0.999651	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.962;0.99;0.998	T	0.71002	-0.4718	10	0.72032	D	0.01	-6.4823	16.6279	0.84984	0.0:0.87:0.13:0.0	.	462;661;619	E7ENV2;Q86VP1;Q86VP1-2	.;TAXB1_HUMAN;.	H	619;619;685;462;661;198	ENSP00000444811:P619H;ENSP00000265393:P619H;ENSP00000386515:P685H;ENSP00000391907:P462H;ENSP00000379612:P661H	ENSP00000265393:P619H	P	+	2	0	TAX1BP1	27823079	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	3.388000	0.52509	1.392000	0.46585	0.655000	0.94253	CCT		0.458	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024	
CREB5	9586	broad.mit.edu	37	7	28843920	28843920	+	Silent	SNP	G	G	A	rs573375434		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:28843920G>A	ENST00000357727.2	+	8	1197	c.807G>A	c.(805-807)acG>acA	p.T269T	CREB5_ENST00000396298.2_Silent_p.T130T|CREB5_ENST00000409603.1_Silent_p.T236T|CREB5_ENST00000396300.2_Silent_p.T262T|CREB5_ENST00000396299.2_Silent_p.T236T	NM_182898.2	NP_878901.2	Q02930	CREB5_HUMAN	cAMP responsive element binding protein 5	269					adipose tissue development (GO:0060612)|fat cell differentiation (GO:0045444)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	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)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T269T(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(13)|prostate(1)|skin(3)	32						AGGACCAGACGccacaccatc	0.587													G|||	1	0.000199681	0.0	0.0	5008	,	,		17283	0.0		0.001	False		,,,				2504	0.0				p.T130T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G390A	7						.						470.0	296.0	355.0					7																	28843920		2203	4300	6503	28810445	SO:0001819	synonymous_variant	9586	exon4			L05515	CCDS5417.1, CCDS5418.1, CCDS43562.1, CCDS43563.1	7p15	2013-01-10			ENSG00000146592	ENSG00000146592		"""basic leucine zipper proteins"""	16844	protein-coding gene	gene with protein product	"""cAMP response element binding protein CRE-Bpa"""					8378084, 8440710	Standard	XM_005249906		Approved	H_GS165L15.1, CRE-BPA	uc003szr.3	Q02930	OTTHUMG00000097081	ENST00000357727.2:c.807G>A	7.37:g.28843920G>A		Somatic		Capture	Illumina HiSeq	Phase_I	28810445	NM_001011666	A8KA51|B4DU13|B5BUH3|C9JK47|Q05886|Q06246|Q75N02|Q86UJ9	Silent	SNP	ENST00000357727.2	37	CCDS5417.1																																																																																				0.587	CREB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214204.4	NM_004904	
CPVL	54504	broad.mit.edu	37	7	29070262	29070262	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:29070262delT	ENST00000409850.1	-	16	1897	c.1251delA	c.(1249-1251)aaafs	p.K417fs	CPVL_ENST00000396276.3_Frame_Shift_Del_p.K417fs|CPVL_ENST00000265394.5_Frame_Shift_Del_p.K417fs			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	417						extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)	p.V418fs*24(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)	28						TCTTCCAAACTTTTTTTTCTG	0.507																																					p.K417fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1251delA	7						.						163.0	155.0	158.0					7																	29070262		2203	4300	6503	29036787	SO:0001589	frameshift_variant	54504	exon12			AF106704	CCDS5419.1	7p15.1	2012-02-10			ENSG00000106066	ENSG00000106066			14399	protein-coding gene	gene with protein product	"""carboxypeptidase WUG"", ""vitellogenic carboxypeptidase-like protein"", ""CP-Mac carboxypeptidase"""	609780				11401439	Standard	XM_005249786		Approved		uc003szw.3	Q9H3G5	OTTHUMG00000023669	ENST00000409850.1:c.1251delA	7.37:g.29070262delT	ENSP00000387164:p.Lys417fs	Somatic		Capture	Illumina HiSeq	Phase_I	29036787	NM_031311	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Frame_Shift_Del	DEL	ENST00000409850.1	37	CCDS5419.1																																																																																				0.507	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029	
WIPF3	644150	broad.mit.edu	37	7	29924036	29924036	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:29924036C>A	ENST00000409290.1	+	4	926	c.926C>A	c.(925-927)cCc>cAc	p.P309H	WIPF3_ENST00000242140.5_Missense_Mutation_p.P309H|WIPF3_ENST00000409123.1_Missense_Mutation_p.P309H	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	309					cell differentiation (GO:0030154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)		p.P309H(1)		breast(2)|large_intestine(3)|lung(6)|ovary(1)	12						GCTTCTTTGCCCGCGCCCCCT	0.682																																					p.P309H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C926A	7						.						6.0	6.0	6.0					7																	29924036		1698	3864	5562	29890561	SO:0001583	missense	644150	exon4			AK094250	CCDS56472.1	7p15.1	2006-10-12			ENSG00000122574	ENSG00000122574			22004	protein-coding gene	gene with protein product		612432					Standard	NM_001080529		Approved	CR16, FLJ36931	uc022aaz.1	A6NGB9	OTTHUMG00000152761	ENST00000409290.1:c.926C>A	7.37:g.29924036C>A	ENSP00000386878:p.Pro309His	Somatic		Capture	Illumina HiSeq	Phase_I	29890561	NM_001080529	B8ZZV2	Missense_Mutation	SNP	ENST00000409290.1	37	CCDS56472.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.209227	0.39003	.	.	ENSG00000122574	ENST00000409123;ENST00000409290;ENST00000242140	T;T;T	0.53423	0.62;0.62;0.62	3.8	3.8	0.43715	.	0.192397	0.31312	N	0.007878	T	0.50667	0.1629	L	0.58101	1.795	0.09310	N	1	D	0.63046	0.992	P	0.49561	0.615	T	0.49969	-0.8882	10	0.87932	D	0	.	11.5339	0.50626	0.0:1.0:0.0:0.0	.	309	A6NGB9	WIPF3_HUMAN	H	309	ENSP00000386790:P309H;ENSP00000386878:P309H;ENSP00000242140:P309H	ENSP00000242140:P309H	P	+	2	0	WIPF3	29890561	0.024000	0.19004	0.073000	0.20177	0.141000	0.21300	1.882000	0.39648	1.836000	0.53414	0.549000	0.68633	CCC		0.682	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1		
CRHR2	1395	broad.mit.edu	37	7	30705225	30705225	+	Missense_Mutation	SNP	C	C	T	rs200310748		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:30705225C>T	ENST00000471646.1	-	4	763	c.346G>A	c.(346-348)Gcc>Acc	p.A116T	CRHR2_ENST00000506074.2_Missense_Mutation_p.A116T|CRHR2_ENST00000348438.4_Missense_Mutation_p.A143T|CRHR2_ENST00000341843.4_Missense_Mutation_p.A102T	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	116					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)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						ACGACAAGGGCGATGCGGTAG	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		19211	0.0		0.001	False		,,,				2504	0.0				p.A116T												.	.	0			c.G346A	7						.						118.0	77.0	91.0					7																	30705225		2200	4289	6489	30671750	SO:0001583	missense	1395	exon4				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.346G>A	7.37:g.30705225C>T	ENSP00000418722:p.Ala116Thr	None		Capture	Illumina HiSeq	Phase_I	30671750	NM_001883	B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Missense_Mutation	SNP	ENST00000471646.1	37	CCDS5429.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.36	3.370006	0.61624	.	.	ENSG00000106113	ENST00000471646;ENST00000348438;ENST00000341843;ENST00000506074	T;T;T;T	0.37411	1.2;1.2;1.2;1.2	5.08	5.08	0.68730	GPCR, family 2-like (1);	0.108090	0.64402	D	0.000007	T	0.47002	0.1422	L	0.31207	0.915	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	0.77004	0.989;0.989;0.988;0.988;0.989	T	0.17077	-1.0381	10	0.23302	T	0.38	.	16.7902	0.85588	0.0:1.0:0.0:0.0	.	115;116;143;102;116	B3SXT0;B3SXS6;Q13324-2;Q13324-3;Q13324	.;.;.;.;CRFR2_HUMAN	T	116;143;102;116	ENSP00000418722:A116T;ENSP00000340943:A143T;ENSP00000344304:A102T;ENSP00000426498:A116T	ENSP00000344304:A102T	A	-	1	0	CRHR2	30671750	1.000000	0.71417	0.913000	0.36048	0.015000	0.08874	7.520000	0.81821	2.736000	0.93811	0.655000	0.94253	GCC		0.632	CRHR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250448.3		
PDE1C	5137	broad.mit.edu	37	7	31855568	31855568	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:31855568C>T	ENST00000396191.1	-	15	2238	c.1783G>A	c.(1783-1785)Gag>Aag	p.E595K	PDE1C_ENST00000396184.3_Missense_Mutation_p.E595K|PDE1C_ENST00000321453.7_Missense_Mutation_p.E595K|PDE1C_ENST00000396193.1_Missense_Mutation_p.E655K|PDE1C_ENST00000479980.1_5'UTR|PDE1C_ENST00000396182.2_Missense_Mutation_p.E595K	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	595					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)	p.E595K(4)|p.E655K(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	GATGACTTCTCGGCTTTGGAG	0.443																																					p.E595K												.	.	5	Substitution - Missense(5)	lung(3)|large_intestine(2)	c.G1783A	7						.						231.0	221.0	224.0					7																	31855568		2203	4300	6503	31822093	SO:0001583	missense	5137	exon15			U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1783G>A	7.37:g.31855568C>T	ENSP00000379494:p.Glu595Lys	Somatic		Capture	Illumina HiSeq	Phase_I	31822093	NM_001191056	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	37	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.924938	0.34002	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.73897	-0.77;-0.79;-0.79;-0.73;-0.73	5.2	5.2	0.72013	.	0.633297	0.14258	N	0.331015	T	0.60586	0.2280	N	0.12182	0.205	0.42369	D	0.992446	B;B;B	0.10296	0.001;0.0;0.003	B;B;B	0.08055	0.003;0.001;0.001	T	0.56269	-0.8007	10	0.51188	T	0.08	.	15.5839	0.76468	0.0:1.0:0.0:0.0	.	595;655;595	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	K	655;595;595;595;595	ENSP00000379496:E655K;ENSP00000379494:E595K;ENSP00000318105:E595K;ENSP00000379487:E595K;ENSP00000379485:E595K	ENSP00000318105:E595K	E	-	1	0	PDE1C	31822093	0.993000	0.37304	0.962000	0.40283	0.101000	0.19017	4.094000	0.57721	2.692000	0.91855	0.655000	0.94253	GAG		0.443	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
BBS9	27241	broad.mit.edu	37	7	33380555	33380555	+	Silent	SNP	C	C	T	rs61764066	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:33380555C>T	ENST00000242067.6	+	11	1766	c.1245C>T	c.(1243-1245)gtC>gtT	p.V415V	BBS9_ENST00000350941.3_Silent_p.V415V|BBS9_ENST00000354265.4_Silent_p.V415V|BBS9_ENST00000396127.2_Silent_p.V415V|BBS9_ENST00000355070.2_Silent_p.V415V	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	415					cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.V415V(2)	BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			ACGTTTCTGTCGTGGTTTCTC	0.333									Bardet-Biedl syndrome				C|||	9	0.00179712	0.0	0.0	5008	,	,		16044	0.0089		0.0	False		,,,				2504	0.0				p.V415V												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1245T	7						.						193.0	179.0	183.0					7																	33380555		2203	4300	6503	33347080	SO:0001819	synonymous_variant	27241	exon11	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507			30000	protein-coding gene	gene with protein product	"""parathyroid hormone responsive B1 gene"""	607968				16380913, 10221542	Standard	XM_005249701		Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.1245C>T	7.37:g.33380555C>T		Somatic		Capture	Illumina HiSeq	Phase_I	33347080	NM_001033605	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Silent	SNP	ENST00000242067.6	37	CCDS43566.1																																																																																				0.333	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1		
NPSR1	387129	broad.mit.edu	37	7	34917701	34917701	+	Missense_Mutation	SNP	C	C	T	rs370072027		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:34917701C>T	ENST00000359791.1	+	9	1167	c.1039C>T	c.(1039-1041)Cgt>Tgt	p.R347C	NPSR1_ENST00000531252.1_Missense_Mutation_p.R336C	NM_207173.1	NP_997056.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	127						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)	p.R347C(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	CATCCGTCTCCGTCAGCTCCA	0.517																																					p.R347C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1039T	7						.	C	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	54.0	45.0	48.0		1039	-4.4	0.0	7		48	0,8600		0,0,4300	no	missense	NPSR1	NM_207173.1	180	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		347/378	34917701	2,13004	2203	4300	6503	34884226	SO:0001583	missense	387129	exon9			AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"""GPCR / Class A : Neuropeptide receptors : S"""	23631	protein-coding gene	gene with protein product		608595	"""G protein-coupled receptor 154"""	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000359791.1:c.1039C>T	7.37:g.34917701C>T	ENSP00000352839:p.Arg347Cys	Somatic		Capture	Illumina HiSeq	Phase_I	34884226	NM_207173	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000359791.1	37	CCDS5443.1	.	.	.	.	.	.	.	.	.	.	c	6.798	0.516333	0.12944	4.54E-4	0.0	ENSG00000187258	ENST00000359791;ENST00000531252	T;T	0.74106	-0.81;-0.43	2.39	-4.45	0.03546	.	.	.	.	.	T	0.46600	0.1401	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.19353	-1.0308	9	0.38643	T	0.18	.	3.8588	0.08986	0.0:0.2351:0.3846:0.3803	.	281;336;347	B7ZMA2;Q6W5P4-5;Q6W5P4-4	.;.;.	C	347;336	ENSP00000352839:R347C;ENSP00000433258:R336C	ENSP00000352839:R347C	R	+	1	0	NPSR1	34884226	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.980000	0.01492	-0.981000	0.03520	-0.192000	0.12808	CGT		0.517	NPSR1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216838.1	NM_207173	
HECW1	23072	broad.mit.edu	37	7	43601459	43601459	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:43601459G>A	ENST00000395891.2	+	30	5360	c.4755G>A	c.(4753-4755)tcG>tcA	p.S1585S	HECW1_ENST00000453890.1_Silent_p.S1551S	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1585	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.S1564S(1)		NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						CGTATCCCTCGTACTCCATGT	0.478																																					p.S1585S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4755A	7						.						141.0	138.0	139.0					7																	43601459		2025	4197	6222	43567984	SO:0001819	synonymous_variant	23072	exon30			AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.4755G>A	7.37:g.43601459G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43567984	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																				0.478	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
BLVRA	644	broad.mit.edu	37	7	43827613	43827613	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:43827613C>T	ENST00000402924.1	+	4	286	c.123C>T	c.(121-123)ggC>ggT	p.G41G	BLVRA_ENST00000265523.4_Silent_p.G41G	NM_001253823.1	NP_001240752.1	P53004	BIEA_HUMAN	biliverdin reductase A	41					heme catabolic process (GO:0042167)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	biliverdin reductase activity (GO:0004074)|zinc ion binding (GO:0008270)	p.G41G(1)		endometrium(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(2)	12						ACCTGATTGGCTTCGTGTCGA	0.557																																					p.G41G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C123T	7						.						227.0	176.0	193.0					7																	43827613		2203	4300	6503	43794138	SO:0001819	synonymous_variant	644	exon3			BC008456	CCDS5472.1	7p13	2012-10-02			ENSG00000106605	ENSG00000106605	1.3.1.24		1062	protein-coding gene	gene with protein product		109750		BLVR			Standard	NM_001253823		Approved		uc003tir.3	P53004	OTTHUMG00000128953	ENST00000402924.1:c.123C>T	7.37:g.43827613C>T		Somatic		Capture	Illumina HiSeq	Phase_I	43794138	NM_000712	A8K747|O95019|Q86UX0|Q96QL4|Q9BRW8	Silent	SNP	ENST00000402924.1	37	CCDS5472.1																																																																																				0.557	BLVRA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339006.1	NM_000712	
MRPS24	64951	broad.mit.edu	37	7	43906396	43906396	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:43906396C>T	ENST00000317534.5	-	4	467	c.406G>A	c.(406-408)Gtg>Atg	p.V136M	URGCP-MRPS24_ENST00000603700.1_3'UTR|MRPS24_ENST00000467084.1_5'Flank	NM_032014.2	NP_114403.1	Q96EL2	RT24_HUMAN	mitochondrial ribosomal protein S24	136					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.V136M(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	5						CTGTAGCCCACGAGGAAGTAG	0.507																																					p.V136M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G406A	7						.						84.0	79.0	80.0					7																	43906396		2203	4300	6503	43872921	SO:0001583	missense	64951	exon4			AB061207	CCDS5473.1	7p14	2012-09-13			ENSG00000062582	ENSG00000062582		"""Mitochondrial ribosomal proteins / small subunits"""	14510	protein-coding gene	gene with protein product		611986				8127713, 11279123	Standard	NM_032014		Approved	MRP-S24, HSPC335	uc003tit.1	Q96EL2	OTTHUMG00000023175	ENST00000317534.5:c.406G>A	7.37:g.43906396C>T	ENSP00000318158:p.Val136Met	Somatic		Capture	Illumina HiSeq	Phase_I	43872921	NM_032014	A4D1U9|P82668|Q96Q23|Q9P047	Missense_Mutation	SNP	ENST00000317534.5	37	CCDS5473.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.088684	0.36855	.	.	ENSG00000062582	ENST00000317534	T	0.46063	0.88	5.09	4.21	0.49690	.	0.228496	0.43260	D	0.000592	T	0.55878	0.1948	M	0.62723	1.935	0.39156	D	0.962328	D	0.89917	1.0	D	0.67382	0.951	T	0.60203	-0.7309	10	0.72032	D	0.01	.	8.0281	0.30448	0.0:0.8148:0.0:0.1852	.	136	Q96EL2	RT24_HUMAN	M	136	ENSP00000318158:V136M	ENSP00000318158:V136M	V	-	1	0	MRPS24	43872921	0.997000	0.39634	0.819000	0.32651	0.051000	0.14879	3.261000	0.51530	1.141000	0.42275	0.655000	0.94253	GTG		0.507	MRPS24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250949.1	NM_032014	
UBE2D4	51619	broad.mit.edu	37	7	43990281	43990281	+	Missense_Mutation	SNP	G	G	A	rs553718857		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:43990281G>A	ENST00000222402.3	+	6	477	c.388G>A	c.(388-390)Gac>Aac	p.D130N	UBE2D4_ENST00000394798.4_Missense_Mutation_p.D92N|POLR2J4_ENST00000427076.1_RNA|RP5-1165K10.2_ENST00000454572.1_RNA	NM_015983.3	NP_057067.1	Q9Y2X8	UB2D4_HUMAN	ubiquitin-conjugating enzyme E2D 4 (putative)	130					protein K11-linked ubiquitination (GO:0070979)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)	p.D130N(1)		endometrium(1)|large_intestine(2)|lung(1)|pancreas(1)	5						CTACAAGGCCGACAGAGAGAA	0.567																																					p.D130N	Esophageal Squamous(27;401 815 16344 30604)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G388A	7						.						135.0	109.0	118.0					7																	43990281		2203	4300	6503	43956806	SO:0001583	missense	51619	exon6			BC004104	CCDS5474.1	7p13	2005-08-11			ENSG00000078967	ENSG00000078967		"""Ubiquitin-conjugating enzymes E2"""	21647	protein-coding gene	gene with protein product						12690205	Standard	NM_015983		Approved	HBUCE1	uc003tja.2	Q9Y2X8	OTTHUMG00000128971	ENST00000222402.3:c.388G>A	7.37:g.43990281G>A	ENSP00000222402:p.Asp130Asn	Somatic		Capture	Illumina HiSeq	Phase_I	43956806	NM_015983	A4D1V0	Missense_Mutation	SNP	ENST00000222402.3	37	CCDS5474.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.799595	0.50208	.	.	ENSG00000078967	ENST00000222402;ENST00000394798	T;T	0.72505	-0.66;-0.66	4.49	1.64	0.23874	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.055354	0.64402	N	0.000002	T	0.49932	0.1586	N	0.16368	0.405	0.47659	D	0.999484	B;B	0.21381	0.055;0.055	B;B	0.17979	0.02;0.02	T	0.26916	-1.0089	10	0.40728	T	0.16	.	8.2239	0.31558	0.2734:0.0:0.7266:0.0	.	92;130	Q9UQL0;Q9Y2X8	.;UB2D4_HUMAN	N	130;92	ENSP00000222402:D130N;ENSP00000378277:D92N	ENSP00000222402:D130N	D	+	1	0	UBE2D4	43956806	1.000000	0.71417	0.989000	0.46669	0.793000	0.44817	2.905000	0.48727	0.029000	0.15352	0.655000	0.94253	GAC		0.567	UBE2D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250958.2	NM_015983	
NPC1L1	29881	broad.mit.edu	37	7	44579613	44579613	+	Missense_Mutation	SNP	G	G	A	rs149337001		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:44579613G>A	ENST00000289547.4	-	2	438	c.383C>T	c.(382-384)aCg>aTg	p.T128M	NPC1L1_ENST00000381160.3_Missense_Mutation_p.T128M|NPC1L1_ENST00000423141.1_Missense_Mutation_p.T128M|NPC1L1_ENST00000546276.1_Missense_Mutation_p.T128M	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	128					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)	p.T128M(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	GGGGCTGCACGTGTTGTGGCA	0.592																																					p.T128M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C383T	7						.	G	MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	88.0	75.0	79.0		383,383	4.0	1.0	7	dbSNP_134	79	0,8600		0,0,4300	no	missense,missense	NPC1L1	NM_001101648.1,NM_013389.2	81,81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	128/1333,128/1360	44579613	1,13005	2203	4300	6503	44546138	SO:0001583	missense	29881	exon2				CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"""NPC1 (Niemann-Pick disease, type C1, gene)-like 1"""			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.383C>T	7.37:g.44579613G>A	ENSP00000289547:p.Thr128Met	Somatic		Capture	Illumina HiSeq	Phase_I	44546138	NM_013389	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Missense_Mutation	SNP	ENST00000289547.4	37	CCDS5491.1	.	.	.	.	.	.	.	.	.	.	g	16.50	3.139753	0.56936	2.27E-4	0.0	ENSG00000015520	ENST00000289547;ENST00000381160;ENST00000546276;ENST00000423141	D;D;D;D	0.97303	-4.33;-4.33;-4.33;-4.33	4.9	3.99	0.46301	.	0.122142	0.53938	D	0.000047	D	0.98283	0.9431	M	0.92026	3.265	0.46167	D	0.998904	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.80764	0.986;0.993;0.99;0.994	D	0.97902	1.0303	10	0.87932	D	0	-36.0232	6.1123	0.20108	0.0961:0.0:0.7155:0.1884	.	128;128;128;128	B7ZLE6;Q9UHC9-3;Q17RV5;D3DVK9	.;.;.;.	M	128	ENSP00000289547:T128M;ENSP00000370552:T128M;ENSP00000438033:T128M;ENSP00000404670:T128M	ENSP00000289547:T128M	T	-	2	0	NPC1L1	44546138	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	3.489000	0.53237	1.011000	0.39340	0.555000	0.69702	ACG		0.592	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389	
CCM2	83605	broad.mit.edu	37	7	45103533	45103533	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:45103533C>T	ENST00000258781.6	+	3	370	c.221C>T	c.(220-222)aCg>aTg	p.T74M	CCM2_ENST00000541586.1_Missense_Mutation_p.T16M|CCM2_ENST00000544363.1_Missense_Mutation_p.T74M|CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000475551.1_Missense_Mutation_p.T68M|CCM2_ENST00000381112.3_Missense_Mutation_p.T95M|CCM2_ENST00000474617.1_Missense_Mutation_p.T68M	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	74	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)		p.T95M(1)		NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						GGTCAGTTAACGTCCATACCA	0.448																																					p.T74M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C221T	7						.						172.0	158.0	163.0					7																	45103533		2203	4300	6503	45070058	SO:0001583	missense	83605	exon3			BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"""malcavernin"""	607929	"""chromosome 7 open reading frame 22"""	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.221C>T	7.37:g.45103533C>T	ENSP00000258781:p.Thr74Met	Somatic		Capture	Illumina HiSeq	Phase_I	45070058	NM_031443	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Missense_Mutation	SNP	ENST00000258781.6	37	CCDS5500.1	.	.	.	.	.	.	.	.	.	.	C	14.74	2.625319	0.46840	.	.	ENSG00000136280	ENST00000258781;ENST00000541586;ENST00000544363;ENST00000475551;ENST00000381112;ENST00000474617	T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78	5.25	3.46	0.39613	Phosphotyrosine interaction domain (1);	0.116152	0.56097	N	0.000028	T	0.61825	0.2378	M	0.66939	2.045	0.49798	D	0.999826	D;B;B;D;B	0.89917	1.0;0.414;0.389;0.999;0.216	D;B;B;P;B	0.72338	0.977;0.031;0.07;0.855;0.021	T	0.59354	-0.7470	10	0.46703	T	0.11	-8.7971	9.0499	0.36369	0.0:0.8286:0.0:0.1714	.	37;95;74;16;74	B7Z8D5;E9PDJ3;F5H0E1;F5H551;Q9BSQ5	.;.;.;.;CCM2_HUMAN	M	74;16;74;68;95;68	ENSP00000258781:T74M;ENSP00000444725:T16M;ENSP00000438035:T74M;ENSP00000417180:T68M;ENSP00000370503:T95M;ENSP00000419474:T68M	ENSP00000258781:T74M	T	+	2	0	CCM2	45070058	1.000000	0.71417	0.974000	0.42286	0.985000	0.73830	7.589000	0.82641	0.622000	0.30249	0.655000	0.94253	ACG		0.448	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443	
SUN3	256979	broad.mit.edu	37	7	48033927	48033927	+	Missense_Mutation	SNP	C	C	A	rs73111110	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:48033927C>A	ENST00000297325.4	-	8	1005	c.846G>T	c.(844-846)aaG>aaT	p.K282N	SUN3_ENST00000473723.1_5'UTR|SUN3_ENST00000395572.2_Missense_Mutation_p.K282N|SUN3_ENST00000412142.1_Missense_Mutation_p.K182N|SUN3_ENST00000453192.2_Missense_Mutation_p.K270N	NM_001030019.1	NP_001025190.1	Q8TAQ9	SUN3_HUMAN	Sad1 and UNC84 domain containing 3	282	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.					integral component of membrane (GO:0016021)|SUN-KASH complex (GO:0034993)		p.K282N(1)		central_nervous_system(1)|endometrium(3)|large_intestine(8)|liver(1)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CAGAAAATTCCTTGGGTGCAC	0.448																																					p.K282N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G846T	7						.						144.0	142.0	143.0					7																	48033927		2203	4300	6503	48000452	SO:0001583	missense	256979	exon9			AF429967	CCDS34636.1, CCDS64647.1	7p12.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164744	ENSG00000164744			22429	protein-coding gene	gene with protein product			"""Sad1 and UNC84 domain containing 1"""	SUNC1			Standard	NM_001284350		Approved	MGC33329	uc003tof.3	Q8TAQ9	OTTHUMG00000155646	ENST00000297325.4:c.846G>T	7.37:g.48033927C>A	ENSP00000297325:p.Lys282Asn	Somatic		Capture	Illumina HiSeq	Phase_I	48000452	NM_152782	A4D2F3|B4DXK1|D3DVM3|E7EWC8|Q4F965|Q7Z4U8	Missense_Mutation	SNP	ENST00000297325.4	37	CCDS34636.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.30|17.30	3.354080|3.354080	0.61293|0.61293	.|.	.|.	ENSG00000164744|ENSG00000164744	ENST00000297325;ENST00000412371;ENST00000412142;ENST00000395572;ENST00000453192;ENST00000438771|ENST00000453071	T;T;T;T;T;T|.	0.62105|.	0.05;0.05;0.05;0.05;0.05;0.05|.	5.21|5.21	3.36|3.36	0.38483|0.38483	Sad1/UNC-like, C-terminal (2);|.	0.189778|.	0.44097|.	D|.	0.000482|.	T|T	0.67804|0.67804	0.2932|0.2932	M|M	0.78344|0.78344	2.41|2.41	0.36488|0.36488	D|D	0.868283|0.868283	P;D;P|.	0.60575|.	0.888;0.988;0.896|.	P;P;P|.	0.53102|.	0.703;0.718;0.572|.	T|T	0.73905|0.73905	-0.3835|-0.3835	10|5	0.87932|.	D|.	0|.	.|.	10.6063|10.6063	0.45396|0.45396	0.0:0.8353:0.0:0.1647|0.0:0.8353:0.0:0.1647	.|.	270;182;282|.	E7EWC8;Q8TAQ9-2;Q8TAQ9|.	.;.;SUN3_HUMAN|.	N|M	282;104;182;282;270;182|206	ENSP00000297325:K282N;ENSP00000406887:K104N;ENSP00000410204:K182N;ENSP00000378939:K282N;ENSP00000387525:K270N;ENSP00000409077:K182N|.	ENSP00000297325:K282N|.	K|R	-|-	3|2	2|0	SUN3|SUN3	48000452|48000452	0.996000|0.996000	0.38824|0.38824	1.000000|1.000000	0.80357|0.80357	0.905000|0.905000	0.53344|0.53344	0.522000|0.522000	0.22909|0.22909	1.224000|1.224000	0.43551|0.43551	0.551000|0.551000	0.68910|0.68910	AAG|AGG		0.448	SUN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340962.1	NM_152782	
ABCA13	154664	broad.mit.edu	37	7	48319363	48319363	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:48319363G>A	ENST00000435803.1	+	18	8596	c.8572G>A	c.(8572-8574)Gga>Aga	p.G2858R		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2858					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.G2858R(1)|p.G2803R(1)		breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						AGCAACCACCGGAAAGAATGT	0.368																																					p.P2803P												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G8409A	7						.						95.0	98.0	97.0					7																	48319363		1812	4080	5892	48289909	SO:0001583	missense	154664	exon16			AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.8572G>A	7.37:g.48319363G>A	ENSP00000411096:p.Gly2858Arg	Somatic		Capture	Illumina HiSeq	Phase_I	48289909	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	G	4.170	0.030083	0.08101	.	.	ENSG00000179869	ENST00000435803	T	0.53857	0.6	5.4	1.53	0.23141	.	0.809916	0.10715	N	0.642430	T	0.24699	0.0599	N	0.11560	0.145	0.09310	N	1	P	0.34826	0.471	B	0.18561	0.022	T	0.09228	-1.0684	10	0.40728	T	0.16	.	4.4554	0.11640	0.2737:0.172:0.5544:0.0	.	2858	Q86UQ4	ABCAD_HUMAN	R	2858	ENSP00000411096:G2858R	ENSP00000411096:G2858R	G	+	1	0	ABCA13	48289909	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	-0.204000	0.09425	0.253000	0.21552	-0.133000	0.14855	GGA		0.368	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
IKZF1	10320	broad.mit.edu	37	7	50455062	50455062	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:50455062T>G	ENST00000331340.3	+	6	764	c.609T>G	c.(607-609)tgT>tgG	p.C203W	IKZF1_ENST00000343574.5_Missense_Mutation_p.C116W|IKZF1_ENST00000439701.1_Intron|IKZF1_ENST00000359197.5_Intron|IKZF1_ENST00000346667.4_Intron|IKZF1_ENST00000349824.4_Intron|IKZF1_ENST00000440768.2_Intron|IKZF1_ENST00000438033.1_Missense_Mutation_p.C116W|IKZF1_ENST00000357364.4_Intron	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	203					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(131)|p.C203W(1)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				CTCACAAATGTGGATATTGTG	0.443			"""D,T"""	BCL6	"""ALL, DLBCL"""																																p.C203W			"""Rec,Dom"""	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	.	132	Unknown(131)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(131)|large_intestine(1)	c.T609G	7						.						53.0	54.0	54.0					7																	50455062		1858	4098	5956	50422556	SO:0001583	missense	10320	exon6			U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13176	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 92"""	603023	"""zinc finger protein, subfamily 1A, 1 (Ikaros)"""	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.609T>G	7.37:g.50455062T>G	ENSP00000331614:p.Cys203Trp	Somatic		Capture	Illumina HiSeq	Phase_I	50422556	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Missense_Mutation	SNP	ENST00000331340.3	37		.	.	.	.	.	.	.	.	.	.	T	18.27	3.586677	0.66105	.	.	ENSG00000185811	ENST00000343574;ENST00000331340;ENST00000438033	D;D;D	0.85258	-1.96;-1.96;-1.96	5.85	4.7	0.59300	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.91436	0.7297	.	.	.	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.91325	0.5085	9	0.87932	D	0	-6.4616	9.7965	0.40737	0.0:0.1381:0.0:0.8619	.	116;203	Q13422-2;Q13422	.;IKZF1_HUMAN	W	116;203;116	ENSP00000342750:C116W;ENSP00000331614:C203W;ENSP00000396554:C116W	ENSP00000331614:C203W	C	+	3	2	IKZF1	50422556	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.496000	0.35638	1.034000	0.39945	0.533000	0.62120	TGT		0.443	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060	
COBL	23242	broad.mit.edu	37	7	51152880	51152880	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:51152880T>C	ENST00000265136.7	-	7	1244	c.1079A>G	c.(1078-1080)aAc>aGc	p.N360S	COBL_ENST00000441453.1_Missense_Mutation_p.N360S|COBL_ENST00000395542.2_Missense_Mutation_p.N385S|COBL_ENST00000395540.2_Missense_Mutation_p.N360S	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	360					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.N360S(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)					GCTCTTCCTGTTCTCCTCCTT	0.597																																					p.N360S	NSCLC(189;2119 2138 12223 30818 34679)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1079G	7						.						197.0	139.0	158.0					7																	51152880		2203	4300	6503	51120374	SO:0001583	missense	23242	exon7			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.1079A>G	7.37:g.51152880T>C	ENSP00000265136:p.Asn360Ser	Somatic		Capture	Illumina HiSeq	Phase_I	51120374	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	.	.	.	.	.	.	.	.	.	.	T	18.03	3.533471	0.64972	.	.	ENSG00000106078	ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542;ENST00000395540;ENST00000441453	T;T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71;0.71	5.46	3.09	0.35607	.	0.732373	0.12271	N	0.483785	T	0.50205	0.1602	L	0.27053	0.805	0.26164	N	0.979954	P;P;P;D;D	0.89917	0.952;0.726;0.952;0.983;1.0	P;B;P;P;D	0.74023	0.474;0.214;0.474;0.659;0.982	T	0.37103	-0.9720	10	0.18710	T	0.47	.	8.8959	0.35465	0.0:0.1533:0.0:0.8467	.	360;360;360;360;385	O75128-3;O75128-5;O75128-7;O75128;O75128-2	.;.;.;COBL_HUMAN;.	S	360;252;188;385;360;360	ENSP00000265136:N360S;ENSP00000401204:N252S;ENSP00000413498:N188S;ENSP00000378912:N385S;ENSP00000378910:N360S;ENSP00000399500:N360S	ENSP00000265136:N360S	N	-	2	0	COBL	51120374	0.998000	0.40836	0.956000	0.39512	0.889000	0.51656	1.805000	0.38883	0.374000	0.24650	0.533000	0.62120	AAC		0.597	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
COBL	23242	broad.mit.edu	37	7	51287484	51287484	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:51287484C>T	ENST00000265136.7	-	2	364	c.199G>A	c.(199-201)Gtg>Atg	p.V67M	COBL_ENST00000441453.1_Missense_Mutation_p.V67M|COBL_ENST00000395542.2_Missense_Mutation_p.V67M|COBL_ENST00000395540.2_Missense_Mutation_p.V67M	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	67					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.V67M(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)					GGCAGGACCACGGTGACGTCC	0.632																																					p.V67M	NSCLC(189;2119 2138 12223 30818 34679)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G199A	7						.						77.0	75.0	75.0					7																	51287484		2203	4300	6503	51254978	SO:0001583	missense	23242	exon2			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.199G>A	7.37:g.51287484C>T	ENSP00000265136:p.Val67Met	Somatic		Capture	Illumina HiSeq	Phase_I	51254978	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.542369	0.85917	.	.	ENSG00000106078	ENST00000265136;ENST00000395542;ENST00000395540;ENST00000441453;ENST00000449281	T;T	0.32023	1.62;1.47	5.73	5.73	0.89815	Cordon-bleu domain (1);	0.000000	0.39759	N	0.001265	T	0.59865	0.2225	M	0.83953	2.67	0.39578	D	0.969396	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.983;0.999;0.999	T	0.65150	-0.6238	10	0.87932	D	0	.	15.7604	0.78076	0.0:1.0:0.0:0.0	.	67;67;67;67	O75128-3;O75128-5;O75128-7;O75128	.;.;.;COBL_HUMAN	M	67;67;67;67;51	ENSP00000265136:V67M;ENSP00000378912:V67M	ENSP00000265136:V67M	V	-	1	0	COBL	51254978	0.993000	0.37304	0.971000	0.41717	0.904000	0.53231	3.967000	0.56802	2.854000	0.98071	0.655000	0.94253	GTG		0.632	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
TMEM248	55069	broad.mit.edu	37	7	66413599	66413599	+	Missense_Mutation	SNP	G	G	A	rs201691446	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:66413599G>A	ENST00000341567.4	+	4	769	c.514G>A	c.(514-516)Gcc>Acc	p.A172T		NM_017994.4	NP_060464.1	Q9NWD8	TM248_HUMAN	transmembrane protein 248	172						integral component of membrane (GO:0016021)		p.A172T(1)									AGATGACTGCGCCCTCCACGG	0.547													G|||	2	0.000399361	0.0	0.0029	5008	,	,		17986	0.0		0.0	False		,,,				2504	0.0				p.A172T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G514A	7						.						74.0	52.0	60.0					7																	66413599		2203	4300	6503	66051034	SO:0001583	missense	55069	exon4				CCDS5536.1	7q11.21	2012-05-30	2012-05-30	2012-05-30	ENSG00000106609	ENSG00000106609			25476	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 42"""	C7orf42		12477932	Standard	XM_005250482		Approved	FLJ10099, FLJ13090	uc003tvk.3	Q9NWD8	OTTHUMG00000129553	ENST00000341567.4:c.514G>A	7.37:g.66413599G>A	ENSP00000340668:p.Ala172Thr	Somatic		Capture	Illumina HiSeq	Phase_I	66051034	NM_017994	Q53H07|Q96FR2	Missense_Mutation	SNP	ENST00000341567.4	37	CCDS5536.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	G	18.01	3.526897	0.64860	.	.	ENSG00000106609	ENST00000341567	.	.	.	6.17	6.17	0.99709	.	0.101017	0.64402	D	0.000002	T	0.31389	0.0795	N	0.14661	0.345	0.41843	D	0.990134	B	0.26708	0.157	B	0.22386	0.039	T	0.19679	-1.0298	9	0.28530	T	0.3	0.3611	13.0796	0.59107	0.0723:0.0:0.9277:0.0	.	172	Q9NWD8	CG042_HUMAN	T	172	.	ENSP00000340668:A172T	A	+	1	0	C7orf42	66051034	1.000000	0.71417	1.000000	0.80357	0.451000	0.32288	6.340000	0.72973	2.941000	0.99782	0.655000	0.94253	GCC		0.547	TMEM248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251745.2	NM_017994	
WBSCR17	64409	broad.mit.edu	37	7	71134961	71134961	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:71134961C>T	ENST00000333538.5	+	8	1905	c.1271C>T	c.(1270-1272)cCg>cTg	p.P424L	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	424					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.P424L(2)		NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				TTTCAGAATCCGGGAATTGAC	0.473																																					p.P424L												.	.	2	Substitution - Missense(2)	large_intestine(1)|pancreas(1)	c.C1271T	7						.						67.0	69.0	68.0					7																	71134961		2203	4300	6503	70772897	SO:0001583	missense	64409	exon8			AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"""Glycosyltransferase family 2 domain containing"""	16347	protein-coding gene	gene with protein product	"""polypeptide N-acetylgalactosaminyltransferase-like 3"", ""polypeptide GalNAc transferase 3"""	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.1271C>T	7.37:g.71134961C>T	ENSP00000329654:p.Pro424Leu	Somatic		Capture	Illumina HiSeq	Phase_I	70772897	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	37	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.181113	0.57800	.	.	ENSG00000185274	ENST00000333538	T	0.68025	-0.3	5.18	5.18	0.71444	.	0.183063	0.48286	D	0.000189	T	0.65165	0.2665	N	0.24115	0.695	0.58432	D	0.999999	D	0.63046	0.992	P	0.53266	0.722	T	0.65639	-0.6119	10	0.37606	T	0.19	.	17.6772	0.88234	0.0:1.0:0.0:0.0	.	424	Q6IS24	GLTL3_HUMAN	L	424	ENSP00000329654:P424L	ENSP00000329654:P424L	P	+	2	0	WBSCR17	70772897	0.998000	0.40836	1.000000	0.80357	0.512000	0.34134	3.875000	0.56108	2.420000	0.82092	0.591000	0.81541	CCG		0.473	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479	
STX1A	6804	broad.mit.edu	37	7	73119551	73119551	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:73119551G>A	ENST00000222812.3	-	4	238	c.212C>T	c.(211-213)aCg>aTg	p.T71M	STX1A_ENST00000395155.3_Missense_Mutation_p.T71M|STX1A_ENST00000395156.3_Missense_Mutation_p.T71M|STX1A_ENST00000395154.3_Missense_Mutation_p.T71M	NM_004603.3	NP_004594.1	Q16623	STX1A_HUMAN	syntaxin 1A (brain)	71					calcium ion-dependent exocytosis (GO:0017156)|cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|neurotransmitter secretion (GO:0007269)|positive regulation of exocytosis (GO:0045921)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of insulin secretion (GO:0050796)|response to gravity (GO:0009629)|secretion by cell (GO:0032940)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)	actomyosin (GO:0042641)|cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|SNARE complex (GO:0031201)|synaptic vesicle membrane (GO:0030672)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex (GO:0070033)	calcium channel inhibitor activity (GO:0019855)	p.T71M(1)		large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(55;0.0908)|all_lung(88;0.198)				CTCCTCCTTCGTCTCTGGGGA	0.587																																					p.T71M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C212T	7						.						151.0	132.0	138.0					7																	73119551		2203	4300	6503	72757487	SO:0001583	missense	6804	exon4				CCDS34655.1, CCDS55120.1	7q11.2	2008-07-18			ENSG00000106089	ENSG00000106089			11433	protein-coding gene	gene with protein product		186590		STX1		1321498	Standard	NM_001165903		Approved	HPC-1, p35-1	uc003tyx.3	Q16623	OTTHUMG00000137422	ENST00000222812.3:c.212C>T	7.37:g.73119551G>A	ENSP00000222812:p.Thr71Met	Somatic		Capture	Illumina HiSeq	Phase_I	72757487	NM_004603	O15447|O15448|Q12936|Q75MD9|Q7Z5K3|Q9BPZ6	Missense_Mutation	SNP	ENST00000222812.3	37	CCDS34655.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.481242	0.44147	.	.	ENSG00000106089	ENST00000222812;ENST00000395156;ENST00000395154;ENST00000395155	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	4.67	4.67	0.58626	t-SNARE (1);Syntaxin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.28234	0.0697	L	0.38175	1.15	0.80722	D	1	P;P;B	0.38729	0.518;0.644;0.113	B;B;B	0.24848	0.04;0.056;0.025	T	0.09378	-1.0677	10	0.23302	T	0.38	-27.0427	15.1034	0.72299	0.0:0.0:1.0:0.0	.	71;71;71	Q7Z5K3;Q16623-3;Q16623	.;.;STX1A_HUMAN	M	71	ENSP00000222812:T71M;ENSP00000378585:T71M;ENSP00000378583:T71M;ENSP00000378584:T71M	ENSP00000222812:T71M	T	-	2	0	STX1A	72757487	1.000000	0.71417	0.984000	0.44739	0.994000	0.84299	7.724000	0.84798	2.421000	0.82119	0.555000	0.69702	ACG		0.587	STX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268422.1	NM_004603	
ELN	2006	broad.mit.edu	37	7	73477688	73477688	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:73477688C>T	ENST00000252034.7	+	28	2306	c.1907C>T	c.(1906-1908)gCc>gTc	p.A636V	ELN_ENST00000380584.4_Missense_Mutation_p.A588V|ELN_ENST00000357036.5_Missense_Mutation_p.A641V|ELN_ENST00000429192.1_Missense_Mutation_p.A622V|ELN_ENST00000414324.1_Missense_Mutation_p.A612V|ELN_ENST00000445912.1_Missense_Mutation_p.A636V|ELN_ENST00000380562.4_Missense_Mutation_p.A642V|ELN_ENST00000458204.1_Missense_Mutation_p.A626V|ELN_ENST00000380575.4_Missense_Mutation_p.A607V|ELN_ENST00000380576.5_Missense_Mutation_p.A617V|ELN_ENST00000380553.4_Missense_Mutation_p.A500V|ELN_ENST00000320399.6_Missense_Mutation_p.A669V|CTB-51J22.1_ENST00000435932.1_RNA|ELN_ENST00000358929.4_Missense_Mutation_p.A704V|ELN_ENST00000320492.7_Missense_Mutation_p.A555V	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.				blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)	p.A636V(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				gctgccaaagccgccCAGTTT	0.662			T	PAX5	B-ALL		"""Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"""																														p.A617V			Dom	yes		7	7q11.23	2006	elastin	yes	L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1850T	7						.						8.0	11.0	10.0					7																	73477688		2048	3986	6034	73115624	SO:0001583	missense	2006	exon27				CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"""tropoelastin"", ""supravalvular aortic stenosis"", ""Williams-Beuren syndrome"""	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1907C>T	7.37:g.73477688C>T	ENSP00000252034:p.Ala636Val	Somatic		Capture	Illumina HiSeq	Phase_I	73115624	NM_001081755	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Missense_Mutation	SNP	ENST00000252034.7	37	CCDS5562.2	.	.	.	.	.	.	.	.	.	.	C	10.23	1.293120	0.23564	.	.	ENSG00000049540	ENST00000445912;ENST00000252034;ENST00000358929;ENST00000320492;ENST00000414324;ENST00000380562;ENST00000380575;ENST00000380584;ENST00000458204;ENST00000357036;ENST00000429192;ENST00000442462;ENST00000380553;ENST00000380576;ENST00000320399	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.41065	1.06;1.02;1.33;1.1;1.04;1.03;1.14;1.01;1.05;1.02;1.06;1.06;1.04;1.13	2.95	2.95	0.34219	.	.	.	.	.	T	0.56514	0.1990	.	.	.	0.32817	D	0.502241	D;D;D;D;D;D;D;D;D;D;D;D;D	0.67145	0.996;0.996;0.996;0.996;0.996;0.996;0.996;0.996;0.996;0.996;0.996;0.996;0.996	D;D;D;D;D;D;D;D;D;D;D;D;D	0.75484	0.971;0.971;0.986;0.971;0.986;0.971;0.986;0.971;0.971;0.986;0.971;0.971;0.971	T	0.61657	-0.7018	8	0.35671	T	0.21	.	9.6925	0.40136	0.0:1.0:0.0:0.0	.	636;555;612;626;642;607;622;641;617;500;547;588;636	E7ENM0;G5E950;G3V0G6;E7EN65;P15502-1;P15502-7;P15502-12;P15502-5;P15502-13;P15502-11;B3KRT8;P15502-8;P15502-2	.;.;.;.;.;.;.;.;.;.;.;.;.	V	636;636;704;555;612;642;607;588;626;641;622;575;500;617;669	ENSP00000389857:A636V;ENSP00000252034:A636V;ENSP00000351807:A704V;ENSP00000315607:A555V;ENSP00000392575:A612V;ENSP00000369936:A642V;ENSP00000369949:A607V;ENSP00000369958:A588V;ENSP00000403162:A626V;ENSP00000349540:A641V;ENSP00000391129:A622V;ENSP00000369926:A500V;ENSP00000369950:A617V;ENSP00000313565:A669V	ENSP00000252034:A636V	A	+	2	0	ELN	73115624	0.994000	0.37717	0.996000	0.52242	0.486000	0.33341	3.386000	0.52492	1.974000	0.57490	0.306000	0.20318	GCC		0.662	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501	
LIMK1	3984	broad.mit.edu	37	7	73523248	73523248	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:73523248G>A	ENST00000336180.2	+	10	1217	c.1166G>A	c.(1165-1167)cGa>cAa	p.R389Q	LIMK1_ENST00000538333.3_Missense_Mutation_p.R355Q|LIMK1_ENST00000418310.1_Missense_Mutation_p.R419Q	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	389	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|nervous system development (GO:0007399)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of axon extension (GO:0045773)|positive regulation of stress fiber assembly (GO:0051496)|protein phosphorylation (GO:0006468)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)	ATP binding (GO:0005524)|heat shock protein binding (GO:0031072)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)	p.R389Q(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21		Lung NSC(55;0.137)			Dabrafenib(DB08912)	AAGGTCATGCGATGCCTGGAA	0.602																																					p.R389Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1166A	7						.						108.0	87.0	94.0					7																	73523248		2203	4300	6503	73161184	SO:0001583	missense	3984	exon10			D26309	CCDS5563.1, CCDS56491.1	7q11.23	2005-01-21			ENSG00000106683	ENSG00000106683			6613	protein-coding gene	gene with protein product		601329				8673124, 8812460	Standard	NM_002314		Approved	LIMK	uc003uaa.2	P53667	OTTHUMG00000023448	ENST00000336180.2:c.1166G>A	7.37:g.73523248G>A	ENSP00000336740:p.Arg389Gln	Somatic		Capture	Illumina HiSeq	Phase_I	73161184	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Missense_Mutation	SNP	ENST00000336180.2	37	CCDS5563.1	.	.	.	.	.	.	.	.	.	.	G	35	5.517042	0.96416	.	.	ENSG00000106683	ENST00000418310;ENST00000419043;ENST00000336180;ENST00000538333	D;D;D	0.82803	-1.65;-1.65;-1.65	5.23	5.23	0.72850	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81837	0.4907	N	0.04724	-0.175	0.80722	D	1	D;D;D	0.89917	1.0;0.993;0.997	D;P;P	0.71656	0.974;0.865;0.719	D	0.86596	0.1863	10	0.87932	D	0	-17.445	16.3479	0.83151	0.0:0.0:1.0:0.0	.	284;355;389	Q59FA3;B7Z6I8;P53667	.;.;LIMK1_HUMAN	Q	419;389;389;355	ENSP00000409717:R419Q;ENSP00000336740:R389Q;ENSP00000444452:R355Q	ENSP00000336740:R389Q	R	+	2	0	LIMK1	73161184	1.000000	0.71417	0.943000	0.38184	0.906000	0.53458	9.364000	0.97136	2.453000	0.82957	0.549000	0.68633	CGA		0.602	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314	
CLIP2	7461	broad.mit.edu	37	7	73770752	73770752	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:73770752C>T	ENST00000395060.1	+	4	816	c.816C>T	c.(814-816)tgC>tgT	p.C272C	CLIP2_ENST00000223398.6_Silent_p.C272C|CLIP2_ENST00000361545.5_Silent_p.C272C			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	272	CAP-Gly 2. {ECO:0000255|PROSITE- ProRule:PRU00045}.					cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)		p.C272C(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						ACTTCCAGTGCCCACCCAAGT	0.602																																					p.C272C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C816T	7						.						118.0	101.0	107.0					7																	73770752		2203	4300	6503	73408688	SO:0001819	synonymous_variant	7461	exon5			AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"""cytoplasmic linker 2"", ""Williams-Beuren syndrome chromosome region 3"""	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.816C>T	7.37:g.73770752C>T		Somatic		Capture	Illumina HiSeq	Phase_I	73408688	NM_003388	O14527|O43611	Silent	SNP	ENST00000395060.1	37	CCDS5569.1																																																																																				0.602	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388	
GTF2IRD1	9569	broad.mit.edu	37	7	73938412	73938412	+	Missense_Mutation	SNP	G	G	A	rs587659375	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:73938412G>A	ENST00000265755.3	+	8	1411	c.1018G>A	c.(1018-1020)Gcc>Acc	p.A340T	GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.A372T|GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.A340T|GTF2IRD1_ENST00000476977.1_Missense_Mutation_p.A340T|GTF2IRD1_ENST00000489094.1_3'UTR	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	340					multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A340T(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GAAGTGGGACGCCTTCATAAA	0.612													G|||	2	0.000399361	0.0	0.0	5008	,	,		12883	0.0		0.0	False		,,,				2504	0.002				p.A340T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1018A	7						.						82.0	61.0	68.0					7																	73938412		2203	4300	6503	73576348	SO:0001583	missense	9569	exon8			AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"""binding factor for early enhancer"""	604318	"""GTF2I repeat domain-containing 1"""	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.1018G>A	7.37:g.73938412G>A	ENSP00000265755:p.Ala340Thr	Somatic		Capture	Illumina HiSeq	Phase_I	73576348	NM_005685	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Missense_Mutation	SNP	ENST00000265755.3	37	CCDS5571.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.272172	0.80469	.	.	ENSG00000006704	ENST00000265755;ENST00000455841;ENST00000424337;ENST00000476977	T;T;T;T	0.33216	1.43;1.42;1.43;1.42	4.63	0.149	0.14863	.	0.432396	0.25430	N	0.030736	T	0.12774	0.0310	N	0.14661	0.345	0.26375	N	0.976836	B;B;P;P	0.48016	0.041;0.396;0.904;0.865	B;B;B;B	0.39217	0.006;0.062;0.154;0.294	T	0.16571	-1.0398	10	0.40728	T	0.16	-12.1664	3.7711	0.08642	0.5028:0.212:0.2852:0.0	.	372;340;340;340	Q6DSU6;E9PFE2;Q9UHL9;Q9UHL9-2	.;.;GT2D1_HUMAN;.	T	340;372;340;340	ENSP00000265755:A340T;ENSP00000397566:A372T;ENSP00000408477:A340T;ENSP00000418383:A340T	ENSP00000265755:A340T	A	+	1	0	GTF2IRD1	73576348	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.246000	0.32803	0.119000	0.18210	0.561000	0.74099	GCC		0.612	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328	
GTF2IRD1	9569	broad.mit.edu	37	7	74009367	74009367	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:74009367C>T	ENST00000265755.3	+	25	3056	c.2663C>T	c.(2662-2664)gCc>gTc	p.A888V	GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.A905V|GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.A873V|GTF2IRD1_ENST00000476977.1_Missense_Mutation_p.A873V	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	888					multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A888V(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TGCAATGATGCCAAGGTGCCA	0.473																																					p.A873V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2618T	7						.						96.0	93.0	94.0					7																	74009367		2203	4300	6503	73647303	SO:0001583	missense	9569	exon25			AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"""binding factor for early enhancer"""	604318	"""GTF2I repeat domain-containing 1"""	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.2663C>T	7.37:g.74009367C>T	ENSP00000265755:p.Ala888Val	Somatic		Capture	Illumina HiSeq	Phase_I	73647303	NM_005685	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Missense_Mutation	SNP	ENST00000265755.3	37	CCDS5571.1	.	.	.	.	.	.	.	.	.	.	C	17.68	3.449807	0.63290	.	.	ENSG00000006704	ENST00000265755;ENST00000455841;ENST00000424337;ENST00000476977	T;T;T;T	0.35421	1.33;1.33;1.33;1.31	4.07	4.07	0.47477	.	0.195944	0.43919	D	0.000509	T	0.34774	0.0909	L	0.54323	1.7	0.44547	D	0.997508	B;B;B;B	0.31054	0.084;0.306;0.087;0.141	B;B;B;B	0.31290	0.063;0.101;0.089;0.127	T	0.23332	-1.0191	10	0.39692	T	0.17	-9.835	14.319	0.66473	0.0:1.0:0.0:0.0	.	905;873;888;873	Q6DSU6;E9PFE2;Q9UHL9;Q9UHL9-2	.;.;GT2D1_HUMAN;.	V	888;905;873;873	ENSP00000265755:A888V;ENSP00000397566:A905V;ENSP00000408477:A873V;ENSP00000418383:A873V	ENSP00000265755:A888V	A	+	2	0	GTF2IRD1	73647303	1.000000	0.71417	0.974000	0.42286	0.994000	0.84299	5.636000	0.67848	2.227000	0.72691	0.561000	0.74099	GCC		0.473	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328	
GSAP	54103	broad.mit.edu	37	7	77006656	77006656	+	Missense_Mutation	SNP	C	C	T	rs201156464		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:77006656C>T	ENST00000257626.7	-	9	706	c.628G>A	c.(628-630)Gtt>Att	p.V210I		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	210					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)	p.V210I(1)									TGAGCCCAAACGAAATCCTCA	0.303																																					p.V210I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G628A	7						.						137.0	144.0	142.0					7																	77006656		2203	4300	6503	76844592	SO:0001583	missense	54103	exon9				CCDS34672.2	7q11.23	2013-04-05	2013-04-05	2013-04-05	ENSG00000186088	ENSG00000186088			28042	protein-coding gene	gene with protein product		613552	"""pigeon homolog (Drosophila)"""	PION		20811458	Standard	NM_017439		Approved	LOC54103	uc003ugf.3	A4D1B5	OTTHUMG00000150504	ENST00000257626.7:c.628G>A	7.37:g.77006656C>T	ENSP00000257626:p.Val210Ile	Somatic		Capture	Illumina HiSeq	Phase_I	76844592	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Missense_Mutation	SNP	ENST00000257626.7	37	CCDS34672.2	.	.	.	.	.	.	.	.	.	.	C	8.246	0.807952	0.16467	.	.	ENSG00000186088	ENST00000257626	T	0.16324	2.35	5.45	3.58	0.41010	.	0.585375	0.14877	U	0.293195	T	0.10895	0.0266	L	0.27053	0.805	0.80722	D	1	B	0.23891	0.093	B	0.18263	0.021	T	0.12400	-1.0549	10	0.27082	T	0.32	.	7.3742	0.26818	0.0:0.7039:0.1403:0.1558	.	210	A4D1B5	GSAP_HUMAN	I	210	ENSP00000257626:V210I	ENSP00000257626:V210I	V	-	1	0	PION	76844592	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	0.768000	0.26590	1.295000	0.44724	0.650000	0.86243	GTT		0.303	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439	
PCLO	27445	broad.mit.edu	37	7	82508670	82508670	+	Missense_Mutation	SNP	G	G	A	rs576824740		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:82508670G>A	ENST00000333891.9	-	10	13974	c.13637C>T	c.(13636-13638)aCg>aTg	p.T4546M	PCLO_ENST00000426442.2_5'UTR|PCLO_ENST00000423517.2_Missense_Mutation_p.T4546M	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein									p.T4546M(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						AAGCTTCCCCGTCTGTTCCGC	0.358													G|||	1	0.000199681	0.0	0.0	5008	,	,		15325	0.0		0.0	False		,,,				2504	0.001				p.T4546M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C13637T	7						.						79.0	72.0	74.0					7																	82508670		1828	4064	5892	82346606	SO:0001583	missense	27445	exon10			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.13637C>T	7.37:g.82508670G>A	ENSP00000334319:p.Thr4546Met	Somatic		Capture	Illumina HiSeq	Phase_I	82346606	NM_033026		De_novo_Start_OutOfFrame	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	12.22	1.873661	0.33069	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000380195	T;T	0.27557	1.66;1.66	4.8	4.8	0.61643	.	.	.	.	.	T	0.41305	0.1153	M	0.75615	2.305	0.80722	D	1	P;P	0.51933	0.949;0.949	B;B	0.44044	0.439;0.439	T	0.53136	-0.8481	9	0.87932	D	0	.	17.8176	0.88639	0.0:0.0:1.0:0.0	.	4546;4546	Q9Y6V0-5;Q9Y6V0-6	.;.	M	4546;4546;42	ENSP00000334319:T4546M;ENSP00000388393:T4546M	ENSP00000334319:T4546M	T	-	2	0	PCLO	82346606	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.787000	0.85759	2.364000	0.80123	0.591000	0.81541	ACG		0.358	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
SEMA3D	223117	broad.mit.edu	37	7	84628805	84628805	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:84628805C>T	ENST00000284136.6	-	17	2328	c.2285G>A	c.(2284-2286)cGa>cAa	p.R762Q	SEMA3D_ENST00000484038.1_5'UTR	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	762	Arg/Lys-rich (basic).				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)	p.R762Q(1)		NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						GTGATGTCTTCGATTTCGTTT	0.448																																					p.R762Q	Ovarian(63;442 1191 17318 29975 31528)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2285A	7						.						174.0	141.0	152.0					7																	84628805		2203	4300	6503	84466741	SO:0001583	missense	223117	exon17			BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"""Semaphorins"", ""Immunoglobulin superfamily / V-set domain containing"""	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.2285G>A	7.37:g.84628805C>T	ENSP00000284136:p.Arg762Gln	Somatic		Capture	Illumina HiSeq	Phase_I	84466741	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.100584	0.76983	.	.	ENSG00000153993	ENST00000284136	T	0.36157	1.27	5.93	5.93	0.95920	.	0.117189	0.64402	D	0.000020	T	0.63010	0.2475	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62139	-0.6917	10	0.62326	D	0.03	.	20.3409	0.98764	0.0:1.0:0.0:0.0	.	762	O95025	SEM3D_HUMAN	Q	762	ENSP00000284136:R762Q	ENSP00000284136:R762Q	R	-	2	0	SEMA3D	84466741	0.997000	0.39634	0.814000	0.32528	0.318000	0.28184	5.538000	0.67193	2.814000	0.96858	0.655000	0.94253	CGA		0.448	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754	
GRM3	2913	broad.mit.edu	37	7	86493631	86493631	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:86493631A>C	ENST00000361669.2	+	6	3699	c.2600A>C	c.(2599-2601)aAt>aCt	p.N867T	GRM3_ENST00000394720.2_Missense_Mutation_p.Q509H|GRM3_ENST00000439827.1_Missense_Mutation_p.Q511H|GRM3_ENST00000536043.1_Missense_Mutation_p.N739T|GRM3_ENST00000546348.1_Missense_Mutation_p.N459T	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	867					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)	p.N867T(1)		NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					ACGGTGTGCAATGGGCGGGAA	0.463																																					p.N867T	GBM(52;969 1098 3139 52280)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2600C	7						.						279.0	228.0	245.0					7																	86493631		2203	4300	6503	86331567	SO:0001583	missense	2913	exon6				CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.2600A>C	7.37:g.86493631A>C	ENSP00000355316:p.Asn867Thr	Somatic		Capture	Illumina HiSeq	Phase_I	86331567	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	37	CCDS5600.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.2|24.2	4.509836|4.509836	0.85282|0.85282	.|.	.|.	ENSG00000198822|ENSG00000198822	ENST00000361669;ENST00000546348;ENST00000536043|ENST00000439827;ENST00000394720	D;D;D|D;D	0.88741|0.88741	-2.42;-2.31;-2.2|-2.42;-2.42	5.99|5.99	5.99|5.99	0.97316|0.97316	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.91503|0.91503	0.7317|0.7317	L|L	0.32530|0.32530	0.975|0.975	0.32100|0.32100	N|N	0.590689|0.590689	D;D;D|D	0.89917|0.64830	1.0;0.999;0.998|0.994	D;D;D|D	0.87578|0.75484	0.998;0.998;0.995|0.986	D|D	0.92541|0.92541	0.6042|0.6042	10|9	0.54805|0.87932	T|D	0.06|0	.|.	15.6754|15.6754	0.77316|0.77316	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	459;739;867|511	B7Z204;F5GYZ2;Q14832|G5E9K2	.;.;GRM3_HUMAN|.	T|H	867;459;739|511;509	ENSP00000355316:N867T;ENSP00000444064:N459T;ENSP00000441407:N739T|ENSP00000398767:Q511H;ENSP00000378209:Q509H	ENSP00000355316:N867T|ENSP00000378209:Q509H	N|Q	+|+	2|3	0|2	GRM3|GRM3	86331567|86331567	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.990000|0.990000	0.78478|0.78478	8.047000|8.047000	0.89440|0.89440	2.291000|2.291000	0.77112|0.77112	0.533000|0.533000	0.62120|0.62120	AAT|CAA		0.463	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2		
ABCB1	5243	broad.mit.edu	37	7	87144725	87144725	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:87144725A>G	ENST00000265724.3	-	26	3521	c.3104T>C	c.(3103-3105)gTc>gCc	p.V1035A	ABCB1_ENST00000488737.2_5'UTR|ABCB1_ENST00000543898.1_Missense_Mutation_p.V971A	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	1035	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)	p.V1035A(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	ACCAAATGTGACATTTCCTTC	0.453																																					p.V1035A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3104C	7						.						62.0	58.0	59.0					7																	87144725		2203	4300	6503	86982661	SO:0001583	missense	5243	exon26			M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"""CD molecules"", ""ATP binding cassette transporters / subfamily B"""	40	protein-coding gene	gene with protein product	"""multidrug resistance protein 1"""	171050	"""colchicin sensitivity"""	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.3104T>C	7.37:g.87144725A>G	ENSP00000265724:p.Val1035Ala	Somatic		Capture	Illumina HiSeq	Phase_I	86982661	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	A	14.48	2.547297	0.45383	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.91686	-2.89;-2.89	5.96	5.96	0.96718	ABC transporter-like (1);	0.203887	0.43260	D	0.000595	D	0.92724	0.7687	M	0.76328	2.33	0.50632	D	0.999882	B;B	0.31459	0.099;0.324	B;B	0.40375	0.036;0.327	D	0.92175	0.5747	10	0.87932	D	0	-11.6692	11.5159	0.50520	0.9284:0.0:0.0716:0.0	.	971;1035	B5AK60;P08183	.;MDR1_HUMAN	A	816;1035;971	ENSP00000265724:V1035A;ENSP00000444095:V971A	ENSP00000265724:V1035A	V	-	2	0	ABCB1	86982661	0.993000	0.37304	1.000000	0.80357	0.313000	0.28021	7.348000	0.79366	2.279000	0.76181	0.533000	0.62120	GTC		0.453	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927	
RUNDC3B	154661	broad.mit.edu	37	7	87400065	87400065	+	Splice_Site	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:87400065G>T	ENST00000338056.3	+	8	1260	c.849G>T	c.(847-849)aaG>aaT	p.K283N	RUNDC3B_ENST00000493037.1_Splice_Site_p.K266N|RUNDC3B_ENST00000394654.3_Splice_Site_p.K266N	NM_001134405.1|NM_138290.2	NP_001127877.1|NP_612147.1	Q96NL0	RUN3B_HUMAN	RUN domain containing 3B	283								p.K283N(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(2)	26	Esophageal squamous(14;0.00164)					TGGAACAGAAGGTATTTTAAA	0.328																																					p.K266N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G798T	7						.						55.0	55.0	55.0					7																	87400065		2203	4300	6503	87238001	SO:0001630	splice_region_variant	154661	exon7				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.849+1G>T	7.37:g.87400065G>T		Somatic		Capture	Illumina HiSeq	Phase_I	87238001	NM_001134405	B4DFD0|E9PBR4|Q8IWW5|Q8NB55|Q8TBG7	Missense_Mutation	SNP	ENST00000338056.3	37	CCDS5609.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.923797	0.92319	.	.	ENSG00000105784	ENST00000338056;ENST00000493037;ENST00000394654	T;T;T	0.59364	0.27;0.27;0.27	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.74145	0.3678	L	0.58810	1.83	0.80722	D	1	D;D;P;D;D	0.76494	0.961;0.961;0.873;0.999;0.998	P;P;P;D;D	0.80764	0.617;0.617;0.544;0.994;0.963	T	0.74213	-0.3738	10	0.52906	T	0.07	-16.0545	19.4269	0.94746	0.0:0.0:1.0:0.0	.	266;266;188;266;283	E9PBR4;B4DFD0;Q96NL0-2;Q96NL0-4;Q96NL0	.;.;.;.;RUN3B_HUMAN	N	283;266;266	ENSP00000337732:K283N;ENSP00000420394:K266N;ENSP00000378149:K266N	ENSP00000337732:K283N	K	+	3	2	RUNDC3B	87238001	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	9.256000	0.95535	2.553000	0.86117	0.650000	0.86243	AAG		0.328	RUNDC3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253679.1	NM_138290	Missense_Mutation
ZNF804B	219578	broad.mit.edu	37	7	88965651	88965651	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:88965651G>A	ENST00000333190.4	+	4	3964	c.3355G>A	c.(3355-3357)Gac>Aac	p.D1119N		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1119							metal ion binding (GO:0046872)	p.D1119N(1)		NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			CTCTTACTATGACAGAACTAT	0.368										HNSCC(36;0.09)																											p.D1119N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3355A	7						.						52.0	52.0	52.0					7																	88965651		2203	4300	6503	88803587	SO:0001583	missense	219578	exon4			AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.3355G>A	7.37:g.88965651G>A	ENSP00000329638:p.Asp1119Asn	Somatic		Capture	Illumina HiSeq	Phase_I	88803587	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.036274	0.75617	.	.	ENSG00000182348	ENST00000333190	T	0.07908	3.15	4.61	4.61	0.57282	.	0.000000	0.64402	D	0.000006	T	0.17109	0.0411	L	0.36672	1.1	0.36611	D	0.875209	D	0.62365	0.991	P	0.57101	0.813	T	0.03374	-1.1043	10	0.59425	D	0.04	-18.5327	18.0083	0.89216	0.0:0.0:1.0:0.0	.	1119	A4D1E1	Z804B_HUMAN	N	1119	ENSP00000329638:D1119N	ENSP00000329638:D1119N	D	+	1	0	ZNF804B	88803587	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.276000	0.65580	2.549000	0.85964	0.655000	0.94253	GAC		0.368	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
AKAP9	10142	broad.mit.edu	37	7	91682216	91682216	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:91682216C>T	ENST00000359028.2	+	23	5806	c.5581C>T	c.(5581-5583)Cga>Tga	p.R1861*	AKAP9_ENST00000356239.3_Nonsense_Mutation_p.R1849*|AKAP9_ENST00000358100.2_Nonsense_Mutation_p.R1861*			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1861	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.R1849*(1)|p.R1861*(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CATTAGCTCTCGACTACAAGC	0.408			T	BRAF	papillary thyroid																																p.R1849X			Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C5545T	7						.						111.0	101.0	104.0					7																	91682216		2203	4300	6503	91520152	SO:0001587	stop_gained	10142	exon22			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.5581C>T	7.37:g.91682216C>T	ENSP00000351922:p.Arg1861*	Somatic		Capture	Illumina HiSeq	Phase_I	91520152	NM_147185	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Nonsense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	C	47	13.438189	0.99742	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120	.	.	.	5.25	5.25	0.73442	.	0.000000	0.30820	N	0.008807	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.1013	0.65056	0.1504:0.8496:0.0:0.0	.	.	.	.	X	1849;1861;1861;1861	.	ENSP00000348573:R1849X	R	+	1	2	AKAP9	91520152	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.199000	0.58426	2.606000	0.88127	0.591000	0.81541	CGA		0.408	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
PEX1	5189	broad.mit.edu	37	7	92123645	92123645	+	Nonsense_Mutation	SNP	G	G	A	rs61750428		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:92123645G>A	ENST00000248633.4	-	19	3087	c.2992C>T	c.(2992-2994)Cga>Tga	p.R998*	AC007566.10_ENST00000441539.1_RNA|AC007566.10_ENST00000427458.1_RNA|PEX1_ENST00000438045.1_Nonsense_Mutation_p.R676*|PEX1_ENST00000428214.1_Nonsense_Mutation_p.R941*	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	998					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)	p.R998*(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TTATCTAGTCGACCAGGCCTA	0.413																																					p.R998X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2992T	7	GRCh37	CM022826	PEX1	M	rs61750428	.						72.0	68.0	70.0					7																	92123645		2203	4300	6503	91961581	SO:0001587	stop_gained	5189	exon19			AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"""ATPases / AAA-type"""	8850	protein-coding gene	gene with protein product		602136	"""peroxisome biogenesis factor 1"", ""Zellweger syndrome 1"", ""Zellweger syndrome"""	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.2992C>T	7.37:g.92123645G>A	ENSP00000248633:p.Arg998*	Somatic		Capture	Illumina HiSeq	Phase_I	91961581	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Nonsense_Mutation	SNP	ENST00000248633.4	37	CCDS5627.1	.	.	.	.	.	.	.	.	.	.	G	41	9.045150	0.99048	.	.	ENSG00000127980	ENST00000438045;ENST00000248633;ENST00000428214	.	.	.	5.74	4.85	0.62838	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.5986	16.3734	0.83374	0.0:0.0:0.8676:0.1324	rs61750428	.	.	.	X	676;998;941	.	ENSP00000248633:R998X	R	-	1	2	PEX1	91961581	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.646000	0.67916	1.408000	0.46895	0.561000	0.74099	CGA		0.413	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466	
CCDC132	55610	broad.mit.edu	37	7	92940556	92940556	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:92940556T>C	ENST00000305866.5	+	20	1955	c.1827T>C	c.(1825-1827)aaT>aaC	p.N609N	CCDC132_ENST00000535481.1_Silent_p.N329N|CCDC132_ENST00000317751.6_Silent_p.N340N|CCDC132_ENST00000541136.1_Silent_p.N420N|CCDC132_ENST00000544910.1_Silent_p.N579N	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	609						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.N609N(1)		endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			TCTTAACAAATACAACATTGA	0.308																																					p.N609N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1827C	7						.						141.0	140.0	140.0					7																	92940556		1827	4068	5895	92778492	SO:0001819	synonymous_variant	55610	exon20			AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.1827T>C	7.37:g.92940556T>C		Somatic		Capture	Illumina HiSeq	Phase_I	92778492	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Silent	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	T	8.284	0.816210	0.16607	.	.	ENSG00000004766	ENST00000458707	.	.	.	5.5	-1.33	0.09172	.	.	.	.	.	T	0.57932	0.2087	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55648	-0.8108	4	.	.	.	-24.9506	11.4203	0.49978	0.0:0.7135:0.0:0.2865	.	.	.	.	T	396	.	.	I	+	2	0	CCDC132	92778492	1.000000	0.71417	0.998000	0.56505	0.859000	0.49053	2.102000	0.41796	-0.070000	0.12908	0.533000	0.62120	ATA		0.308	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	
COL1A2	1278	broad.mit.edu	37	7	94040249	94040249	+	Missense_Mutation	SNP	G	G	A	rs550867796		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:94040249G>A	ENST00000297268.6	+	22	1717	c.1246G>A	c.(1246-1248)Gtc>Atc	p.V416I		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	416					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)	p.V416I(1)	COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	CAGAGCTGGCGTCATGGTAAG	0.463										HNSCC(75;0.22)			G|||	1	0.000199681	0.0	0.0	5008	,	,		18582	0.0		0.0	False		,,,				2504	0.001				p.V416I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1246A	7						.						147.0	142.0	144.0					7																	94040249		2203	4300	6503	93878185	SO:0001583	missense	1278	exon22			Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.1246G>A	7.37:g.94040249G>A	ENSP00000297268:p.Val416Ile	Somatic		Capture	Illumina HiSeq	Phase_I	93878185	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.288759	0.59976	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.93547	-3.24	5.84	5.84	0.93424	.	0.125811	0.56097	D	0.000038	D	0.89880	0.6843	N	0.25647	0.755	0.32029	N	0.599745	B	0.22909	0.077	B	0.20767	0.031	D	0.86456	0.1776	10	0.51188	T	0.08	.	20.5276	0.99231	0.0:0.0:1.0:0.0	.	416	P08123	CO1A2_HUMAN	I	416;417	ENSP00000297268:V416I	ENSP00000297268:V416I	V	+	1	0	COL1A2	93878185	1.000000	0.71417	1.000000	0.80357	0.574000	0.36063	5.818000	0.69236	2.937000	0.99478	0.650000	0.86243	GTC		0.463	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
COL1A2	1278	broad.mit.edu	37	7	94055131	94055131	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:94055131G>A	ENST00000297268.6	+	44	3376	c.2905G>A	c.(2905-2907)Gtg>Atg	p.V969M		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	969					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)	p.V969M(1)	COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TCATGGCCCCGTGGGTCCTGC	0.537										HNSCC(75;0.22)																											p.V969M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2905A	7						.						93.0	89.0	90.0					7																	94055131		2203	4300	6503	93893067	SO:0001583	missense	1278	exon44			Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.2905G>A	7.37:g.94055131G>A	ENSP00000297268:p.Val969Met	Somatic		Capture	Illumina HiSeq	Phase_I	93893067	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.964964	0.53507	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	D	0.93604	-3.25	5.32	4.44	0.53790	.	0.275088	0.36628	N	0.002485	D	0.88160	0.6362	L	0.28274	0.84	0.37478	D	0.915879	B	0.34226	0.443	B	0.28991	0.097	D	0.89645	0.3865	10	0.62326	D	0.03	.	15.9651	0.79966	0.0:0.0:0.8644:0.1356	.	969	P08123	CO1A2_HUMAN	M	969;970	ENSP00000297268:V969M	ENSP00000297268:V969M	V	+	1	0	COL1A2	93893067	0.998000	0.40836	0.913000	0.36048	0.803000	0.45373	2.941000	0.49011	1.618000	0.50286	0.655000	0.94253	GTG		0.537	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
SMURF1	57154	broad.mit.edu	37	7	98658280	98658280	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:98658280G>T	ENST00000361125.1	-	3	464	c.145C>A	c.(145-147)Cac>Aac	p.H49N	SMURF1_ENST00000480055.1_5'UTR|SMURF1_ENST00000361368.2_Missense_Mutation_p.H49N	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	49	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)	p.H49N(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			TCGGTTGAGTGGCACTGCCCA	0.522																																					p.H49N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C145A	7						.						141.0	100.0	114.0					7																	98658280		2203	4300	6503	98496216	SO:0001583	missense	57154	exon3			AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.145C>A	7.37:g.98658280G>T	ENSP00000354621:p.His49Asn	Somatic		Capture	Illumina HiSeq	Phase_I	98496216	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Missense_Mutation	SNP	ENST00000361125.1	37	CCDS34690.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.010414	0.93346	.	.	ENSG00000198742	ENST00000361368;ENST00000361125	T;T	0.69435	-0.4;-0.4	5.08	5.08	0.68730	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.048216	0.85682	D	0.000000	D	0.83603	0.5290	M	0.83692	2.655	0.80722	D	1	D;D;D	0.89917	0.998;0.997;1.0	D;D;D	0.79784	0.962;0.983;0.993	D	0.86052	0.1526	10	0.72032	D	0.01	.	18.8294	0.92132	0.0:0.0:1.0:0.0	.	49;49;49	Q9HCE7-2;Q9HCE7;B9EGV3	.;SMUF1_HUMAN;.	N	49	ENSP00000355326:H49N;ENSP00000354621:H49N	ENSP00000354621:H49N	H	-	1	0	SMURF1	98496216	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.813000	0.99286	2.503000	0.84419	0.655000	0.94253	CAC		0.522	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429	
ARPC1B	10095	broad.mit.edu	37	7	98985759	98985759	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:98985759G>A	ENST00000451682.1	+	6	576	c.267G>A	c.(265-267)acG>acA	p.T89T	ARPC1A_ENST00000432884.2_3'UTR|ARPC1B_ENST00000474880.1_3'UTR|ARPC1B_ENST00000252725.5_Silent_p.T89T			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	89					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.T89T(2)		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)			GGAAGCCCACGCTGGTCATCC	0.642																																					p.T89T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G267A	7						.						63.0	60.0	61.0					7																	98985759		2203	4300	6503	98823695	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.267G>A	7.37:g.98985759G>A		Somatic		Capture	Illumina HiSeq	Phase_I	98823695	NM_005720	Q9BU00	Silent	SNP	ENST00000451682.1	37	CCDS5661.1																																																																																				0.642	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720	
PDAP1	11333	broad.mit.edu	37	7	98995605	98995605	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:98995605G>A	ENST00000350498.3	-	5	647	c.367C>T	c.(367-369)Cgt>Tgt	p.R123C	PDAP1_ENST00000496335.1_5'Flank	NM_014891.6	NP_055706.1	Q13442	HAP28_HUMAN	PDGFA associated protein 1	123					cell proliferation (GO:0008283)|signal transduction (GO:0007165)		poly(A) RNA binding (GO:0044822)	p.R123C(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2)|prostate(1)|skin(1)	9	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)			TTCATGTAACGCTCTTTTGCC	0.542																																					p.R123C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C367T	7						.						141.0	138.0	139.0					7																	98995605		2203	4300	6503	98833541	SO:0001583	missense	11333	exon5			U41745	CCDS5662.1	7q	2008-07-18			ENSG00000106244	ENSG00000106244			14634	protein-coding gene	gene with protein product	"""PDGF associated protein"""	607075				8780057	Standard	NM_014891		Approved	PAP1, PAP, HASPP28	uc003uqe.3	Q13442	OTTHUMG00000154629	ENST00000350498.3:c.367C>T	7.37:g.98995605G>A	ENSP00000222968:p.Arg123Cys	Somatic		Capture	Illumina HiSeq	Phase_I	98833541	NM_014891	D6W5S5|Q92906	Missense_Mutation	SNP	ENST00000350498.3	37	CCDS5662.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.939751	0.73557	.	.	ENSG00000106244	ENST00000350498	.	.	.	4.99	4.04	0.47022	Casein kinase substrate, phosphoprotein PP28 (1);	0.000000	0.85682	D	0.000000	T	0.80974	0.4727	M	0.91561	3.22	0.80722	D	1	D	0.76494	0.999	D	0.65987	0.94	D	0.85075	0.0942	8	.	.	.	-5.1726	13.0898	0.59160	0.0:0.0:0.762:0.238	.	123	Q13442	HAP28_HUMAN	C	123	.	.	R	-	1	0	PDAP1	98833541	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.795000	0.55499	2.465000	0.83290	0.650000	0.86243	CGT		0.542	PDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336388.2	NM_014891	
CYP3A7	1551	broad.mit.edu	37	7	99313529	99313529	+	Splice_Site	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:99313529G>A	ENST00000336374.2	-	7	524	c.522C>T	c.(520-522)caC>caT	p.H174H	AC069294.1_ENST00000408560.1_RNA	NM_000765.3	NP_000756.2	P24462	CP3A7_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 7	174					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)	p.H174H(1)		autonomic_ganglia(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	32	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Alfentanil(DB00802)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amlodipine(DB00381)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atorvastatin(DB01076)|Buprenorphine(DB00921)|Buspirone(DB00490)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clotrimazole(DB00257)|Cocaine(DB00907)|Codeine(DB00318)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diltiazem(DB00343)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Eplerenone(DB00700)|Erythromycin(DB00199)|Estradiol(DB00783)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluticasone Propionate(DB00588)|Fluvoxamine(DB00176)|Gestodene(DB06730)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nifedipine(DB01115)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Testosterone(DB00624)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	CCCCAAAGACGCTGAGTGGAG	0.463																																					p.H174H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C522T	7						.						139.0	125.0	130.0					7																	99313529		2203	4300	6503	99151465	SO:0001630	splice_region_variant	1551	exon7			AF315325	CCDS5673.1	7q21-q22.1	2007-12-14	2003-01-14		ENSG00000160870	ENSG00000160870		"""Cytochrome P450s"""	2640	protein-coding gene	gene with protein product		605340	"""cytochrome P450, subfamily IIIA, polypeptide 7"""			2722762	Standard	NM_000765		Approved	CP37, P450-HFLA		P24462	OTTHUMG00000156726	ENST00000336374.2:c.522-1C>T	7.37:g.99313529G>A		Somatic		Capture	Illumina HiSeq	Phase_I	99151465	NM_000765	A4D288|Q9H241	Silent	SNP	ENST00000336374.2	37	CCDS5673.1																																																																																				0.463	CYP3A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345484.1		Silent
ZKSCAN1	7586	broad.mit.edu	37	7	99631486	99631486	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:99631486G>A	ENST00000324306.6	+	6	1592	c.1358G>A	c.(1357-1359)cGc>cAc	p.R453H	ZKSCAN1_ENST00000426572.1_Missense_Mutation_p.R417H|ZKSCAN1_ENST00000535170.1_Missense_Mutation_p.R240H	NM_003439.1	NP_003430.1	P17029	ZKSC1_HUMAN	zinc finger with KRAB and SCAN domains 1	453					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.R453H(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(181;0.0211)|all_lung(186;0.0323)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			CTCCATCAGCGCATCCACTCT	0.522																																					p.R453H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1358A	7						.						171.0	174.0	173.0					7																	99631486		2203	4300	6503	99469422	SO:0001583	missense	7586	exon6			X52349	CCDS34698.1, CCDS69349.1, CCDS75640.1	7q22	2013-01-09	2004-11-16	2004-11-17	ENSG00000106261	ENSG00000106261		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13101	protein-coding gene	gene with protein product		601260	"""zinc finger protein 36 (KOX 18)"""	ZNF139, ZNF36			Standard	NM_001287055		Approved	KOX18, PHZ-37, ZSCAN33	uc003usk.1	P17029	OTTHUMG00000156534	ENST00000324306.6:c.1358G>A	7.37:g.99631486G>A	ENSP00000323148:p.Arg453His	Somatic		Capture	Illumina HiSeq	Phase_I	99469422	NM_003439	A4D294|P52745|Q2M1U1|Q8TBW5|Q8TEK7	Missense_Mutation	SNP	ENST00000324306.6	37	CCDS34698.1	.	.	.	.	.	.	.	.	.	.	G	19.98	3.927530	0.73327	.	.	ENSG00000106261	ENST00000324306;ENST00000426572;ENST00000535170	T;T;T	0.02446	4.29;4.29;4.29	5.08	5.08	0.68730	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000036	T	0.14960	0.0361	M	0.84511	2.7	0.38329	D	0.943754	D	0.89917	1.0	D	0.75484	0.986	T	0.00094	-1.2079	10	0.87932	D	0	.	9.691	0.40127	0.0923:0.0:0.9077:0.0	.	453	P17029	ZKSC1_HUMAN	H	453;417;240	ENSP00000323148:R453H;ENSP00000409172:R417H;ENSP00000443508:R240H	ENSP00000323148:R453H	R	+	2	0	ZKSCAN1	99469422	0.848000	0.29623	0.965000	0.40720	0.883000	0.51084	2.088000	0.41663	2.802000	0.96397	0.563000	0.77884	CGC		0.522	ZKSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344550.2	NM_003439	
MBLAC1	255374	broad.mit.edu	37	7	99725556	99725556	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:99725556G>A	ENST00000398075.2	+	2	937	c.538G>A	c.(538-540)Gcc>Acc	p.A180T	RP11-506M12.1_ENST00000494221.1_RNA	NM_203397.1	NP_981942.1	A4D2B0	MBLC1_HUMAN	metallo-beta-lactamase domain containing 1	180							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.A180T(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|skin(1)	7						CGTGGTGGTGGCCGGCACGGC	0.731																																					p.A180T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G538A	7						.						23.0	29.0	27.0					7																	99725556		2053	4185	6238	99563492	SO:0001583	missense	255374	exon2			BC031288	CCDS43620.1	7q22	2014-02-12	2009-04-08		ENSG00000214309	ENSG00000214309			22180	protein-coding gene	gene with protein product							Standard	XM_005250250		Approved	MGC49416	uc003utp.3	A4D2B0	OTTHUMG00000154846	ENST00000398075.2:c.538G>A	7.37:g.99725556G>A	ENSP00000381150:p.Ala180Thr	Somatic		Capture	Illumina HiSeq	Phase_I	99563492	NM_203397	Q8N5X8	Missense_Mutation	SNP	ENST00000398075.2	37	CCDS43620.1	.	.	.	.	.	.	.	.	.	.	G	10.11	1.259498	0.23051	.	.	ENSG00000214309	ENST00000398075	T	0.28454	1.61	4.68	1.79	0.24919	Beta-lactamase-like (2);	0.463200	0.17726	U	0.164058	T	0.15219	0.0367	N	0.25825	0.765	0.09310	N	1	B	0.16603	0.018	B	0.19666	0.026	T	0.19679	-1.0298	10	0.14656	T	0.56	.	1.8349	0.03138	0.1832:0.1596:0.4931:0.1642	.	180	A4D2B0	MBLC1_HUMAN	T	180	ENSP00000381150:A180T	ENSP00000381150:A180T	A	+	1	0	MBLAC1	99563492	0.385000	0.25172	0.750000	0.31169	0.530000	0.34684	1.011000	0.29911	0.581000	0.29539	0.561000	0.74099	GCC		0.731	MBLAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337353.1	NM_203397	
PILRB	29990	broad.mit.edu	37	7	99956505	99956505	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:99956505C>T	ENST00000452089.1	+	7	1316	c.257C>T	c.(256-258)cCg>cTg	p.P86L	PILRB_ENST00000609309.1_Missense_Mutation_p.P86L|PILRB_ENST00000448382.1_Intron|STAG3L5P-PVRIG2P-PILRB_ENST00000310771.4_RNA|PILRB_ENST00000610247.1_Missense_Mutation_p.P86L|PILRB_ENST00000444073.1_Missense_Mutation_p.P86L			Q9UKJ0	PILRB_HUMAN	paired immunoglobin-like type 2 receptor beta	86	Ig-like V-type.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)		p.P86L(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	13	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGCACAAGGCCGCCTTCCATT	0.542																																					p.P86L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C257T	7						.						117.0	120.0	119.0					7																	99956505		2203	4300	6503	99794441	SO:0001583	missense	29990	exon2			AF161081, AJ400845	CCDS43622.1	7q22.1	2014-05-16			ENSG00000121716	ENSG00000121716		"""Immunoglobulin superfamily / V-set domain containing"""	18297	protein-coding gene	gene with protein product		605342				10660620	Standard	NM_178238		Approved	FDFACT1, FDFACT2	uc022ail.1	Q9UKJ0	OTTHUMG00000155363	ENST00000452089.1:c.257C>T	7.37:g.99956505C>T	ENSP00000391748:p.Pro86Leu	Somatic		Capture	Illumina HiSeq	Phase_I	99794441	NM_178238	Q69YF9|Q9HBS0	Missense_Mutation	SNP	ENST00000452089.1	37	CCDS43622.1	.	.	.	.	.	.	.	.	.	.	C	3.027	-0.200555	0.06219	.	.	ENSG00000121716	ENST00000310771;ENST00000420688;ENST00000452089;ENST00000457519;ENST00000443526;ENST00000419749;ENST00000422808;ENST00000444073;ENST00000413850;ENST00000438231	T;T;T;T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88;2.88;2.88;2.88	2.48	-1.58	0.08479	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.285170	0.05594	N	0.575114	T	0.12518	0.0304	N	0.14661	0.345	0.09310	N	1	D	0.89917	1.0	D	0.71184	0.972	T	0.12293	-1.0553	9	.	.	.	.	1.1776	0.01838	0.2426:0.4103:0.1967:0.1503	.	86	Q9UKJ0	PILRB_HUMAN	L	86;86;86;86;86;86;86;86;191;86	ENSP00000311153:P86L;ENSP00000391748:P86L;ENSP00000411261:P86L;ENSP00000403757:P86L;ENSP00000404321:P86L;ENSP00000389856:P86L;ENSP00000410764:P86L;ENSP00000408425:P86L	.	P	+	2	0	PILRB	99794441	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.328000	0.02680	-0.618000	0.05656	-0.335000	0.08231	CCG		0.542	PILRB-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339923.2	NM_178238	
PILRA	29992	broad.mit.edu	37	7	99971859	99971859	+	Missense_Mutation	SNP	C	C	T	rs146090442	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:99971859C>T	ENST00000198536.2	+	2	469	c.257C>T	c.(256-258)cCg>cTg	p.P86L	PILRA_ENST00000474013.1_3'UTR|PILRA_ENST00000394000.2_Missense_Mutation_p.P86L|PILRA_ENST00000453419.1_Missense_Mutation_p.P86L|PILRA_ENST00000350573.2_Missense_Mutation_p.P86L	NM_013439.2	NP_038467.2	Q9UKJ1	PILRA_HUMAN	paired immunoglobin-like type 2 receptor alpha	86	Ig-like V-type.				signal transduction (GO:0007165)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P86L(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	15	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGCACAAGGCCGCCTTCCATT	0.547													c|||	8	0.00159744	0.0053	0.0014	5008	,	,		16565	0.0		0.0	False		,,,				2504	0.0				p.P86L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C257T	7						.	C	LEU/PRO,LEU/PRO,LEU/PRO	20,4386	27.2+/-55.0	0,20,2183	85.0	95.0	92.0		257,257,257	-4.5	0.0	7	dbSNP_134	92	0,8598		0,0,4299	no	missense,missense,missense	PILRA	NM_013439.2,NM_178272.1,NM_178273.1	98,98,98	0,20,6482	TT,TC,CC		0.0,0.4539,0.1538	probably-damaging,probably-damaging,probably-damaging	86/304,86/231,86/176	99971859	20,12984	2203	4299	6502	99809795	SO:0001583	missense	29992	exon2			AF161080	CCDS5691.1, CCDS5692.1, CCDS47660.1	7q22.1	2013-01-11			ENSG00000085514	ENSG00000085514		"""Immunoglobulin superfamily / V-set domain containing"""	20396	protein-coding gene	gene with protein product		605341				10660620	Standard	NM_178272		Approved	FDF03	uc003uuo.1	Q9UKJ1	OTTHUMG00000155248	ENST00000198536.2:c.257C>T	7.37:g.99971859C>T	ENSP00000198536:p.Pro86Leu	Somatic		Capture	Illumina HiSeq	Phase_I	99809795	NM_178272	Q8NHI1	Missense_Mutation	SNP	ENST00000198536.2	37	CCDS5691.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	7.014	0.557346	0.13436	0.004539	0.0	ENSG00000085514	ENST00000432297;ENST00000198536;ENST00000453419;ENST00000394000;ENST00000350573	T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88	3.28	-4.52	0.03472	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.300430	0.05499	N	0.558179	T	0.11196	0.0273	N	0.12961	0.28	0.09310	N	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.998;0.999	D;D;D;P;D	0.71184	0.972;0.962;0.953;0.866;0.909	T	0.12192	-1.0557	9	.	.	.	.	0.3838	0.00399	0.314:0.1974:0.2738:0.2149	.	86;86;86;86;86	C9JJ79;C9JGG1;Q9UKJ1-4;Q9UKJ1-3;Q9UKJ1	.;.;.;.;PILRA_HUMAN	L	86	ENSP00000415111:P86L;ENSP00000198536:P86L;ENSP00000390026:P86L;ENSP00000377569:P86L;ENSP00000340109:P86L	.	P	+	2	0	PILRA	99809795	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.254000	0.00538	-1.085000	0.03088	0.313000	0.20887	CCG		0.547	PILRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339016.1	NM_013439	
PILRA	29992	broad.mit.edu	37	7	99972029	99972029	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:99972029G>A	ENST00000198536.2	+	2	639	c.427G>A	c.(427-429)Gag>Aag	p.E143K	PILRA_ENST00000474013.1_3'UTR|PILRA_ENST00000394000.2_Missense_Mutation_p.E143K|PILRA_ENST00000453419.1_Missense_Mutation_p.E143K|PILRA_ENST00000350573.2_Missense_Mutation_p.E143K	NM_013439.2	NP_038467.2	Q9UKJ1	PILRA_HUMAN	paired immunoglobin-like type 2 receptor alpha	143	Ig-like V-type.				signal transduction (GO:0007165)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E143K(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	15	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCAGTCCATCGAGGGGACCAA	0.592																																					p.E143K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G427A	7						.						80.0	77.0	78.0					7																	99972029		2203	4300	6503	99809965	SO:0001583	missense	29992	exon2			AF161080	CCDS5691.1, CCDS5692.1, CCDS47660.1	7q22.1	2013-01-11			ENSG00000085514	ENSG00000085514		"""Immunoglobulin superfamily / V-set domain containing"""	20396	protein-coding gene	gene with protein product		605341				10660620	Standard	NM_178272		Approved	FDF03	uc003uuo.1	Q9UKJ1	OTTHUMG00000155248	ENST00000198536.2:c.427G>A	7.37:g.99972029G>A	ENSP00000198536:p.Glu143Lys	Somatic		Capture	Illumina HiSeq	Phase_I	99809965	NM_178272	Q8NHI1	Missense_Mutation	SNP	ENST00000198536.2	37	CCDS5691.1	.	.	.	.	.	.	.	.	.	.	G	2.309	-0.358464	0.05138	.	.	ENSG00000085514	ENST00000432297;ENST00000198536;ENST00000453419;ENST00000394000;ENST00000350573	T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01	3.38	-6.76	0.01732	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	7.298260	0.00357	N	0.000032	T	0.12305	0.0299	L	0.34521	1.04	0.09310	N	1	P;B;B;B;B	0.35745	0.518;0.045;0.04;0.282;0.06	B;B;B;B;B	0.20577	0.03;0.007;0.006;0.02;0.015	T	0.10382	-1.0632	9	.	.	.	.	7.7511	0.28898	0.2645:0.1099:0.5505:0.0751	.	143;143;143;143;143	C9JJ79;C9JGG1;Q9UKJ1-4;Q9UKJ1-3;Q9UKJ1	.;.;.;.;PILRA_HUMAN	K	143	ENSP00000415111:E143K;ENSP00000198536:E143K;ENSP00000390026:E143K;ENSP00000377569:E143K;ENSP00000340109:E143K	.	E	+	1	0	PILRA	99809965	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-9.279000	0.00012	-4.148000	0.00069	-2.640000	0.00151	GAG		0.592	PILRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339016.1	NM_013439	
NYAP1	222950	broad.mit.edu	37	7	100086319	100086319	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:100086319G>A	ENST00000300179.2	+	4	1134	c.975G>A	c.(973-975)ccG>ccA	p.P325P	NYAP1_ENST00000423930.1_Silent_p.P325P|NYAP1_ENST00000454988.1_Silent_p.P268P	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	325	Pro-rich.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)			p.P325P(1)									AAATCCCCCCGCCCTTCCCCA	0.682																																					p.P325P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G975A	7						.						50.0	49.0	49.0					7																	100086319		2200	4295	6495	99924255	SO:0001819	synonymous_variant	222950	exon4			AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"""chromosome 7 open reading frame 51"", ""KIAA1486-like"""	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.975G>A	7.37:g.100086319G>A		Somatic		Capture	Illumina HiSeq	Phase_I	99924255	NM_173564	Q6U9Y3|Q8N1V0	Silent	SNP	ENST00000300179.2	37	CCDS5696.1																																																																																				0.682	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564	
CCDC71L	168455	broad.mit.edu	37	7	106301008	106301008	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:106301008delG	ENST00000523505.1	-	1	434	c.335delC	c.(334-336)ccgfs	p.P112fs		NM_175884.4	NP_787080.2	Q8N9Z2	CC71L_HUMAN	coiled-coil domain containing 71-like	112	Pro-rich.									endometrium(1)	1						AGGGGGCCCCGGGGGGTCGGG	0.761																																					p.P112fs												.	.	0			c.335delC	7						.						5.0	6.0	6.0					7																	106301008		1773	3978	5751	106088244	SO:0001589	frameshift_variant	168455	exon1				CCDS55151.1	7q22.3	2011-12-12	2011-12-12	2011-12-12	ENSG00000253276	ENSG00000253276			26685	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 74"""	C7orf74		12477932	Standard	NM_175884		Approved	FLJ36031	uc003vdt.3	Q8N9Z2	OTTHUMG00000164150	ENST00000523505.1:c.335delC	7.37:g.106301008delG	ENSP00000430897:p.Pro112fs	Somatic		Capture	Illumina HiSeq	Phase_I	106088244	NM_175884	Q7Z756	Frame_Shift_Del	DEL	ENST00000523505.1	37	CCDS55151.1																																																																																				0.761	CCDC71L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377493.1	NM_175884	
UBE3C	9690	broad.mit.edu	37	7	157046761	157046761	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr7:157046761C>T	ENST00000348165.5	+	20	3168	c.2808C>T	c.(2806-2808)tgC>tgT	p.C936C		NM_014671.2	NP_055486.2	Q15386	UBE3C_HUMAN	ubiquitin protein ligase E3C	936	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.C936C(1)		central_nervous_system(2)|endometrium(3)|kidney(16)|large_intestine(13)|lung(25)|ovary(2)|prostate(1)|urinary_tract(1)	63		all_hematologic(28;0.0185)|all_epithelial(9;0.0664)	OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)		GCCAGCACTGCCTGGCTTTCC	0.562																																					p.C936C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2808T	7						.						57.0	54.0	55.0					7																	157046761		2203	4300	6503	156739522	SO:0001819	synonymous_variant	9690	exon20			AK127280	CCDS34789.1	7q36.3	2004-05-04			ENSG00000009335	ENSG00000009335			16803	protein-coding gene	gene with protein product		614454				7584026, 11278995	Standard	NM_014671		Approved	KIAA0010, KIAA10	uc010lqs.3	Q15386	OTTHUMG00000157239	ENST00000348165.5:c.2808C>T	7.37:g.157046761C>T		Somatic		Capture	Illumina HiSeq	Phase_I	156739522	NM_014671	A4D235|A6NCP3|Q8TC15|Q96CR4|Q9UDU3	Silent	SNP	ENST00000348165.5	37	CCDS34789.1																																																																																				0.562	UBE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348108.1	NM_014671	
VPS13B	157680	broad.mit.edu	37	8	100844859	100844859	+	Missense_Mutation	SNP	G	G	A	rs544366805		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:100844859G>A	ENST00000358544.2	+	52	9779	c.9668G>A	c.(9667-9669)cGg>cAg	p.R3223Q	VPS13B_ENST00000357162.2_Missense_Mutation_p.R3198Q|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3223					protein transport (GO:0015031)			p.R3223Q(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)			GGGAATTTCCGGGAAAATGGA	0.468													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15769	0.0		0.0	False		,,,				2504	0.0				p.R3198Q	Colon(161;2205 2542 7338 31318)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G9593A	8						.						49.0	53.0	51.0					8																	100844859		2203	4300	6503	100914035	SO:0001583	missense	157680	exon52			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.9668G>A	8.37:g.100844859G>A	ENSP00000351346:p.Arg3223Gln	Somatic		Capture	Illumina HiSeq	Phase_I	100914035	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	G	8.747	0.920266	0.17982	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.67345	-0.26;-0.26	5.62	3.72	0.42706	.	0.391022	0.27744	N	0.018022	T	0.45677	0.1354	L	0.29908	0.895	0.09310	N	1	B;B	0.29481	0.018;0.245	B;B	0.14578	0.011;0.011	T	0.19160	-1.0314	10	0.14656	T	0.56	.	7.8745	0.29586	0.1514:0.2141:0.6345:0.0	.	3198;3223	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	Q	3198;3223	ENSP00000349685:R3198Q;ENSP00000351346:R3223Q	ENSP00000349685:R3198Q	R	+	2	0	VPS13B	100914035	0.015000	0.18098	0.758000	0.31321	0.506000	0.33950	0.695000	0.25527	1.369000	0.46134	0.557000	0.71058	CGG		0.468	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
SPAG1	6674	broad.mit.edu	37	8	101237483	101237483	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:101237483C>T	ENST00000388798.2	+	14	1962	c.1771C>T	c.(1771-1773)Cca>Tca	p.P591S	SPAG1_ENST00000523302.1_3'UTR|SPAG1_ENST00000251809.3_Missense_Mutation_p.P591S	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	591					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)	p.P591S(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		TGCTTCTGTGCCACTGCAAGC	0.512																																					p.P591S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1771T	8						.						64.0	59.0	61.0					8																	101237483		2203	4300	6503	101306659	SO:0001583	missense	6674	exon14			AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"""Tetratricopeptide (TTC) repeat domain containing"""	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.1771C>T	8.37:g.101237483C>T	ENSP00000373450:p.Pro591Ser	Somatic		Capture	Illumina HiSeq	Phase_I	101306659	NM_003114	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	37	CCDS34930.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.523365	0.27299	.	.	ENSG00000104450	ENST00000251809;ENST00000388798	T;T	0.60548	0.18;0.18	5.57	4.68	0.58851	.	0.456623	0.26180	N	0.025877	T	0.45716	0.1356	L	0.36672	1.1	0.31857	N	0.621451	B	0.31769	0.339	B	0.27500	0.08	T	0.54132	-0.8339	10	0.32370	T	0.25	-6.8624	13.2905	0.60269	0.1587:0.8413:0.0:0.0	.	591	Q07617	SPAG1_HUMAN	S	591	ENSP00000251809:P591S;ENSP00000373450:P591S	ENSP00000251809:P591S	P	+	1	0	SPAG1	101306659	0.998000	0.40836	0.013000	0.15412	0.074000	0.17049	4.795000	0.62489	1.452000	0.47756	0.650000	0.86243	CCA		0.512	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218	
RP1L1	94137	broad.mit.edu	37	8	10464779	10464779	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:10464779G>A	ENST00000382483.3	-	4	7052	c.6829C>T	c.(6829-6831)Ccc>Tcc	p.P2277S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2357	25 X 16 AA approximate tandem repeats of [ED]-[AT]-[PQ]-[ED]-[AVT]-E-[GKE]-[ED]- [AMT]-Q-[EPK]-[EAT]-[TSELP]-[EG]- [EGSQDI]-[AVIE].				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)		p.P2277S(1)		breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GGTGGAGTGGGCCTGTCCTCA	0.597																																					p.P2277S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6829T	8						.						121.0	126.0	124.0					8																	10464779		1960	4146	6106	10502189	SO:0001583	missense	94137	exon4			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.6829C>T	8.37:g.10464779G>A	ENSP00000371923:p.Pro2277Ser	Somatic		Capture	Illumina HiSeq	Phase_I	10502189	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	G	1.591	-0.529027	0.04112	.	.	ENSG00000183638	ENST00000382483	T	0.04406	3.63	4.48	-1.03	0.10102	.	0.582703	0.13119	U	0.412337	T	0.02047	0.0064	N	0.08118	0	0.09310	N	1	B	0.30281	0.275	B	0.30029	0.11	T	0.43940	-0.9360	10	0.35671	T	0.21	-3.2798	1.693	0.02856	0.2418:0.2495:0.3816:0.1272	.	2277	A6NKC6	.	S	2277	ENSP00000371923:P2277S	ENSP00000371923:P2277S	P	-	1	0	RP1L1	10502189	.	.	0.015000	0.15790	0.064000	0.16182	.	.	0.111000	0.17947	-0.361000	0.07541	CCC		0.597	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
RP1L1	94137	broad.mit.edu	37	8	10466421	10466421	+	Silent	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:10466421C>A	ENST00000382483.3	-	4	5410	c.5187G>T	c.(5185-5187)ggG>ggT	p.G1729G		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1809					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)		p.G1729G(1)		breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CCGGCCCCAGCCCTCCCTCAG	0.657																																					p.G1729G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G5187T	8						.						73.0	81.0	79.0					8																	10466421		1962	4146	6108	10503831	SO:0001819	synonymous_variant	94137	exon4			AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.5187G>T	8.37:g.10466421C>A		Somatic		Capture	Illumina HiSeq	Phase_I	10503831	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																				0.657	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
SNX31	169166	broad.mit.edu	37	8	101620766	101620766	+	Missense_Mutation	SNP	C	C	T	rs138819788	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:101620766C>T	ENST00000311812.2	-	8	787	c.637G>A	c.(637-639)Gtg>Atg	p.V213M	SNX31_ENST00000428383.2_Missense_Mutation_p.V114M	NM_152628.3	NP_689841.3	Q8N9S9	SNX31_HUMAN	sorting nexin 31	213					protein transport (GO:0015031)	protein complex (GO:0043234)	phosphatidylinositol binding (GO:0035091)	p.V213M(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|skin(3)|urinary_tract(1)	26	all_cancers(14;4.01e-05)|all_epithelial(15;1.26e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;1.21e-11)|all cancers(13;2.62e-09)|OV - Ovarian serous cystadenocarcinoma(57;3.22e-06)|STAD - Stomach adenocarcinoma(118;0.206)			TCCATCAGCACGGAGTCGAGG	0.527													C|||	3	0.000599042	0.0023	0.0	5008	,	,		20236	0.0		0.0	False		,,,				2504	0.0				p.V213M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G637A	8						.	C	MET/VAL	6,4400	11.4+/-27.6	0,6,2197	123.0	103.0	110.0		637	-7.0	0.0	8	dbSNP_134	110	0,8600		0,0,4300	yes	missense	SNX31	NM_152628.3	21	0,6,6497	TT,TC,CC		0.0,0.1362,0.0461	benign	213/441	101620766	6,13000	2203	4300	6503	101689942	SO:0001583	missense	169166	exon8				CCDS6288.1	8q22.3	2011-05-03			ENSG00000174226	ENSG00000174226		"""Sorting nexins"""	28605	protein-coding gene	gene with protein product						16782399	Standard	NM_152628		Approved	MGC39715	uc003yjr.3	Q8N9S9	OTTHUMG00000164725	ENST00000311812.2:c.637G>A	8.37:g.101620766C>T	ENSP00000312368:p.Val213Met	Somatic		Capture	Illumina HiSeq	Phase_I	101689942	NM_152628	C9J6L9|Q8N0U9	Missense_Mutation	SNP	ENST00000311812.2	37	CCDS6288.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	7.580	0.668626	0.14776	0.001362	0.0	ENSG00000174226	ENST00000311812;ENST00000428383	T;T	0.21932	2.29;1.98	6.16	-6.97	0.01616	.	1.413740	0.04354	N	0.356261	T	0.08268	0.0206	N	0.03209	-0.39	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.33523	-0.9865	10	0.41790	T	0.15	3.4498	7.0361	0.24995	0.0:0.3331:0.3377:0.3292	.	114;213	Q8N9S9-2;Q8N9S9	.;SNX31_HUMAN	M	213;114	ENSP00000312368:V213M;ENSP00000405024:V114M	ENSP00000312368:V213M	V	-	1	0	SNX31	101689942	0.000000	0.05858	0.001000	0.08648	0.196000	0.23810	-2.029000	0.01430	-1.571000	0.01663	-0.295000	0.09555	GTG		0.527	SNX31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379910.1	NM_152628	
LRP12	29967	broad.mit.edu	37	8	105509340	105509340	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:105509340G>A	ENST00000276654.5	-	5	1548	c.1440C>T	c.(1438-1440)agC>agT	p.S480S	LRP12_ENST00000424843.2_Silent_p.S461S|LRP12_ENST00000518375.1_5'Flank	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	480	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)	p.S480S(2)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			TTTCTTCATCGCTGCCATCAC	0.448																																					p.S480S												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C1440T	8						.						144.0	121.0	129.0					8																	105509340		2203	4300	6503	105578516	SO:0001819	synonymous_variant	29967	exon5			AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"""Low density lipoprotein receptors"""	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.1440C>T	8.37:g.105509340G>A		Somatic		Capture	Illumina HiSeq	Phase_I	105578516	NM_013437	A8K137|B4DRQ2	Silent	SNP	ENST00000276654.5	37	CCDS6303.1																																																																																				0.448	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437	
OXR1	55074	broad.mit.edu	37	8	107705011	107705011	+	Missense_Mutation	SNP	G	G	A	rs149485264		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:107705011G>A	ENST00000442977.2	+	6	683	c.584G>A	c.(583-585)cGa>cAa	p.R195Q	OXR1_ENST00000517566.2_Missense_Mutation_p.R194Q|OXR1_ENST00000497705.1_Missense_Mutation_p.R127Q|OXR1_ENST00000445937.1_Missense_Mutation_p.R194Q|OXR1_ENST00000312046.6_Missense_Mutation_p.R187Q|OXR1_ENST00000531443.1_Missense_Mutation_p.R194Q|OXR1_ENST00000452423.2_5'UTR	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	195					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)	p.R106Q(1)|p.R195Q(1)		NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			ACTGGTATTCGACCTGCACGA	0.343													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14643	0.0		0.0	False		,,,				2504	0.0				p.R187Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G560A	8						.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	3,4403	6.2+/-15.9	0,3,2200	85.0	85.0	85.0		584,581,581,560	3.2	1.0	8	dbSNP_134	85	0,8600		0,0,4300	yes	missense,missense,missense,missense	OXR1	NM_001198532.1,NM_001198533.1,NM_018002.3,NM_181354.4	43,43,43,43	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging	195/875,194/874,194/847,187/840	107705011	3,13003	2203	4300	6503	107774187	SO:0001583	missense	55074	exon5			AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 3"""	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.584G>A	8.37:g.107705011G>A	ENSP00000405424:p.Arg195Gln	Somatic		Capture	Illumina HiSeq	Phase_I	107774187	NM_181354	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Missense_Mutation	SNP	ENST00000442977.2	37	CCDS56548.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.51|15.51	2.855985|2.855985	0.51376|0.51376	6.81E-4|6.81E-4	0.0|0.0	ENSG00000164830|ENSG00000164830	ENST00000517455|ENST00000445937;ENST00000531443;ENST00000517566;ENST00000442977;ENST00000497705;ENST00000312046	.|T;T;T;T;T;T	.|0.23754	.|2.72;2.72;2.7;2.7;1.89;2.69	5.06|5.06	3.25|3.25	0.37280|0.37280	.|.	.|0.066956	.|0.64402	.|D	.|0.000010	T|T	0.40398|0.40398	0.1115|0.1115	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|0.999;0.998;1.0;0.999	.|D;P;D;D	.|0.71414	.|0.932;0.856;0.973;0.932	T|T	0.10154|0.10154	-1.0642|-1.0642	5|10	.|0.35671	.|T	.|0.21	-13.8266|-13.8266	11.4862|11.4862	0.50354|0.50354	0.1515:0.0:0.8485:0.0|0.1515:0.0:0.8485:0.0	.|.	.|187;195;127;194	.|Q8N573-2;Q8N573;Q8N573-3;Q8N573-5	.|.;OXR1_HUMAN;.;.	N|Q	111|194;194;194;195;127;187	.|ENSP00000402918:R194Q;ENSP00000431966:R194Q;ENSP00000429205:R194Q;ENSP00000405424:R195Q;ENSP00000431014:R127Q;ENSP00000311026:R187Q	.|ENSP00000311026:R187Q	D|R	+|+	1|2	0|0	OXR1|OXR1	107774187|107774187	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.152000|0.152000	0.21847|0.21847	5.033000|5.033000	0.64146|0.64146	1.131000|1.131000	0.42111|0.42111	-0.350000|-0.350000	0.07774|0.07774	GAC|CGA		0.343	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354	
EIF3E	3646	broad.mit.edu	37	8	109215282	109215282	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:109215282C>T	ENST00000220849.5	-	12	1291	c.1229G>A	c.(1228-1230)aGc>aAc	p.S410N	EIF3E_ENST00000519517.1_5'Flank|EIF3E_ENST00000519030.1_Missense_Mutation_p.S317N	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E									p.S410N(1)	EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			AAAGGAAAGGCTTTTGGTCTT	0.398																																					p.S410N	GBM(15;360 410 8460 34179 52246)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1229A	8						.						155.0	140.0	145.0					8																	109215282		2203	4298	6501	109284458	SO:0001583	missense	3646	exon12			U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408			3277	protein-coding gene	gene with protein product		602210	"""eukaryotic translation initiation factor 3, subunit 6 48kDa"""	INT6, EIF3S6		9403073, 9295280	Standard	NM_001568		Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.1229G>A	8.37:g.109215282C>T	ENSP00000220849:p.Ser410Asn	Somatic		Capture	Illumina HiSeq	Phase_I	109284458	NM_001568		Missense_Mutation	SNP	ENST00000220849.5	37	CCDS6308.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.361246	0.61403	.	.	ENSG00000104408	ENST00000220849;ENST00000519030	T;T	0.42900	0.96;0.96	5.7	5.7	0.88788	Proteasome component (PCI) domain (1);	0.000000	0.85682	D	0.000000	T	0.30696	0.0773	N	0.17474	0.49	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.07986	-1.0744	10	0.18710	T	0.47	-14.6532	19.8276	0.96624	0.0:1.0:0.0:0.0	.	410	P60228	EIF3E_HUMAN	N	410;317	ENSP00000220849:S410N;ENSP00000428796:S317N	ENSP00000220849:S410N	S	-	2	0	EIF3E	109284458	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.089000	0.71384	2.697000	0.92050	0.585000	0.79938	AGC		0.398	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568	
PKHD1L1	93035	broad.mit.edu	37	8	110408348	110408348	+	Missense_Mutation	SNP	G	G	A	rs369575692		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:110408348G>A	ENST00000378402.5	+	11	1008	c.904G>A	c.(904-906)Gtc>Atc	p.V302I		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	302	IPT/TIG 3.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.V304I(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AGATTTCCCCGTCAGAGTTCT	0.393										HNSCC(38;0.096)																											p.V302I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G904A	8						.	G	ILE/VAL	0,3926		0,0,1963	74.0	63.0	67.0		904	4.0	0.7	8		67	1,8329		0,1,4164	no	missense	PKHD1L1	NM_177531.4	29	0,1,6127	AA,AG,GG		0.012,0.0,0.0082	benign	302/4244	110408348	1,12255	1963	4165	6128	110477524	SO:0001583	missense	93035	exon11			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.904G>A	8.37:g.110408348G>A	ENSP00000367655:p.Val302Ile	Somatic		Capture	Illumina HiSeq	Phase_I	110477524	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	9.650	1.141288	0.21205	0.0	1.2E-4	ENSG00000205038	ENST00000378402	T	0.76839	-1.05	5.81	3.96	0.45880	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.390219	0.25338	N	0.031382	T	0.69043	0.3067	L	0.45470	1.425	0.20873	N	0.999838	B	0.28258	0.205	B	0.18871	0.023	T	0.52895	-0.8514	10	0.30078	T	0.28	.	12.8882	0.58055	0.1558:0.0:0.8442:0.0	.	302	Q86WI1	PKHL1_HUMAN	I	302	ENSP00000367655:V302I	ENSP00000367655:V302I	V	+	1	0	PKHD1L1	110477524	0.799000	0.28903	0.678000	0.29963	0.541000	0.35023	2.198000	0.42705	0.353000	0.24079	-0.797000	0.03246	GTC		0.393	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
DEFB135	613209	broad.mit.edu	37	8	11842043	11842043	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:11842043A>G	ENST00000382208.2	+	2	178	c.178A>G	c.(178-180)Act>Gct	p.T60A		NM_001033017.2	NP_001028189.2	Q30KP9	DB135_HUMAN	defensin, beta 135	60					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.T60A(1)		endometrium(1)|large_intestine(2)|prostate(1)	4						TTTGTGTGATACTATACATTT	0.383																																					p.T60A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A178G	8						.						113.0	112.0	112.0					8																	11842043		1869	4102	5971	11879452	SO:0001583	missense	613209	exon2			DQ012025	CCDS43710.1	8p23.1	2009-05-27			ENSG00000205883	ENSG00000205883		"""Defensins, beta"""	32400	protein-coding gene	gene with protein product						16033865	Standard	NM_001033017		Approved		uc003wuw.1	Q30KP9	OTTHUMG00000158719	ENST00000382208.2:c.178A>G	8.37:g.11842043A>G	ENSP00000371643:p.Thr60Ala	Somatic		Capture	Illumina HiSeq	Phase_I	11879452	NM_001033017	Q4QY37	Missense_Mutation	SNP	ENST00000382208.2	37	CCDS43710.1	.	.	.	.	.	.	.	.	.	.	A	9.322	1.058361	0.19987	.	.	ENSG00000205883	ENST00000382208	T	0.11277	2.79	3.34	-6.69	0.01772	.	1.216860	0.06387	N	0.716371	T	0.05227	0.0139	.	.	.	0.09310	N	1	P	0.35033	0.481	B	0.33042	0.157	T	0.26538	-1.0100	9	0.40728	T	0.16	1.0567	0.5449	0.00652	0.2214:0.1475:0.2065:0.4246	.	60	Q30KP9	DB135_HUMAN	A	60	ENSP00000371643:T60A	ENSP00000371643:T60A	T	+	1	0	DEFB135	11879452	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-0.718000	0.04980	-1.436000	0.01970	0.459000	0.35465	ACT		0.383	DEFB135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351888.1	NM_001033017	
USP17L2	377630	broad.mit.edu	37	8	11996002	11996002	+	Missense_Mutation	SNP	A	A	G	rs371801443		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:11996002A>G	ENST00000333796.3	-	1	584	c.268T>C	c.(268-270)Tac>Cac	p.Y90H	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	90	USP.				apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.Y90H(1)		central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						GCGTTCTCGTAGCAGGTATTT	0.577																																					p.Y90H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T268C	8						.						34.0	40.0	38.0					8																	11996002		1376	2825	4201	12033411	SO:0001583	missense	377630	exon1			BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"""deubiquitinating enzyme 3"""	610186	"""ubiquitin specific peptidase 17-like 2"""				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.268T>C	8.37:g.11996002A>G	ENSP00000333329:p.Tyr90His	Somatic		Capture	Illumina HiSeq	Phase_I	12033411	NM_201402		Missense_Mutation	SNP	ENST00000333796.3	37	CCDS43713.1	.	.	.	.	.	.	.	.	.	.	a	14.68	2.607705	0.46527	.	.	ENSG00000223443	ENST00000333796	T	0.20069	2.1	0.902	0.902	0.19290	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.288427	0.28442	N	0.015324	T	0.54013	0.1832	H	0.97440	4.005	0.36992	D	0.894831	D	0.89917	1.0	D	0.91635	0.999	T	0.62374	-0.6868	10	0.87932	D	0	.	6.1024	0.20055	1.0:0.0:0.0:0.0	.	90	Q6R6M4	U17L2_HUMAN	H	90	ENSP00000333329:Y90H	ENSP00000333329:Y90H	Y	-	1	0	USP17L2	12033411	1.000000	0.71417	0.007000	0.13788	0.017000	0.09413	5.878000	0.69682	0.696000	0.31696	0.386000	0.25728	TAC		0.577	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402	
PKHD1L1	93035	broad.mit.edu	37	8	110474050	110474050	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:110474050A>G	ENST00000378402.5	+	48	7400	c.7296A>G	c.(7294-7296)atA>atG	p.I2432M		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2432					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.I2434M(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GAGAAGAAATAGGAAGTGACC	0.393										HNSCC(38;0.096)																											p.I2432M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A7296G	8						.						65.0	69.0	68.0					8																	110474050		2039	4205	6244	110543226	SO:0001583	missense	93035	exon48			AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.7296A>G	8.37:g.110474050A>G	ENSP00000367655:p.Ile2432Met	Somatic		Capture	Illumina HiSeq	Phase_I	110543226	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	A	13.19	2.163868	0.38217	.	.	ENSG00000205038	ENST00000378402	D	0.86030	-2.06	5.64	0.66	0.17868	.	0.310463	0.33712	N	0.004640	T	0.66992	0.2846	N	0.13272	0.32	0.24675	N	0.993397	B	0.20550	0.046	B	0.17098	0.017	T	0.53662	-0.8407	10	0.36615	T	0.2	.	4.0322	0.09714	0.6:0.0:0.253:0.147	.	2432	Q86WI1	PKHL1_HUMAN	M	2432	ENSP00000367655:I2432M	ENSP00000367655:I2432M	I	+	3	3	PKHD1L1	110543226	0.958000	0.32768	0.999000	0.59377	0.998000	0.95712	0.031000	0.13710	0.091000	0.17302	0.528000	0.53228	ATA		0.393	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
FER1L6	654463	broad.mit.edu	37	8	125131972	125131972	+	Missense_Mutation	SNP	G	G	A	rs367724676		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:125131972G>A	ENST00000522917.1	+	41	5721	c.5515G>A	c.(5515-5517)Gtc>Atc	p.V1839I	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6_ENST00000399018.1_Missense_Mutation_p.V1839I	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1839						integral component of membrane (GO:0016021)		p.V1839I(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			catcttcctcgtccttttcat	0.458																																					p.V1839I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5515A	8						.	G	ILE/VAL	1,4159		0,1,2079	210.0	222.0	218.0		5515	6.0	1.0	8		218	0,8414		0,0,4207	no	missense	FER1L6	NM_001039112.2	29	0,1,6286	AA,AG,GG		0.0,0.024,0.0080	benign	1839/1858	125131972	1,12573	2080	4207	6287	125201153	SO:0001583	missense	654463	exon41			AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"""fer-1-like 6 (C. elegans)"""				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.5515G>A	8.37:g.125131972G>A	ENSP00000428280:p.Val1839Ile	Somatic		Capture	Illumina HiSeq	Phase_I	125201153	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.900097	0.92035	2.4E-4	0.0	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.82344	-1.6;-1.6	6.03	6.03	0.97812	.	0.241743	0.33631	U	0.004714	D	0.87370	0.6160	M	0.80422	2.495	0.58432	D	0.999997	D	0.63880	0.993	P	0.49683	0.619	D	0.83803	0.0237	10	0.13853	T	0.58	-2.8111	20.5568	0.99304	0.0:0.0:1.0:0.0	.	1839	Q2WGJ9	FR1L6_HUMAN	I	1839	ENSP00000428280:V1839I;ENSP00000381982:V1839I	ENSP00000381982:V1839I	V	+	1	0	FER1L6	125201153	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.950000	0.87804	2.861000	0.98227	0.655000	0.94253	GTC		0.458	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
LONRF1	91694	broad.mit.edu	37	8	12583334	12583334	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:12583334A>T	ENST00000398246.3	-	11	2134	c.2065T>A	c.(2065-2067)Tct>Act	p.S689T	MIR3926-2_ENST00000578598.1_RNA|LONRF1_ENST00000525024.1_Missense_Mutation_p.S115T|LONRF1_ENST00000533751.1_Missense_Mutation_p.S332T	NM_152271.3	NP_689484.3	Q17RB8	LONF1_HUMAN	LON peptidase N-terminal domain and ring finger 1	689	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)	p.S689T(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19				READ - Rectum adenocarcinoma(644;0.236)		CAGGCTTGAGAGTAAACCAAA	0.418																																					p.S689T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2065A	8						.						85.0	82.0	83.0					8																	12583334		1833	4084	5917	12627705	SO:0001583	missense	91694	exon11			AK074329	CCDS5987.2	8p23.1	2013-01-09			ENSG00000154359	ENSG00000154359		"""RING-type (C3HC4) zinc fingers"""	26302	protein-coding gene	gene with protein product						18253036	Standard	XM_005273685		Approved	FLJ23749, RNF191	uc003wwd.1	Q17RB8	OTTHUMG00000165475	ENST00000398246.3:c.2065T>A	8.37:g.12583334A>T	ENSP00000381298:p.Ser689Thr	Somatic		Capture	Illumina HiSeq	Phase_I	12627705	NM_152271	B4DM29|B4DU84|Q8TEA0|Q9BSV1	Missense_Mutation	SNP	ENST00000398246.3	37	CCDS5987.2	.	.	.	.	.	.	.	.	.	.	A	15.29	2.789328	0.49997	.	.	ENSG00000154359	ENST00000398246;ENST00000525024;ENST00000533751;ENST00000524526	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.36	5.36	0.76844	Peptidase S16, lon N-terminal (1);PUA-like domain (1);	0.327243	0.33253	N	0.005103	T	0.21550	0.0519	N	0.08118	0	0.33212	D	0.553487	B;B	0.16396	0.014;0.017	B;B	0.24006	0.03;0.05	T	0.22417	-1.0217	10	0.27082	T	0.32	-12.6733	6.7998	0.23744	0.6946:0.1269:0.0:0.1785	.	678;689	Q17RB8-2;Q17RB8	.;LONF1_HUMAN	T	689;115;332;292	ENSP00000381298:S689T;ENSP00000436770:S115T;ENSP00000432130:S332T;ENSP00000433327:S292T	ENSP00000381298:S689T	S	-	1	0	LONRF1	12627705	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.414000	0.44627	2.333000	0.79357	0.482000	0.46254	TCT		0.418	LONRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251693.2	NM_152271	
KIAA0196	9897	broad.mit.edu	37	8	126056844	126056844	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:126056844G>A	ENST00000318410.7	-	21	2950	c.2601C>T	c.(2599-2601)acC>acT	p.T867T	KIAA0196-AS1_ENST00000519140.1_RNA|KIAA0196_ENST00000517845.1_Silent_p.T719T	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	867					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)		p.T867T(1)		NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			AGGTTCCCAAGGTGGTCTGGA	0.438																																					p.T867T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2601T	8						.						167.0	177.0	174.0					8																	126056844		2203	4300	6503	126126026	SO:0001819	synonymous_variant	9897	exon21				CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"""strumpellin"""	610657	"""spastic paraplegia 8 (autosomal dominant)"""	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.2601C>T	8.37:g.126056844G>A		Somatic		Capture	Illumina HiSeq	Phase_I	126126026	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	37	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	G	8.582	0.882464	0.17467	.	.	ENSG00000164961	ENST00000523273	.	.	.	5.41	-2.54	0.06307	.	.	.	.	.	T	0.38081	0.1027	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28776	-1.0033	4	.	.	.	-21.3337	0.7027	0.00910	0.2219:0.3018:0.1703:0.306	.	.	.	.	L	484	.	.	P	-	2	0	KIAA0196	126126026	0.620000	0.27068	0.043000	0.18650	0.686000	0.39977	-0.119000	0.10676	-0.802000	0.04421	-0.175000	0.13238	CCT		0.438	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846	
KCNQ3	3786	broad.mit.edu	37	8	133141603	133141603	+	Missense_Mutation	SNP	G	G	A	rs202163980		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:133141603G>A	ENST00000388996.4	-	15	2945	c.2525C>T	c.(2524-2526)aCg>aTg	p.T842M	KCNQ3_ENST00000519445.1_Missense_Mutation_p.T830M|KCNQ3_ENST00000521134.1_Missense_Mutation_p.T722M	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	842					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.T842M(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GAAGGGGTCCGTGTCTGTGTC	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		18635	0.0		0.001	False		,,,				2504	0.0				p.T842M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2525T	8						.						83.0	70.0	74.0					8																	133141603		2203	4300	6503	133210785	SO:0001583	missense	3786	exon15			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.2525C>T	8.37:g.133141603G>A	ENSP00000373648:p.Thr842Met	Somatic		Capture	Illumina HiSeq	Phase_I	133210785	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	25.4	4.629352	0.87560	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	T;T;T	0.50813	0.73;0.73;0.73	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.63815	0.2543	L	0.44542	1.39	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	T	0.64609	-0.6367	10	0.87932	D	0	-15.8721	18.9552	0.92655	0.0:0.0:1.0:0.0	.	830;842	E7ET42;O43525	.;KCNQ3_HUMAN	M	842;722;830;819;721	ENSP00000373648:T842M;ENSP00000429799:T722M;ENSP00000428790:T830M	ENSP00000373648:T842M	T	-	2	0	KCNQ3	133210785	1.000000	0.71417	0.966000	0.40874	0.991000	0.79684	9.230000	0.95299	2.714000	0.92807	0.655000	0.94253	ACG		0.572	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
KCNQ3	3786	broad.mit.edu	37	8	133141866	133141866	+	Silent	SNP	G	G	C	rs555827251		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:133141866G>C	ENST00000388996.4	-	15	2682	c.2262C>G	c.(2260-2262)ctC>ctG	p.L754L	KCNQ3_ENST00000519445.1_Silent_p.L742L|KCNQ3_ENST00000521134.1_Silent_p.L634L	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	754					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.L754L(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	CTCGGGAGTCGAGAAGAGTCA	0.612																																					p.L754L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2262G	8						.						33.0	35.0	34.0					8																	133141866		2203	4300	6503	133211048	SO:0001819	synonymous_variant	3786	exon15			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.2262C>G	8.37:g.133141866G>C		Somatic		Capture	Illumina HiSeq	Phase_I	133211048	NM_004519	A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	37	CCDS34943.1																																																																																				0.612	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
KCNQ3	3786	broad.mit.edu	37	8	133142133	133142133	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:133142133C>T	ENST00000388996.4	-	15	2415	c.1995G>A	c.(1993-1995)tcG>tcA	p.S665S	KCNQ3_ENST00000519445.1_Silent_p.S653S|KCNQ3_ENST00000521134.1_Silent_p.S545S	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	665					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.S665S(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	CTTCAGCTGGCGAGGAGGTGC	0.532																																					p.S665S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1995A	8						.						136.0	115.0	122.0					8																	133142133		2203	4300	6503	133211315	SO:0001819	synonymous_variant	3786	exon15			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.1995G>A	8.37:g.133142133C>T		Somatic		Capture	Illumina HiSeq	Phase_I	133211315	NM_004519	A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	37	CCDS34943.1																																																																																				0.532	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
KCNQ3	3786	broad.mit.edu	37	8	133153411	133153411	+	Missense_Mutation	SNP	C	C	T	rs141821338		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:133153411C>T	ENST00000388996.4	-	10	1850	c.1430G>A	c.(1429-1431)cGc>cAc	p.R477H	KCNQ3_ENST00000519445.1_Missense_Mutation_p.R477H|KCNQ3_ENST00000521134.1_Missense_Mutation_p.R357H	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	477					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.R477H(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GGCTTTCATGCGGAAGGCCGT	0.473																																					p.R477H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1430A	8						.						119.0	124.0	122.0					8																	133153411		2203	4300	6503	133222593	SO:0001583	missense	3786	exon10			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.1430G>A	8.37:g.133153411C>T	ENSP00000373648:p.Arg477His	Somatic		Capture	Illumina HiSeq	Phase_I	133222593	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.011674	0.93346	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.99735	-6.58;-6.58;-6.58	5.63	5.63	0.86233	Potassium channel, voltage dependent, KCNQ, C-terminal (1);	0.118141	0.56097	D	0.000027	D	0.99600	0.9855	M	0.64170	1.965	0.52099	D	0.999943	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98327	1.0531	10	0.87932	D	0	-16.6136	18.6978	0.91607	0.0:1.0:0.0:0.0	.	477;477	E7ET42;O43525	.;KCNQ3_HUMAN	H	477;357;477;466;356	ENSP00000373648:R477H;ENSP00000429799:R357H;ENSP00000428790:R477H	ENSP00000373648:R477H	R	-	2	0	KCNQ3	133222593	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.524000	0.60552	2.652000	0.90054	0.655000	0.94253	CGC		0.473	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
PHF20L1	51105	broad.mit.edu	37	8	133848922	133848922	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:133848922C>T	ENST00000395386.2	+	16	2346	c.2047C>T	c.(2047-2049)Cga>Tga	p.R683*	AF230666.2_ENST00000429151.1_RNA|PHF20L1_ENST00000395390.2_Nonsense_Mutation_p.R658*|AF230666.2_ENST00000608375.1_RNA|PHF20L1_ENST00000220847.7_Nonsense_Mutation_p.R70*	NM_016018.4	NP_057102.4	A8MW92	P20L1_HUMAN	PHD finger protein 20-like 1	683							zinc ion binding (GO:0008270)	p.R657*(2)		breast(1)|endometrium(1)|large_intestine(1)|lung(10)|ovary(2)	15	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TGAAATTGTGCGATGTATTTG	0.408																																					p.R683X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C2047T	8						.						190.0	183.0	185.0					8																	133848922		1969	4147	6116	133918104	SO:0001587	stop_gained	51105	exon16			AF230666	CCDS6367.2, CCDS6368.1, CCDS75791.1	8q24.22	2014-03-24			ENSG00000129292	ENSG00000129292		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	24280	protein-coding gene	gene with protein product	"""tudor domain containing 20B"""					10810093, 24492612	Standard	NM_016018		Approved	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B	uc003ytt.3	A8MW92	OTTHUMG00000148656	ENST00000395386.2:c.2047C>T	8.37:g.133848922C>T	ENSP00000378784:p.Arg683*	Somatic		Capture	Illumina HiSeq	Phase_I	133918104	NM_016018	A8MZC9|Q86U89|Q86W43|Q96BT0|Q9H702|Q9HBK3|Q9NYR3|Q9Y381	Nonsense_Mutation	SNP	ENST00000395386.2	37	CCDS6367.2	.	.	.	.	.	.	.	.	.	.	C	38	7.083629	0.98051	.	.	ENSG00000129292	ENST00000395386;ENST00000220847;ENST00000395390	.	.	.	5.14	3.02	0.34903	.	0.103999	0.38111	U	0.001810	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.6783	12.4875	0.55881	0.3889:0.6111:0.0:0.0	.	.	.	.	X	683;70;658	.	ENSP00000220847:R70X	R	+	1	2	PHF20L1	133918104	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	2.219000	0.42899	1.289000	0.44618	0.544000	0.68410	CGA		0.408	PHF20L1-008	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308949.3	NM_016018	
KCNK9	51305	broad.mit.edu	37	8	140631061	140631061	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:140631061C>T	ENST00000520439.1	-	2	628	c.565G>A	c.(565-567)Gcc>Acc	p.A189T	KCNK9_ENST00000303015.1_Missense_Mutation_p.A189T|KCNK9_ENST00000523477.1_5'Flank	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	189					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.A189T(1)		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)	TAGTAGTAGGCGTGGAAGAAG	0.592																																					p.A189T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G565A	8						.						89.0	86.0	87.0					8																	140631061		2203	4300	6503	140700243	SO:0001583	missense	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.565G>A	8.37:g.140631061C>T	ENSP00000430676:p.Ala189Thr	Somatic		Capture	Illumina HiSeq	Phase_I	140700243	NM_016601	Q2M290|Q540F2	Missense_Mutation	SNP	ENST00000520439.1	37	CCDS6377.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.111318	0.77210	.	.	ENSG00000169427	ENST00000522317;ENST00000303015;ENST00000520439	T;T;T	0.36699	1.24;1.24;1.24	5.85	5.85	0.93711	Ion transport 2 (1);	0.063633	0.64402	D	0.000004	T	0.66577	0.2803	M	0.91300	3.195	0.48696	D	0.999695	D	0.76494	0.999	D	0.69142	0.962	T	0.73623	-0.3924	10	0.87932	D	0	.	14.0418	0.64681	0.1507:0.8493:0.0:0.0	.	189	Q9NPC2	KCNK9_HUMAN	T	189	ENSP00000429847:A189T;ENSP00000302166:A189T;ENSP00000430676:A189T	ENSP00000302166:A189T	A	-	1	0	KCNK9	140700243	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.546000	0.60705	2.753000	0.94483	0.655000	0.94253	GCC		0.592	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601	
KCNK9	51305	broad.mit.edu	37	8	140715158	140715158	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:140715158G>A	ENST00000520439.1	-	1	141	c.78C>T	c.(76-78)ttC>ttT	p.F26F	KCNK9_ENST00000303015.1_Silent_p.F26F	NM_001282534.1	NP_001269463.1	Q9NPC2	KCNK9_HUMAN	potassium channel, subfamily K, member 9	26					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.F26F(1)		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)	CGAGGGCGTCGAACACGGCGG	0.627																																					p.F26F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C78T	8						.						64.0	55.0	58.0					8																	140715158		2203	4300	6503	140784340	SO:0001819	synonymous_variant	51305	exon1			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.78C>T	8.37:g.140715158G>A		Somatic		Capture	Illumina HiSeq	Phase_I	140784340	NM_016601	Q2M290|Q540F2	Silent	SNP	ENST00000520439.1	37	CCDS6377.1																																																																																				0.627	KCNK9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378473.1	NM_016601	
AGO2	27161	broad.mit.edu	37	8	141551327	141551327	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:141551327G>A	ENST00000220592.5	-	15	2082	c.1970C>T	c.(1969-1971)aCg>aTg	p.T657M	AGO2_ENST00000519980.1_Missense_Mutation_p.T657M	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	657	Interaction with GW182 family members. {ECO:0000255}.|Piwi. {ECO:0000255|HAMAP-Rule:MF_03031}.				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)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|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)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)	p.T657M(1)									CTTGAAGCGCGTGGACTTGTA	0.627																																					p.T657M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1970T	8						.						117.0	91.0	99.0					8																	141551327		2202	4300	6502	141620509	SO:0001583	missense	27161	exon15			AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"""Argonaute/PIWI family"""	3263	protein-coding gene	gene with protein product	"""argonaute 2"""	606229	"""eukaryotic translation initiation factor 2C, 2"""	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.1970C>T	8.37:g.141551327G>A	ENSP00000220592:p.Thr657Met	Somatic		Capture	Illumina HiSeq	Phase_I	141620509	NM_001164623	Q8TCZ5|Q8WV58|Q96ID1	Missense_Mutation	SNP	ENST00000220592.5	37	CCDS6380.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.990124	0.93106	.	.	ENSG00000123908	ENST00000220592;ENST00000519980	T;T	0.32515	1.45;1.45	5.36	5.36	0.76844	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.63462	0.2513	M	0.87758	2.905	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.79108	0.986;0.992	T	0.69781	-0.5052	10	0.87932	D	0	-8.7099	19.4371	0.94799	0.0:0.0:1.0:0.0	.	657;657	Q9UKV8-2;Q9UKV8	.;AGO2_HUMAN	M	657	ENSP00000220592:T657M;ENSP00000430176:T657M	ENSP00000220592:T657M	T	-	2	0	EIF2C2	141620509	1.000000	0.71417	0.973000	0.42090	0.992000	0.81027	9.774000	0.98992	2.642000	0.89623	0.650000	0.86243	ACG		0.627	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4		
AGO2	27161	broad.mit.edu	37	8	141559336	141559336	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:141559336G>A	ENST00000220592.5	-	12	1577	c.1465C>T	c.(1465-1467)Ccg>Tcg	p.P489S	AGO2_ENST00000519980.1_Missense_Mutation_p.P489S	NM_012154.3	NP_036286.2	Q9UKV8	AGO2_HUMAN	argonaute RISC catalytic component 2	489					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)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|negative regulation of translational initiation (GO:0045947)|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)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|RISC complex (GO:0016442)	endoribonuclease activity (GO:0004521)|endoribonuclease activity, cleaving siRNA-paired mRNA (GO:0070551)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA 7-methylguanosine cap binding (GO:0000340)|siRNA binding (GO:0035197)|translation initiation factor activity (GO:0003743)	p.P489S(1)									CAGAAGCACGGCTGGCCCTGG	0.622																																					p.P489S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1465T	8						.						47.0	45.0	45.0					8																	141559336		2203	4300	6503	141628518	SO:0001583	missense	27161	exon12			AF121255	CCDS6380.1, CCDS55279.1	8q24.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000123908	ENSG00000123908		"""Argonaute/PIWI family"""	3263	protein-coding gene	gene with protein product	"""argonaute 2"""	606229	"""eukaryotic translation initiation factor 2C, 2"""	EIF2C2		10534406, 12906857	Standard	NM_012154		Approved	hAGO2, Q10	uc003yvn.3	Q9UKV8	OTTHUMG00000164232	ENST00000220592.5:c.1465C>T	8.37:g.141559336G>A	ENSP00000220592:p.Pro489Ser	Somatic		Capture	Illumina HiSeq	Phase_I	141628518	NM_001164623	Q8TCZ5|Q8WV58|Q96ID1	Missense_Mutation	SNP	ENST00000220592.5	37	CCDS6380.1	.	.	.	.	.	.	.	.	.	.	G	33	5.216286	0.95104	.	.	ENSG00000123908	ENST00000220592;ENST00000519980	T;T	0.13538	2.58;2.58	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.50582	0.1624	M	0.93638	3.44	0.80722	D	1	D;D	0.71674	0.998;0.993	D;D	0.77557	0.99;0.951	T	0.64136	-0.6478	10	0.87932	D	0	-15.5564	19.2786	0.94042	0.0:0.0:1.0:0.0	.	489;489	Q9UKV8-2;Q9UKV8	.;AGO2_HUMAN	S	489	ENSP00000220592:P489S;ENSP00000430176:P489S	ENSP00000220592:P489S	P	-	1	0	EIF2C2	141628518	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.707000	0.98725	2.641000	0.89580	0.563000	0.77884	CCG		0.622	AGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377866.4		
MROH5	389690	broad.mit.edu	37	8	142458137	142458137	+	RNA	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:142458137C>T	ENST00000430863.1	-	0	2769				SNORD5_ENST00000458800.1_RNA	NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5																		CCCTCCTGCACGGCCTGCTTG	0.657																																					p.V897M												.	.	0			c.G2689A	8						.						29.0	35.0	33.0					8																	142458137		2052	4185	6237	142527319			389690	exon21					8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"""maestro heat-like repeat containing"""	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142458137C>T		Somatic		Capture	Illumina HiSeq	Phase_I	142527319	NM_207414		Missense_Mutation	SNP	ENST00000430863.1	37																																																																																					0.657	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4	NM_207414	
BAI1	575	broad.mit.edu	37	8	143561076	143561076	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:143561076G>T	ENST00000517894.1	+	9	2643	c.1749G>T	c.(1747-1749)gaG>gaT	p.E583D	BAI1_ENST00000323289.5_Missense_Mutation_p.E583D			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	583					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.E583D(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					TCTGTGATGAGGACAACTTTG	0.642																																					p.E583D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1749T	8						.						83.0	90.0	88.0					8																	143561076		2009	4169	6178	143558078	SO:0001583	missense	575	exon8			AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"""-"", ""GPCR / Class B : Orphans"""	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.1749G>T	8.37:g.143561076G>T	ENSP00000430945:p.Glu583Asp	Somatic		Capture	Illumina HiSeq	Phase_I	143558078	NM_001702		Missense_Mutation	SNP	ENST00000517894.1	37		.	.	.	.	.	.	.	.	.	.	g	12.52	1.961984	0.34659	.	.	ENSG00000181790	ENST00000517894;ENST00000323289	T;T	0.28255	1.62;1.62	4.67	2.53	0.30540	.	0.000000	0.64402	U	0.000001	T	0.23451	0.0567	L	0.43923	1.385	0.34236	D	0.677048	B	0.30281	0.275	B	0.33620	0.167	T	0.24261	-1.0165	10	0.14656	T	0.56	.	9.3208	0.37964	0.2437:0.0:0.7563:0.0	.	583	E9PBK0	.	D	583	ENSP00000430945:E583D;ENSP00000313046:E583D	ENSP00000313046:E583D	E	+	3	2	BAI1	143558078	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	1.413000	0.34725	0.968000	0.38212	0.306000	0.20318	GAG		0.642	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702	
ARC	23237	broad.mit.edu	37	8	143694937	143694937	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:143694937G>A	ENST00000356613.2	-	1	1896	c.696C>T	c.(694-696)ggC>ggT	p.G232G	ARC_ENST00000581404.1_5'Flank	NM_015193.4	NP_056008.1	O60936	NOL3_HUMAN	activity-regulated cytoskeleton-associated protein	0					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|response to hypoxia (GO:0001666)|response to injury involved in regulation of muscle adaptation (GO:0014876)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|sarcoplasm (GO:0016528)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)	p.G232G(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	13	all_cancers(97;3.55e-12)|all_epithelial(106;1.03e-08)|Lung NSC(106;0.000353)|all_lung(105;0.00092)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.0279)				CCTCAGAGCCGCCCACCTGCC	0.637																																					p.G232G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C696T	8						.						27.0	28.0	28.0					8																	143694937		2177	4264	6441	143691939	SO:0001819	synonymous_variant	23237	exon1			AF193421	CCDS34950.1	8q24.3	2008-08-01			ENSG00000198576	ENSG00000198576			648	protein-coding gene	gene with protein product		612461				10970730, 17466953	Standard	NM_015193		Approved	KIAA0278, Arg3.1	uc003ywn.2	Q7LC44	OTTHUMG00000134310	ENST00000356613.2:c.696C>T	8.37:g.143694937G>A		Somatic		Capture	Illumina HiSeq	Phase_I	143691939	NM_015193	B4DFL0|O60937	Silent	SNP	ENST00000356613.2	37	CCDS34950.1																																																																																				0.637	ARC-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259274.2		
LYPD2	137797	broad.mit.edu	37	8	143832561	143832561	+	Missense_Mutation	SNP	G	G	A	rs374454038		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:143832561G>A	ENST00000359228.3	-	2	168	c.86C>T	c.(85-87)cCg>cTg	p.P29L		NM_205545.1	NP_991108.1	Q6UXB3	LYPD2_HUMAN	LY6/PLAUR domain containing 2	29	UPAR/Ly6.					anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.P29L(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(2)	7	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)					TGTGGGCTCCGGACAGACGTA	0.637																																					p.P29L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C86T	8						.	G	LEU/PRO	0,4406		0,0,2203	175.0	140.0	152.0		86	-10.0	0.0	8		152	1,8599	1.2+/-3.3	0,1,4299	no	missense	LYPD2	NM_205545.1	98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	29/126	143832561	1,13005	2203	4300	6503	143829563	SO:0001583	missense	137797	exon2			AY358432	CCDS6388.1	8q24.3	2005-08-30		2005-08-30	ENSG00000197353	ENSG00000197353			25215	protein-coding gene	gene with protein product				LYPDC2		12975309	Standard	NM_205545		Approved	RGTR430, UNQ430	uc003ywz.3	Q6UXB3	OTTHUMG00000164686	ENST00000359228.3:c.86C>T	8.37:g.143832561G>A	ENSP00000352163:p.Pro29Leu	Somatic		Capture	Illumina HiSeq	Phase_I	143829563	NM_205545	A8K2R6|Q0VD64|Q0VF31	Missense_Mutation	SNP	ENST00000359228.3	37	CCDS6388.1	.	.	.	.	.	.	.	.	.	.	G	10.04	1.241968	0.22796	0.0	1.16E-4	ENSG00000197353	ENST00000359228	T	0.76968	-1.06	5.0	-10.0	0.00425	Ly-6 antigen / uPA receptor -like (1);CD59 antigen, conserved site (1);CD59 antigen (1);	2.214490	0.02018	N	0.047563	T	0.60881	0.2303	L	0.33485	1.01	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48305	-0.9047	10	0.40728	T	0.16	.	4.0546	0.09811	0.2906:0.0736:0.4705:0.1653	.	29	Q6UXB3	LYPD2_HUMAN	L	29	ENSP00000352163:P29L	ENSP00000352163:P29L	P	-	2	0	LYPD2	143829563	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-6.689000	0.00057	-2.739000	0.00380	-1.550000	0.00899	CCG		0.637	LYPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379742.1	NM_205545	
TOP1MT	116447	broad.mit.edu	37	8	144400005	144400005	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:144400005C>T	ENST00000329245.4	-	10	1252	c.1218G>A	c.(1216-1218)acG>acA	p.T406T	TOP1MT_ENST00000521193.1_Silent_p.T308T|TOP1MT_ENST00000519148.1_Silent_p.T308T|TOP1MT_ENST00000523676.1_Silent_p.T308T|AC087793.1_ENST00000585120.1_RNA	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	406					DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)	p.T406T(1)		endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	TCAGGCTGGTCGTCTGGGGAG	0.602																																					p.T406T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1218A	8						.						62.0	57.0	59.0					8																	144400005		2203	4300	6503	144471380	SO:0001819	synonymous_variant	116447	exon10			AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.1218G>A	8.37:g.144400005C>T		Somatic		Capture	Illumina HiSeq	Phase_I	144471380	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Silent	SNP	ENST00000329245.4	37	CCDS6400.1																																																																																				0.602	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963	
MAPK15	225689	broad.mit.edu	37	8	144803812	144803812	+	Missense_Mutation	SNP	C	C	T	rs372002074		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:144803812C>T	ENST00000338033.4	+	12	1417	c.1298C>T	c.(1297-1299)gCg>gTg	p.A433V	RP11-429J17.5_ENST00000527908.1_RNA	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	433					MAPK cascade (GO:0000165)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|SH3 domain binding (GO:0017124)	p.A452V(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|stomach(1)	12	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CCCCCTGGGGCGAAGGAAGCG	0.642																																					p.A433V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1298T	8						.	C	VAL/ALA	1,3813		0,1,1906	72.0	83.0	79.0		1298	1.4	0.0	8		79	0,8232		0,0,4116	no	missense	MAPK15	NM_139021.2	64	0,1,6022	TT,TC,CC		0.0,0.0262,0.0083	possibly-damaging	433/545	144803812	1,12045	1907	4116	6023	144875800	SO:0001583	missense	225689	exon12			AY065978	CCDS6409.2	8q24.3	2011-06-09			ENSG00000181085	ENSG00000181085		"""Mitogen-activated protein kinase cascade / Kinases"""	24667	protein-coding gene	gene with protein product	"""extracellular signal regulated kinase 8"""					11875070	Standard	XM_006716528		Approved	ERK8, ERK7	uc003yzj.3	Q8TD08	OTTHUMG00000146450	ENST00000338033.4:c.1298C>T	8.37:g.144803812C>T	ENSP00000337691:p.Ala433Val	Somatic		Capture	Illumina HiSeq	Phase_I	144875800	NM_139021	Q2TCF9|Q8N362	Missense_Mutation	SNP	ENST00000338033.4	37	CCDS6409.2	.	.	.	.	.	.	.	.	.	.	c	4.369	0.068042	0.08436	2.62E-4	0.0	ENSG00000181085	ENST00000338033	T	0.73469	-0.75	2.25	1.35	0.21983	.	12.505500	0.01643	N	0.024178	T	0.59609	0.2206	N	0.19112	0.55	0.09310	N	0.999999	B	0.12013	0.005	B	0.08055	0.003	T	0.43048	-0.9415	10	0.29301	T	0.29	-13.8569	4.7356	0.12986	0.0:0.811:0.0:0.189	.	433	Q8TD08	MK15_HUMAN	V	433	ENSP00000337691:A433V	ENSP00000337691:A433V	A	+	2	0	MAPK15	144875800	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	-0.422000	0.07043	0.497000	0.27926	0.306000	0.20318	GCG		0.642	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021	
SCRIB	23513	broad.mit.edu	37	8	144894548	144894548	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:144894548A>C	ENST00000320476.3	-	9	800	c.794T>G	c.(793-795)cTg>cGg	p.L265R	SCRIB_ENST00000377533.3_Missense_Mutation_p.L184R|MIR937_ENST00000401271.1_RNA|SCRIB_ENST00000356994.2_Missense_Mutation_p.L265R	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	265	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)		p.L265R(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			TAGCTGCTTCAGCTGACCTGG	0.612																																					p.L265R	Pancreas(51;966 1133 10533 14576 29674)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T794G	8						.						104.0	90.0	95.0					8																	144894548		2203	4300	6503	144966536	SO:0001583	missense	23513	exon9			AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.794T>G	8.37:g.144894548A>C	ENSP00000322938:p.Leu265Arg	Somatic		Capture	Illumina HiSeq	Phase_I	144966536	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	37	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.856622	0.51376	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533	T;T;T	0.61392	1.83;0.11;1.43	4.21	4.21	0.49690	.	.	.	.	.	T	0.76926	0.4056	M	0.85041	2.73	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.981;0.996	T	0.81219	-0.1032	9	0.87932	D	0	.	12.6097	0.56544	1.0:0.0:0.0:0.0	.	265;265	Q14160;Q14160-3	SCRIB_HUMAN;.	R	265;265;184	ENSP00000349486:L265R;ENSP00000322938:L265R;ENSP00000366756:L184R	ENSP00000322938:L265R	L	-	2	0	SCRIB	144966536	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	6.929000	0.75852	1.741000	0.51731	0.460000	0.39030	CTG		0.612	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	
PLEC	5339	broad.mit.edu	37	8	144995173	144995173	+	Missense_Mutation	SNP	C	C	T	rs375208309		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:144995173C>T	ENST00000322810.4	-	32	9396	c.9227G>A	c.(9226-9228)cGg>cAg	p.R3076Q	PLEC_ENST00000436759.2_Missense_Mutation_p.R2966Q|PLEC_ENST00000356346.3_Missense_Mutation_p.R2925Q|PLEC_ENST00000345136.3_Missense_Mutation_p.R2939Q|PLEC_ENST00000398774.2_Missense_Mutation_p.R2907Q|PLEC_ENST00000354958.2_Missense_Mutation_p.R2917Q|PLEC_ENST00000357649.2_Missense_Mutation_p.R2943Q|PLEC_ENST00000354589.3_Missense_Mutation_p.R2939Q|PLEC_ENST00000527096.1_Missense_Mutation_p.R2962Q	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3076	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)	p.R2966Q(1)|p.R3076Q(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CAGCAGGTCCCGCCGCTGCTC	0.602																																					p.R2943Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G8828A	8						.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4329		0,1,2164	44.0	52.0	49.0		8897,8774,8750,9227,8720,8816,8828,8816	4.8	1.0	8		49	1,8537		0,1,4268	no	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	43,43,43,43,43,43,43,43	0,2,6432	TT,TC,CC		0.0117,0.0231,0.0155	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	2966/4575,2925/4534,2917/4526,3076/4685,2907/4516,2939/4548,2943/4552,2939/4548	144995173	2,12866	2165	4269	6434	145067161	SO:0001583	missense	5339	exon32			U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.9227G>A	8.37:g.144995173C>T	ENSP00000323856:p.Arg3076Gln	Somatic		Capture	Illumina HiSeq	Phase_I	145067161	NM_201383	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.190544	0.38707	2.31E-4	1.17E-4	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.78364	-1.14;-1.14;-1.17;-1.17;-1.15;-1.14;-1.14;-1.14;-1.14	4.82	4.82	0.62117	.	0.183542	0.32231	U	0.006390	T	0.72930	0.3522	N	0.25144	0.715	0.37760	D	0.926276	D;D;D;D;D;D;D;D	0.62365	0.991;0.991;0.991;0.985;0.991;0.991;0.991;0.991	P;P;P;B;P;P;P;P	0.49708	0.62;0.62;0.62;0.416;0.62;0.62;0.62;0.62	T	0.76011	-0.3115	10	0.35671	T	0.21	.	17.0298	0.86458	0.0:1.0:0.0:0.0	.	2966;2925;2917;3076;2907;2939;2943;2939	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	Q	2939;2943;2939;2907;3076;2917;2925;2966;2962	ENSP00000344848:R2939Q;ENSP00000350277:R2943Q;ENSP00000346602:R2939Q;ENSP00000381756:R2907Q;ENSP00000323856:R3076Q;ENSP00000347044:R2917Q;ENSP00000348702:R2925Q;ENSP00000388180:R2966Q;ENSP00000434583:R2962Q	ENSP00000323856:R3076Q	R	-	2	0	PLEC	145067161	0.992000	0.36948	0.998000	0.56505	0.972000	0.66771	2.990000	0.49401	2.404000	0.81709	0.448000	0.29417	CGG		0.602	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
DLGAP2	9228	broad.mit.edu	37	8	1497408	1497408	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:1497408G>A	ENST00000421627.2	+	2	683	c.549G>A	c.(547-549)gcG>gcA	p.A183A		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	262					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)		p.A205A(1)		breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		ACGGCCGGGCGGACGACCACC	0.667																																					p.A183A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G549A	8						.						16.0	23.0	21.0					8																	1497408		2176	4285	6461	1484815	SO:0001819	synonymous_variant	9228	exon2			AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"""discs, large (Drosophila) homolog-associated protein 2"""			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.549G>A	8.37:g.1497408G>A		Somatic		Capture	Illumina HiSeq	Phase_I	1484815	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Silent	SNP	ENST00000421627.2	37	CCDS47760.1	.	.	.	.	.	.	.	.	.	.	G	0.203	-1.043428	0.01997	.	.	ENSG00000198010	ENST00000520901	.	.	.	5.57	-0.867	0.10655	.	.	.	.	.	T	0.42017	0.1184	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25257	-1.0137	4	.	.	.	-2.1129	2.2903	0.04136	0.2009:0.235:0.443:0.1211	.	.	.	.	Q	200	.	.	R	+	2	0	DLGAP2	1484815	0.805000	0.28982	0.003000	0.11579	0.010000	0.07245	0.157000	0.16402	-0.204000	0.10235	-0.819000	0.03115	CGG		0.667	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745	
DLGAP2	9228	broad.mit.edu	37	8	1497737	1497737	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:1497737C>T	ENST00000421627.2	+	2	1012	c.878C>T	c.(877-879)aCg>aTg	p.T293M		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	372					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)		p.T315M(1)		breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		TCCTGGTCTACGCTGACGGTC	0.652																																					p.T293M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C878T	8						.						17.0	19.0	18.0					8																	1497737		2181	4275	6456	1485144	SO:0001583	missense	9228	exon2			AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"""discs, large (Drosophila) homolog-associated protein 2"""			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.878C>T	8.37:g.1497737C>T	ENSP00000400258:p.Thr293Met	Somatic		Capture	Illumina HiSeq	Phase_I	1485144	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	ENST00000421627.2	37	CCDS47760.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.4|25.4	4.631983|4.631983	0.87660|0.87660	.|.	.|.	ENSG00000198010|ENSG00000198010	ENST00000520901|ENST00000356067;ENST00000421627	.|T	.|0.32023	.|1.47	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.64405|0.64405	0.2595|0.2595	M|M	0.88906|0.88906	2.99|2.99	0.51482|0.51482	D|D	0.999928|0.999928	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.992	T|T	0.72137|0.72137	-0.4381|-0.4381	5|10	.|0.87932	.|D	.|0	-7.7439|-7.7439	18.9482|18.9482	0.92630|0.92630	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|372;372	.|Q9P1A6-2;Q9P1A6	.|.;DLGP2_HUMAN	C|M	310|338;293	.|ENSP00000400258:T293M	.|ENSP00000348366:T338M	R|T	+|+	1|2	0|0	DLGAP2|DLGAP2	1485144|1485144	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.849000|0.849000	0.48306|0.48306	7.058000|7.058000	0.76676|0.76676	2.463000|2.463000	0.83235|0.83235	0.655000|0.655000	0.94253|0.94253	CGC|ACG		0.652	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745	
ARHGEF10	9639	broad.mit.edu	37	8	1905259	1905259	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:1905259G>A	ENST00000398564.1	+	29	3940	c.3940G>A	c.(3940-3942)Gtc>Atc	p.V1314I	ARHGEF10_ENST00000521927.1_3'UTR|ARHGEF10_ENST00000518288.1_Missense_Mutation_p.V1313I|ARHGEF10_ENST00000262112.6_Missense_Mutation_p.V1285I|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.V1289I|ARHGEF10_ENST00000520359.1_Missense_Mutation_p.V1251I			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1314					centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V1314I(1)|p.V1066I(1)		endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		GAAGGATCCTGTCTCGCTGAG	0.617																																					p.V1289I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3865A	8						.						50.0	48.0	49.0					8																	1905259		2203	4300	6503	1892666	SO:0001583	missense	9639	exon29			AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"""Rho guanine nucleotide exchange factors"""	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.3940G>A	8.37:g.1905259G>A	ENSP00000381571:p.Val1314Ile	Somatic		Capture	Illumina HiSeq	Phase_I	1892666	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Missense_Mutation	SNP	ENST00000398564.1	37		.	.	.	.	.	.	.	.	.	.	G	7.744	0.701883	0.15172	.	.	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398564;ENST00000262112;ENST00000522435	T;T;T;T;T;T	0.58506	0.35;0.35;0.34;0.34;0.33;0.41	5.71	-8.1	0.01086	.	0.759254	0.12895	N	0.430244	T	0.27063	0.0663	N	0.08118	0	0.09310	N	1	B;B	0.12630	0.004;0.006	B;B	0.09377	0.001;0.004	T	0.15378	-1.0439	10	0.22706	T	0.39	-0.0279	9.5527	0.39319	0.3788:0.0:0.5108:0.1104	.	1251;1289	O15013-7;O15013-5	.;.	I	1289;1251;1313;1314;1285;933	ENSP00000340297:V1289I;ENSP00000427909:V1251I;ENSP00000431012:V1313I;ENSP00000381571:V1314I;ENSP00000262112:V1285I;ENSP00000427768:V933I	ENSP00000262112:V1285I	V	+	1	0	ARHGEF10	1892666	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.045000	0.14013	-1.895000	0.01104	-0.768000	0.03414	GTC		0.617	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
CSMD1	64478	broad.mit.edu	37	8	2949073	2949073	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:2949073G>A	ENST00000520002.1	-	49	7808	c.7253C>T	c.(7252-7254)gCc>gTc	p.A2418V	CSMD1_ENST00000537824.1_Missense_Mutation_p.A2417V|CSMD1_ENST00000400186.3_Missense_Mutation_p.A2418V|CSMD1_ENST00000542608.1_Missense_Mutation_p.A2417V|CSMD1_ENST00000602723.1_Missense_Mutation_p.A2418V|CSMD1_ENST00000602557.1_Missense_Mutation_p.A2418V			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2418	CUB 14. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)		p.A2146V(1)|p.A2417V(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)		CTTACTGGTGGCATGGTCAGT	0.353																																					p.C2417C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C7251T	8						.						115.0	109.0	111.0					8																	2949073		1847	4085	5932	2936480	SO:0001583	missense	64478	exon48					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.7253C>T	8.37:g.2949073G>A	ENSP00000430733:p.Ala2418Val	Somatic		Capture	Illumina HiSeq	Phase_I	2936480	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	G	29.9	5.042354	0.93685	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.78	5.78	0.91487	CUB (5);	0.000000	0.64402	D	0.000001	T	0.41213	0.1149	L	0.56769	1.78	0.80722	D	1	D;P;D	0.76494	0.978;0.949;0.999	P;P;D	0.87578	0.715;0.792;0.998	T	0.01858	-1.1259	10	0.38643	T	0.18	.	20.0013	0.97409	0.0:0.0:1.0:0.0	.	2418;2418;2417	E5RIG2;Q96PZ7;F5H2I8	.;CSMD1_HUMAN;.	V	2418;2418;2279;2417;2417	ENSP00000383047:A2418V;ENSP00000430733:A2418V;ENSP00000441462:A2417V;ENSP00000446243:A2417V	ENSP00000320445:A2279V	A	-	2	0	CSMD1	2936480	1.000000	0.71417	0.860000	0.33809	0.519000	0.34347	9.520000	0.98027	2.723000	0.93209	0.542000	0.68232	GCC		0.353	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
CSMD1	64478	broad.mit.edu	37	8	3245111	3245111	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:3245111G>A	ENST00000520002.1	-	19	3245	c.2690C>T	c.(2689-2691)aCt>aTt	p.T897I	CSMD1_ENST00000537824.1_Missense_Mutation_p.T896I|CSMD1_ENST00000400186.3_Missense_Mutation_p.T897I|CSMD1_ENST00000542608.1_Missense_Mutation_p.T896I|CSMD1_ENST00000539096.1_Missense_Mutation_p.T896I|CSMD1_ENST00000602723.1_Missense_Mutation_p.T897I|CSMD1_ENST00000602557.1_Missense_Mutation_p.T897I			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	897	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.T625I(1)|p.T896I(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)		ACAGCTGAAAGTCACTGTGGA	0.612																																					p.D896D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2688T	8						.						47.0	55.0	52.0					8																	3245111		2115	4218	6333	3232518	SO:0001583	missense	64478	exon18					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.2690C>T	8.37:g.3245111G>A	ENSP00000430733:p.Thr897Ile	Somatic		Capture	Illumina HiSeq	Phase_I	3232518	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	G	16.89	3.246357	0.59103	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11	5.11	5.11	0.69529	Complement control module (2);Sushi/SCR/CCP (3);	0.075502	0.56097	D	0.000039	T	0.75997	0.3926	M	0.63169	1.94	0.49915	D	0.999833	D;P;B	0.89917	1.0;0.844;0.185	D;P;B	0.87578	0.998;0.747;0.132	T	0.71108	-0.4688	10	0.18276	T	0.48	.	18.5306	0.90990	0.0:0.0:1.0:0.0	.	897;897;897	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	I	897;897;759;896;896;896	ENSP00000383047:T897I;ENSP00000430733:T897I;ENSP00000441462:T896I;ENSP00000446243:T896I;ENSP00000441675:T896I	ENSP00000320445:T759I	T	-	2	0	CSMD1	3232518	1.000000	0.71417	0.911000	0.35937	0.004000	0.04260	7.790000	0.85794	2.374000	0.81015	0.650000	0.86243	ACT		0.612	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
MCPH1	79648	broad.mit.edu	37	8	6303024	6303024	+	Missense_Mutation	SNP	C	C	T	rs115033462	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:6303024C>T	ENST00000344683.5	+	8	1857	c.1781C>T	c.(1780-1782)aCg>aTg	p.T594M	MCPH1_ENST00000522905.1_Missense_Mutation_p.T546M|MCPH1_ENST00000519480.1_Missense_Mutation_p.T594M	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	594					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)	p.T594M(1)	AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		AACATGGAGACGTCTACAGAA	0.418													C|||	18	0.00359425	0.0136	0.0	5008	,	,		20632	0.0		0.0	False		,,,				2504	0.0				p.T594M	Colon(95;1448 1467 8277 34473 35819)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1781T	8						.	C	MET/THR,MET/THR,MET/THR	32,3716		1,30,1843	61.0	55.0	57.0		1781,1637,1781	-6.4	0.0	8	dbSNP_132	57	0,8210		0,0,4105	yes	missense,missense,missense	MCPH1	NM_001172574.1,NM_001172575.1,NM_024596.3	81,81,81	1,30,5948	TT,TC,CC		0.0,0.8538,0.2676	possibly-damaging,possibly-damaging,possibly-damaging	594/611,546/563,594/836	6303024	32,11926	1874	4105	5979	6290432	SO:0001583	missense	79648	exon8			AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"""BRCT-repeat inhibitor of TERT expression 1"""	607117	"""microcephaly, primary autosomal recessive 1"""			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.1781C>T	8.37:g.6303024C>T	ENSP00000342924:p.Thr594Met	Somatic		Capture	Illumina HiSeq	Phase_I	6290432	NM_024596	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	37	CCDS43689.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	10.02	1.236559	0.22711	0.008538	0.0	ENSG00000147316	ENST00000344683;ENST00000519480;ENST00000522905	T;T;T	0.11277	2.79;2.79;2.79	4.69	-6.41	0.01938	.	2.705550	0.00892	N	0.002246	T	0.05731	0.0150	L	0.38175	1.15	0.09310	N	1	B;B;B	0.23377	0.027;0.084;0.045	B;B;B	0.26202	0.01;0.067;0.017	T	0.32877	-0.9890	10	0.72032	D	0.01	8.4485	2.4636	0.04547	0.2212:0.406:0.2518:0.121	.	546;594;594	E9PH63;Q8NEM0;E9PGU5	.;MCPH1_HUMAN;.	M	594;594;546	ENSP00000342924:T594M;ENSP00000430962:T594M;ENSP00000430768:T546M	ENSP00000342924:T594M	T	+	2	0	MCPH1	6290432	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.899000	0.04101	-1.159000	0.02807	-2.209000	0.00301	ACG		0.418	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
ANGPT2	285	broad.mit.edu	37	8	6385152	6385152	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:6385152A>G	ENST00000325203.5	-	3	964	c.490T>C	c.(490-492)Tcc>Ccc	p.S164P	ANGPT2_ENST00000523120.1_Missense_Mutation_p.S164P|ANGPT2_ENST00000338312.6_Missense_Mutation_p.S112P|ANGPT2_ENST00000415216.1_Missense_Mutation_p.S164P|MCPH1_ENST00000344683.5_Intron			O15123	ANGP2_HUMAN	angiopoietin 2	164					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to growth factor stimulus (GO:0071363)|germ cell development (GO:0007281)|glomerulus vasculature development (GO:0072012)|leukocyte migration (GO:0050900)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of positive chemotaxis (GO:0050928)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|Tie signaling pathway (GO:0048014)	cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)	p.S164P(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		GTCGAGAGGGAGTGTTCCAAG	0.308																																					p.S112P												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T334C	8						.						162.0	149.0	153.0					8																	6385152		2203	4300	6503	6372560	SO:0001583	missense	285	exon2			AF004327	CCDS5958.1, CCDS47761.1	8p23	2013-02-06			ENSG00000091879	ENSG00000091879		"""Fibrinogen C domain containing"""	485	protein-coding gene	gene with protein product		601922				9545648	Standard	NM_001147		Approved	Ang2	uc003wqj.4	O15123	OTTHUMG00000090365	ENST00000325203.5:c.490T>C	8.37:g.6385152A>G	ENSP00000314897:p.Ser164Pro	Somatic		Capture	Illumina HiSeq	Phase_I	6372560	NM_001118888	A0AV38|A8K205|B7ZLM7|Q9NRR7|Q9P2Y7	Missense_Mutation	SNP	ENST00000325203.5	37	CCDS5958.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.262314	0.80358	.	.	ENSG00000091879	ENST00000325203;ENST00000415216;ENST00000338312;ENST00000523120	T;T;D;T	0.82893	0.42;0.41;-1.66;1.08	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.90480	0.7018	M	0.77313	2.365	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;0.993;1.0;0.99	D	0.91520	0.5234	10	0.72032	D	0.01	.	13.267	0.60139	1.0:0.0:0.0:0.0	.	112;164;164;164	O15123-2;E7EVQ3;O15123-3;O15123	.;.;.;ANGP2_HUMAN	P	164;164;112;164	ENSP00000314897:S164P;ENSP00000400782:S164P;ENSP00000343517:S112P;ENSP00000428023:S164P	ENSP00000314897:S164P	S	-	1	0	ANGPT2	6372560	1.000000	0.71417	0.981000	0.43875	0.800000	0.45204	8.739000	0.91574	2.023000	0.59567	0.533000	0.62120	TCC		0.308	ANGPT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206737.1	NM_001147	
XKR5	389610	broad.mit.edu	37	8	6681155	6681155	+	RNA	SNP	T	T	C	rs539008683		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:6681155T>C	ENST00000518724.1	-	0	675							Q6UX68	XKR5_HUMAN	XK, Kell blood group complex subunit-related family, member 5							integral component of membrane (GO:0016021)		p.P175P(1)		endometrium(1)|large_intestine(1)|lung(1)	3			STAD - Stomach adenocarcinoma(24;0.0984)	READ - Rectum adenocarcinoma(644;0.137)|COAD - Colon adenocarcinoma(149;0.166)		GGGCGGCCCATGGCATGGCCA	0.587													T|||	1	0.000199681	0.0	0.0	5008	,	,		19137	0.001		0.0	False		,,,				2504	0.0				p.P175P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A525G	8						.						24.0	28.0	27.0					8																	6681155		1990	4157	6147	6668565			389610	exon4			AY358489		8p23.1	2006-01-12	2006-01-12		ENSG00000186530	ENSG00000275591			20782	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 5"""				Standard	NM_207411		Approved		uc022aqv.1	Q6UX68	OTTHUMG00000153652		8.37:g.6681155T>C		Somatic		Capture	Illumina HiSeq	Phase_I	6668565	NM_207411	Q5GH74	Silent	SNP	ENST00000518724.1	37																																																																																					0.587	XKR5-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000331969.2	NM_207411	
SGK223	157285	broad.mit.edu	37	8	8233777	8233777	+	Silent	SNP	C	C	T	rs184277103	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:8233777C>T	ENST00000520004.1	-	3	2406	c.2142G>A	c.(2140-2142)ccG>ccA	p.P714P	SGK223_ENST00000330777.4_Silent_p.P714P			Q86YV5	SG223_HUMAN		716	Poly-Pro.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.P714P(1)									ACTTTGGAGGCGGAGGAGGAG	0.532													C|||	4	0.000798722	0.0	0.0	5008	,	,		19699	0.0		0.0	False		,,,				2504	0.0041				p.P714P	GBM(34;731 755 10259 33573 33867)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2142A	8						.						94.0	104.0	101.0					8																	8233777		1952	4150	6102	8271187	SO:0001819	synonymous_variant	157285	exon2																														ENST00000520004.1:c.2142G>A	8.37:g.8233777C>T		Somatic		Capture	Illumina HiSeq	Phase_I	8271187	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																				0.532	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
MFHAS1	9258	broad.mit.edu	37	8	8747829	8747829	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:8747829A>G	ENST00000276282.6	-	1	3326	c.2740T>C	c.(2740-2742)Ttt>Ctt	p.F914L		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	914								p.F914L(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		AAGATCTGAAATTTACCATCC	0.488																																					p.F914L	Melanoma(103;1201 2045 17515 28966)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2740C	8						.						79.0	81.0	80.0					8																	8747829		2203	4300	6503	8785239	SO:0001583	missense	9258	exon1			AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.2740T>C	8.37:g.8747829A>G	ENSP00000276282:p.Phe914Leu	Somatic		Capture	Illumina HiSeq	Phase_I	8785239	NM_004225	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	A	8.598	0.886198	0.17540	.	.	ENSG00000147324	ENST00000276282	T	0.34072	1.38	5.04	2.82	0.32997	.	0.409870	0.24920	N	0.034558	T	0.21881	0.0527	L	0.36672	1.1	0.32132	N	0.586659	B	0.02656	0.0	B	0.01281	0.0	T	0.18335	-1.0340	10	0.11794	T	0.64	.	5.7977	0.18396	0.7191:0.0:0.2809:0.0	.	914	Q9Y4C4	MFHA1_HUMAN	L	914	ENSP00000276282:F914L	ENSP00000276282:F914L	F	-	1	0	MFHAS1	8785239	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.387000	0.44389	1.111000	0.41721	0.533000	0.62120	TTT		0.488	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
MFHAS1	9258	broad.mit.edu	37	8	8748980	8748980	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:8748980G>A	ENST00000276282.6	-	1	2175	c.1589C>T	c.(1588-1590)gCg>gTg	p.A530V		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	530	Roc. {ECO:0000255|PROSITE- ProRule:PRU00758}.							p.A530V(1)		endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		GCACACCACCGCGTGGGGCAC	0.622																																					p.A530V	Melanoma(103;1201 2045 17515 28966)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1589T	8						.						31.0	28.0	29.0					8																	8748980		2199	4299	6498	8786390	SO:0001583	missense	9258	exon1			AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.1589C>T	8.37:g.8748980G>A	ENSP00000276282:p.Ala530Val	Somatic		Capture	Illumina HiSeq	Phase_I	8786390	NM_004225	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.937962	0.73557	.	.	ENSG00000147324	ENST00000276282	T	0.78595	-1.19	5.42	5.42	0.78866	ROC GTPase (1);	0.000000	0.85682	D	0.000000	D	0.87803	0.6269	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.88238	0.2908	10	0.72032	D	0.01	.	18.3864	0.90468	0.0:0.0:1.0:0.0	.	530	Q9Y4C4	MFHA1_HUMAN	V	530	ENSP00000276282:A530V	ENSP00000276282:A530V	A	-	2	0	MFHAS1	8786390	1.000000	0.71417	0.940000	0.37924	0.499000	0.33736	7.603000	0.82811	2.817000	0.96982	0.563000	0.77884	GCG		0.622	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
PCM1	5108	broad.mit.edu	37	8	17813022	17813022	+	Silent	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:17813022C>A	ENST00000519253.1	+	10	1583	c.1332C>A	c.(1330-1332)ccC>ccA	p.P444P	PCM1_ENST00000325083.8_Silent_p.P444P|PCM1_ENST00000524226.1_Silent_p.P444P|PCM1_ENST00000518537.1_Silent_p.P483P			Q15154	PCM1_HUMAN	pericentriolar material 1	444					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)	p.P444P(1)	PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		CTTCAGCTCCCTCTGCTTCTG	0.423			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""																																p.P444P			Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1332A	8						.						78.0	74.0	75.0					8																	17813022		1939	4132	6071	17857302	SO:0001819	synonymous_variant	5108	exon10				CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.1332C>A	8.37:g.17813022C>A		Somatic		Capture	Illumina HiSeq	Phase_I	17857302	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Silent	SNP	ENST00000519253.1	37																																																																																					0.423	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
LPL	4023	broad.mit.edu	37	8	19819726	19819726	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:19819726G>T	ENST00000311322.8	+	9	1893	c.1423G>T	c.(1423-1425)Ggc>Tgc	p.G475C		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	475					chylomicron remodeling (GO:0034371)|fatty acid biosynthetic process (GO:0006633)|lipoprotein metabolic process (GO:0042157)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of sequestering of triglyceride (GO:0010890)|response to cold (GO:0009409)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle remodeling (GO:0034372)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phospholipase activity (GO:0004620)|receptor binding (GO:0005102)|triglyceride binding (GO:0017129)|triglyceride lipase activity (GO:0004806)	p.G475C(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	AST-120(DB05269)|Tyloxapol(DB06439)	TAAGAAGTCAGGCTGGTGAGC	0.498																																					p.G475C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1423T	8						.						131.0	120.0	124.0					8																	19819726		2203	4300	6503	19864006	SO:0001583	missense	4023	exon9				CCDS6012.1	8p22	2012-10-02			ENSG00000175445	ENSG00000175445	3.1.1.34		6677	protein-coding gene	gene with protein product		609708		LIPD			Standard	NM_000237		Approved		uc003wzk.4	P06858	OTTHUMG00000036645	ENST00000311322.8:c.1423G>T	8.37:g.19819726G>T	ENSP00000309757:p.Gly475Cys	Somatic		Capture	Illumina HiSeq	Phase_I	19864006	NM_000237	B2R5T9|Q16282|Q16283|Q96FC4	Missense_Mutation	SNP	ENST00000311322.8	37	CCDS6012.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.708915	0.68615	.	.	ENSG00000175445	ENST00000311322;ENST00000535763	D	0.89123	-2.47	5.81	3.03	0.35002	.	0.881184	0.10230	N	0.699733	D	0.86661	0.5986	N	0.08118	0	0.46849	D	0.999220	D	0.89917	1.0	D	0.70935	0.971	T	0.83095	-0.0131	8	.	.	.	.	10.002	0.41935	0.229:0.0:0.771:0.0	.	475	P06858	LIPL_HUMAN	C	475;461	ENSP00000309757:G475C	.	G	+	1	0	LPL	19864006	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	2.234000	0.43035	0.804000	0.34136	0.655000	0.94253	GGC		0.498	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3		
LZTS1	11178	broad.mit.edu	37	8	20110664	20110664	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:20110664C>T	ENST00000381569.1	-	3	1135	c.778G>A	c.(778-780)Gag>Aag	p.E260K	LZTS1_ENST00000522290.1_Missense_Mutation_p.E260K|LZTS1_ENST00000265801.6_Missense_Mutation_p.E260K			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	260					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E260K(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		ATGCTGCACTCGTCCGTGGAG	0.632																																					p.E260K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G778A	8						.						58.0	53.0	55.0					8																	20110664		2198	4287	6485	20154944	SO:0001583	missense	11178	exon2			AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"""F37/Esophageal cancer-related gene-coding leucine-zipper motif"""			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.778G>A	8.37:g.20110664C>T	ENSP00000370981:p.Glu260Lys	Somatic		Capture	Illumina HiSeq	Phase_I	20154944	NM_021020	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Missense_Mutation	SNP	ENST00000381569.1	37	CCDS6015.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.804826	0.70682	.	.	ENSG00000061337	ENST00000381569;ENST00000265801;ENST00000522290;ENST00000360248	T;T;T	0.30182	1.9;1.9;1.54	5.63	4.75	0.60458	.	0.217233	0.48286	D	0.000195	T	0.45377	0.1339	M	0.79926	2.475	0.54753	D	0.999982	P;P	0.44260	0.83;0.704	P;B	0.46320	0.512;0.181	T	0.53514	-0.8428	10	0.66056	D	0.02	-33.3758	15.1256	0.72481	0.0:0.8508:0.1492:0.0	.	260;260	Q9Y250-4;Q9Y250	.;LZTS1_HUMAN	K	260	ENSP00000370981:E260K;ENSP00000265801:E260K;ENSP00000429263:E260K	ENSP00000265801:E260K	E	-	1	0	LZTS1	20154944	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	6.053000	0.71089	1.376000	0.46267	0.561000	0.74099	GAG		0.632	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020	
LGI3	203190	broad.mit.edu	37	8	22005884	22005884	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:22005884C>T	ENST00000306317.2	-	8	1725	c.1436G>A	c.(1435-1437)cGc>cAc	p.R479H	LGI3_ENST00000424267.2_Missense_Mutation_p.R455H	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	479					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)	p.R479H(1)		endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		TGCCAGGTAGCGGCGGCCACC	0.642																																					p.R479H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1436A	8						.						41.0	36.0	37.0					8																	22005884		2203	4300	6503	22061829	SO:0001583	missense	203190	exon8			AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.1436G>A	8.37:g.22005884C>T	ENSP00000302297:p.Arg479His	Somatic		Capture	Illumina HiSeq	Phase_I	22061829	NM_139278	A5PLP2|Q86TL4|Q8N296	Missense_Mutation	SNP	ENST00000306317.2	37	CCDS6025.1	.	.	.	.	.	.	.	.	.	.	C	10.99	1.506661	0.26949	.	.	ENSG00000168481	ENST00000306317;ENST00000424267	T;T	0.79141	-1.24;-1.24	5.19	5.19	0.71726	Six-bladed beta-propeller, TolB-like (1);	0.158912	0.47093	D	0.000249	T	0.55417	0.1919	N	0.01576	-0.805	0.34972	D	0.753273	D;D	0.61697	0.99;0.979	P;B	0.48738	0.588;0.433	T	0.63655	-0.6588	10	0.19147	T	0.46	-35.0029	9.7807	0.40647	0.0:0.9063:0.0:0.0937	.	455;479	A5PLP2;Q8N145	.;LGI3_HUMAN	H	479;455	ENSP00000302297:R479H;ENSP00000399121:R455H	ENSP00000302297:R479H	R	-	2	0	LGI3	22061829	0.990000	0.36364	1.000000	0.80357	0.998000	0.95712	1.889000	0.39718	2.396000	0.81511	0.561000	0.74099	CGC		0.642	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1		
RHOBTB2	23221	broad.mit.edu	37	8	22863640	22863640	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:22863640C>T	ENST00000251822.6	+	4	1001	c.464C>T	c.(463-465)gCt>gTt	p.A155V	RP11-875O11.1_ENST00000502083.2_RNA|RHOBTB2_ENST00000519685.1_Missense_Mutation_p.A177V|RHOBTB2_ENST00000523918.1_3'UTR|RP11-875O11.1_ENST00000523884.1_RNA|RHOBTB2_ENST00000522948.1_Missense_Mutation_p.A162V	NM_015178.2	NP_055993.2	Q9BYZ6	RHBT2_HUMAN	Rho-related BTB domain containing 2	155	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.A155V(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	31		Prostate(55;0.0513)|Breast(100;0.214)		Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)		GTCAACAGGGCTAGGCGACCC	0.602																																					p.A177V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C530T	8						.						142.0	136.0	138.0					8																	22863640		2203	4300	6503	22919585	SO:0001583	missense	23221	exon6			AF315385	CCDS6034.1, CCDS55210.1, CCDS55211.1	8p21.2	2013-01-08			ENSG00000008853	ENSG00000008853		"""BTB/POZ domain containing"""	18756	protein-coding gene	gene with protein product		607352				11222756	Standard	NM_001160036		Approved	KIAA0717, DBC2	uc011kzp.1	Q9BYZ6	OTTHUMG00000097827	ENST00000251822.6:c.464C>T	8.37:g.22863640C>T	ENSP00000251822:p.Ala155Val	Somatic		Capture	Illumina HiSeq	Phase_I	22919585	NM_001160036	A8K9Z8|D3DSR8|E9PBU2|E9PEI7|O94825|Q8N4A8|Q9BZK6	Missense_Mutation	SNP	ENST00000251822.6	37	CCDS6034.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634957	0.87760	.	.	ENSG00000008853	ENST00000519685;ENST00000524077;ENST00000522948;ENST00000251822	T;T;T;T	0.27890	2.91;1.64;2.91;2.91	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.45236	0.1332	L	0.35341	1.055	0.58432	D	0.999999	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.79108	0.987;0.987;0.992	T	0.18650	-1.0330	10	0.32370	T	0.25	.	17.682	0.88246	0.0:1.0:0.0:0.0	.	162;155;177	E9PEI7;Q9BYZ6;E9PBU2	.;RHBT2_HUMAN;.	V	177;177;162;155	ENSP00000427926:A177V;ENSP00000430785:A177V;ENSP00000429141:A162V;ENSP00000251822:A155V	ENSP00000251822:A155V	A	+	2	0	RHOBTB2	22919585	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.808000	0.86044	2.505000	0.84491	0.563000	0.77884	GCT		0.602	RHOBTB2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215101.2		
SLC25A37	51312	broad.mit.edu	37	8	23429120	23429120	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:23429120G>A	ENST00000519973.1	+	4	967	c.769G>A	c.(769-771)Gtc>Atc	p.V257I	FP15737_ENST00000399967.3_5'Flank	NM_016612.2	NP_057696.2	Q9NYZ2	MFRN1_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 37	257					iron ion homeostasis (GO:0055072)|mitochondrial iron ion transport (GO:0048250)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	iron ion transmembrane transporter activity (GO:0005381)	p.V257I(1)		NS(1)|endometrium(3)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Prostate(55;0.114)		Colorectal(74;0.0198)|COAD - Colon adenocarcinoma(73;0.0751)		CCCCCTGGACGTCTGTAAGAC	0.672																																					p.V257I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G769A	8						.						28.0	30.0	30.0					8																	23429120		1917	4097	6014	23485065	SO:0001583	missense	51312	exon4			AF495725	CCDS47828.1	8p21.2	2013-05-22	2012-03-29		ENSG00000147454	ENSG00000147454		"""Solute carriers"""	29786	protein-coding gene	gene with protein product	"""mitoferrin"""	610387	"""solute carrier family 25, member 37"""			16511496	Standard	XM_006716352		Approved	MSCP, MFRN, MFRN1	uc003xdo.3	Q9NYZ2	OTTHUMG00000163865	ENST00000519973.1:c.769G>A	8.37:g.23429120G>A	ENSP00000429200:p.Val257Ile	Somatic		Capture	Illumina HiSeq	Phase_I	23485065	NM_016612	A2RU93|Q53FT7|Q69YJ8|Q969S1|Q9P0J2	Missense_Mutation	SNP	ENST00000519973.1	37	CCDS47828.1	.	.	.	.	.	.	.	.	.	.	G	34	5.305863	0.95629	.	.	ENSG00000147454	ENST00000519973	D	0.82803	-1.65	5.8	5.8	0.92144	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.93194	0.7832	M	0.91768	3.24	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.94096	0.7357	10	0.87932	D	0	-12.414	18.6148	0.91299	0.0:0.0:1.0:0.0	.	257	Q9NYZ2	MFRN1_HUMAN	I	257	ENSP00000429200:V257I	ENSP00000429200:V257I	V	+	1	0	SLC25A37	23485065	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.476000	0.97823	2.740000	0.93945	0.650000	0.86243	GTC		0.672	SLC25A37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376039.1	NM_016612	
DOCK5	80005	broad.mit.edu	37	8	25159871	25159871	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:25159871C>T	ENST00000276440.7	+	10	921	c.877C>T	c.(877-879)Cgc>Tgc	p.R293C	DOCK5_ENST00000481100.1_Missense_Mutation_p.R293C	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	293					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.R293C(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		CATCCGGCCCCGCGTCAGCCT	0.567																																					p.R293C	Pancreas(145;34 1887 3271 10937 30165)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C877T	8						.						95.0	75.0	82.0					8																	25159871		2203	4300	6503	25215788	SO:0001583	missense	80005	exon10				CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.877C>T	8.37:g.25159871C>T	ENSP00000276440:p.Arg293Cys	Somatic		Capture	Illumina HiSeq	Phase_I	25215788	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.8|21.8	4.208423|4.208423	0.79240|0.79240	.|.	.|.	ENSG00000147459|ENSG00000147459	ENST00000444569|ENST00000481100;ENST00000276440	T|T;T	0.17054|0.18810	2.3|2.19;2.19	5.55|5.55	4.59|4.59	0.56863|0.56863	.|.	.|0.271361	.|0.28914	.|N	.|0.013737	T|T	0.39911|0.39911	0.1096|0.1096	M|M	0.66939|0.66939	2.045|2.045	0.54753|0.54753	D|D	0.999986|0.999986	.|D;D	.|0.76494	.|0.999;0.998	.|P;P	.|0.60886	.|0.88;0.816	T|T	0.21895|0.21895	-1.0232|-1.0232	7|10	0.54805|0.87932	T|D	0.06|0	.|.	13.0012|13.0012	0.58676|0.58676	0.2694:0.7306:0.0:0.0|0.2694:0.7306:0.0:0.0	.|.	.|68;293	.|Q68DL4;Q9H7D0	.|.;DOCK5_HUMAN	L|C	64|293	ENSP00000414125:P64L|ENSP00000429737:R293C;ENSP00000276440:R293C	ENSP00000414125:P64L|ENSP00000276440:R293C	P|R	+|+	2|1	0|0	DOCK5|DOCK5	25215788|25215788	0.733000|0.733000	0.28132|0.28132	1.000000|1.000000	0.80357|0.80357	0.861000|0.861000	0.49209|0.49209	1.789000|1.789000	0.38724|0.38724	2.607000|2.607000	0.88179|0.88179	0.650000|0.650000	0.86243|0.86243	CCG|CGC		0.567	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
PPP2R2A	5520	broad.mit.edu	37	8	26227751	26227751	+	Missense_Mutation	SNP	G	G	A	rs369862992		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:26227751G>A	ENST00000380737.3	+	10	1495	c.1166G>A	c.(1165-1167)cGc>cAc	p.R389H	PPP2R2A_ENST00000315985.7_Missense_Mutation_p.R399H	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	389					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)	p.R389H(1)		kidney(1)|large_intestine(2)|ovary(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;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		AATAAGCCTCGCACAGTTCTG	0.413																																					p.R399H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1196A	8						.	G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	78.0	75.0	76.0		1196,1166	4.4	1.0	8		76	0,8600		0,0,4300	no	missense,missense	PPP2R2A	NM_001177591.1,NM_002717.3	29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	399/458,389/448	26227751	1,13005	2203	4300	6503	26283668	SO:0001583	missense	5520	exon10			M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9304	protein-coding gene	gene with protein product	"""PP2A subunit B isoform alpha"""	604941	"""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"""			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.1166G>A	8.37:g.26227751G>A	ENSP00000370113:p.Arg389His	Somatic		Capture	Illumina HiSeq	Phase_I	26283668	NM_001177591	B2RBU8|B4E1T7|P50409|Q00007	Missense_Mutation	SNP	ENST00000380737.3	37	CCDS34867.1	.	.	.	.	.	.	.	.	.	.	G	10.42	1.345085	0.24426	2.27E-4	0.0	ENSG00000221914	ENST00000380737;ENST00000524169;ENST00000315985	T;T;T	0.46451	1.46;0.87;1.46	5.25	4.38	0.52667	WD40 repeat-like-containing domain (1);	0.267600	0.30392	U	0.009723	T	0.36468	0.0968	M	0.62154	1.92	0.40672	D	0.982222	B;B;P	0.43607	0.002;0.005;0.812	B;B;B	0.31812	0.001;0.005;0.136	T	0.42344	-0.9457	10	0.42905	T	0.14	-31.0147	14.2581	0.66065	0.0714:0.0:0.9285:0.0	.	399;389;390	B4E1T7;P63151;Q6ZP32	.;2ABA_HUMAN;.	H	389;168;399	ENSP00000370113:R389H;ENSP00000430320:R168H;ENSP00000325074:R399H	ENSP00000325074:R399H	R	+	2	0	PPP2R2A	26283668	0.996000	0.38824	1.000000	0.80357	0.865000	0.49528	4.218000	0.58554	1.587000	0.49959	-0.136000	0.14681	CGC		0.413	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717	
SCARA5	286133	broad.mit.edu	37	8	27779210	27779210	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:27779210G>A	ENST00000354914.3	-	4	1279	c.794C>T	c.(793-795)gCg>gTg	p.A265V	SCARA5_ENST00000301906.4_Missense_Mutation_p.A222V|SCARA5_ENST00000380385.2_Intron|SCARA5_ENST00000518030.1_Missense_Mutation_p.A222V|SCARA5_ENST00000524352.1_Missense_Mutation_p.A265V	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	265					cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)	p.A265V(1)		central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		GCCTACGTGCGCCAGGCGCAG	0.687																																					p.A265V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C794T	8						.						52.0	37.0	42.0					8																	27779210		2202	4300	6502	27835129	SO:0001583	missense	286133	exon4			AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"""scavenger receptor class A, member 5 (putative)"""			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.794C>T	8.37:g.27779210G>A	ENSP00000346990:p.Ala265Val	Somatic		Capture	Illumina HiSeq	Phase_I	27835129	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	Missense_Mutation	SNP	ENST00000354914.3	37	CCDS6064.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.269942	0.23221	.	.	ENSG00000168079	ENST00000354914;ENST00000517320;ENST00000524352;ENST00000518030;ENST00000301906	D;D;D;D	0.90444	-2.32;-2.67;-2.62;-2.62	4.76	-0.796	0.10912	.	0.387908	0.26935	N	0.021754	T	0.67534	0.2903	N	0.01267	-0.92	0.09310	N	0.999995	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.60875	-0.7176	10	0.07813	T	0.8	.	8.4848	0.33065	0.5957:0.0:0.4043:0.0	.	265;222;265	Q6ZMJ2-2;Q6ZMJ2-3;Q6ZMJ2	.;.;SCAR5_HUMAN	V	265;65;265;222;222	ENSP00000346990:A265V;ENSP00000428663:A265V;ENSP00000430713:A222V;ENSP00000301906:A222V	ENSP00000301906:A222V	A	-	2	0	SCARA5	27835129	0.058000	0.20735	0.689000	0.30133	0.861000	0.49209	1.922000	0.40045	-0.424000	0.07382	0.456000	0.33151	GCG		0.687	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833	
ZNF395	55893	broad.mit.edu	37	8	28214287	28214287	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:28214287G>A	ENST00000344423.5	-	4	614	c.483C>T	c.(481-483)gaC>gaT	p.D161D	ZNF395_ENST00000523202.1_Silent_p.D161D|ZNF395_ENST00000523095.1_Silent_p.D161D	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	161					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D161D(1)		cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		TTTCCACTGCGTCCGACTTCC	0.572																																					p.D161D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C483T	8						.						121.0	110.0	114.0					8																	28214287		2203	4300	6503	28270206	SO:0001819	synonymous_variant	55893	exon4			AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"""Zinc fingers, C2H2-type"""	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.483C>T	8.37:g.28214287G>A		Somatic		Capture	Illumina HiSeq	Phase_I	28270206	NM_018660	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Silent	SNP	ENST00000344423.5	37	CCDS6067.1																																																																																				0.572	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1		
KIF13B	23303	broad.mit.edu	37	8	28989877	28989877	+	Missense_Mutation	SNP	C	C	T	rs12549991		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:28989877C>T	ENST00000524189.1	-	23	2928	c.2890G>A	c.(2890-2892)Gcc>Acc	p.A964T	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	964					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)	p.A964T(1)		endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		TCCCACAGGGCGGGGTTTTTC	0.393																																					p.A964T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2890A	8						.						77.0	81.0	80.0					8																	28989877		1808	4072	5880	29045796	SO:0001583	missense	23303	exon23			AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"""Kinesins"""	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.2890G>A	8.37:g.28989877C>T	ENSP00000427900:p.Ala964Thr	Somatic		Capture	Illumina HiSeq	Phase_I	29045796	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	37	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.193582	0.38707	.	.	ENSG00000197892	ENST00000524189	T	0.76709	-1.04	4.63	3.76	0.43208	.	0.052144	0.85682	D	0.000000	T	0.59211	0.2177	N	0.11756	0.17	0.80722	D	1	B	0.19583	0.037	B	0.16722	0.016	T	0.52873	-0.8517	10	0.26408	T	0.33	.	11.2887	0.49237	0.0:0.8462:0.0:0.1538	.	964	F8VPJ2	.	T	964	ENSP00000427900:A964T	ENSP00000427900:A964T	A	-	1	0	KIF13B	29045796	0.989000	0.36119	1.000000	0.80357	0.664000	0.39144	2.205000	0.42770	1.180000	0.42898	0.467000	0.42956	GCC		0.393	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1		
DUSP4	1846	broad.mit.edu	37	8	29194905	29194905	+	Missense_Mutation	SNP	G	G	A	rs375453930		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:29194905G>A	ENST00000240100.2	-	4	1212	c.823C>T	c.(823-825)Cgc>Tgc	p.R275C	DUSP4_ENST00000240101.2_Missense_Mutation_p.R184C	NM_001394.6	NP_001385.1	Q13115	DUS4_HUMAN	dual specificity phosphatase 4	275	Tyrosine-protein phosphatase.				endoderm formation (GO:0001706)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein dephosphorylation (GO:0006470)|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)	nucleoplasm (GO:0005654)|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)|protein tyrosine/threonine phosphatase activity (GO:0008330)	p.R275C(1)		endometrium(1)|large_intestine(1)|lung(4)	6				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		ACCAGCACGCGCCCACGGCAG	0.657																																					p.R275C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C823T	8						.	G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	49.0	46.0	47.0		823,550	2.8	0.5	8		47	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense	DUSP4	NM_001394.6,NM_057158.3	180,180	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	275/395,184/304	29194905	1,13001	2203	4298	6501	29250824	SO:0001583	missense	1846	exon4			U21108	CCDS6072.1, CCDS6073.1	8p12-p11	2011-06-09			ENSG00000120875	ENSG00000120875		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3070	protein-coding gene	gene with protein product	"""VH1 homologous phosphatase 2"", ""MAP kinase phosphatase 2"""	602747				7535768, 9205128	Standard	NM_001394		Approved	HVH2, MKP-2, TYP	uc003xhm.3	Q13115	OTTHUMG00000133395	ENST00000240100.2:c.823C>T	8.37:g.29194905G>A	ENSP00000240100:p.Arg275Cys	Somatic		Capture	Illumina HiSeq	Phase_I	29250824	NM_001394	B2RBU5|D3DSU4|G5E930|Q13524	Missense_Mutation	SNP	ENST00000240100.2	37	CCDS6072.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.114640	0.77210	0.0	1.16E-4	ENSG00000120875	ENST00000240100;ENST00000240101	T;T	0.61274	0.12;0.12	4.67	2.81	0.32909	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.050282	0.85682	N	0.000000	T	0.67116	0.2859	L	0.56124	1.755	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.66027	-0.6025	10	0.72032	D	0.01	.	7.8818	0.29627	0.0888:0.0:0.7507:0.1605	.	275;184	Q13115;G5E930	DUS4_HUMAN;.	C	275;184	ENSP00000240100:R275C;ENSP00000240101:R184C	ENSP00000240100:R275C	R	-	1	0	DUSP4	29250824	1.000000	0.71417	0.525000	0.27900	0.982000	0.71751	3.950000	0.56676	0.611000	0.30052	0.462000	0.41574	CGC		0.657	DUSP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257249.1	NM_001394	
LEPROTL1	23484	broad.mit.edu	37	8	29961958	29961958	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:29961958G>A	ENST00000321250.8	+	3	350	c.235G>A	c.(235-237)Gtg>Atg	p.V79M	LEPROTL1_ENST00000523116.1_Missense_Mutation_p.V79M|LEPROTL1_ENST00000442880.2_Missense_Mutation_p.V79M|LEPROTL1_ENST00000518001.1_Missense_Mutation_p.V18M|LEPROTL1_ENST00000518192.1_Missense_Mutation_p.V102M	NM_015344.2	NP_056159.2	O95214	LERL1_HUMAN	leptin receptor overlapping transcript-like 1	79						integral component of membrane (GO:0016021)		p.V79M(1)		endometrium(1)|kidney(1)|large_intestine(3)	5				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		GGGCATTGTCGTGTCAGCTTT	0.368																																					p.V79M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G235A	8						.						201.0	186.0	191.0					8																	29961958		2203	4300	6503	30081500	SO:0001583	missense	23484	exon3			AF063605	CCDS6075.1, CCDS47834.1	8p12	2014-09-11			ENSG00000104660	ENSG00000104660			6555	protein-coding gene	gene with protein product		607338				11342119	Standard	NM_015344		Approved	my047, Vps55	uc003xhx.2	O95214	OTTHUMG00000163820	ENST00000321250.8:c.235G>A	8.37:g.29961958G>A	ENSP00000314625:p.Val79Met	Somatic		Capture	Illumina HiSeq	Phase_I	30081500	NM_001128208	E9PHP8|Q9BW48	Missense_Mutation	SNP	ENST00000321250.8	37	CCDS6075.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.862256	0.71949	.	.	ENSG00000104660	ENST00000321250;ENST00000518001;ENST00000520682;ENST00000442880;ENST00000523116;ENST00000518192	.	.	.	5.79	5.79	0.91817	.	0.060619	0.64402	D	0.000003	T	0.78984	0.4370	M	0.71871	2.18	0.51233	D	0.999914	D;P	0.89917	1.0;0.891	D;P	0.77004	0.989;0.713	T	0.80341	-0.1423	9	0.87932	D	0	.	17.5131	0.87765	0.0:0.0:1.0:0.0	.	79;79	E9PHP8;O95214	.;LERL1_HUMAN	M	79;18;79;79;79;102	.	ENSP00000314625:V79M	V	+	1	0	LEPROTL1	30081500	1.000000	0.71417	0.999000	0.59377	0.779000	0.44077	6.028000	0.70889	2.722000	0.93159	0.591000	0.81541	GTG		0.368	LEPROTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375771.2		
TTI2	80185	broad.mit.edu	37	8	33361294	33361294	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:33361294C>T	ENST00000431156.2	-	5	1705	c.1087G>A	c.(1087-1089)Gca>Aca	p.A363T	TTI2_ENST00000520636.1_Missense_Mutation_p.A332T|TTI2_ENST00000360742.5_Missense_Mutation_p.A363T|TTI2_ENST00000519356.1_5'UTR	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	363								p.A363T(1)									AGGTTTCTTGCGTAGGTCCTG	0.517																																					p.A363T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1087A	8						.						42.0	37.0	39.0					8																	33361294		2203	4300	6503	33480836	SO:0001583	missense	80185	exon4			AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"""chromosome 8 open reading frame 41"", ""Tel2 interacting protein 2 homolog (S. pombe)"""	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.1087G>A	8.37:g.33361294C>T	ENSP00000411169:p.Ala363Thr	Somatic		Capture	Illumina HiSeq	Phase_I	33480836	NM_025115	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	37	CCDS6090.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.153062	0.78001	.	.	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636	T;T;T	0.78003	-0.24;-0.24;-1.14	5.5	4.61	0.57282	.	0.063153	0.64402	D	0.000008	D	0.84392	0.5462	M	0.67953	2.075	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.58520	0.84;0.84	D	0.86279	0.1666	10	0.62326	D	0.03	-12.0214	15.474	0.75461	0.1398:0.8602:0.0:0.0	.	363;332	Q6NXR4;E5RIH5	TTI2_HUMAN;.	T	363;363;363;332	ENSP00000353971:A363T;ENSP00000411169:A363T;ENSP00000428401:A332T	ENSP00000353971:A363T	A	-	1	0	C8orf41	33480836	1.000000	0.71417	0.088000	0.20740	0.554000	0.35429	4.686000	0.61700	1.532000	0.49169	0.650000	0.86243	GCA		0.517	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115	
UNC5D	137970	broad.mit.edu	37	8	35541226	35541226	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:35541226G>A	ENST00000404895.2	+	5	1060	c.732G>A	c.(730-732)tcG>tcA	p.S244S	UNC5D_ENST00000420357.1_Silent_p.S244S|UNC5D_ENST00000453357.2_Silent_p.S239S|UNC5D_ENST00000416672.1_Silent_p.S244S|UNC5D_ENST00000287272.2_Silent_p.S244S	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	244	Ig-like C2-type.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|pyramidal neuron differentiation (GO:0021859)|regulation of neuron migration (GO:2001222)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.S239S(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(56)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(6)|urinary_tract(2)	112				READ - Rectum adenocarcinoma(1;1.31e-05)|Colorectal(1;0.000723)		GAAGCCTGTCGGCCACTGTTG	0.507																																					p.S244S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G732A	8						.						53.0	47.0	49.0					8																	35541226		2203	4300	6503	35660768	SO:0001819	synonymous_variant	137970	exon5			AB055056	CCDS6093.2	8p12	2013-01-11			ENSG00000156687	ENSG00000156687		"""Immunoglobulin superfamily / I-set domain containing"""	18634	protein-coding gene	gene with protein product						18402767	Standard	NM_080872		Approved	KIAA1777, Unc5h4	uc003xjr.2	Q6UXZ4	OTTHUMG00000157145	ENST00000404895.2:c.732G>A	8.37:g.35541226G>A		Somatic		Capture	Illumina HiSeq	Phase_I	35660768	NM_080872	Q8WYP7	Silent	SNP	ENST00000404895.2	37	CCDS6093.2																																																																																				0.507	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2		
FGFR1	2260	broad.mit.edu	37	8	38314905	38314905	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:38314905G>A	ENST00000447712.2	-	2	1001	c.60C>T	c.(58-60)acC>acT	p.T20T	FGFR1_ENST00000341462.5_Silent_p.T20T|FGFR1_ENST00000397103.1_Silent_p.T20T|FGFR1_ENST00000326324.6_Silent_p.T20T|FGFR1_ENST00000532791.1_Silent_p.T20T|FGFR1_ENST00000356207.5_Silent_p.T20T|FGFR1_ENST00000425967.3_Silent_p.T53T|FGFR1_ENST00000397108.4_Silent_p.T20T|FGFR1_ENST00000397091.5_Silent_p.T20T|FGFR1_ENST00000335922.5_5'UTR|FGFR1_ENST00000397113.2_Silent_p.T20T	NM_001174063.1|NM_015850.3|NM_023110.2	NP_001167534.1|NP_056934.2|NP_075598.2	P11362	FGFR1_HUMAN	fibroblast growth factor receptor 1	20					angiogenesis (GO:0001525)|auditory receptor cell development (GO:0060117)|axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell maturation (GO:0048469)|cell migration (GO:0016477)|chondrocyte differentiation (GO:0002062)|chordate embryonic development (GO:0043009)|embryonic limb morphogenesis (GO:0030326)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lung-associated mesenchyme development (GO:0060484)|MAPK cascade (GO:0000165)|mesenchymal cell differentiation (GO:0048762)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|outer ear morphogenesis (GO:0042473)|paraxial mesoderm development (GO:0048339)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|regulation of cell differentiation (GO:0045595)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of lateral mesodermal cell fate specification (GO:0048378)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ventricular zone neuroblast division (GO:0021847)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.T20T(3)	FGFR1/ZNF703(2)	breast(2)|central_nervous_system(7)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	50	all_cancers(2;9.05e-47)|all_epithelial(2;2.64e-50)|all_lung(3;1.71e-23)|Lung NSC(2;3.61e-23)|Colorectal(12;0.000442)	Breast(189;1.48e-05)|all_lung(54;0.00354)|Lung NSC(58;0.0138)|Hepatocellular(245;0.065)	Epithelial(3;3.96e-34)|all cancers(3;3.06e-30)|BRCA - Breast invasive adenocarcinoma(5;2.28e-21)|COAD - Colon adenocarcinoma(9;0.24)		Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	ACGGCCTAGCGGTGCAGAGTG	0.617		1	T	"""BCR, FOP, ZNF198, CEP1"""	"""MPD, NHL"""		"""Pfeiffer syndrome, Kallman syndrome"""																														p.T20T	Melanoma(146;1153 1840 21453 21841 43625)		Dom	yes		8	8p11.2-p11.1	2260	fibroblast growth factor receptor 1	yes	L	.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C60T	8						.						68.0	60.0	62.0					8																	38314905		2203	4300	6503	38434062	SO:0001819	synonymous_variant	2260	exon2			M34185	CCDS6107.2, CCDS43730.1, CCDS43731.1, CCDS43732.1, CCDS55221.1, CCDS55222.1, CCDS55223.1	8p11.23-p11.22	2014-04-03	2008-08-01		ENSG00000077782	ENSG00000077782	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3688	protein-coding gene	gene with protein product	"""Pfeiffer syndrome"""	136350	"""fms-related tyrosine kinase 2"""	FLT2, KAL2		2162671	Standard	NM_015850		Approved	H2, H3, H4, H5, CEK, FLG, BFGFR, N-SAM, CD331	uc011lbu.2	P11362	OTTHUMG00000147366	ENST00000447712.2:c.60C>T	8.37:g.38314905G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38434062	NM_001174065	A8K6T9|A8K8V5|C1KBH8|P17049|Q02063|Q02065|Q14306|Q14307|Q53H63|Q59H40|Q5BJG2|Q8N685|Q9UD50|Q9UDF0|Q9UDF1|Q9UDF2	Silent	SNP	ENST00000447712.2	37	CCDS6107.2																																																																																				0.617	FGFR1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
TACC1	6867	broad.mit.edu	37	8	38677516	38677516	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:38677516G>A	ENST00000317827.4	+	3	1133	c.754G>A	c.(754-756)Gct>Act	p.A252T	TACC1_ENST00000330691.6_Intron|TACC1_ENST00000379931.3_Missense_Mutation_p.A252T|TACC1_ENST00000348567.4_Intron|TACC1_ENST00000520611.1_5'Flank|TACC1_ENST00000520340.1_Missense_Mutation_p.A216T|TACC1_ENST00000522752.1_Intron|TACC1_ENST00000520615.1_Missense_Mutation_p.A57T|TACC1_ENST00000518415.1_Missense_Mutation_p.A207T|TACC1_ENST00000276520.8_Intron|TACC1_ENST00000443286.2_Missense_Mutation_p.A268T|TACC1_ENST00000520973.1_Missense_Mutation_p.A57T|TACC1_ENST00000519416.1_Missense_Mutation_p.A57T	NM_006283.2	NP_006274.2	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing protein 1	252	Interaction with TDRD7.|Interaction with YEATS4.|SPAZ 1.				cell cycle (GO:0007049)|cell division (GO:0051301)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.A252T(2)		breast(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(3)	17		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			AGACACCAACGCTGCTGTGGA	0.537																																					p.A252T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G754A	8						.						42.0	42.0	42.0					8																	38677516		2203	4299	6502	38796673	SO:0001583	missense	6867	exon3			AF049910	CCDS6109.1, CCDS47845.1, CCDS55224.1	8p11	2012-12-20			ENSG00000147526	ENSG00000147526			11522	protein-coding gene	gene with protein product		605301					Standard	NM_006283		Approved		uc010lwp.3	O75410	OTTHUMG00000164018	ENST00000317827.4:c.754G>A	8.37:g.38677516G>A	ENSP00000321703:p.Ala252Thr	Somatic		Capture	Illumina HiSeq	Phase_I	38796673	NM_006283	B2RBD9|D3DSX6|Q6Y687|Q86YG7|Q8IUJ2|Q8IUJ3|Q8IUJ4|Q8IZG2|Q8NEY7|Q9UPP9	Missense_Mutation	SNP	ENST00000317827.4	37	CCDS6109.1	.	.	.	.	.	.	.	.	.	.	G	0.651	-0.809591	0.02798	.	.	ENSG00000147526	ENST00000519416;ENST00000520615;ENST00000443388;ENST00000443286;ENST00000518415;ENST00000522904;ENST00000317827;ENST00000379931;ENST00000520973;ENST00000521935;ENST00000524193	T;T;T;T;T;T;T;T;T;T	0.30182	2.98;2.98;3.16;3.16;2.98;3.16;3.15;2.98;1.65;1.54	5.27	-10.5	0.00291	.	2.477800	0.01232	N	0.008372	T	0.12902	0.0313	N	0.16478	0.41	0.09310	N	1	B;B;B;B;B;B;B;B	0.09022	0.0;0.0;0.002;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.001;0.0;0.0;0.0	T	0.10989	-1.0606	10	0.21014	T	0.42	1.17	2.6314	0.04946	0.23:0.2455:0.3639:0.1605	.	57;57;57;268;252;252;57;207	B7Z3G3;E7EVI4;B4DH49;B4E302;O75410-2;O75410;E7ET87;O75410-7	.;.;.;.;.;TACC1_HUMAN;.;.	T	57;57;57;268;207;224;252;252;57;57;57	ENSP00000428687:A57T;ENSP00000428450:A57T;ENSP00000393647:A268T;ENSP00000428706:A207T;ENSP00000430355:A224T;ENSP00000321703:A252T;ENSP00000369263:A252T;ENSP00000430959:A57T;ENSP00000428175:A57T;ENSP00000429330:A57T	ENSP00000321703:A252T	A	+	1	0	TACC1	38796673	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.268000	0.02836	-1.619000	0.01566	-1.311000	0.01308	GCT		0.537	TACC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376768.1	NM_006283	
ADAM9	8754	broad.mit.edu	37	8	38934836	38934836	+	Missense_Mutation	SNP	G	G	A	rs138482520		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:38934836G>A	ENST00000487273.2	+	16	1865	c.1787G>A	c.(1786-1788)cGa>cAa	p.R596Q	ADAM9_ENST00000484143.1_3'UTR	NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	596	Cys-rich.				activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.R596Q(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			ACGCCTAGTCGAGGCACCAAA	0.438													G|||	1	0.000199681	0.0	0.0	5008	,	,		14302	0.0		0.001	False		,,,				2504	0.0				p.R596Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1787A	8						.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	119.0	112.0	114.0		1787	1.8	0.2	8	dbSNP_134	114	0,8600		0,0,4300	no	missense	ADAM9	NM_003816.2	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	596/820	38934836	1,13005	2203	4300	6503	39053993	SO:0001583	missense	8754	exon16			U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"""ADAM metallopeptidase domain containing"""	216	protein-coding gene	gene with protein product	"""meltrin gamma"""	602713	"""a disintegrin and metalloproteinase domain 9 (meltrin gamma)"", ""cone rod dystrophy 9"""	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.1787G>A	8.37:g.38934836G>A	ENSP00000419446:p.Arg596Gln	Somatic		Capture	Illumina HiSeq	Phase_I	39053993	NM_003816	B7ZLN7|Q10718|Q8NFM6	Missense_Mutation	SNP	ENST00000487273.2	37	CCDS6112.1	.	.	.	.	.	.	.	.	.	.	G	7.312	0.615215	0.14129	2.27E-4	0.0	ENSG00000168615	ENST00000487273	T	0.22134	1.97	5.55	1.78	0.24846	ADAM, cysteine-rich (2);	0.663371	0.15992	N	0.234779	T	0.10294	0.0252	N	0.11131	0.1	0.09310	N	1	B	0.06786	0.001	B	0.12837	0.008	T	0.36529	-0.9744	10	0.18276	T	0.48	.	10.0638	0.42290	0.4684:0.0:0.5316:0.0	.	596	Q13443	ADAM9_HUMAN	Q	596	ENSP00000419446:R596Q	ENSP00000369249:R596Q	R	+	2	0	ADAM9	39053993	0.001000	0.12720	0.153000	0.22517	0.851000	0.48451	0.083000	0.14871	0.111000	0.17947	0.557000	0.71058	CGA		0.438	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2		
ANK1	286	broad.mit.edu	37	8	41551436	41551436	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:41551436C>T	ENST00000347528.4	-	29	3595	c.3512G>A	c.(3511-3513)cGc>cAc	p.R1171H	ANK1_ENST00000396942.1_Missense_Mutation_p.R1171H|ANK1_ENST00000265709.8_Missense_Mutation_p.R1212H|ANK1_ENST00000352337.4_Missense_Mutation_p.R1171H|ANK1_ENST00000289734.7_Missense_Mutation_p.R1171H|ANK1_ENST00000396945.1_Missense_Mutation_p.R1171H|ANK1_ENST00000379758.2_Missense_Mutation_p.R1171H	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	1171	ZU5 2. {ECO:0000255|PROSITE- ProRule:PRU00485}.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.R1171H(1)		breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			GCAAAGCAGGCGCAGGCTGGT	0.647																																					p.R1171H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3512A	8						.						31.0	28.0	29.0					8																	41551436		2203	4300	6503	41670593	SO:0001583	missense	286	exon29			M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.3512G>A	8.37:g.41551436C>T	ENSP00000339620:p.Arg1171His	Somatic		Capture	Illumina HiSeq	Phase_I	41670593	NM_020475	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	37	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	C	35	5.421819	0.96111	.	.	ENSG00000029534	ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	T;T;T;T;T;T;T	0.73469	-0.72;-0.72;-0.69;-0.68;-0.69;-0.67;-0.75	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.87018	0.6073	M	0.80183	2.485	0.80722	D	1	D;D;D;P;D;D	0.89917	0.988;0.996;0.994;0.914;0.988;1.0	D;P;P;P;D;D	0.73708	0.91;0.821;0.677;0.498;0.91;0.981	D	0.88810	0.3291	10	0.87932	D	0	.	18.7318	0.91738	0.0:1.0:0.0:0.0	.	1212;1171;1171;1171;1171;487	P16157-21;P16157-4;P16157;P16157-5;P16157-3;B3KX39	.;.;ANK1_HUMAN;.;.;.	H	1171;1171;1171;1171;1171;1171;1212;1171	ENSP00000339620:R1171H;ENSP00000289734:R1171H;ENSP00000369082:R1171H;ENSP00000380149:R1171H;ENSP00000380147:R1171H;ENSP00000309131:R1171H;ENSP00000265709:R1212H	ENSP00000265709:R1212H	R	-	2	0	ANK1	41670593	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.794000	0.85869	2.493000	0.84123	0.313000	0.20887	CGC		0.647	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
SLC20A2	6575	broad.mit.edu	37	8	42294776	42294776	+	Silent	SNP	G	G	A	rs115234947	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:42294776G>A	ENST00000342228.3	-	8	1623	c.1254C>T	c.(1252-1254)ggC>ggT	p.G418G	SLC20A2_ENST00000520179.1_Silent_p.G418G|SLC20A2_ENST00000520262.1_Silent_p.G418G	NM_006749.4	NP_006740.1	Q08357	S20A2_HUMAN	solute carrier family 20 (phosphate transporter), member 2	418					ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic phosphate transmembrane transporter activity (GO:0005315)|receptor activity (GO:0004872)|sodium:phosphate symporter activity (GO:0005436)|virus receptor activity (GO:0001618)	p.G418G(1)		breast(1)|endometrium(6)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|stomach(1)	26	all_lung(13;8.33e-12)|Lung NSC(13;1.41e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;5.73e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00419)|Lung(22;0.0302)|LUSC - Lung squamous cell carcinoma(45;0.0869)			ACACGGTGTCGCCCACCAGCT	0.632													G|||	108	0.0215655	0.0809	0.0014	5008	,	,		17338	0.0		0.0	False		,,,				2504	0.0				p.G418G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1254T	8						.	G		254,4152	146.5+/-181.1	7,240,1956	69.0	63.0	65.0		1254	-11.7	0.0	8	dbSNP_132	65	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	SLC20A2	NM_006749.3		7,245,6251	AA,AG,GG		0.0581,5.7649,1.9914		418/653	42294776	259,12747	2203	4300	6503	42413933	SO:0001819	synonymous_variant	6575	exon8				CCDS6132.1	8p11.21	2013-05-22			ENSG00000168575	ENSG00000168575		"""Solute carriers"""	10947	protein-coding gene	gene with protein product		158378		MLVAR, GLVR2		7745689, 16790504	Standard	NM_001257180		Approved	PiT-2, Glvr-2	uc010lxm.4	Q08357	OTTHUMG00000164169	ENST00000342228.3:c.1254C>T	8.37:g.42294776G>A		Somatic		Capture	Illumina HiSeq	Phase_I	42413933	NM_006749		Silent	SNP	ENST00000342228.3	37	CCDS6132.1																																																																																				0.632	SLC20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377578.1		
POMK	84197	broad.mit.edu	37	8	42958821	42958821	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:42958821G>A	ENST00000331373.5	+	4	385	c.130G>A	c.(130-132)Gct>Act	p.A44T		NM_001277971.1|NM_032237.3	NP_001264900.1|NP_115613.1	Q9H5K3	SG196_HUMAN	protein-O-mannose kinase	44					brain development (GO:0007420)|carbohydrate phosphorylation (GO:0046835)|learning or memory (GO:0007611)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|protein O-linked glycosylation (GO:0006493)|sensory perception of pain (GO:0019233)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|carbohydrate kinase activity (GO:0019200)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)|protein kinase activity (GO:0004672)	p.A44T(1)									CTTCTTCATCGCTCCTCGACA	0.577																																					p.A44T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G130A	8						.						167.0	137.0	147.0					8																	42958821		2203	4300	6503	43077978	SO:0001583	missense	84197	exon4				CCDS6141.1	8p11.21	2013-08-22			ENSG00000185900	ENSG00000185900			26267	protein-coding gene	gene with protein product		615247				16879967, 23519211	Standard	NM_001277971		Approved	FLJ23356, SgK196		Q9H5K3	OTTHUMG00000164100	ENST00000331373.5:c.130G>A	8.37:g.42958821G>A	ENSP00000331258:p.Ala44Thr	Somatic		Capture	Illumina HiSeq	Phase_I	43077978	NM_032237		Missense_Mutation	SNP	ENST00000331373.5	37	CCDS6141.1	.	.	.	.	.	.	.	.	.	.	G	8.754	0.921955	0.17982	.	.	ENSG00000185900	ENST00000518991;ENST00000331373	T;T	0.69806	-0.43;-0.43	5.16	-1.84	0.07809	.	0.663946	0.15744	N	0.246754	T	0.33498	0.0865	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.14172	-1.0482	10	0.13470	T	0.59	-14.3861	2.3743	0.04338	0.1414:0.1445:0.4517:0.2623	.	44	Q9H5K3	SG196_HUMAN	T	44	ENSP00000429090:A44T;ENSP00000331258:A44T	ENSP00000331258:A44T	A	+	1	0	AC113191.1	43077978	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.227000	0.09126	-0.321000	0.08627	-0.535000	0.04281	GCT		0.577	POMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377291.2	NM_032237	
HGSNAT	138050	broad.mit.edu	37	8	43037306	43037306	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:43037306G>A	ENST00000458501.2	+	11	1115	c.1115G>A	c.(1114-1116)cGc>cAc	p.R372H	HGSNAT_ENST00000379644.4_Missense_Mutation_p.R344H|HGSNAT_ENST00000297798.7_Missense_Mutation_p.R76H|HGSNAT_ENST00000521576.1_Missense_Mutation_p.R61H			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	372			R -> C (in MPS3C; results in a negligible amount of protein synthesis and very low enzyme activity; retained in the endoplasmic reticulum). {ECO:0000269|PubMed:17033958, ECO:0000269|PubMed:18024218, ECO:0000269|PubMed:19479962}.|R -> H (in MPS3C; Retained in the endoplasmic reticulum and loss of enzymatic activity). {ECO:0000269|PubMed:17033958}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lysosomal transport (GO:0007041)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	heparan-alpha-glucosaminide N-acetyltransferase activity (GO:0015019)|transferase activity, transferring acyl groups (GO:0016746)	p.R372H(1)|p.R76H(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(6)	13	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			GACAAGGTGCGCATTCCTGGT	0.493																																					p.R344H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1031A	8	GRCh37	CM065258	HGSNAT	M		.						415.0	416.0	416.0					8																	43037306		2121	4233	6354	43156463	SO:0001583	missense	138050	exon11				CCDS47852.1	8p11.1	2011-11-16	2006-09-05	2006-08-16	ENSG00000165102	ENSG00000165102	2.3.1.78		26527	protein-coding gene	gene with protein product		610453	"""transmembrane protein 76"""	TMEM76		17033958, 16960811	Standard	NM_152419		Approved	FLJ32731, HGNAT	uc003xpx.4	Q68CP4	OTTHUMG00000164102	ENST00000458501.2:c.1115G>A	8.37:g.43037306G>A	ENSP00000389524:p.Arg372His	Somatic		Capture	Illumina HiSeq	Phase_I	43156463	NM_152419	B4E2V0	Missense_Mutation	SNP	ENST00000458501.2	37		.	.	.	.	.	.	.	.	.	.	G	23.9	4.466195	0.84425	.	.	ENSG00000165102	ENST00000458501;ENST00000379644;ENST00000522082;ENST00000521576;ENST00000297798	D;D;D;D;D	0.91945	-2.94;-2.94;-2.94;-2.13;-2.13	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.97269	0.9107	H	0.96269	3.795	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.98150	1.0441	10	0.87932	D	0	-6.3407	14.4965	0.67691	0.0:0.0:1.0:0.0	.	372	Q68CP4	HGNAT_HUMAN	H	372;344;91;61;76	ENSP00000389524:R372H;ENSP00000368965:R344H;ENSP00000430151:R91H;ENSP00000429029:R61H;ENSP00000297798:R76H	ENSP00000297798:R76H	R	+	2	0	HGSNAT	43156463	1.000000	0.71417	0.831000	0.32960	0.851000	0.48451	7.754000	0.85163	2.562000	0.86427	0.650000	0.86243	CGC		0.493	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038	
PRKDC	5591	broad.mit.edu	37	8	48736523	48736523	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:48736523G>A	ENST00000314191.2	-	65	8871	c.8815C>T	c.(8815-8817)Cgt>Tgt	p.R2939C	PRKDC_ENST00000338368.3_Missense_Mutation_p.R2939C|PRKDC_ENST00000523565.1_5'UTR	NM_006904.6	NP_008835.5	P78527	PRKDC_HUMAN	protein kinase, DNA-activated, catalytic polypeptide	2940	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.|KIP-binding.				B cell lineage commitment (GO:0002326)|brain development (GO:0007420)|cellular protein modification process (GO:0006464)|cellular response to insulin stimulus (GO:0032869)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|ectopic germ cell programmed cell death (GO:0035234)|heart development (GO:0007507)|immunoglobulin V(D)J recombination (GO:0033152)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of protein phosphorylation (GO:0001933)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|pro-B cell differentiation (GO:0002328)|protein destabilization (GO:0031648)|regulation of circadian rhythm (GO:0042752)|response to gamma radiation (GO:0010332)|rhythmic process (GO:0048511)|signal transduction involved in mitotic G1 DNA damage checkpoint (GO:0072431)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell receptor V(D)J recombination (GO:0033153)|telomere maintenance (GO:0000723)	cytosol (GO:0005829)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription factor binding (GO:0008134)	p.R2940C(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(9)|cervix(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(30)|lung(56)|ovary(6)|pancreas(1)|prostate(8)|skin(7)	147		all_cancers(86;0.0336)|all_epithelial(80;0.00111)|Lung NSC(129;0.00363)|all_lung(136;0.00391)			Caffeine(DB00201)	AAAATCCCACGGAGGACGTCG	0.363								Non-homologous end-joining																													p.S2939S	Esophageal Squamous(79;1091 1253 12329 31680 40677)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C8817T	8						.						104.0	96.0	98.0					8																	48736523		1834	4092	5926	48899076	SO:0001583	missense	5591	exon64				CCDS75734.1, CCDS75735.1	8q11	2014-09-17				ENSG00000253729	2.7.11.1		9413	protein-coding gene	gene with protein product		600899		HYRC, HYRC1		7638222	Standard	NM_001081640		Approved	DNPK1, p350, DNAPK, XRCC7, DNA-PKcs	uc003xqi.3	P78527		ENST00000314191.2:c.8815C>T	8.37:g.48736523G>A	ENSP00000313420:p.Arg2939Cys	Somatic		Capture	Illumina HiSeq	Phase_I	48899076	NM_001081640	P78528|Q13327|Q13337|Q14175|Q59H99|Q7Z611|Q96SE6|Q9UME3	Missense_Mutation	SNP	ENST00000314191.2	37		.	.	.	.	.	.	.	.	.	.	G	22.1	4.241465	0.79912	.	.	ENSG00000253729	ENST00000314191;ENST00000338368	T;T	0.02787	4.23;4.16	5.29	5.29	0.74685	PIK-related kinase (1);	0.131816	0.52532	D	0.000071	T	0.16085	0.0387	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.66497	0.912;0.944	T	0.00092	-1.2082	10	0.87932	D	0	.	19.3298	0.94281	0.0:0.0:1.0:0.0	.	2939;2940	E7EUY0;P78527	.;PRKDC_HUMAN	C	2939	ENSP00000313420:R2939C;ENSP00000345182:R2939C	ENSP00000313420:R2939C	R	-	1	0	PRKDC	48899076	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	5.944000	0.70219	2.649000	0.89929	0.650000	0.86243	CGT		0.363	PRKDC-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001081640	
UBE2V2	7336	broad.mit.edu	37	8	48955657	48955657	+	Silent	SNP	C	C	T	rs545217661		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:48955657C>T	ENST00000523111.2	+	2	136	c.81C>T	c.(79-81)ggC>ggT	p.G27G	UBE2V2_ENST00000520809.1_5'UTR|UBE2V2_ENST00000521346.1_5'UTR|UBE2V2_ENST00000517630.1_5'UTR	NM_003350.2	NP_003341.1	Q15819	UB2V2_HUMAN	ubiquitin-conjugating enzyme E2 variant 2	27					cell proliferation (GO:0008283)|DNA double-strand break processing (GO:0000729)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of DNA repair (GO:0045739)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of synapse assembly (GO:0051965)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of DNA repair (GO:0006282)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|UBC13-MMS2 complex (GO:0031372)	acid-amino acid ligase activity (GO:0016881)	p.G27G(1)		large_intestine(1)|lung(2)	3		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00171)|all_lung(136;0.00196)				AAGGAGTAGGCGACGGTACAG	0.408								Rad6 pathway					C|||	1	0.000199681	0.0008	0.0	5008	,	,		15610	0.0		0.0	False		,,,				2504	0.0				p.G27G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C81T	8						.						140.0	138.0	139.0					8																	48955657		1934	4130	6064	49118210	SO:0001819	synonymous_variant	7336	exon2			X98091	CCDS43738.1	8q11.21	2008-02-05			ENSG00000169139	ENSG00000169139		"""Ubiquitin-conjugating enzymes E2"""	12495	protein-coding gene	gene with protein product		603001				9418904, 9199207	Standard	NM_003350		Approved	UEV-2, DDVit-1, EDPF-1, MMS2	uc003xqm.3	Q15819	OTTHUMG00000164206	ENST00000523111.2:c.81C>T	8.37:g.48955657C>T		Somatic		Capture	Illumina HiSeq	Phase_I	49118210	NM_003350		Silent	SNP	ENST00000523111.2	37	CCDS43738.1	.	.	.	.	.	.	.	.	.	.	C	9.516	1.107102	0.20714	.	.	ENSG00000169139	ENST00000324746	.	.	.	5.76	-0.24	0.13047	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.6929	5.0844	0.14675	0.2352:0.2558:0.0:0.509	.	.	.	.	X	23	.	.	R	+	1	2	UBE2V2	49118210	0.061000	0.20836	0.996000	0.52242	0.992000	0.81027	-0.848000	0.04326	-0.111000	0.12001	-0.140000	0.14226	CGA		0.408	UBE2V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377808.3	NM_003350	
RB1CC1	9821	broad.mit.edu	37	8	53570062	53570062	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:53570062C>T	ENST00000025008.5	-	15	2850	c.2327G>A	c.(2326-2328)cGa>cAa	p.R776Q	RB1CC1_ENST00000435644.2_Missense_Mutation_p.R776Q|RB1CC1_ENST00000521611.1_Intron|RB1CC1_ENST00000539297.1_Missense_Mutation_p.R776Q	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	776					autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)		p.R776Q(1)		NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				ATCCTGCATTCGTCTACTGTC	0.398																																					p.R776Q	GBM(180;1701 2102 13475 42023 52570)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2327A	8						.						151.0	139.0	143.0					8																	53570062		2203	4300	6503	53732615	SO:0001583	missense	9821	exon15			AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"""200 kDa FAK family kinase-interacting protein"", ""phosphatase 1, regulatory subunit 131"""	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.2327G>A	8.37:g.53570062C>T	ENSP00000025008:p.Arg776Gln	Somatic		Capture	Illumina HiSeq	Phase_I	53732615	NM_001083617	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	ENST00000025008.5	37	CCDS34892.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.289935	0.80914	.	.	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	T;T;T	0.28069	1.63;1.63;1.63	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.46814	0.1412	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.992	T	0.14727	-1.0462	10	0.24483	T	0.36	-11.7423	19.3789	0.94523	0.0:1.0:0.0:0.0	.	776;776	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	Q	776	ENSP00000025008:R776Q;ENSP00000396067:R776Q;ENSP00000445960:R776Q	ENSP00000025008:R776Q	R	-	2	0	RB1CC1	53732615	1.000000	0.71417	0.912000	0.35992	0.839000	0.47603	7.445000	0.80570	2.652000	0.90054	0.563000	0.77884	CGA		0.398	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781	
RGS20	8601	broad.mit.edu	37	8	54866663	54866663	+	Silent	SNP	C	C	T	rs561000130		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:54866663C>T	ENST00000297313.3	+	5	863	c.771C>T	c.(769-771)aaC>aaT	p.N257N	RGS20_ENST00000276500.4_Silent_p.N110N|RGS20_ENST00000522225.1_5'UTR|RGS20_ENST00000517405.1_3'UTR|RGS20_ENST00000344277.6_Silent_p.N142N	NM_170587.2	NP_733466.1	O76081	RGS20_HUMAN	regulator of G-protein signaling 20	257					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)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.N257N(1)		breast(2)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)			AAGAAGTCAACGCCTGGGCTC	0.453													C|||	1	0.000199681	0.0	0.0	5008	,	,		17698	0.001		0.0	False		,,,				2504	0.0				p.N257N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C771T	8						.						70.0	72.0	71.0					8																	54866663		2203	4300	6503	55029216	SO:0001819	synonymous_variant	8601	exon5			AF074979	CCDS6155.1, CCDS6156.1, CCDS69482.1	8q11.23	2008-07-25	2007-08-14		ENSG00000147509	ENSG00000147509		"""Regulators of G-protein signaling"""	14600	protein-coding gene	gene with protein product		607193	"""regulator of G-protein signalling 20"""			9748279, 9748280	Standard	NM_003702		Approved	RGSZ1, ZGAP1	uc003xrp.3	O76081	OTTHUMG00000164750	ENST00000297313.3:c.771C>T	8.37:g.54866663C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55029216	NM_170587	Q96BG9	De_novo_Start_OutOfFrame	SNP	ENST00000297313.3	37	CCDS6155.1																																																																																				0.453	RGS20-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380058.1		
CLVS1	157807	broad.mit.edu	37	8	62212687	62212687	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:62212687C>T	ENST00000519846.1	+	3	773	c.301C>T	c.(301-303)Cgc>Tgc	p.R101C	RP11-787D18.1_ENST00000521801.1_RNA|RP11-787D18.1_ENST00000518064.1_RNA|CLVS1_ENST00000325897.4_Missense_Mutation_p.R101C|CLVS1_ENST00000518592.1_Intron			Q8IUQ0	CLVS1_HUMAN	clavesin 1	101					lysosome organization (GO:0007040)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|transporter activity (GO:0005215)	p.R101C(1)		endometrium(3)|kidney(4)|large_intestine(4)|lung(21)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	41						TTTCCAGTACCGCCAGCTAAA	0.498																																					p.R101C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C301T	8						.						67.0	65.0	66.0					8																	62212687		2203	4300	6503	62375241	SO:0001583	missense	157807	exon2			AY094971	CCDS6176.1	8q12.1	2009-10-14	2009-10-14	2009-10-14		ENSG00000177182			23139	protein-coding gene	gene with protein product		611292	"""retinaldehyde binding protein 1-like 1"""	RLBP1L1		16802092, 19651769	Standard	NM_173519		Approved	MGC34646, CRALBPL, C6orf212L	uc003xuh.3	Q8IUQ0		ENST00000519846.1:c.301C>T	8.37:g.62212687C>T	ENSP00000428402:p.Arg101Cys	Somatic		Capture	Illumina HiSeq	Phase_I	62375241	NM_173519	B2R7M5|C8UZT3|Q8NB32	Missense_Mutation	SNP	ENST00000519846.1	37	CCDS6176.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.180846	0.78677	.	.	ENSG00000177182	ENST00000519846;ENST00000325897	D;D	0.89485	-2.52;-2.52	5.79	5.79	0.91817	Phosphatidylinositol transfer protein-like, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96291	0.8790	M	0.94021	3.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.961;0.996	D	0.96682	0.9504	9	.	.	.	-14.0481	20.0313	0.97540	0.0:1.0:0.0:0.0	.	101;101	Q8IUQ0;Q8IUQ0-2	CLVS1_HUMAN;.	C	101	ENSP00000428402:R101C;ENSP00000325506:R101C	.	R	+	1	0	CLVS1	62375241	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.092000	0.50207	2.746000	0.94184	0.655000	0.94253	CGC		0.498	CLVS1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378323.1	NM_173519	
ASPH	444	broad.mit.edu	37	8	62596709	62596709	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:62596709C>T	ENST00000379454.4	-	2	329	c.142G>A	c.(142-144)Gga>Aga	p.G48R	ASPH_ENST00000522603.1_Missense_Mutation_p.G19R|ASPH_ENST00000517847.2_Missense_Mutation_p.G19R|ASPH_ENST00000445642.3_Missense_Mutation_p.G19R|ASPH_ENST00000517661.1_Missense_Mutation_p.G19R|ASPH_ENST00000522835.1_Missense_Mutation_p.G19R|ASPH_ENST00000517903.1_Missense_Mutation_p.G19R|ASPH_ENST00000389204.4_Missense_Mutation_p.G19R|ASPH_ENST00000518068.1_Missense_Mutation_p.G48R|ASPH_ENST00000541428.1_Missense_Mutation_p.G19R|ASPH_ENST00000517856.1_Missense_Mutation_p.G48R|ASPH_ENST00000379449.6_Missense_Mutation_p.G48R|ASPH_ENST00000356457.5_Missense_Mutation_p.G48R	NM_004318.3	NP_004309.2	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase	48					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular response to calcium ion (GO:0071277)|detection of calcium ion (GO:0005513)|face morphogenesis (GO:0060325)|limb morphogenesis (GO:0035108)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|palate development (GO:0060021)|pattern specification process (GO:0007389)|peptidyl-aspartic acid hydroxylation (GO:0042264)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteolysis (GO:0045862)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|regulation of protein depolymerization (GO:1901879)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|response to ATP (GO:0033198)	calcium channel complex (GO:0034704)|cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|electron carrier activity (GO:0009055)|ion channel binding (GO:0044325)|peptide-aspartate beta-dioxygenase activity (GO:0004597)|structural constituent of muscle (GO:0008307)|structural molecule activity (GO:0005198)	p.G48R(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(5)|lung(16)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	CCTGAGAGTCCGCCTTTCCTC	0.398																																					p.G19R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G55A	8						.						173.0	146.0	155.0					8																	62596709		2203	4300	6503	62759263	SO:0001583	missense	444	exon2			AF224468	CCDS34898.1, CCDS34899.1, CCDS34900.1, CCDS43742.1, CCDS47866.1, CCDS55234.1, CCDS55235.1, CCDS55236.1, CCDS55237.1, CCDS55238.1, CCDS75746.1	8q12.1	2008-02-05			ENSG00000198363	ENSG00000198363	1.14.11.16		757	protein-coding gene	gene with protein product	"""junctin"", ""humbug"", ""junctate"""	600582				7821814, 10974562	Standard	NM_004318		Approved	CASQ2BP1, BAH, JCTN, HAAH	uc003xuj.3	Q12797	OTTHUMG00000164375	ENST00000379454.4:c.142G>A	8.37:g.62596709C>T	ENSP00000368767:p.Gly48Arg	Somatic		Capture	Illumina HiSeq	Phase_I	62759263	NM_001164753	A6NDF4|A6NHI2|B4DIC9|B4E2K4|B7ZM95|E5RGP5|F5H667|Q6NXR7|Q8TB28|Q9H291|Q9H2C4|Q9NRI0|Q9NRI1|Q9Y4J0	Missense_Mutation	SNP	ENST00000379454.4	37	CCDS34898.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.045881	0.93685	.	.	ENSG00000198363	ENST00000389213;ENST00000541428;ENST00000379454;ENST00000522349;ENST00000356457;ENST00000519234;ENST00000518068;ENST00000517903;ENST00000445642;ENST00000517847;ENST00000522835;ENST00000518306;ENST00000517856;ENST00000389204;ENST00000522603;ENST00000379449;ENST00000517661	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.59083	0.29;0.29;0.29;0.29;0.29;0.29;0.29;0.29;0.29;0.29;0.29;0.29;0.29;0.29;0.29;0.29	5.96	5.96	0.96718	Aspartyl beta-hydroxylase/Triadin domain (1);	0.062198	0.64402	D	0.000009	T	0.75324	0.3834	L	0.59436	1.845	0.58432	D	0.999993	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;1.0;1.0;1.0;0.997;1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D;D;P;D;D;D;D;D;D	0.97110	0.93;0.93;0.997;1.0;1.0;1.0;1.0;0.874;1.0;0.977;0.997;0.995;1.0;0.943	T	0.75428	-0.3321	10	0.87932	D	0	-17.3541	20.4082	0.99013	0.0:1.0:0.0:0.0	.	19;19;48;19;19;19;19;48;48;48;48;48;19;48	Q12797-4;Q12797-3;B8Y0L3;B4DIC9;B7ZM95;B7ZM96;F5H667;E5RG56;Q6NXR7;F8W7A9;Q8TB28;Q12797-2;Q9H291;Q12797	.;.;.;.;.;.;.;.;.;.;.;.;.;ASPH_HUMAN	R	48;19;48;19;48;48;48;19;19;19;19;19;48;19;19;48;19	ENSP00000437864:G19R;ENSP00000368767:G48R;ENSP00000429718:G19R;ENSP00000348841:G48R;ENSP00000427823:G48R;ENSP00000429286:G48R;ENSP00000430245:G19R;ENSP00000394013:G19R;ENSP00000429954:G19R;ENSP00000429160:G19R;ENSP00000427877:G19R;ENSP00000429743:G48R;ENSP00000373856:G19R;ENSP00000436188:G19R;ENSP00000368762:G48R;ENSP00000428060:G19R	ENSP00000348841:G48R	G	-	1	0	ASPH	62759263	0.997000	0.39634	0.997000	0.53966	0.798000	0.45092	5.364000	0.66110	2.814000	0.96858	0.655000	0.94253	GGA		0.398	ASPH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378510.3	NM_004318	
ARMC1	55156	broad.mit.edu	37	8	66517676	66517676	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:66517676C>T	ENST00000276569.3	-	5	807	c.563G>A	c.(562-564)cGt>cAt	p.R188H	ARMC1_ENST00000458464.2_Missense_Mutation_p.R86H	NM_018120.4	NP_060590.1	Q9NVT9	ARMC1_HUMAN	armadillo repeat containing 1	188					metal ion transport (GO:0030001)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)	p.R188H(1)		cervix(1)|endometrium(3)|large_intestine(1)|lung(8)|skin(1)	14			Epithelial(68;0.103)|OV - Ovarian serous cystadenocarcinoma(28;0.235)			CAAATCTGAACGGATTCGCAC	0.338																																					p.R188H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G563A	8						.						73.0	73.0	73.0					8																	66517676		2203	4300	6503	66680230	SO:0001583	missense	55156	exon5			BC011607	CCDS6181.1, CCDS69490.1	8q12.3	2013-02-14			ENSG00000104442	ENSG00000104442		"""Armadillo repeat containing"""	17684	protein-coding gene	gene with protein product							Standard	XM_005251264		Approved	FLJ10511, Arcp	uc003xvl.3	Q9NVT9	OTTHUMG00000164374	ENST00000276569.3:c.563G>A	8.37:g.66517676C>T	ENSP00000276569:p.Arg188His	Somatic		Capture	Illumina HiSeq	Phase_I	66680230	NM_018120	B4E2W7|Q9H018|Q9H820	Missense_Mutation	SNP	ENST00000276569.3	37	CCDS6181.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.996834	0.74818	.	.	ENSG00000104442	ENST00000276569;ENST00000458464;ENST00000518908	T;T;T	0.46451	0.87;0.87;0.87	5.36	5.36	0.76844	Heavy metal-associated domain, HMA (1);	0.000000	0.85682	D	0.000000	T	0.58666	0.2138	L	0.41632	1.29	0.80722	D	1	D;P	0.89917	1.0;0.816	D;B	0.83275	0.996;0.103	T	0.60801	-0.7191	10	0.72032	D	0.01	.	19.0996	0.93269	0.0:1.0:0.0:0.0	.	86;188	B4E2W7;Q9NVT9	.;ARMC1_HUMAN	H	188;86;188	ENSP00000276569:R188H;ENSP00000388572:R86H;ENSP00000429191:R188H	ENSP00000276569:R188H	R	-	2	0	ARMC1	66680230	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.656000	0.67988	2.507000	0.84556	0.555000	0.69702	CGT		0.338	ARMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378480.1	NM_018120	
TRIM55	84675	broad.mit.edu	37	8	67066426	67066426	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:67066426C>A	ENST00000315962.4	+	9	1754	c.1381C>A	c.(1381-1383)Cca>Aca	p.P461T	TRIM55_ENST00000350034.4_Intron|TRIM55_ENST00000276573.7_Missense_Mutation_p.P461T|TRIM55_ENST00000353317.5_Intron	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	461					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.P461T(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			ACCTTGCACCCCAGGGAGCGA	0.577																																					p.P461T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1381A	8						.						66.0	63.0	64.0					8																	67066426		2203	4300	6503	67228980	SO:0001583	missense	84675	exon9			AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	14215	protein-coding gene	gene with protein product		606469	"""ring finger protein 29"", ""tripartite motif-containing 55"""	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.1381C>A	8.37:g.67066426C>A	ENSP00000323913:p.Pro461Thr	Somatic		Capture	Illumina HiSeq	Phase_I	67228980	NM_184085	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Missense_Mutation	SNP	ENST00000315962.4	37	CCDS6184.1	.	.	.	.	.	.	.	.	.	.	C	1.743	-0.491279	0.04322	.	.	ENSG00000147573	ENST00000315962;ENST00000276573	T;T	0.26957	1.7;1.71	5.89	3.07	0.35406	.	0.770143	0.11832	N	0.525156	T	0.13884	0.0336	L	0.27053	0.805	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.14615	-1.0466	10	0.02654	T	1	.	6.758	0.23524	0.1282:0.5857:0.2212:0.0649	.	461;461	Q9BYV6;Q9BYV6-3	TRI55_HUMAN;.	T	461	ENSP00000323913:P461T;ENSP00000276573:P461T	ENSP00000276573:P461T	P	+	1	0	TRIM55	67228980	0.052000	0.20516	1.000000	0.80357	0.998000	0.95712	0.403000	0.20982	0.364000	0.24374	0.650000	0.86243	CCA		0.577	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085	
ADHFE1	137872	broad.mit.edu	37	8	67361186	67361186	+	Missense_Mutation	SNP	A	A	C	rs553493479		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:67361186A>C	ENST00000396623.3	+	8	746	c.715A>C	c.(715-717)Agt>Cgt	p.S239R	ADHFE1_ENST00000496501.1_3'UTR|ADHFE1_ENST00000415254.1_Missense_Mutation_p.S191R|ADHFE1_ENST00000379385.4_Missense_Mutation_p.S239R	NM_144650.2	NP_653251.2	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	239					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|molecular hydrogen transport (GO:0015993)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacid-oxoacid transhydrogenase activity (GO:0047988)|metal ion binding (GO:0046872)	p.S191R(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	29		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			GGTCGCCAACAGTGGCTTTGA	0.502																																					p.S239R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A715C	8						.						169.0	159.0	163.0					8																	67361186		2203	4300	6503	67523740	SO:0001583	missense	137872	exon8			AK056992	CCDS6190.2	8q12.3	2013-05-21			ENSG00000147576	ENSG00000147576	1.1.99.24	"""Alcohol dehydrogenases"""	16354	protein-coding gene	gene with protein product	"""hydroxyacid-oxoacid transhydrogenase"""	611083				12592711	Standard	NM_144650		Approved	ADHFe1, FLJ32430	uc003xwb.4	Q8IWW8	OTTHUMG00000150215	ENST00000396623.3:c.715A>C	8.37:g.67361186A>C	ENSP00000379865:p.Ser239Arg	Somatic		Capture	Illumina HiSeq	Phase_I	67523740	NM_144650	B4DTJ8|Q49A19|Q68CI7|Q6P2B6|Q96MF9	Missense_Mutation	SNP	ENST00000396623.3	37	CCDS6190.2	.	.	.	.	.	.	.	.	.	.	A	26.8	4.776252	0.90195	.	.	ENSG00000147576	ENST00000379385;ENST00000396623;ENST00000415254	T;T;T	0.51574	0.7;0.7;0.7	6.05	6.05	0.98169	Alcohol dehydrogenase, iron-type (1);	0.000000	0.85682	D	0.000000	T	0.75413	0.3846	M	0.94021	3.485	0.80722	D	1	P	0.49783	0.928	P	0.61070	0.883	T	0.82090	-0.0629	10	0.87932	D	0	-11.862	16.5932	0.84781	1.0:0.0:0.0:0.0	.	239	Q8IWW8	HOT_HUMAN	R	239;239;191	ENSP00000368695:S239R;ENSP00000379865:S239R;ENSP00000407115:S191R	ENSP00000368695:S239R	S	+	1	0	ADHFE1	67523740	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	9.339000	0.96797	2.320000	0.78422	0.528000	0.53228	AGT		0.502	ADHFE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316867.3	NM_144650	
ADHFE1	137872	broad.mit.edu	37	8	67372691	67372691	+	Silent	SNP	G	G	A	rs200821866		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:67372691G>A	ENST00000396623.3	+	13	1342	c.1311G>A	c.(1309-1311)acG>acA	p.T437T	ADHFE1_ENST00000496501.1_3'UTR|C8orf46_ENST00000482608.2_3'UTR|ADHFE1_ENST00000415254.1_Silent_p.T389T	NM_144650.2	NP_653251.2	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	437					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|molecular hydrogen transport (GO:0015993)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacid-oxoacid transhydrogenase activity (GO:0047988)|metal ion binding (GO:0046872)	p.T389T(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	29		Lung NSC(129;0.197)	Epithelial(68;0.0321)|all cancers(69;0.0751)|BRCA - Breast invasive adenocarcinoma(89;0.0855)|OV - Ovarian serous cystadenocarcinoma(28;0.226)			TGAAAGGAACGCTGCCCCAGG	0.552																																					p.T437T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1311A	8						.						76.0	73.0	74.0					8																	67372691		2203	4300	6503	67535245	SO:0001819	synonymous_variant	137872	exon13			AK056992	CCDS6190.2	8q12.3	2013-05-21			ENSG00000147576	ENSG00000147576	1.1.99.24	"""Alcohol dehydrogenases"""	16354	protein-coding gene	gene with protein product	"""hydroxyacid-oxoacid transhydrogenase"""	611083				12592711	Standard	NM_144650		Approved	ADHFe1, FLJ32430	uc003xwb.4	Q8IWW8	OTTHUMG00000150215	ENST00000396623.3:c.1311G>A	8.37:g.67372691G>A		Somatic		Capture	Illumina HiSeq	Phase_I	67535245	NM_144650	B4DTJ8|Q49A19|Q68CI7|Q6P2B6|Q96MF9	Silent	SNP	ENST00000396623.3	37	CCDS6190.2																																																																																				0.552	ADHFE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316867.3	NM_144650	
ARFGEF1	10565	broad.mit.edu	37	8	68115362	68115362	+	Missense_Mutation	SNP	G	G	A	rs140098688	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:68115362G>A	ENST00000262215.3	-	36	5473	c.5084C>T	c.(5083-5085)gCg>gTg	p.A1695V	ARFGEF1_ENST00000517955.1_5'Flank|ARFGEF1_ENST00000520381.1_Missense_Mutation_p.A1149V|ARFGEF1_ENST00000518230.1_Missense_Mutation_p.A533V	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1695					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)	p.A1695V(1)		breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			GGAATTAAACGCTTTTGCAAA	0.423																																					p.A1695V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5084T	8						.	G	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	154.0	128.0	137.0		5084	4.8	1.0	8	dbSNP_134	137	0,8600		0,0,4300	no	missense	ARFGEF1	NM_006421.4	64	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	1695/1850	68115362	2,13004	2203	4300	6503	68277916	SO:0001583	missense	10565	exon36			AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.5084C>T	8.37:g.68115362G>A	ENSP00000262215:p.Ala1695Val	Somatic		Capture	Illumina HiSeq	Phase_I	68277916	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.241415	0.79912	4.54E-4	0.0	ENSG00000066777	ENST00000520381;ENST00000262215;ENST00000518789;ENST00000518230	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.42449	0.1203	L	0.52573	1.65	0.80722	D	1	P;P;B;P	0.46656	0.882;0.668;0.403;0.668	B;B;B;B	0.37943	0.261;0.048;0.043;0.048	T	0.40942	-0.9536	10	0.31617	T	0.26	.	17.7834	0.88530	0.0:0.0:1.0:0.0	.	1695;1173;519;1149	Q9Y6D6;Q59FY5;B3KMS9;E5RIF2	BIG1_HUMAN;.;.;.	V	1149;1695;26;533	ENSP00000428429:A1149V;ENSP00000262215:A1695V;ENSP00000429560:A26V;ENSP00000430891:A533V	ENSP00000262215:A1695V	A	-	2	0	ARFGEF1	68277916	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	7.819000	0.86621	2.357000	0.79964	0.650000	0.86243	GCG		0.423	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421	
NCOA2	10499	broad.mit.edu	37	8	71039179	71039179	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:71039179G>T	ENST00000452400.2	-	19	3966	c.3785C>A	c.(3784-3786)aCt>aAt	p.T1262N	NCOA2_ENST00000267974.4_Missense_Mutation_p.T350N	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	1262					cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|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)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)	p.T1262N(1)	PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			CATCATCAAAGTTCGTTGCTG	0.488			T	"""RUNXBP2, HEY1"""	"""AML, Chondrosarcoma"""																																p.T1262N			Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3785A	8						.						155.0	141.0	146.0					8																	71039179		1987	4172	6159	71201733	SO:0001583	missense	10499	exon19			X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.3785C>A	8.37:g.71039179G>T	ENSP00000399968:p.Thr1262Asn	Somatic		Capture	Illumina HiSeq	Phase_I	71201733	NM_006540	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	37	CCDS47872.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.45|18.45	3.626143|3.626143	0.66901|0.66901	.|.	.|.	ENSG00000140396|ENSG00000140396	ENST00000518363|ENST00000452400;ENST00000267974	.|T;T	.|0.06768	.|4.81;3.26	5.97|5.97	5.97|5.97	0.96955|0.96955	.|.	.|0.153318	.|0.56097	.|D	.|0.000024	T|T	0.15782|0.15782	0.0380|0.0380	L|L	0.44542|0.44542	1.39|1.39	0.26847|0.26847	N|N	0.968248|0.968248	.|P;P	.|0.49090	.|0.919;0.514	.|P;B	.|0.49252	.|0.604;0.212	T|T	0.01630|0.01630	-1.1308|-1.1308	5|10	.|0.39692	.|T	.|0.17	.|.	20.4387|20.4387	0.99107|0.99107	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|350;1262	.|F8WAJ2;Q15596	.|.;NCOA2_HUMAN	I|N	363|1262;350	.|ENSP00000399968:T1262N;ENSP00000267974:T350N	.|ENSP00000267974:T350N	L|T	-|-	1|2	0|0	NCOA2|NCOA2	71201733|71201733	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.953000|0.953000	0.61014|0.61014	4.504000|4.504000	0.60414|0.60414	2.836000|2.836000	0.97738|0.97738	0.655000|0.655000	0.94253|0.94253	CTT|ACT		0.488	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1		
NCOA2	10499	broad.mit.edu	37	8	71068490	71068490	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:71068490C>T	ENST00000452400.2	-	11	2291	c.2110G>A	c.(2110-2112)Gcc>Acc	p.A704T	NCOA2_ENST00000524223.1_5'UTR	NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	704	CASP8AP2-binding. {ECO:0000250}.				cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of glucose metabolic process (GO:0010906)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|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)|signal transducer activity (GO:0004871)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)	p.A704T(1)	PAX3/NCOA2(4)|HEY1/NCOA2(10)	NS(1)|breast(4)|endometrium(7)|kidney(4)|large_intestine(10)|lung(25)|ovary(1)|pancreas(2)|prostate(2)|skin(4)	60	Breast(64;0.201)		Epithelial(68;0.0147)|OV - Ovarian serous cystadenocarcinoma(28;0.0455)|all cancers(69;0.0606)			GTTAACTTGGCCAAGTCCACA	0.522			T	"""RUNXBP2, HEY1"""	"""AML, Chondrosarcoma"""																																p.A704T			Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2110A	8						.						49.0	49.0	49.0					8																	71068490		1916	4131	6047	71231044	SO:0001583	missense	10499	exon11			X97674	CCDS47872.1	8q13.3	2011-07-01			ENSG00000140396	ENSG00000140396		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7669	protein-coding gene	gene with protein product		601993				9111344, 8670870	Standard	XM_005251128		Approved	TIF2, GRIP1, NCoA-2, KAT13C, bHLHe75	uc003xyn.1	Q15596	OTTHUMG00000164671	ENST00000452400.2:c.2110G>A	8.37:g.71068490C>T	ENSP00000399968:p.Ala704Thr	Somatic		Capture	Illumina HiSeq	Phase_I	71231044	NM_006540	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	37	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	C	12.65	2.000242	0.35320	.	.	ENSG00000140396	ENST00000452400	T	0.55234	0.53	5.77	4.83	0.62350	Steroid receptor coactivator (1);Nuclear receptor coactivator Src-1 (1);	0.048608	0.85682	N	0.000000	T	0.64182	0.2575	L	0.46741	1.465	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60959	-0.7159	10	0.30854	T	0.27	.	13.2219	0.59892	0.0:0.9156:0.0:0.0844	.	704	Q15596	NCOA2_HUMAN	T	704	ENSP00000399968:A704T	ENSP00000399968:A704T	A	-	1	0	NCOA2	71231044	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.946000	0.63576	1.298000	0.44778	0.655000	0.94253	GCC		0.522	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1		
ZFHX4	79776	broad.mit.edu	37	8	77763849	77763849	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:77763849delT	ENST00000521891.2	+	10	5140	c.4692delT	c.(4690-4692)tctfs	p.S1564fs	ZFHX4_ENST00000050961.6_Frame_Shift_Del_p.S1519fs|ZFHX4_ENST00000455469.2_Frame_Shift_Del_p.S1519fs|ZFHX4_ENST00000518282.1_Frame_Shift_Del_p.S1538fs	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1519					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.H1565fs*5(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			ATTCAGTTTCTCACTTGCATA	0.403										HNSCC(33;0.089)																											p.S1564fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.4692delT	8						.						41.0	40.0	40.0					8																	77763849		1899	4121	6020	77926404	SO:0001589	frameshift_variant	79776	exon10				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.4692delT	8.37:g.77763849delT	ENSP00000430497:p.Ser1564fs	Somatic		Capture	Illumina HiSeq	Phase_I	77926404	NM_024721	G3V138|Q18PS0|Q6ZN20	Frame_Shift_Del	DEL	ENST00000521891.2	37	CCDS47878.2																																																																																				0.403	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
TPD52	7163	broad.mit.edu	37	8	80950413	80950413	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:80950413C>T	ENST00000379097.3	-	6	975	c.613G>A	c.(613-615)Gct>Act	p.A205T	TPD52_ENST00000520527.1_Missense_Mutation_p.A228T|TPD52_ENST00000537855.1_Intron|TPD52_ENST00000523395.1_5'UTR|TPD52_ENST00000518937.1_Missense_Mutation_p.A188T|TPD52_ENST00000517427.1_Missense_Mutation_p.A214T|TPD52_ENST00000448733.2_Missense_Mutation_p.A219T|TPD52_ENST00000519303.2_Missense_Mutation_p.A41T|TPD52_ENST00000379096.5_Missense_Mutation_p.A165T	NM_001025252.1	NP_001020423.1	P55327	TPD52_HUMAN	tumor protein D52	205					anatomical structure morphogenesis (GO:0009653)|B cell differentiation (GO:0030183)|positive regulation of cell proliferation (GO:0008284)|secretion (GO:0046903)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.A205T(1)		endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	8	all_epithelial(4;1.13e-09)|Lung NSC(7;9.71e-07)|all_lung(9;3.75e-06)	Lung NSC(129;3.55e-06)|all_lung(136;1.53e-05)|Acute lymphoblastic leukemia(644;0.158)	BRCA - Breast invasive adenocarcinoma(6;0.00181)|Epithelial(68;0.0149)|all cancers(69;0.0612)			GCATTTGCAGCCGAATTCAAG	0.453																																					p.A205T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G613A	8						.						132.0	111.0	118.0					8																	80950413		2203	4300	6503	81112968	SO:0001583	missense	7163	exon6			U18914	CCDS34912.1, CCDS47879.1, CCDS55249.1, CCDS75757.1, CCDS75758.1, CCDS75759.1	8q21.13	2014-06-24			ENSG00000076554	ENSG00000076554			12005	protein-coding gene	gene with protein product		604068				7796418	Standard	NM_001287144		Approved	D52, hD52, N8L	uc003ybr.1	P55327	OTTHUMG00000164565	ENST00000379097.3:c.613G>A	8.37:g.80950413C>T	ENSP00000368391:p.Ala205Thr	Somatic		Capture	Illumina HiSeq	Phase_I	81112968	NM_001025252	B7Z414|C9J502|D0UFD1|D0UFD2|D0UFD3|D0UFD4|D0UFD5|E5RKB4|Q13056|Q53EK8|Q6FGP3|Q6FGS3|Q86YZ2|Q9UCX8	Missense_Mutation	SNP	ENST00000379097.3	37	CCDS34912.1	.	.	.	.	.	.	.	.	.	.	C	2.818	-0.245415	0.05906	.	.	ENSG00000076554	ENST00000379096;ENST00000518937;ENST00000520527;ENST00000517427;ENST00000448733;ENST00000379097;ENST00000425513;ENST00000519303	T;T;T;T;T;T;T	0.24723	1.84;1.84;1.84;1.84;1.84;1.84;1.84	5.35	2.84	0.33178	.	0.445877	0.27371	N	0.019663	T	0.09069	0.0224	N	0.04043	-0.29	0.80722	D	1	B;B;B	0.16396	0.001;0.017;0.002	B;B;B	0.21708	0.007;0.036;0.01	T	0.25328	-1.0135	10	0.02654	T	1	-4.1592	7.0979	0.25319	0.0:0.4718:0.0:0.5281	.	165;188;205	P55327-2;E5RKB4;P55327	.;.;TPD52_HUMAN	T	165;188;228;214;219;205;165;41	ENSP00000368390:A165T;ENSP00000429915:A188T;ENSP00000429309:A228T;ENSP00000429351:A214T;ENSP00000410222:A219T;ENSP00000368391:A205T;ENSP00000428951:A41T	ENSP00000368390:A165T	A	-	1	0	TPD52	81112968	0.916000	0.31088	0.896000	0.35187	0.985000	0.73830	1.490000	0.35573	0.410000	0.25675	-0.345000	0.07892	GCT		0.453	TPD52-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379539.2	NM_005079	
PDP1	54704	broad.mit.edu	37	8	94935625	94935625	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:94935625A>G	ENST00000297598.4	+	2	1607	c.1338A>G	c.(1336-1338)atA>atG	p.I446M	PDP1_ENST00000517764.1_Missense_Mutation_p.I446M|PDP1_ENST00000396200.3_Missense_Mutation_p.I471M|PDP1_ENST00000520728.1_Missense_Mutation_p.I446M	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	446					cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.I446M(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						AACAGCCAATAGCTGTTGGTG	0.488																																					p.I471M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1413G	8						.						80.0	81.0	81.0					8																	94935625		2203	4300	6503	95004801	SO:0001583	missense	54704	exon3			AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9279	protein-coding gene	gene with protein product		605993	"""protein phosphatase 2C, magnesium-dependent, catalytic subunit"""	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.1338A>G	8.37:g.94935625A>G	ENSP00000297598:p.Ile446Met	Somatic		Capture	Illumina HiSeq	Phase_I	95004801	NM_001161779	B3KX71|J3KPU0|Q5U5K1	Missense_Mutation	SNP	ENST00000297598.4	37	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	A	5.472	0.272055	0.10349	.	.	ENSG00000164951	ENST00000297598;ENST00000520728;ENST00000396200;ENST00000517764	T;T;T;T	0.44881	0.92;0.92;0.91;0.92	6.03	4.92	0.64577	Protein phosphatase 2C-like (3);	0.127835	0.64402	D	0.000016	T	0.28200	0.0696	N	0.14661	0.345	0.42311	D	0.992211	P;P	0.41597	0.756;0.635	B;B	0.40534	0.332;0.332	T	0.07462	-1.0771	10	0.27785	T	0.31	-7.6316	14.2696	0.66143	0.8499:0.1501:0.0:0.0	.	497;446	B4DYX8;Q9P0J1	.;PDP1_HUMAN	M	446;446;471;446	ENSP00000297598:I446M;ENSP00000428317:I446M;ENSP00000379503:I471M;ENSP00000430380:I446M	ENSP00000297598:I446M	I	+	3	3	PDP1	95004801	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.761000	0.38440	2.308000	0.77769	0.533000	0.62120	ATA		0.488	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444	
CDH17	1015	broad.mit.edu	37	8	95161012	95161012	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:95161012G>A	ENST00000027335.3	-	14	2011	c.1887C>T	c.(1885-1887)gcC>gcT	p.A629A	CDH17_ENST00000450165.2_Silent_p.A629A|CDH17_ENST00000441892.2_Silent_p.A415A	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	629	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)	p.A629A(1)		NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			ATGGACTTCCGGCTTCTCTGT	0.413																																					p.A629A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1887T	8						.						88.0	73.0	78.0					8																	95161012		2203	4300	6503	95230188	SO:0001819	synonymous_variant	1015	exon14			X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.1887C>T	8.37:g.95161012G>A		Somatic		Capture	Illumina HiSeq	Phase_I	95230188	NM_001144663	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																				0.413	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
RAD54B	25788	broad.mit.edu	37	8	95404068	95404068	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:95404068A>G	ENST00000336148.5	-	10	1702	c.1578T>C	c.(1576-1578)ttT>ttC	p.F526F		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	526					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)	p.F526F(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			TTCTAAGGATAAAGAGTCCAG	0.368								Direct reversal of damage;Homologous recombination																													p.F526F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1578C	8						.						102.0	115.0	111.0					8																	95404068		2203	4300	6503	95473244	SO:0001819	synonymous_variant	25788	exon10			AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.1578T>C	8.37:g.95404068A>G		Somatic		Capture	Illumina HiSeq	Phase_I	95473244	NM_012415	F6WBS8	Silent	SNP	ENST00000336148.5	37	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	A	9.280	1.047836	0.19827	.	.	ENSG00000197275	ENST00000546218	.	.	.	4.89	2.4	0.29515	.	.	.	.	.	T	0.64011	0.2560	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63028	-0.6728	5	0.87932	D	0	-15.5363	8.7492	0.34605	0.775:0.0:0.225:0.0	.	.	.	.	S	199	.	ENSP00000442273:L199S	L	-	2	0	RAD54B	95473244	1.000000	0.71417	0.987000	0.45799	0.997000	0.91878	2.326000	0.43849	0.266000	0.21894	0.528000	0.53228	TTA		0.368	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415	
KIAA1429	25962	broad.mit.edu	37	8	95523708	95523708	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:95523708C>T	ENST00000297591.5	-	13	3170	c.3095G>A	c.(3094-3096)cGt>cAt	p.R1032H	KIAA1429_ENST00000523405.1_5'UTR|KIAA1429_ENST00000421249.2_Missense_Mutation_p.R1032H|KIAA1429_ENST00000437199.1_Missense_Mutation_p.R1032H	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	1032					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R1032H(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)			TGAAGGAACACGCATGTCCTT	0.418																																					p.R1032H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3095A	8						.						81.0	76.0	77.0					8																	95523708		2203	4300	6503	95592884	SO:0001583	missense	25962	exon13			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.3095G>A	8.37:g.95523708C>T	ENSP00000297591:p.Arg1032His	Somatic		Capture	Illumina HiSeq	Phase_I	95592884	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	37	CCDS34923.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.031229	0.75504	.	.	ENSG00000164944	ENST00000297591;ENST00000437199;ENST00000421249	T;T;T	0.66280	-0.2;-0.2;0.62	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.71626	0.3362	L	0.29908	0.895	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.74368	-0.3688	10	0.72032	D	0.01	-13.4601	19.5048	0.95111	0.0:1.0:0.0:0.0	.	1032;1032	Q69YN4-4;Q69YN4	.;VIR_HUMAN	H	1032	ENSP00000297591:R1032H;ENSP00000395600:R1032H;ENSP00000398390:R1032H	ENSP00000297591:R1032H	R	-	2	0	KIAA1429	95592884	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.445000	0.80570	2.678000	0.91216	0.650000	0.86243	CGT		0.418	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
KCNS2	3788	broad.mit.edu	37	8	99440584	99440584	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:99440584G>A	ENST00000287042.4	+	2	727	c.377G>A	c.(376-378)cGc>cAc	p.R126H	KCNS2_ENST00000521839.1_Missense_Mutation_p.R126H	NM_020697.2	NP_065748.1	Q9ULS6	KCNS2_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 2	126					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.R126H(1)		autonomic_ganglia(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	31	Breast(36;2.4e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.0448)			TACCATGGCCGCAAAGTAGAG	0.552																																					p.R126H	Pancreas(138;844 2489 9202 24627)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G377A	8						.						85.0	91.0	89.0					8																	99440584		2203	4300	6503	99509760	SO:0001583	missense	3788	exon2			AB032970	CCDS6279.1	8q22	2011-07-05			ENSG00000156486	ENSG00000156486		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6301	protein-coding gene	gene with protein product		602906				9305895, 16382104	Standard	NM_020697		Approved	Kv9.2	uc003yin.3	Q9ULS6	OTTHUMG00000044337	ENST00000287042.4:c.377G>A	8.37:g.99440584G>A	ENSP00000287042:p.Arg126His	Somatic		Capture	Illumina HiSeq	Phase_I	99509760	NM_020697	A8KAN1	Missense_Mutation	SNP	ENST00000287042.4	37	CCDS6279.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.054137	0.75960	.	.	ENSG00000156486	ENST00000287042;ENST00000521839	T;T	0.46451	0.87;0.87	5.31	5.31	0.75309	BTB/POZ-like (1);BTB/POZ fold (1);	0.136406	0.47093	D	0.000244	T	0.59445	0.2194	M	0.67397	2.05	0.44798	D	0.997809	D	0.76494	0.999	D	0.73380	0.98	T	0.56408	-0.7984	10	0.33141	T	0.24	.	12.3465	0.55124	0.0775:0.0:0.9225:0.0	.	126	Q9ULS6	KCNS2_HUMAN	H	126	ENSP00000287042:R126H;ENSP00000430712:R126H	ENSP00000287042:R126H	R	+	2	0	KCNS2	99509760	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.869000	0.99810	2.470000	0.83445	0.563000	0.77884	CGC		0.552	KCNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103134.1	NM_020697	
PARP10	84875	broad.mit.edu	37	8	145057506	145057506	+	Missense_Mutation	SNP	G	G	A	rs140734015		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr8:145057506G>A	ENST00000313028.7	-	8	2345	c.2251C>T	c.(2251-2253)Cgt>Tgt	p.R751C	PARP10_ENST00000525773.1_Missense_Mutation_p.R763C|PARP10_ENST00000524918.1_Missense_Mutation_p.R742C|PARP10_ENST00000533665.1_5'Flank	NM_032789.3	NP_116178.2	Q53GL7	PAR10_HUMAN	poly (ADP-ribose) polymerase family, member 10	751	Myc binding.				negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of gene expression (GO:0010629)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of protein K63-linked ubiquitination (GO:1900045)|negative regulation of viral genome replication (GO:0045071)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein poly-ADP-ribosylation (GO:0070212)|regulation of chromatin assembly (GO:0010847)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.R751C(1)		NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(2)	27	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.31e-40)|Epithelial(56;1.16e-39)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AGGCGAGCACGCAGCTCTGCA	0.706													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17732	0.0		0.0	False		,,,				2504	0.0				p.R751C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2251T	8						.		CYS/ARG	1,4401		0,1,2200	21.0	21.0	21.0		2251	-4.3	0.0	8	dbSNP_134	21	0,8596		0,0,4298	no	missense	PARP10	NM_032789.3	180	0,1,6498	AA,AG,GG		0.0,0.0227,0.0077	benign	751/1026	145057506	1,12997	2201	4298	6499	145129494	SO:0001583	missense	84875	exon8			AK027370	CCDS34960.1	8q24	2010-02-16				ENSG00000178685		"""Poly (ADP-ribose) polymerases"""	25895	protein-coding gene	gene with protein product		609564				15273990	Standard	NM_032789		Approved	FLJ14464	uc003zal.4	Q53GL7		ENST00000313028.7:c.2251C>T	8.37:g.145057506G>A	ENSP00000325618:p.Arg751Cys	Somatic		Capture	Illumina HiSeq	Phase_I	145129494	NM_032789	Q8N2I0|Q8WV05|Q96CH7|Q96K72	Missense_Mutation	SNP	ENST00000313028.7	37	CCDS34960.1	.	.	.	.	.	.	.	.	.	.	G	4.061	0.009004	0.07912	2.27E-4	0.0	ENSG00000178685	ENST00000524918;ENST00000534861;ENST00000313028;ENST00000525773	T;T;T	0.09538	2.98;2.97;2.97	5.24	-4.26	0.03755	.	1.233990	0.05669	N	0.588255	T	0.03695	0.0105	N	0.01874	-0.695	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43130	-0.9410	10	0.34782	T	0.22	.	6.4686	0.21995	0.3398:0.2711:0.3891:0.0	.	763;751	E9PNI7;Q53GL7	.;PAR10_HUMAN	C	742;457;751;763	ENSP00000431620:R742C;ENSP00000325618:R751C;ENSP00000434776:R763C	ENSP00000325618:R751C	R	-	1	0	PARP10	145129494	0.000000	0.05858	0.000000	0.03702	0.047000	0.14425	-0.580000	0.05827	-0.982000	0.03515	-1.037000	0.02385	CGT		0.706	PARP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383866.1	NM_032789	
TMEM246	84302	broad.mit.edu	37	9	104238739	104238739	+	Silent	SNP	G	G	A	rs147343270		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:104238739G>A	ENST00000374851.1	-	4	1783	c.636C>T	c.(634-636)gaC>gaT	p.D212D	RP11-490D19.6_ENST00000431507.1_RNA|RP11-490D19.6_ENST00000425734.1_RNA|RP11-490D19.6_ENST00000450109.1_RNA|RP11-490D19.6_ENST00000424154.1_RNA|TMEM246_ENST00000374848.3_Silent_p.D212D|TMEM246_ENST00000374847.1_Silent_p.D212D			Q9BRR3	TM246_HUMAN	transmembrane protein 246	212						integral component of membrane (GO:0016021)		p.D212D(2)									GTACAGCATCGTCTTCTACCA	0.512																																					p.D212D												.	.	2	Substitution - coding silent(2)	upper_aerodigestive_tract(1)|large_intestine(1)	c.C636T	9						.	G		0,4406		0,0,2203	92.0	75.0	81.0		636	-4.1	0.9	9	dbSNP_134	81	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C9orf125	NM_032342.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		212/404	104238739	1,13005	2203	4300	6503	103278560	SO:0001819	synonymous_variant	84302	exon2			BC006115	CCDS6757.1	9q31.1	2012-04-02	2012-04-02	2012-04-02	ENSG00000165152	ENSG00000165152			28180	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 125"""	C9orf125		12477932	Standard	NM_032342		Approved	MGC12992	uc004bbm.3	Q9BRR3	OTTHUMG00000020381	ENST00000374851.1:c.636C>T	9.37:g.104238739G>A		Somatic		Capture	Illumina HiSeq	Phase_I	103278560	NM_032342	Q49AQ4	Silent	SNP	ENST00000374851.1	37	CCDS6757.1																																																																																				0.512	TMEM246-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053444.1	NM_032342	
FKTN	2218	broad.mit.edu	37	9	108397344	108397344	+	Silent	SNP	G	G	A	rs141886790		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:108397344G>A	ENST00000223528.2	+	10	1309	c.1185G>A	c.(1183-1185)ccG>ccA	p.P395P	FKTN_ENST00000540160.1_Missense_Mutation_p.E265K|FKTN_ENST00000602661.1_Silent_p.P395P|FKTN_ENST00000448551.2_Silent_p.P395P|FKTN_ENST00000357998.5_Silent_p.P395P	NM_006731.2	NP_006722.2	O75072	FKTN_HUMAN	fukutin	395					muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|negative regulation of JNK cascade (GO:0046329)|nervous system development (GO:0007399)|regulation of protein glycosylation (GO:0060049)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	transferase activity (GO:0016740)	p.P395P(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	25						ACCTGTTTCCGAAGTTTACAC	0.453																																					p.P395P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1185A	9						.						170.0	152.0	158.0					9																	108397344		2203	4300	6503	107437165	SO:0001819	synonymous_variant	2218	exon11				CCDS6766.1	9q31-q33	2014-09-17	2007-11-21	2007-11-21	ENSG00000106692	ENSG00000106692			3622	protein-coding gene	gene with protein product		607440	"""Fukuyama type congenital muscular dystrophy (fukutin)"""	FCMD		8275093, 17036286, 17044012	Standard	NM_001079802		Approved	LGMD2M	uc004bcs.3	O75072	OTTHUMG00000020425	ENST00000223528.2:c.1185G>A	9.37:g.108397344G>A		Somatic		Capture	Illumina HiSeq	Phase_I	107437165	NM_001079802	B4DUX9|J3KP13|Q3MIJ1|Q96TE1|Q9P295	Silent	SNP	ENST00000223528.2	37	CCDS6766.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.36|11.36	1.617082|1.617082	0.28801|0.28801	.|.	.|.	ENSG00000106692|ENSG00000106692	ENST00000540160|ENST00000457847	D|.	0.81996|.	-1.56|.	6.17|6.17	1.79|1.79	0.24919|0.24919	.|.	.|.	.|.	.|.	.|.	T|T	0.23451|0.23451	0.0567|0.0567	.|.	.|.	.|.	0.25036|0.25036	N|N	0.991231|0.991231	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.20874|0.20874	-1.0262|-1.0262	8|4	0.72032|.	D|.	0.01|.	-0.3343|-0.3343	2.7309|2.7309	0.05227|0.05227	0.2259:0.4725:0.1123:0.1894|0.2259:0.4725:0.1123:0.1894	.|.	265|.	B4E2W4|.	.|.	K|Q	265|92	ENSP00000439423:E265K|.	ENSP00000439423:E265K|.	E|R	+|+	1|2	0|0	FKTN|FKTN	107437165|107437165	0.847000|0.847000	0.29606|0.29606	1.000000|1.000000	0.80357|0.80357	0.532000|0.532000	0.34746|0.34746	-0.038000|-0.038000	0.12144|0.12144	0.476000|0.476000	0.27440|0.27440	-0.863000|-0.863000	0.03009|0.03009	GAA|CGA		0.453	FKTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053505.1	NM_006731	
AKAP2	11217	broad.mit.edu	37	9	112898625	112898625	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:112898625C>T	ENST00000259318.7	+	2	315	c.108C>T	c.(106-108)ggC>ggT	p.G36G	PALM2-AKAP2_ENST00000374530.3_Silent_p.G267G|AKAP2_ENST00000555236.1_Silent_p.G267G|AKAP2_ENST00000434623.2_Silent_p.G125G|PALM2-AKAP2_ENST00000302798.7_Silent_p.G267G|AKAP2_ENST00000374525.1_Silent_p.G125G|AKAP2_ENST00000510514.5_Silent_p.G267G	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	36								p.G267G(1)|p.G125G(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						CGCATAATGGCCTCCTTACTG	0.502																																					p.G267G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C801T	9						.						181.0	161.0	168.0					9																	112898625		2203	4300	6503	111938446	SO:0001819	synonymous_variant	445815	exon8			AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.108C>T	9.37:g.112898625C>T		Somatic		Capture	Illumina HiSeq	Phase_I	111938446	NM_147150	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Silent	SNP	ENST00000259318.7	37	CCDS48003.1																																																																																				0.502	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065	
SVEP1	79987	broad.mit.edu	37	9	113141773	113141773	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:113141773T>C	ENST00000401783.2	-	44	10598	c.10262A>G	c.(10261-10263)cAc>cGc	p.H3421R	SVEP1_ENST00000297826.5_Missense_Mutation_p.H1347R|SVEP1_ENST00000374469.1_Missense_Mutation_p.H3398R	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3421	Sushi 34. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.H3424R(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						ATTTTCTACGTGAGCTGGTGG	0.413																																					p.H3421R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A10262G	9						.						81.0	73.0	75.0					9																	113141773		1935	4141	6076	112181594	SO:0001583	missense	79987	exon44			AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.10262A>G	9.37:g.113141773T>C	ENSP00000384917:p.His3421Arg	Somatic		Capture	Illumina HiSeq	Phase_I	112181594	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	T	9.345	1.063995	0.20067	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.63096	-0.02;-0.02;-0.02	5.87	4.72	0.59763	Complement control module (2);Sushi/SCR/CCP (3);	0.324306	0.37053	N	0.002269	T	0.38532	0.1044	N	0.05510	-0.035	0.32137	N	0.586012	B	0.32653	0.379	B	0.33890	0.172	T	0.46062	-0.9218	10	0.22109	T	0.4	.	8.4655	0.32953	0.1303:0.0:0.1367:0.733	.	3421	Q4LDE5	SVEP1_HUMAN	R	3421;3398;1347	ENSP00000384917:H3421R;ENSP00000363593:H3398R;ENSP00000297826:H1347R	ENSP00000297826:H1347R	H	-	2	0	SVEP1	112181594	0.992000	0.36948	0.017000	0.16124	0.247000	0.25773	2.230000	0.42999	1.028000	0.39785	0.533000	0.62120	CAC		0.413	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ZNF483	158399	broad.mit.edu	37	9	114304662	114304662	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:114304662A>G	ENST00000309235.5	+	6	1605	c.1447A>G	c.(1447-1449)Aca>Gca	p.T483A	ZNF483_ENST00000358151.4_Intron	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	483					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.T483A(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(11)|ovary(1)|skin(5)	31						TTCATCGCTCACACCACATCA	0.413																																					p.T483A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1447G	9						.						48.0	50.0	49.0					9																	114304662		2203	4300	6503	113344483	SO:0001583	missense	158399	exon6			AB075842	CCDS35105.1, CCDS35106.1	9q32	2013-01-09			ENSG00000173258	ENSG00000173258		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23384	protein-coding gene	gene with protein product							Standard	NM_001007169		Approved	ZKSCAN16, KIAA1962, ZSCAN48	uc004bff.2	Q8TF39	OTTHUMG00000020490	ENST00000309235.5:c.1447A>G	9.37:g.114304662A>G	ENSP00000311679:p.Thr483Ala	Somatic		Capture	Illumina HiSeq	Phase_I	113344483	NM_133464	Q5VZN2|Q8NAE1	Missense_Mutation	SNP	ENST00000309235.5	37	CCDS35106.1	.	.	.	.	.	.	.	.	.	.	A	11.15	1.555203	0.27739	.	.	ENSG00000173258	ENST00000309235	T	0.06849	3.25	4.44	3.27	0.37495	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.466924	0.18329	N	0.144545	T	0.06554	0.0168	L	0.35249	1.045	0.44207	D	0.997038	B	0.06786	0.001	B	0.08055	0.003	T	0.28170	-1.0052	10	0.23891	T	0.37	-2.387	8.7593	0.34665	0.9077:0.0:0.0923:0.0	.	483	Q8TF39	ZN483_HUMAN	A	483	ENSP00000311679:T483A	ENSP00000311679:T483A	T	+	1	0	ZNF483	113344483	0.001000	0.12720	0.064000	0.19789	0.016000	0.09150	1.636000	0.37144	1.007000	0.39238	0.533000	0.62120	ACA		0.413	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567	
C9orf43	257169	broad.mit.edu	37	9	116175875	116175875	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:116175875C>T	ENST00000288462.4	+	2	548	c.102C>T	c.(100-102)ggC>ggT	p.G34G	POLE3_ENST00000374171.4_5'Flank|C9orf43_ENST00000374165.1_Silent_p.G34G|C9orf43_ENST00000490544.1_3'UTR	NM_152786.1	NP_689999.1	Q8TAL5	CI043_HUMAN	chromosome 9 open reading frame 43	34								p.G34G(1)		breast(2)|large_intestine(6)|lung(2)|ovary(1)|pancreas(1)|prostate(3)	15						TTGAGAGGGGCCATCCTCGAA	0.547																																					p.G34G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C102T	9						.						89.0	83.0	85.0					9																	116175875		2203	4300	6503	115215696	SO:0001819	synonymous_variant	257169	exon2			BC026884	CCDS6796.1	9q33.1	2012-03-15			ENSG00000157653	ENSG00000157653			23570	protein-coding gene	gene with protein product						12477932	Standard	NM_152786		Approved	MGC17358	uc004bhp.3	Q8TAL5	OTTHUMG00000020526	ENST00000288462.4:c.102C>T	9.37:g.116175875C>T		Somatic		Capture	Illumina HiSeq	Phase_I	115215696	NM_152786		Silent	SNP	ENST00000288462.4	37	CCDS6796.1																																																																																				0.547	C9orf43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053739.1	NM_152786	
RGS3	5998	broad.mit.edu	37	9	116246449	116246449	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:116246449G>A	ENST00000374140.2	+	7	766	c.557G>A	c.(556-558)cGc>cAc	p.R186H	RGS3_ENST00000350696.5_Missense_Mutation_p.R186H|RGS3_ENST00000317613.6_Missense_Mutation_p.R74H	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	186	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				inactivation of MAPK activity (GO:0000188)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.R82H(1)|p.R186H(1)		cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						AGTAGACTACGCCACCAGAAG	0.512																																					p.R186H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G557A	9						.						79.0	78.0	78.0					9																	116246449		2203	4300	6503	115286270	SO:0001583	missense	5998	exon7			AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.557G>A	9.37:g.116246449G>A	ENSP00000363255:p.Arg186His	Somatic		Capture	Illumina HiSeq	Phase_I	115286270	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.272746	0.23221	.	.	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000317613	T;T;T	0.69175	-0.38;-0.38;-0.38	4.99	-1.68	0.08212	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	1.199840	0.05960	N	0.640427	T	0.52175	0.1718	N	0.04132	-0.27	0.09310	N	1	D;P;D	0.61697	0.987;0.941;0.99	P;B;P	0.54312	0.644;0.297;0.748	T	0.44467	-0.9326	10	0.28530	T	0.3	.	6.9429	0.24502	0.3946:0.1152:0.4903:0.0	.	76;74;186	B3KWG8;P49796-5;P49796	.;.;RGS3_HUMAN	H	186;186;74	ENSP00000363255:R186H;ENSP00000259406:R186H;ENSP00000312844:R74H	ENSP00000312844:R74H	R	+	2	0	RGS3	115286270	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.047000	0.11963	-0.907000	0.03862	-1.851000	0.00568	CGC		0.512	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
RGS3	5998	broad.mit.edu	37	9	116259663	116259663	+	Missense_Mutation	SNP	C	C	T	rs564374250		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:116259663C>T	ENST00000374140.2	+	10	1029	c.820C>T	c.(820-822)Cgg>Tgg	p.R274W	RGS3_ENST00000317613.6_Missense_Mutation_p.R162W|RGS3_ENST00000350696.5_Missense_Mutation_p.R274W	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	274					inactivation of MAPK activity (GO:0000188)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.R170W(2)|p.R274W(2)		cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						GGTGGCCAGGCGGCGACTGCG	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		19482	0.0		0.0	False		,,,				2504	0.001				p.R274W												.	.	4	Substitution - Missense(4)	large_intestine(2)|prostate(2)	c.C820T	9						.						64.0	58.0	60.0					9																	116259663		2203	4300	6503	115299484	SO:0001583	missense	5998	exon10			AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.820C>T	9.37:g.116259663C>T	ENSP00000363255:p.Arg274Trp	Somatic		Capture	Illumina HiSeq	Phase_I	115299484	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.034177	0.75617	.	.	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000317613	T;T;T	0.51325	0.71;0.71;1.09	5.69	4.78	0.61160	.	0.178973	0.38959	N	0.001504	T	0.64843	0.2635	M	0.62723	1.935	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	T	0.67968	-0.5533	10	0.87932	D	0	.	12.6469	0.56740	0.2985:0.7015:0.0:0.0	.	164;162;274	B3KWG8;P49796-5;P49796	.;.;RGS3_HUMAN	W	274;274;162	ENSP00000363255:R274W;ENSP00000259406:R274W;ENSP00000312844:R162W	ENSP00000312844:R162W	R	+	1	2	RGS3	115299484	0.806000	0.28996	0.998000	0.56505	0.993000	0.82548	1.116000	0.31221	1.364000	0.46038	0.650000	0.86243	CGG		0.622	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
RGS3	5998	broad.mit.edu	37	9	116357881	116357881	+	Missense_Mutation	SNP	G	G	A	rs375907877		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:116357881G>A	ENST00000374140.2	+	25	3456	c.3247G>A	c.(3247-3249)Ggg>Agg	p.G1083R	RGS3_ENST00000343817.5_Missense_Mutation_p.G802R|RGS3_ENST00000350696.5_Missense_Mutation_p.G1083R|RGS3_ENST00000342620.5_Missense_Mutation_p.G53R|RGS3_ENST00000374134.3_Missense_Mutation_p.G404R|RGS3_ENST00000462403.1_Missense_Mutation_p.G196R|RGS3_ENST00000394646.3_Missense_Mutation_p.G476R|RGS3_ENST00000462143.1_Missense_Mutation_p.G404R	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	1083	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				inactivation of MAPK activity (GO:0000188)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.G1083R(1)|p.G1083W(1)|p.G196R(1)|p.G196W(1)|p.G979W(1)|p.G979R(1)		cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						CCTCACAGACGGGTTAGCAGT	0.522																																					p.G1083R												.	.	6	Substitution - Missense(6)	large_intestine(3)|lung(3)	c.G3247A	9						.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	157.0	129.0	139.0		1210,2404,157,3247,586	5.4	0.9	9		139	0,8600		0,0,4300	no	missense,missense,missense,missense,missense	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4,NM_144489.2	125,125,125,125,125	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	404/520,802/918,53/169,1083/1199,196/312	116357881	1,13005	2203	4300	6503	115397702	SO:0001583	missense	5998	exon25			AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.3247G>A	9.37:g.116357881G>A	ENSP00000363255:p.Gly1083Arg	Somatic		Capture	Illumina HiSeq	Phase_I	115397702	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.245691	0.80024	2.27E-4	0.0	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000343817;ENST00000394646;ENST00000474719;ENST00000462143;ENST00000342620;ENST00000374134;ENST00000462403	T;T;T;T;T;T;T;T	0.02944	4.1;4.1;4.1;4.1;4.1;4.1;4.1;4.1	5.37	5.37	0.77165	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);Regulator of G-protein signaling, domain 1 (1);	0.000000	0.64402	D	0.000001	T	0.26846	0.0657	H	0.96430	3.82	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	0.994;0.999;1.0;1.0;1.0;1.0	T	0.41770	-0.9490	10	0.87932	D	0	.	18.1493	0.89669	0.0:0.0:1.0:0.0	.	476;196;979;802;973;1083	B3KUB2;Q5VZ06;P49796-6;P49796-4;B3KWG8;P49796	.;.;.;.;.;RGS3_HUMAN	R	1083;1083;802;476;251;404;53;404;196	ENSP00000363255:G1083R;ENSP00000259406:G1083R;ENSP00000340284:G802R;ENSP00000378141:G476R;ENSP00000420356:G404R;ENSP00000343359:G53R;ENSP00000363249:G404R;ENSP00000436168:G196R	ENSP00000343359:G53R	G	+	1	0	RGS3	115397702	1.000000	0.71417	0.890000	0.34922	0.332000	0.28634	9.799000	0.99117	2.507000	0.84556	0.456000	0.33151	GGG		0.522	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
ZNF618	114991	broad.mit.edu	37	9	116811804	116811804	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:116811804C>T	ENST00000374126.5	+	15	2321	c.2222C>T	c.(2221-2223)cCg>cTg	p.P741L	ZNF618_ENST00000470105.1_3'UTR|ZNF618_ENST00000288466.7_Missense_Mutation_p.P648L			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	741					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.P648L(1)		breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						ATCCTGACGCCGGTGAAGCAG	0.602																																					p.P648L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1943T	9						.						35.0	38.0	37.0					9																	116811804		2133	4229	6362	115851625	SO:0001583	missense	114991	exon14			BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"""Zinc fingers, C2H2-type"""	29416	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 10"""					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.2222C>T	9.37:g.116811804C>T	ENSP00000363241:p.Pro741Leu	Somatic		Capture	Illumina HiSeq	Phase_I	115851625	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Missense_Mutation	SNP	ENST00000374126.5	37		.	.	.	.	.	.	.	.	.	.	C	19.87	3.908141	0.72868	.	.	ENSG00000157657	ENST00000374126;ENST00000288466	T;T	0.26373	1.74;1.74	5.03	5.03	0.67393	Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.54143	0.1840	.	.	.	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.992;0.998;0.999	T	0.59451	-0.7452	9	0.87932	D	0	-19.7971	17.7125	0.88326	0.0:1.0:0.0:0.0	.	708;741;648	B9EG82;Q5T7W0;Q5T7W0-2	.;ZN618_HUMAN;.	L	741;648	ENSP00000363241:P741L;ENSP00000288466:P648L	ENSP00000288466:P648L	P	+	2	0	ZNF618	115851625	1.000000	0.71417	0.842000	0.33263	0.968000	0.65278	7.221000	0.78016	2.503000	0.84419	0.561000	0.74099	CCG		0.602	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
ORM1	5004	broad.mit.edu	37	9	117087392	117087392	+	Missense_Mutation	SNP	G	G	A	rs139631990		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:117087392G>A	ENST00000259396.8	+	5	578	c.500G>A	c.(499-501)cGc>cAc	p.R167H	ORM1_ENST00000477456.1_3'UTR	NM_000607.2	NP_000598.2	P02763	A1AG1_HUMAN	orosomucoid 1	167			R -> C (in dbSNP:rs3182034). {ECO:0000269|PubMed:15489334}.		acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.R167H(1)		endometrium(2)|large_intestine(4)|lung(2)	8		Myeloproliferative disorder(63;0.163)			Abiraterone(DB05812)|Acenocoumarol(DB01418)|Ajmaline(DB01426)|Alfentanil(DB00802)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aprindine(DB01429)|Bupropion(DB01156)|Canagliflozin(DB08907)|Celecoxib(DB00482)|Chlorpromazine(DB00477)|Desipramine(DB01151)|Disopyramide(DB00280)|Doxazosin(DB00590)|Doxepin(DB01142)|Erlotinib(DB00530)|Fluoxetine(DB00472)|Gefitinib(DB00317)|Imatinib(DB00619)|Imipramine(DB00458)|Ivacaftor(DB08820)|Maprotiline(DB00934)|Mirabegron(DB08893)|Nateglinide(DB00731)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxycodone(DB00497)|Penbutolol(DB01359)|Pethidine(DB00454)|Phenprocoumon(DB00946)|Pitavastatin(DB08860)|Prazosin(DB00457)|Propranolol(DB00571)|Quinidine(DB00908)|Saquinavir(DB01232)|Tacrolimus(DB00864)|Tamsulosin(DB00706)|Telaprevir(DB05521)|Thalidomide(DB01041)|Trazodone(DB00656)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Vismodegib(DB08828)|Warfarin(DB00682)	GACTGCTTGCGCATTCCCAAG	0.562																																					p.R167H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G500A	9						.						132.0	145.0	141.0					9																	117087392		2203	4300	6503	116127213	SO:0001583	missense	5004	exon5				CCDS6803.1	9q32	2013-09-19			ENSG00000229314	ENSG00000229314		"""Lipocalins"""	8498	protein-coding gene	gene with protein product		138600					Standard	NM_000607		Approved		uc004bik.4	P02763	OTTHUMG00000021012	ENST00000259396.8:c.500G>A	9.37:g.117087392G>A	ENSP00000259396:p.Arg167His	Somatic		Capture	Illumina HiSeq	Phase_I	116127213	NM_000607	B7ZKQ5|Q5T539|Q5U067|Q8TC16	Missense_Mutation	SNP	ENST00000259396.8	37	CCDS6803.1	.	.	.	.	.	.	.	.	.	.	-	10.59	1.393706	0.25205	.	.	ENSG00000229314	ENST00000259396	T	0.09723	2.95	4.24	1.82	0.25136	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.463309	0.24305	N	0.039689	T	0.03739	0.0106	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37686	-0.9695	10	0.52906	T	0.07	-18.8371	7.1315	0.25504	0.2735:0.0:0.7265:0.0	.	167	P02763	A1AG1_HUMAN	H	167	ENSP00000259396:R167H	ENSP00000259396:R167H	R	+	2	0	ORM1	116127213	0.024000	0.19004	0.005000	0.12908	0.039000	0.13416	0.065000	0.14466	0.250000	0.21479	-1.026000	0.02426	CGC		0.562	ORM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055426.1		
DFNB31	25861	broad.mit.edu	37	9	117228645	117228645	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:117228645A>G	ENST00000362057.3	-	3	1033	c.865T>C	c.(865-867)Tcc>Ccc	p.S289P	DFNB31_ENST00000265134.6_5'UTR	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	289	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)		p.S289P(1)		central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						AGGCCCAGGGACCGGCCGTCC	0.627																																					p.S289P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T865C	9						.						71.0	72.0	72.0					9																	117228645		2203	4300	6503	116268466	SO:0001583	missense	25861	exon3			AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"""whirlin"""	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.865T>C	9.37:g.117228645A>G	ENSP00000354623:p.Ser289Pro	Somatic		Capture	Illumina HiSeq	Phase_I	116268466	NM_015404	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Missense_Mutation	SNP	ENST00000362057.3	37	CCDS6806.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.449458	0.84101	.	.	ENSG00000095397	ENST00000362057	T	0.17213	2.29	5.01	5.01	0.66863	PDZ/DHR/GLGF (4);	0.052033	0.85682	D	0.000000	T	0.27489	0.0675	L	0.28054	0.825	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74348	0.983;0.977	T	0.02352	-1.1172	10	0.35671	T	0.21	-23.8709	13.996	0.64402	1.0:0.0:0.0:0.0	.	289;289	B9EGE6;Q9P202	.;WHRN_HUMAN	P	289	ENSP00000354623:S289P	ENSP00000354623:S289P	S	-	1	0	DFNB31	116268466	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	6.651000	0.74372	2.006000	0.58801	0.402000	0.26972	TCC		0.627	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404	
C9orf91	203197	broad.mit.edu	37	9	117379514	117379514	+	Silent	SNP	C	C	T	rs376587972		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:117379514C>T	ENST00000288502.4	+	2	476	c.39C>T	c.(37-39)ggC>ggT	p.G13G	AL160275.1_ENST00000606438.1_RNA|Y_RNA_ENST00000364879.1_RNA|C9orf91_ENST00000374049.4_Silent_p.G13G|C9orf91_ENST00000471206.1_3'UTR			Q5VZI3	CI091_HUMAN	chromosome 9 open reading frame 91	13						integral component of membrane (GO:0016021)		p.G13G(1)		endometrium(2)|large_intestine(3)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	13						GGGCCACTGGCCCATTGCCCC	0.617																																					p.G13G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C39T	9						.	C		0,4406		0,0,2203	35.0	40.0	38.0		39	0.4	0.2	9		38	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C9orf91	NM_153045.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		13/343	117379514	1,13005	2203	4300	6503	116419335	SO:0001819	synonymous_variant	203197	exon2			BX649023	CCDS6808.1	9q33.1	2008-02-05			ENSG00000157693	ENSG00000157693			24513	protein-coding gene	gene with protein product						14702039	Standard	NM_153045		Approved	DKFZp547P234, FLJ38045	uc004bjd.4	Q5VZI3	OTTHUMG00000020541	ENST00000288502.4:c.39C>T	9.37:g.117379514C>T		Somatic		Capture	Illumina HiSeq	Phase_I	116419335	NM_153045	A0PJA3|Q3KNS4|Q5VZI2|Q6P5Z7|Q8N1P3|Q8ND43	Silent	SNP	ENST00000288502.4	37	CCDS6808.1																																																																																				0.617	C9orf91-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000053780.1	NM_153045	
TNFSF15	9966	broad.mit.edu	37	9	117553069	117553069	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:117553069A>C	ENST00000374045.4	-	4	532	c.419T>G	c.(418-420)cTg>cGg	p.L140R	TNFSF15_ENST00000374044.1_Missense_Mutation_p.L63R|AL390240.1_ENST00000408807.1_RNA	NM_001204344.1|NM_005118.3	NP_001191273.1|NP_005109.2	O95150	TNF15_HUMAN	tumor necrosis factor (ligand) superfamily, member 15	140					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cytokine metabolic process (GO:0042107)|immune response (GO:0006955)|positive regulation of cytokine secretion (GO:0050715)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.L140R(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(1)	11						CTCTGGGATCAGCAGGAATTT	0.488																																					p.L140R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T419G	9						.						115.0	111.0	112.0					9																	117553069		2203	4300	6503	116592890	SO:0001583	missense	9966	exon4			AF039390	CCDS6809.1	9q32	2008-07-21			ENSG00000181634	ENSG00000181634		"""Tumor necrosis factor (ligand) superfamily"""	11931	protein-coding gene	gene with protein product	"""vascular endothelial cell growth inhibitor"", ""TNF superfamily ligand TL1A"", ""TNF ligand-related molecule 1"", ""vascular endothelial growth inhibitor-192A"""	604052				9434163	Standard	NM_005118		Approved	TL1, VEGI, TL1A, VEGI192A, MGC129934, MGC129935	uc004bjh.3	O95150	OTTHUMG00000021011	ENST00000374045.4:c.419T>G	9.37:g.117553069A>C	ENSP00000363157:p.Leu140Arg	Somatic		Capture	Illumina HiSeq	Phase_I	116592890	NM_005118	Q3SX69|Q5VJK8|Q5VWH1|Q8NFE9	Missense_Mutation	SNP	ENST00000374045.4	37	CCDS6809.1	.	.	.	.	.	.	.	.	.	.	A	10.11	1.259487	0.23051	.	.	ENSG00000181634	ENST00000374045;ENST00000374044	D;D	0.94497	-3.44;-3.44	5.93	5.93	0.95920	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.430200	0.23859	N	0.043876	D	0.86422	0.5929	N	0.24115	0.695	0.24682	N	0.993358	P;P	0.43392	0.805;0.627	B;B	0.33339	0.162;0.155	T	0.80919	-0.1167	10	0.45353	T	0.12	-14.0029	6.6588	0.23002	0.7918:0.0:0.0712:0.137	.	140;81	O95150;O95150-2	TNF15_HUMAN;.	R	140;63	ENSP00000363157:L140R;ENSP00000363156:L63R	ENSP00000363156:L63R	L	-	2	0	TNFSF15	116592890	1.000000	0.71417	1.000000	0.80357	0.613000	0.37349	3.895000	0.56258	2.271000	0.75665	0.533000	0.62120	CTG		0.488	TNFSF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055424.2	NM_005118	
TNC	3371	broad.mit.edu	37	9	117836064	117836064	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:117836064T>C	ENST00000350763.4	-	10	3443	c.3032A>G	c.(3031-3033)aAa>aGa	p.K1011R	TNC_ENST00000341037.4_Missense_Mutation_p.K1011R|TNC_ENST00000535648.1_Missense_Mutation_p.K1011R|TNC_ENST00000346706.3_Missense_Mutation_p.K1011R|TNC_ENST00000542877.1_Missense_Mutation_p.K1011R|TNC_ENST00000423613.2_Missense_Mutation_p.K1011R|TNC_ENST00000340094.3_Missense_Mutation_p.K1011R|TNC_ENST00000345230.3_Missense_Mutation_p.K1011R|TNC_ENST00000537320.1_Missense_Mutation_p.K1011R	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1011	Fibronectin type-III 5. {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.K1011R(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						GCGGTCAAATTTGGCCAACGG	0.557																																					p.K1011R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3032G	9						.						84.0	83.0	83.0					9																	117836064		2203	4300	6503	116875885	SO:0001583	missense	3371	exon10				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.3032A>G	9.37:g.117836064T>C	ENSP00000265131:p.Lys1011Arg	Somatic		Capture	Illumina HiSeq	Phase_I	116875885	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.052850	0.75960	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36	5.85	5.85	0.93711	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.046277	0.85682	D	0.000000	T	0.63931	0.2553	L	0.45422	1.42	0.58432	D	0.999994	P;P	0.49961	0.859;0.93	P;P	0.61722	0.759;0.893	T	0.63088	-0.6715	10	0.46703	T	0.11	.	16.2186	0.82243	0.0:0.0:0.0:1.0	.	1011;1011	E9PC84;P24821	.;TENA_HUMAN	R	1011	ENSP00000344400:K1011R;ENSP00000438152:K1011R;ENSP00000344555:K1011R;ENSP00000345861:K1011R;ENSP00000265131:K1011R;ENSP00000339553:K1011R;ENSP00000411406:K1011R;ENSP00000443478:K1011R;ENSP00000442242:K1011R	ENSP00000344400:K1011R	K	-	2	0	TNC	116875885	1.000000	0.71417	1.000000	0.80357	0.768000	0.43524	7.542000	0.82095	2.238000	0.73509	0.459000	0.35465	AAA		0.557	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
TNC	3371	broad.mit.edu	37	9	117849181	117849181	+	Missense_Mutation	SNP	C	C	T	rs145121881	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:117849181C>T	ENST00000350763.4	-	3	1240	c.829G>A	c.(829-831)Gat>Aat	p.D277N	TNC_ENST00000341037.4_Missense_Mutation_p.D277N|TNC_ENST00000535648.1_Missense_Mutation_p.D277N|TNC_ENST00000346706.3_Missense_Mutation_p.D277N|TNC_ENST00000542877.1_Missense_Mutation_p.D277N|TNC_ENST00000423613.2_Missense_Mutation_p.D277N|TNC_ENST00000340094.3_Missense_Mutation_p.D277N|TNC_ENST00000345230.3_Missense_Mutation_p.D277N|TNC_ENST00000537320.1_Missense_Mutation_p.D277N	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	277	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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.D277N(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						TTGCAGTCATCGCCTGCAAAG	0.567																																					p.D277N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G829A	9						.	C	ASN/ASP	5,4401	11.4+/-27.6	0,5,2198	182.0	132.0	149.0		829	2.1	0.0	9	dbSNP_134	149	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TNC	NM_002160.3	23	0,6,6497	TT,TC,CC		0.0116,0.1135,0.0461	benign	277/2202	117849181	6,13000	2203	4300	6503	116889002	SO:0001583	missense	3371	exon3				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.829G>A	9.37:g.117849181C>T	ENSP00000265131:p.Asp277Asn	Somatic		Capture	Illumina HiSeq	Phase_I	116889002	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	C	7.782	0.709697	0.15239	0.001135	1.16E-4	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.03524	3.91;3.91;3.9;3.91;3.91;3.91;3.91;3.91;3.91	5.13	2.14	0.27477	EGF, extracellular (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);	0.766799	0.12916	N	0.428517	T	0.04907	0.0132	L	0.31926	0.97	0.09310	N	1	P;P	0.51147	0.942;0.657	P;B	0.45406	0.479;0.217	T	0.38950	-0.9637	10	0.59425	D	0.04	.	11.1001	0.48168	0.1356:0.6032:0.2613:0.0	.	277;277	E9PC84;P24821	.;TENA_HUMAN	N	277	ENSP00000344400:D277N;ENSP00000438152:D277N;ENSP00000344555:D277N;ENSP00000345861:D277N;ENSP00000265131:D277N;ENSP00000339553:D277N;ENSP00000411406:D277N;ENSP00000443478:D277N;ENSP00000442242:D277N	ENSP00000344400:D277N	D	-	1	0	TNC	116889002	0.001000	0.12720	0.041000	0.18516	0.027000	0.11550	0.434000	0.21494	0.365000	0.24400	0.563000	0.77884	GAT		0.567	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
CDK5RAP2	55755	broad.mit.edu	37	9	123199604	123199604	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:123199604C>T	ENST00000349780.4	-	25	4103	c.3924G>A	c.(3922-3924)ctG>ctA	p.L1308L	CDK5RAP2_ENST00000359309.3_Silent_p.L1267L|CDK5RAP2_ENST00000360190.4_Silent_p.L1308L|CDK5RAP2_ENST00000360822.3_Silent_p.L1276L	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	1308					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)	p.L1308L(1)		breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						ATTTCTCCAGCAGCTCAGCAC	0.493																																					p.L1308L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3924A	9						.						159.0	120.0	133.0					9																	123199604		2203	4300	6503	122239425	SO:0001819	synonymous_variant	55755	exon25			BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.3924G>A	9.37:g.123199604C>T		Somatic		Capture	Illumina HiSeq	Phase_I	122239425	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Silent	SNP	ENST00000349780.4	37	CCDS6823.1																																																																																				0.493	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249	
CDK5RAP2	55755	broad.mit.edu	37	9	123220814	123220814	+	Silent	SNP	G	G	A	rs36001459	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:123220814G>A	ENST00000349780.4	-	20	2468	c.2289C>T	c.(2287-2289)caC>caT	p.H763H	CDK5RAP2_ENST00000359309.3_Silent_p.H763H|CDK5RAP2_ENST00000360190.4_Silent_p.H763H|CDK5RAP2_ENST00000360822.3_Silent_p.H731H	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	763					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)	p.H763H(1)		breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						AGCCAGGTGCGTGGGCCCCAT	0.453													G|||	5	0.000998403	0.0008	0.0	5008	,	,		20098	0.0		0.001	False		,,,				2504	0.0031				p.H763H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2289T	9						.	G	,	0,4406		0,0,2203	103.0	99.0	100.0		2289,2289	1.4	0.0	9	dbSNP_126	100	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous	CDK5RAP2	NM_001011649.1,NM_018249.4	,	0,12,6491	AA,AG,GG		0.1395,0.0,0.0923	,	763/1815,763/1894	123220814	12,12994	2203	4300	6503	122260635	SO:0001819	synonymous_variant	55755	exon20			BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.2289C>T	9.37:g.123220814G>A		Somatic		Capture	Illumina HiSeq	Phase_I	122260635	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Silent	SNP	ENST00000349780.4	37	CCDS6823.1																																																																																				0.453	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249	
PSMD5	5711	broad.mit.edu	37	9	123593725	123593725	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:123593725G>T	ENST00000210313.3	-	4	519	c.445C>A	c.(445-447)Ctg>Atg	p.L149M	PSMD5_ENST00000373904.5_Intron|PSMD5-AS1_ENST00000589026.1_RNA	NM_001270427.1|NM_005047.3	NP_001257356.1|NP_005038.1	Q16401	PSMD5_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5	149					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 regulatory particle assembly (GO:0070682)|protein folding (GO:0006457)|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)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)		p.L149M(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|prostate(1)	10						ATTCTTGACAGGGATTTGATA	0.343																																					p.L149M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C445A	9						.						120.0	112.0	115.0					9																	123593725		2203	4300	6503	122633546	SO:0001583	missense	5711	exon4			AK001065	CCDS6824.1, CCDS59143.1	9q34.11	2008-02-05			ENSG00000095261	ENSG00000095261		"""Proteasome (prosome, macropain) subunits"""	9563	protein-coding gene	gene with protein product		604452				7559544	Standard	NM_005047		Approved	S5B, KIAA0072	uc004bko.4	Q16401	OTTHUMG00000020573	ENST00000210313.3:c.445C>A	9.37:g.123593725G>T	ENSP00000210313:p.Leu149Met	Somatic		Capture	Illumina HiSeq	Phase_I	122633546	NM_005047	B4DZM8|Q15045|Q4VXG8	Missense_Mutation	SNP	ENST00000210313.3	37	CCDS6824.1	.	.	.	.	.	.	.	.	.	.	G	16.97	3.267877	0.59540	.	.	ENSG00000095261	ENST00000210313	T	0.51325	0.71	5.68	3.84	0.44239	Armadillo-like helical (1);Armadillo-type fold (1);	0.145987	0.45867	D	0.000324	T	0.60038	0.2238	M	0.72118	2.19	0.80722	D	1	D	0.60160	0.987	D	0.64321	0.924	T	0.59220	-0.7495	10	0.51188	T	0.08	.	6.5456	0.22404	0.1512:0.0:0.704:0.1448	.	149	Q16401	PSMD5_HUMAN	M	149	ENSP00000210313:L149M	ENSP00000210313:L149M	L	-	1	2	PSMD5	122633546	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.233000	0.43027	0.863000	0.35553	0.650000	0.86243	CTG		0.343	PSMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053825.2	NM_005047	
DAB2IP	153090	broad.mit.edu	37	9	124530781	124530781	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:124530781C>T	ENST00000408936.3	+	10	1950	c.1768C>T	c.(1768-1770)Cgc>Tgc	p.R590C	DAB2IP_ENST00000259371.2_Missense_Mutation_p.R562C|DAB2IP_ENST00000309989.1_Missense_Mutation_p.R466C			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	590					activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|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)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)	p.R466C(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						CAACATGCAGCGCTTCCTGCT	0.572																																					p.R562C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1684T	9						.						137.0	121.0	127.0					9																	124530781		2203	4300	6503	123570602	SO:0001583	missense	153090	exon10			AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"""nGAP-like protein"", ""DOC-2/DAB2 interactive protein"", ""ASK-interacting protein"", ""ASK1-interacting protein 1"""	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.1768C>T	9.37:g.124530781C>T	ENSP00000386183:p.Arg590Cys	Somatic		Capture	Illumina HiSeq	Phase_I	123570602	NM_032552	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Missense_Mutation	SNP	ENST00000408936.3	37		.	.	.	.	.	.	.	.	.	.	C	19.01	3.744115	0.69418	.	.	ENSG00000136848	ENST00000259371;ENST00000408936;ENST00000373782;ENST00000309989	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	4.82	4.82	0.62117	Rho GTPase activation protein (1);Ras GTPase-activating protein (2);	0.054579	0.64402	D	0.000001	T	0.25791	0.0628	L	0.55103	1.725	0.80722	D	1	D;B	0.76494	0.999;0.354	P;B	0.51806	0.68;0.06	T	0.01074	-1.1460	10	0.87932	D	0	.	11.2618	0.49087	0.2912:0.7088:0.0:0.0	.	590;562	Q5VWQ8;G3XA90	DAB2P_HUMAN;.	C	562;590;499;466	ENSP00000259371:R562C;ENSP00000386183:R590C;ENSP00000362887:R499C;ENSP00000310827:R466C	ENSP00000259371:R562C	R	+	1	0	DAB2IP	123570602	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	2.568000	0.45965	2.391000	0.81399	0.557000	0.71058	CGC		0.572	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552	
DAB2IP	153090	broad.mit.edu	37	9	124544647	124544647	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:124544647G>A	ENST00000408936.3	+	16	3622	c.3440G>A	c.(3439-3441)cGc>cAc	p.R1147H	DAB2IP_ENST00000259371.2_Missense_Mutation_p.R1119H|DAB2IP_ENST00000309989.1_Missense_Mutation_p.R1023H			Q5VWQ8	DAB2P_HUMAN	DAB2 interacting protein	1147					activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|angiogenesis (GO:0001525)|cell cycle (GO:0007049)|cell motility involved in cerebral cortex radial glia guided migration (GO:0021814)|cellular protein catabolic process (GO:0044257)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|layer formation in cerebral cortex (GO:0021819)|negative regulation of angiogenesis (GO:0016525)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of G0 to G1 transition (GO:0070317)|negative regulation of GTPase activity (GO:0034260)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase activity (GO:0043553)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|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)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuron projection morphogenesis (GO:0048812)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of dendrite development (GO:1900006)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron migration (GO:2001224)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of synapse maturation (GO:0090129)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of ARF GTPase activity (GO:0032312)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein complex assembly (GO:0043254)|response to unfolded protein (GO:0006986)|transformed cell apoptotic process (GO:0006927)|tube formation (GO:0035148)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	axon (GO:0030424)|cerebellar mossy fiber (GO:0044300)|climbing fiber (GO:0044301)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|neuronal cell body (GO:0043025)|neuronal cell body membrane (GO:0032809)|parallel fiber (GO:1990032)|plasma membrane (GO:0005886)	14-3-3 protein binding (GO:0071889)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|mitogen-activated protein kinase kinase binding (GO:0031434)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase 2A binding (GO:0051721)|Ras GTPase activator activity (GO:0005099)|SH3 domain binding (GO:0017124)|signaling adaptor activity (GO:0035591)|vascular endothelial growth factor receptor 2 binding (GO:0043184)	p.R1023H(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(8)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	27						GCCAATGCCCGCCTCATGAGT	0.572																																					p.R1119H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3356A	9						.						144.0	129.0	134.0					9																	124544647		2203	4300	6503	123584468	SO:0001583	missense	153090	exon16			AF367051	CCDS6832.1, CCDS6833.2	9q33.1-q33.3	2008-07-21			ENSG00000136848	ENSG00000136848			17294	protein-coding gene	gene with protein product	"""nGAP-like protein"", ""DOC-2/DAB2 interactive protein"", ""ASK-interacting protein"", ""ASK1-interacting protein 1"""	609205				11944990, 11812785	Standard	XM_005251721		Approved	AF9Q34, DIP1/2, KIAA1743, AIP1	uc004bln.3	Q5VWQ8	OTTHUMG00000020595	ENST00000408936.3:c.3440G>A	9.37:g.124544647G>A	ENSP00000386183:p.Arg1147His	Somatic		Capture	Illumina HiSeq	Phase_I	123584468	NM_032552	A6H8V2|A6NHI9|B0QZB1|G3XA90|Q8TDL2|Q96SE1|Q9C0C0	Missense_Mutation	SNP	ENST00000408936.3	37		.	.	.	.	.	.	.	.	.	.	G	22.6	4.312756	0.81358	.	.	ENSG00000136848	ENST00000259371;ENST00000408936;ENST00000373782;ENST00000309989	T;T;T;T	0.16597	2.33;2.33;2.33;2.33	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.45013	0.1321	M	0.79123	2.44	0.58432	D	0.999999	B;D	0.89917	0.056;1.0	B;D	0.79784	0.027;0.993	T	0.48340	-0.9044	10	0.87932	D	0	.	17.4385	0.87559	0.0:0.0:1.0:0.0	.	1147;1119	Q5VWQ8;G3XA90	DAB2P_HUMAN;.	H	1119;1147;1056;1023	ENSP00000259371:R1119H;ENSP00000386183:R1147H;ENSP00000362887:R1056H;ENSP00000310827:R1023H	ENSP00000259371:R1119H	R	+	2	0	DAB2IP	123584468	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.745000	0.98856	2.357000	0.79964	0.455000	0.32223	CGC		0.572	DAB2IP-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317857.1	NM_032552	
PDCL	5082	broad.mit.edu	37	9	125588985	125588985	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:125588985C>T	ENST00000259467.4	-	2	247	c.82G>A	c.(82-84)Gag>Aag	p.E28K		NM_005388.4	NP_005379.3	Q13371	PHLP_HUMAN	phosducin-like	28					heterotrimeric G-protein complex assembly (GO:1902605)|intracellular signal transduction (GO:0035556)|negative regulation of protein refolding (GO:0061084)|protein folding (GO:0006457)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|visual perception (GO:0007601)	cytoplasm (GO:0005737)	receptor signaling protein activity (GO:0005057)	p.E28K(1)		endometrium(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	10						TCCTTGTCCTCGTGGTCACTG	0.532																																					p.E28K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G82A	9						.						149.0	120.0	130.0					9																	125588985		2203	4300	6503	124628806	SO:0001583	missense	5082	exon2			AF083325	CCDS6845.1	9q12-q13	2008-07-21			ENSG00000136940	ENSG00000136940			8770	protein-coding gene	gene with protein product		604421				10095058	Standard	NM_005388		Approved	PhLP, DKFZp564M1863	uc004bmz.2	Q13371	OTTHUMG00000020624	ENST00000259467.4:c.82G>A	9.37:g.125588985C>T	ENSP00000259467:p.Glu28Lys	Somatic		Capture	Illumina HiSeq	Phase_I	124628806	NM_005388	Q4VXB6|Q96AF1|Q9UEW7|Q9UFL0|Q9UNX1|Q9UNX2	Missense_Mutation	SNP	ENST00000259467.4	37	CCDS6845.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.69|18.69	3.678492|3.678492	0.68042|0.68042	.|.	.|.	ENSG00000136940|ENSG00000136940	ENST00000259467|ENST00000394285	T|.	0.47869|.	0.83|.	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	0.092482|.	0.64402|.	D|.	0.000001|.	T|T	0.69043|0.69043	0.3067|0.3067	L|L	0.48362|0.48362	1.52|1.52	0.80722|0.80722	D|D	1|1	B;B|.	0.15141|.	0.012;0.012|.	B;B|.	0.08055|.	0.003;0.003|.	T|T	0.65043|0.65043	-0.6264|-0.6264	9|5	.|.	.|.	.|.	-19.8572|-19.8572	18.4395|18.4395	0.90660|0.90660	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	28;28|.	Q4VXB6;Q13371|.	.;PHLP_HUMAN|.	K|Q	28|16	ENSP00000259467:E28K|.	.|.	E|R	-|-	1|2	0|0	PDCL|PDCL	124628806|124628806	1.000000|1.000000	0.71417|0.71417	0.954000|0.954000	0.39281|0.39281	0.837000|0.837000	0.47467|0.47467	5.453000|5.453000	0.66645|0.66645	2.577000|2.577000	0.86979|0.86979	0.655000|0.655000	0.94253|0.94253	GAG|CGA		0.532	PDCL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053956.1	NM_005388	
RC3H2	54542	broad.mit.edu	37	9	125621109	125621109	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:125621109G>A	ENST00000373670.1	-	11	2722	c.2122C>T	c.(2122-2124)Cga>Tga	p.R708*	RC3H2_ENST00000357244.2_Nonsense_Mutation_p.R708*|RC3H2_ENST00000423239.2_Nonsense_Mutation_p.R708*			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	708					B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R708*(1)		breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						ATGTCATCTCGTTGGTACATA	0.478																																					p.R708X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2122T	9						.						136.0	134.0	135.0					9																	125621109		1933	4142	6075	124660930	SO:0001587	stop_gained	54542	exon12			AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCCH-type domain containing"""	21461	protein-coding gene	gene with protein product		615231	"""membrane associated DNA binding protein"", ""ring finger and CCCH-type zinc finger domains 2"""	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.2122C>T	9.37:g.125621109G>A	ENSP00000362774:p.Arg708*	Somatic		Capture	Illumina HiSeq	Phase_I	124660930	NM_018835	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Nonsense_Mutation	SNP	ENST00000373670.1	37	CCDS43874.1	.	.	.	.	.	.	.	.	.	.	G	40	7.965678	0.98585	.	.	ENSG00000056586	ENST00000373670;ENST00000357244;ENST00000373663;ENST00000423239	.	.	.	5.39	5.39	0.77823	.	0.115799	0.64402	D	0.000020	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.4201	16.327	0.82987	0.0:0.0:1.0:0.0	.	.	.	.	X	708;708;579;708	.	ENSP00000349783:R708X	R	-	1	2	RC3H2	124660930	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.662000	0.46766	2.525000	0.85131	0.655000	0.94253	CGA		0.478	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835	
DENND1A	57706	broad.mit.edu	37	9	126146018	126146018	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:126146018C>T	ENST00000373624.2	-	21	1953	c.1752G>A	c.(1750-1752)ctG>ctA	p.L584L	DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000394219.3_Silent_p.L595L|DENND1A_ENST00000542603.1_Silent_p.L369L	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	584					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.L584L(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						CCAGTGGCTGCAGTGCGGCCT	0.622																																					p.L584L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1752A	9						.						77.0	71.0	73.0					9																	126146018		2203	4300	6503	125185839	SO:0001819	synonymous_variant	57706	exon21			AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"""DENN/MADD domain containing"""	29324	protein-coding gene	gene with protein product		613633	"""KIAA1608"""	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.1752G>A	9.37:g.126146018C>T		Somatic		Capture	Illumina HiSeq	Phase_I	125185839	NM_020946	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Silent	SNP	ENST00000373624.2	37	CCDS35133.1																																																																																				0.622	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820	
LHX2	9355	broad.mit.edu	37	9	126777417	126777417	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:126777417C>T	ENST00000373615.4	+	3	1079	c.340C>T	c.(340-342)Cgc>Tgc	p.R114C		NM_004789.3	NP_004780.3	P50458	LHX2_HUMAN	LIM homeobox 2	114					axon extension (GO:0048675)|axon guidance (GO:0007411)|cerebral cortex development (GO:0021987)|dorsal/ventral pattern formation (GO:0009953)|mesoderm development (GO:0007498)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|neural tube closure (GO:0001843)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|retina development in camera-type eye (GO:0060041)|telencephalon regionalization (GO:0021978)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.R114C(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)	10						CTCTGTGCAGCGCTGCGCCCG	0.637																																					p.R114C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C340T	9						.						65.0	67.0	67.0					9																	126777417		2203	4300	6503	125817238	SO:0001583	missense	9355	exon3			U11701	CCDS6853.1	9q33.3	2011-06-20			ENSG00000106689	ENSG00000106689		"""Homeoboxes / LIM class"""	6594	protein-coding gene	gene with protein product		603759				8649822, 10051612	Standard	NM_004789		Approved	LH-2, hLhx2	uc004boe.1	P50458	OTTHUMG00000020647	ENST00000373615.4:c.340C>T	9.37:g.126777417C>T	ENSP00000362717:p.Arg114Cys	Somatic		Capture	Illumina HiSeq	Phase_I	125817238	NM_004789	O95860|Q52M57|Q8N1Z3	Missense_Mutation	SNP	ENST00000373615.4	37	CCDS6853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.6|21.6	4.166087|4.166087	0.78339|0.78339	.|.	.|.	ENSG00000106689|ENSG00000106689	ENST00000446480|ENST00000373615	.|D	.|0.88201	.|-2.35	4.55|4.55	4.55|4.55	0.56014|0.56014	.|Zinc finger, LIM-type (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.93278|0.93278	0.7858|0.7858	M|M	0.84156|0.84156	2.68|2.68	0.58432|0.58432	D|D	0.999995|0.999995	.|D;D	.|0.89917	.|0.989;1.0	.|P;D	.|0.65443	.|0.531;0.935	D|D	0.93004|0.93004	0.6426|0.6426	5|10	.|0.51188	.|T	.|0.08	.|.	10.25|10.25	0.43364|0.43364	0.3125:0.6875:0.0:0.0|0.3125:0.6875:0.0:0.0	.|.	.|114;114	.|B3KNJ5;P50458	.|.;LHX2_HUMAN	V|C	119|114	.|ENSP00000362717:R114C	.|ENSP00000362717:R114C	A|R	+|+	2|1	0|0	LHX2|LHX2	125817238|125817238	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	2.766000|2.766000	0.47629|0.47629	2.347000|2.347000	0.79759|0.79759	0.561000|0.561000	0.74099|0.74099	GCG|CGC		0.637	LHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054010.2		
NEK6	10783	broad.mit.edu	37	9	127089684	127089684	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:127089684C>T	ENST00000320246.5	+	7	727	c.582C>T	c.(580-582)ggC>ggT	p.G194G	NEK6_ENST00000539416.1_Silent_p.G219G|NEK6_ENST00000545174.1_Silent_p.G194G|NEK6_ENST00000540326.1_Silent_p.G212G|NEK6_ENST00000373603.1_Silent_p.G194G|NEK6_ENST00000546191.1_Silent_p.G194G|NEK6_ENST00000394199.2_Silent_p.G228G|NEK6_ENST00000373600.3_Silent_p.G228G	NM_014397.5	NP_055212.2	Q9HC98	NEK6_HUMAN	NIMA-related kinase 6	194	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cellular senescence (GO:2000772)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|signal transduction (GO:0007165)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinesin binding (GO:0019894)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)	p.G187G(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)	15						TTGGTCTGGGCCGCTTCTTCA	0.637																																					p.G212G	NSCLC(122;934 1785 18647 44295 45571)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C636T	9						.						216.0	190.0	199.0					9																	127089684		2203	4300	6503	126129505	SO:0001819	synonymous_variant	10783	exon7			AF087909	CCDS6854.1, CCDS48015.1, CCDS55338.1, CCDS55339.1	9q33.3-q34.11	2012-11-15	2012-11-15		ENSG00000119408	ENSG00000119408			7749	protein-coding gene	gene with protein product	"""putative serine-threonine protein kinase"""	604884	"""NIMA (never in mitosis gene a)-related kinase 6"""			10702691	Standard	NM_001145001		Approved	SID6-1512	uc004boh.3	Q9HC98	OTTHUMG00000020650	ENST00000320246.5:c.582C>T	9.37:g.127089684C>T		Somatic		Capture	Illumina HiSeq	Phase_I	126129505	NM_001166167	B7Z2D9|Q5TBG3|Q5TBG9|Q6FG86|Q6IAR3|Q96E83|Q9ULX2	Silent	SNP	ENST00000320246.5	37	CCDS6854.1																																																																																				0.637	NEK6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054016.1	NM_014397	
FAM129B	64855	broad.mit.edu	37	9	130270408	130270408	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:130270408C>T	ENST00000373312.3	-	12	1719	c.1506G>A	c.(1504-1506)ccG>ccA	p.P502P	FAM129B_ENST00000468379.1_Intron|FAM129B_ENST00000373314.3_Silent_p.P489P	NM_022833.2	NP_073744.2	Q96TA1	NIBL1_HUMAN	family with sequence similarity 129, member B	502					negative regulation of apoptotic process (GO:0043066)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P502P(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						TGAGCAGGAACGGGATGCTGA	0.627																																					p.P502P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1506A	9						.						65.0	69.0	67.0					9																	130270408		2203	4300	6503	129310229	SO:0001819	synonymous_variant	64855	exon12			AF151783	CCDS35144.1, CCDS35145.1	9q34.13	2010-02-01	2006-11-23	2006-11-23	ENSG00000136830	ENSG00000136830			25282	protein-coding gene	gene with protein product		614045	"""chromosome 9 open reading frame 88"""	C9orf88		14702039, 19362540	Standard	XM_005252135		Approved	DKFZP434H0820, FLJ13518, FLJ22151, FLJ22298, bA356B19.6, MINERVA	uc004brh.3	Q96TA1	OTTHUMG00000020705	ENST00000373312.3:c.1506G>A	9.37:g.130270408C>T		Somatic		Capture	Illumina HiSeq	Phase_I	129310229	NM_022833	Q4LE55|Q5VVW6|Q5VVW7|Q9BUS2|Q9NT35	Silent	SNP	ENST00000373312.3	37	CCDS35145.1																																																																																				0.627	FAM129B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054196.1	NM_022833	
ENG	2022	broad.mit.edu	37	9	130580414	130580414	+	Silent	SNP	G	G	A	rs369135742		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:130580414G>A	ENST00000373203.4	-	12	2071	c.1671C>T	c.(1669-1671)acC>acT	p.T557T	ENG_ENST00000344849.3_Silent_p.T557T|RP11-228B15.4_ENST00000439298.1_RNA|ENG_ENST00000480266.1_5'UTR|RP11-228B15.4_ENST00000425991.1_RNA	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	557	Ser/Thr-rich.				artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in endocardial cushion formation (GO:0003273)|cell motility (GO:0048870)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|chronological cell aging (GO:0001300)|detection of hypoxia (GO:0070483)|extracellular matrix constituent secretion (GO:0070278)|extracellular matrix disassembly (GO:0022617)|heart looping (GO:0001947)|intracellular signal transduction (GO:0035556)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|patterning of blood vessels (GO:0001569)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of gene expression (GO:0010628)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of phosphorylation (GO:0042325)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to corticosteroid (GO:0031960)|response to hypoxia (GO:0001666)|response to statin (GO:0036273)|response to transforming growth factor beta (GO:0071559)|smooth muscle tissue development (GO:0048745)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	activin binding (GO:0048185)|galactose binding (GO:0005534)|glycosaminoglycan binding (GO:0005539)|protein homodimerization activity (GO:0042803)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane signaling receptor activity (GO:0004888)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)	p.T557T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	17						CTTGAGACCCGGTCTTGGGAC	0.637									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia																												p.T557T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1671T	9						.	G	,	0,4406		0,0,2203	55.0	53.0	54.0		1671,1671	2.9	0.0	9		54	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ENG	NM_000118.2,NM_001114753.1	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	557/626,557/659	130580414	1,13005	2203	4300	6503	129620235	SO:0001819	synonymous_variant	2022	exon12	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	AF035753	CCDS6880.1, CCDS48029.1, CCDS75906.1	9q34.11	2014-09-17	2008-09-04		ENSG00000106991	ENSG00000106991		"""CD molecules"""	3349	protein-coding gene	gene with protein product		131195	"""Osler-Rendu-Weber syndrome 1"""	ORW1, ORW		8404038, 10548503	Standard	NM_001278138		Approved	END, HHT1, CD105	uc031tfe.1	P17813	OTTHUMG00000020723	ENST00000373203.4:c.1671C>T	9.37:g.130580414G>A		Somatic		Capture	Illumina HiSeq	Phase_I	129620235	NM_001114753	Q14248|Q14926|Q5T9C0	Silent	SNP	ENST00000373203.4	37	CCDS48029.1																																																																																				0.637	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1		
ST6GALNAC6	30815	broad.mit.edu	37	9	130652968	130652968	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:130652968C>T	ENST00000373146.1	-	5	831	c.652G>A	c.(652-654)Ggc>Agc	p.G218S	ST6GALNAC6_ENST00000291839.5_Missense_Mutation_p.G218S|ST6GALNAC6_ENST00000485320.1_5'UTR|ST6GALNAC6_ENST00000542456.1_Intron|ST6GALNAC6_ENST00000373142.1_Missense_Mutation_p.G218S|ST6GALNAC6_ENST00000373144.3_Missense_Mutation_p.G184S|ST6GALNAC6_ENST00000373141.1_Missense_Mutation_p.G184S			Q969X2	SIA7F_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	218					cell-cell recognition (GO:0009988)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide metabolic process (GO:0006677)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)	p.G218S(1)		endometrium(3)|large_intestine(3)|lung(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CGCATGCGGCCGGGAGAGACG	0.652																																					p.G218S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G652A	9						.						42.0	44.0	43.0					9																	130652968		2203	4297	6500	129692789	SO:0001583	missense	30815	exon5			BC006564	CCDS6882.1, CCDS69668.1, CCDS69669.1, CCDS75908.1	9q34.13	2013-03-01		2005-02-07	ENSG00000160408	ENSG00000160408		"""Sialyltransferases"""	23364	protein-coding gene	gene with protein product		610135	"""sialytransferase 7 ((alpha-N-acetylneuraminyl 2,3-betagalactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialytransferase) F"""	SIAT7F		12668675	Standard	XM_005251952		Approved	ST6GALNACVI	uc004bso.1	Q969X2	OTTHUMG00000020718	ENST00000373146.1:c.652G>A	9.37:g.130652968C>T	ENSP00000362239:p.Gly218Ser	Somatic		Capture	Illumina HiSeq	Phase_I	129692789	NM_013443	B3KQ01|Q5T9C4|Q5T9C5|Q9H8A2|Q9ULB8	Missense_Mutation	SNP	ENST00000373146.1	37	CCDS6882.1	.	.	.	.	.	.	.	.	.	.	C	3.092	-0.186656	0.06340	.	.	ENSG00000160408	ENST00000373146;ENST00000373141;ENST00000373142;ENST00000373144;ENST00000291839;ENST00000447681	T;T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;1.65;1.65	5.81	-4.26	0.03755	.	0.954309	0.08833	N	0.886972	T	0.11067	0.0270	N	0.04297	-0.235	0.20563	N	0.999881	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.40590	-0.9555	10	0.08179	T	0.78	-0.2583	9.5821	0.39495	0.0:0.3583:0.0972:0.5445	.	184;218	Q969X2-2;Q969X2	.;SIA7F_HUMAN	S	218;184;218;184;218;184	ENSP00000362239:G218S;ENSP00000362234:G184S;ENSP00000362235:G218S;ENSP00000362237:G184S;ENSP00000291839:G218S;ENSP00000405326:G184S	ENSP00000291839:G218S	G	-	1	0	ST6GALNAC6	129692789	0.000000	0.05858	0.110000	0.21437	0.265000	0.26407	-0.293000	0.08320	-0.707000	0.05022	-0.302000	0.09304	GGC		0.652	ST6GALNAC6-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054278.1	NM_013443	
FAM102A	399665	broad.mit.edu	37	9	130716179	130716179	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:130716179G>A	ENST00000373095.1	-	2	547	c.172C>T	c.(172-174)Cgg>Tgg	p.R58W		NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	58								p.R58W(1)		breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						TTTCGCCACCGCACACAGTTC	0.612																																					p.R58W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C172T	9						.						89.0	80.0	83.0					9																	130716179		2203	4300	6503	129756000	SO:0001583	missense	399665	exon2				CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"""sym-3 homolog A (C. elegans)"""	610891	"""chromosome 9 open reading frame 132"""	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.172C>T	9.37:g.130716179G>A	ENSP00000362187:p.Arg58Trp	Somatic		Capture	Illumina HiSeq	Phase_I	129756000	NM_001035254	A2A329|Q8TEL4	Missense_Mutation	SNP	ENST00000373095.1	37	CCDS35150.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.981365	0.74474	.	.	ENSG00000167106	ENST00000373095	T	0.45668	0.89	5.9	5.9	0.94986	.	0.112416	0.64402	D	0.000007	T	0.40570	0.1122	L	0.43701	1.375	0.80722	D	1	B	0.26081	0.141	B	0.22880	0.042	T	0.19614	-1.0300	10	0.62326	D	0.03	-19.424	18.8411	0.92184	0.0:0.0:1.0:0.0	.	58	Q5T9C2	F102A_HUMAN	W	58	ENSP00000362187:R58W	ENSP00000362187:R58W	R	-	1	2	FAM102A	129756000	1.000000	0.71417	0.987000	0.45799	0.997000	0.91878	7.880000	0.87243	2.788000	0.95919	0.655000	0.94253	CGG		0.612	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2		
PTGES2	80142	broad.mit.edu	37	9	130883508	130883508	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:130883508G>A	ENST00000338961.6	-	7	1794	c.1050C>T	c.(1048-1050)ttC>ttT	p.F350F	PTGES2_ENST00000483625.1_5'Flank|RP11-395P17.3_ENST00000418747.1_RNA|RP11-395P17.3_ENST00000536815.1_RNA|PTGES2_ENST00000277462.5_Silent_p.F159F	NM_001256335.1|NM_025072.6	NP_001243264.1|NP_079348.1	Q9H7Z7	PGES2_HUMAN	prostaglandin E synthase 2	350	GST C-terminal.				cell redox homeostasis (GO:0045454)|positive regulation of transcription, DNA-templated (GO:0045893)|prostaglandin biosynthetic process (GO:0001516)|secretion (GO:0046903)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|glutathione binding (GO:0043295)|heme binding (GO:0020037)|lyase activity (GO:0016829)|prostaglandin-E synthase activity (GO:0050220)|protein disulfide oxidoreductase activity (GO:0015035)	p.F350F(1)		endometrium(1)|large_intestine(1)|lung(2)	4						TCAGGTCATCGAACGCATCCA	0.627																																					p.F350F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1050T	9						.						110.0	80.0	90.0					9																	130883508		2200	4299	6499	129923329	SO:0001819	synonymous_variant	80142	exon7			AK024100	CCDS6891.1	9q34.12	2008-05-06	2002-06-13	2002-06-14	ENSG00000148334	ENSG00000148334			17822	protein-coding gene	gene with protein product		608152	"""chromosome 9 open reading frame 15"""	C9orf15		11866447	Standard	NM_025072		Approved	FLJ14038	uc004bti.4	Q9H7Z7	OTTHUMG00000020730	ENST00000338961.6:c.1050C>T	9.37:g.130883508G>A		Somatic		Capture	Illumina HiSeq	Phase_I	129923329	NM_025072	Q53EW9|Q5SYV6|Q96GI0|Q96GL2	Silent	SNP	ENST00000338961.6	37	CCDS6891.1																																																																																				0.627	PTGES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054339.1		
DNM1	1759	broad.mit.edu	37	9	130982522	130982522	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:130982522G>A	ENST00000372923.3	+	6	843	c.751G>A	c.(751-753)Gcc>Acc	p.A251T	DNM1_ENST00000393594.3_Missense_Mutation_p.A251T|DNM1_ENST00000475805.1_Missense_Mutation_p.A251T|DNM1_ENST00000486160.1_Missense_Mutation_p.A251T|DNM1_ENST00000341179.7_Missense_Mutation_p.A251T	NM_004408.2	NP_004399.2	Q05193	DYN1_HUMAN	dynamin 1	251	Dynamin-type G.				endocytosis (GO:0006897)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)	extracellular vesicular exosome (GO:0070062)|membrane coat (GO:0030117)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.A251T(4)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(15)|lung(6)|ovary(2)|urinary_tract(2)	32						CATTACCGCCGCCTTGGCTGC	0.542																																					p.A251T	GBM(113;146 1575 2722 28670 29921)											.	.	4	Substitution - Missense(4)	large_intestine(4)	c.G751A	9						.						188.0	172.0	178.0					9																	130982522		2203	4300	6503	130022343	SO:0001583	missense	1759	exon6			L07807	CCDS6895.1, CCDS43882.1, CCDS75911.1, CCDS75912.1	9q34	2013-01-10			ENSG00000106976	ENSG00000106976		"""Pleckstrin homology (PH) domain containing"""	2972	protein-coding gene	gene with protein product		602377		DNM		2144893, 9143509	Standard	XM_005251763		Approved		uc022bob.1	Q05193	OTTHUMG00000020733	ENST00000372923.3:c.751G>A	9.37:g.130982522G>A	ENSP00000362014:p.Ala251Thr	Somatic		Capture	Illumina HiSeq	Phase_I	130022343	NM_001005336	A6NLM6|Q5SYX0|Q5SYX2|Q6P3T6|Q86VD2	Missense_Mutation	SNP	ENST00000372923.3	37	CCDS6895.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.502424	0.85176	.	.	ENSG00000106976	ENST00000475805;ENST00000341179;ENST00000372923;ENST00000393589;ENST00000393594;ENST00000486160	T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11	5.71	5.71	0.89125	Dynamin central domain (1);	0.099589	0.64402	D	0.000001	D	0.90854	0.7127	M	0.90705	3.14	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.998	D	0.92020	0.5625	10	0.87932	D	0	-14.6002	19.8432	0.96699	0.0:0.0:1.0:0.0	.	251;251;251	Q05193;Q05193-3;Q05193-2	DYN1_HUMAN;.;.	T	251;251;251;246;251;251	ENSP00000419225:A251T;ENSP00000345680:A251T;ENSP00000362014:A251T;ENSP00000377219:A251T;ENSP00000420045:A251T	ENSP00000345680:A251T	A	+	1	0	DNM1	130022343	1.000000	0.71417	0.956000	0.39512	0.194000	0.23727	9.835000	0.99442	2.700000	0.92200	0.462000	0.41574	GCC		0.542	DNM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054367.1	NM_004408	
GOLGA2	2801	broad.mit.edu	37	9	131019662	131019662	+	Missense_Mutation	SNP	G	G	A	rs201662917		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:131019662G>A	ENST00000421699.2	-	25	2792	c.2780C>T	c.(2779-2781)gCc>gTc	p.A927V	AL590708.1_ENST00000408370.1_RNA|GOLGA2_ENST00000609374.1_Missense_Mutation_p.A915V	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	927					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)		p.A915V(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						CTGCTGGTTGGCAGCCCCAAG	0.662																																					p.A927V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2780T	9						.	G	VAL/ALA	0,4402		0,0,2201	19.0	23.0	22.0		2780	0.8	0.0	9		22	3,8585		0,3,4291	no	missense	GOLGA2	NM_004486.4	64	0,3,6492	AA,AG,GG		0.0349,0.0,0.0231	benign	927/1003	131019662	3,12987	2201	4294	6495	130059483	SO:0001583	missense	2801	exon25			L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"""Golgi matrix protein GM130"", ""SY11 protein"""	602580	"""golgi autoantigen, golgin subfamily a, 2"""			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.2780C>T	9.37:g.131019662G>A	ENSP00000416097:p.Ala927Val	Somatic		Capture	Illumina HiSeq	Phase_I	130059483	NM_004486	Q6GRM9|Q9BRB0|Q9NYF9	Missense_Mutation	SNP	ENST00000421699.2	37	CCDS6896.2	.	.	.	.	.	.	.	.	.	.	g	11.85	1.762696	0.31228	0.0	3.49E-4	ENSG00000167110	ENST00000421699;ENST00000342583	T	0.23950	1.88	4.8	0.823	0.18812	.	1.289190	0.04856	N	0.443258	T	0.19525	0.0469	L	0.41906	1.305	0.09310	N	1	B;B	0.30236	0.274;0.002	B;B	0.28709	0.093;0.009	T	0.26538	-1.0100	10	0.52906	T	0.07	.	1.3231	0.02120	0.2519:0.1493:0.4459:0.153	.	927;545	Q08379;Q08379-2	GOGA2_HUMAN;.	V	927;211	ENSP00000416097:A927V	ENSP00000342692:A211V	A	-	2	0	GOLGA2	130059483	0.005000	0.15991	0.000000	0.03702	0.002000	0.02628	1.492000	0.35594	-0.124000	0.11724	0.555000	0.69702	GCC		0.662	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486	
GOLGA2	2801	broad.mit.edu	37	9	131022860	131022860	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:131022860G>A	ENST00000421699.2	-	17	1573	c.1561C>T	c.(1561-1563)Cgc>Tgc	p.R521C	AL590708.1_ENST00000408370.1_RNA|GOLGA2_ENST00000609374.1_Missense_Mutation_p.R509C	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	521					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)		p.R509C(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						ATTTGCCTGCGCGCCTCCGCC	0.662																																					p.R521C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1561T	9						.						87.0	98.0	94.0					9																	131022860		2203	4300	6503	130062681	SO:0001583	missense	2801	exon17			L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"""Golgi matrix protein GM130"", ""SY11 protein"""	602580	"""golgi autoantigen, golgin subfamily a, 2"""			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.1561C>T	9.37:g.131022860G>A	ENSP00000416097:p.Arg521Cys	Somatic		Capture	Illumina HiSeq	Phase_I	130062681	NM_004486	Q6GRM9|Q9BRB0|Q9NYF9	Missense_Mutation	SNP	ENST00000421699.2	37	CCDS6896.2	.	.	.	.	.	.	.	.	.	.	g	19.27	3.796093	0.70567	.	.	ENSG00000167110	ENST00000421699	T	0.31769	1.48	5.31	4.39	0.52855	.	0.114616	0.56097	D	0.000039	T	0.54631	0.1870	M	0.79805	2.47	0.51767	D	0.999935	D	0.89917	1.0	D	0.69307	0.963	T	0.57183	-0.7855	10	0.42905	T	0.14	.	12.969	0.58501	0.0:0.0:0.5804:0.4195	.	521	Q08379	GOGA2_HUMAN	C	521	ENSP00000416097:R521C	ENSP00000416097:R521C	R	-	1	0	GOLGA2	130062681	1.000000	0.71417	0.011000	0.14972	0.879000	0.50718	2.631000	0.46502	1.183000	0.42943	0.313000	0.20887	CGC		0.662	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486	
GOLGA2	2801	broad.mit.edu	37	9	131024929	131024929	+	Silent	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:131024929C>A	ENST00000421699.2	-	13	978	c.966G>T	c.(964-966)cgG>cgT	p.R322R	GOLGA2_ENST00000609374.1_Silent_p.R310R	NM_004486.4	NP_004477.3	Q08379	GOGA2_HUMAN	golgin A2	322					mitotic cell cycle (GO:0000278)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)		p.R310R(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34						TCACTAGGACCCGAAGCTTCT	0.468																																					p.R322R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G966T	9						.						125.0	110.0	115.0					9																	131024929		2203	4300	6503	130064750	SO:0001819	synonymous_variant	2801	exon13			L06147	CCDS6896.2	9q34.13	2010-06-28	2010-02-12		ENSG00000167110	ENSG00000167110			4425	protein-coding gene	gene with protein product	"""Golgi matrix protein GM130"", ""SY11 protein"""	602580	"""golgi autoantigen, golgin subfamily a, 2"""			8315394	Standard	NM_004486		Approved	GM130, golgin-95	uc011maw.2	Q08379	OTTHUMG00000020732	ENST00000421699.2:c.966G>T	9.37:g.131024929C>A		Somatic		Capture	Illumina HiSeq	Phase_I	130064750	NM_004486	Q6GRM9|Q9BRB0|Q9NYF9	Silent	SNP	ENST00000421699.2	37	CCDS6896.2																																																																																				0.468	GOLGA2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054358.2	NM_004486	
SPTAN1	6709	broad.mit.edu	37	9	131374040	131374040	+	Silent	SNP	C	C	T	rs539062498		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:131374040C>T	ENST00000372731.4	+	37	4916	c.4806C>T	c.(4804-4806)aaC>aaT	p.N1602N	SPTAN1_ENST00000372739.3_Silent_p.N1607N|SPTAN1_ENST00000358161.5_Silent_p.N1607N	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1602					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.N1602N(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						TGCATGCCAACGCTGACCGGA	0.507													C|||	1	0.000199681	0.0	0.0	5008	,	,		18492	0.001		0.0	False		,,,				2504	0.0				p.N1582N	NSCLC(120;833 1744 2558 35612 37579)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4746T	9						.						72.0	62.0	65.0					9																	131374040		2203	4300	6503	130413861	SO:0001819	synonymous_variant	6709	exon36			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.4806C>T	9.37:g.131374040C>T		Somatic		Capture	Illumina HiSeq	Phase_I	130413861	NM_001195532	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																				0.507	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
ZER1	10444	broad.mit.edu	37	9	131513413	131513413	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:131513413C>T	ENST00000291900.2	-	7	1579	c.1173G>A	c.(1171-1173)ctG>ctA	p.L391L	snoU13_ENST00000459043.1_RNA|ZER1_ENST00000494461.1_5'Flank	NM_006336.2	NP_006327.2	Q7Z7L7	ZER1_HUMAN	zyg-11 related, cell cycle regulator	391					protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein transferase activity (GO:0051438)	Cul2-RING ubiquitin ligase complex (GO:0031462)	ubiquitin-protein transferase activity (GO:0004842)	p.L391L(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	15						TCAGGGCCCGCAGCAGCTGGT	0.652																																					p.L391L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1173A	9						.						36.0	33.0	34.0					9																	131513413		2201	4299	6500	130553234	SO:0001819	synonymous_variant	10444	exon7			X99802	CCDS6910.1	9q33.3	2013-01-17	2012-12-10	2007-01-04	ENSG00000160445	ENSG00000160445		"""ZYG11 cell cycle regulator family"""	30960	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 60"", ""zyg-11 homolog B (C. elegans)-like"", ""zer-1 homolog (C. elegans)"""	C9orf60, ZYG11BL		11719588	Standard	NM_006336		Approved	ZYG, Hzyg	uc004bwa.2	Q7Z7L7	OTTHUMG00000020759	ENST00000291900.2:c.1173G>A	9.37:g.131513413C>T		Somatic		Capture	Illumina HiSeq	Phase_I	130553234	NM_006336	O00156|Q5T272|Q5T273	Silent	SNP	ENST00000291900.2	37	CCDS6910.1																																																																																				0.652	ZER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054491.1	NM_006336	
TBC1D13	54662	broad.mit.edu	37	9	131568287	131568287	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:131568287C>T	ENST00000372648.5	+	10	1218	c.1068C>T	c.(1066-1068)tgC>tgT	p.C356C	TBC1D13_ENST00000539497.1_Silent_p.C175C|TBC1D13_ENST00000223865.8_Silent_p.C231C	NM_018201.3	NP_060671.3	Q9NVG8	TBC13_HUMAN	TBC1 domain family, member 13	356							Rab GTPase activator activity (GO:0005097)	p.C356C(2)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	6						TCGTCTGCTGCGCCATGCTCA	0.617																																					p.C356C												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C1068T	9						.						96.0	66.0	77.0					9																	131568287		2203	4300	6503	130608108	SO:0001819	synonymous_variant	54662	exon10			AK001605	CCDS6911.1, CCDS69677.1	9q34.13	2013-07-09			ENSG00000107021	ENSG00000107021			25571	protein-coding gene	gene with protein product						22762500	Standard	XM_005252060		Approved	FLJ10743	uc010myj.3	Q9NVG8	OTTHUMG00000020760	ENST00000372648.5:c.1068C>T	9.37:g.131568287C>T		Somatic		Capture	Illumina HiSeq	Phase_I	130608108	NM_018201	A7E2E7|B3KW04|B9EGJ8|Q5T270|Q5T271	Silent	SNP	ENST00000372648.5	37	CCDS6911.1																																																																																				0.617	TBC1D13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054496.1	NM_018201	
CCBL1	883	broad.mit.edu	37	9	131595886	131595886	+	Missense_Mutation	SNP	G	G	A	rs377314110		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:131595886G>A	ENST00000302586.3	-	13	1408	c.1246C>T	c.(1246-1248)Cgg>Tgg	p.R416W	CCBL1_ENST00000436267.2_Missense_Mutation_p.R510W|CCBL1_ENST00000320665.6_Missense_Mutation_p.R366W|CCBL1_ENST00000483599.1_5'UTR	NM_001122671.1|NM_004059.4	NP_001116143.1|NP_004050.3	Q16773	KAT1_HUMAN	cysteine conjugate-beta lyase, cytoplasmic	416					cellular amino acid biosynthetic process (GO:0008652)|cellular modified amino acid metabolic process (GO:0006575)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine catabolic process (GO:0097053)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|glutamine-phenylpyruvate transaminase activity (GO:0047316)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-glutamine:pyruvate aminotransferase activity (GO:0047945)|L-phenylalanine-oxaloacetate transaminase activity (GO:0036141)|L-phenylalanine:pyruvate aminotransferase activity (GO:0047312)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)	p.R416W(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)	18					L-Glutamine(DB00130)	TTCCACTTCCGCAGCTTCTCG	0.587																																					p.R366W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1096T	9						.	G	TRP/ARG,TRP/ARG,TRP/ARG	1,4245		0,1,2122	85.0	97.0	93.0		1246,1096,1246	3.6	0.9	9		93	0,8478		0,0,4239	no	missense,missense,missense	CCBL1	NM_001122671.1,NM_001122672.1,NM_004059.4	101,101,101	0,1,6361	AA,AG,GG		0.0,0.0236,0.0079	probably-damaging,probably-damaging,probably-damaging	416/423,366/373,416/423	131595886	1,12723	2123	4239	6362	130635707	SO:0001583	missense	883	exon12			Y17448	CCDS43884.1, CCDS48038.1, CCDS75915.1	9q34.11	2008-03-11	2008-03-11		ENSG00000171097	ENSG00000171097	2.6.1.64		1564	protein-coding gene	gene with protein product	"""glutamine transaminase K"", ""kyneurenine aminotransferase"""	600547	"""cysteine conjugate-beta lyase; cytoplasmic (glutamine transaminase K, kyneurenine aminotransferase)"""			7883047	Standard	NM_001122671		Approved	KATI, GTK	uc004bwh.3	Q16773	OTTHUMG00000020767	ENST00000302586.3:c.1246C>T	9.37:g.131595886G>A	ENSP00000302227:p.Arg416Trp	Somatic		Capture	Illumina HiSeq	Phase_I	130635707	NM_001122672	Q5T275|Q8N191	Missense_Mutation	SNP	ENST00000302586.3	37	CCDS43884.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.762452	0.31228	2.36E-4	0.0	ENSG00000171097	ENST00000302586;ENST00000320665;ENST00000436267	T;D;T	0.81659	-1.0;-1.52;-1.03	5.46	3.57	0.40892	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.460130	0.24587	N	0.037242	D	0.82848	0.5126	M	0.66439	2.03	0.25006	N	0.99144	D;D;D;D	0.65815	0.989;0.989;0.995;0.989	B;B;P;B	0.52710	0.288;0.288;0.707;0.288	T	0.75614	-0.3257	10	0.72032	D	0.01	-11.2983	10.1486	0.42780	0.1645:0.0:0.8355:0.0	.	510;416;366;416	B7Z4W5;A8K563;Q16773-2;Q16773	.;.;.;KAT1_HUMAN	W	416;366;510	ENSP00000302227:R416W;ENSP00000317342:R366W;ENSP00000399415:R510W	ENSP00000302227:R416W	R	-	1	2	CCBL1	130635707	0.848000	0.29623	0.881000	0.34555	0.106000	0.19336	2.220000	0.42908	1.278000	0.44430	0.436000	0.28706	CGG		0.587	CCBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054521.2		
LRRC8A	56262	broad.mit.edu	37	9	131669596	131669596	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:131669596G>T	ENST00000259324.5	+	3	676	c.153G>T	c.(151-153)aaG>aaT	p.K51N	LRRC8A_ENST00000372600.4_Missense_Mutation_p.K51N|LRRC8A_ENST00000372599.3_Missense_Mutation_p.K51N	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	51					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.K51N(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						CCCAAGACAAGATGATCTGCC	0.587																																					p.K51N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G153T	9						.						88.0	71.0	77.0					9																	131669596		2203	4300	6503	130709417	SO:0001583	missense	56262	exon3			AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"""leucine rich repeat containing 8"""	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.153G>T	9.37:g.131669596G>T	ENSP00000259324:p.Lys51Asn	Somatic		Capture	Illumina HiSeq	Phase_I	130709417	NM_019594	Q6UXM2|Q8NCI0|Q9P2B1	Missense_Mutation	SNP	ENST00000259324.5	37	CCDS35155.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.652438	0.47362	.	.	ENSG00000136802	ENST00000372600;ENST00000372599;ENST00000259324	T;T;T	0.30714	1.52;1.52;1.52	5.56	5.56	0.83823	Leucine-rich repeat-containing protein 8, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.42268	0.1195	L	0.39147	1.195	0.58432	D	0.999991	D	0.63880	0.993	D	0.63488	0.915	T	0.11299	-1.0593	10	0.41790	T	0.15	.	11.8367	0.52327	0.0884:0.0:0.9116:0.0	.	51	Q8IWT6	LRC8A_HUMAN	N	51	ENSP00000361682:K51N;ENSP00000361680:K51N;ENSP00000259324:K51N	ENSP00000259324:K51N	K	+	3	2	LRRC8A	130709417	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	4.471000	0.60182	2.607000	0.88179	0.563000	0.77884	AAG		0.587	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594	
PHYHD1	254295	broad.mit.edu	37	9	131689360	131689360	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:131689360C>T	ENST00000372592.3	+	4	1010	c.77C>T	c.(76-78)gCg>gTg	p.A26V	PHYHD1_ENST00000421063.2_Missense_Mutation_p.A26V|PHYHD1_ENST00000308941.5_Missense_Mutation_p.A26V|PHYHD1_ENST00000353176.5_Missense_Mutation_p.A26V	NM_001100876.1	NP_001094346.1	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	26							dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)	p.A26V(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(1)|stomach(3)	10						TTCTTGTCTGCGGAAGAGTGT	0.542																																					p.A26V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C77T	9						.						209.0	172.0	185.0					9																	131689360		2203	4300	6503	130729181	SO:0001583	missense	254295	exon4			BC051300	CCDS6914.1, CCDS43885.1, CCDS43886.1	9q34.13	2010-08-13			ENSG00000175287	ENSG00000175287			23396	protein-coding gene	gene with protein product						12477932	Standard	NM_174933		Approved	MGC16638	uc004bwp.2	Q5SRE7	OTTHUMG00000020764	ENST00000372592.3:c.77C>T	9.37:g.131689360C>T	ENSP00000361673:p.Ala26Val	Somatic		Capture	Illumina HiSeq	Phase_I	130729181	NM_174933	A6PWN9|A6PWP0|B3KT57|B4E3X8|Q5SRE9|Q5SRF0|Q7Z623|Q7Z7P9|Q96GM4	Missense_Mutation	SNP	ENST00000372592.3	37	CCDS43885.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.476318	0.44044	.	.	ENSG00000175287	ENST00000372592;ENST00000428610;ENST00000308941;ENST00000419552;ENST00000353176;ENST00000426694;ENST00000421063	D;D;D;D;D;D;D	0.91124	-2.79;-2.79;-2.79;-2.79;-2.79;-2.79;-2.79	5.57	1.68	0.24146	.	0.283735	0.40302	N	0.001123	D	0.82287	0.5004	L	0.57536	1.79	0.23277	N	0.997991	P;P;D	0.56746	0.51;0.951;0.977	B;B;B	0.32724	0.102;0.06;0.151	T	0.73817	-0.3863	10	0.39692	T	0.17	-0.7651	6.1099	0.20094	0.1323:0.6587:0.0:0.209	.	26;26;26	Q5SRE7-2;Q5SRE7;Q5SRE7-3	.;PHYD1_HUMAN;.	V	26	ENSP00000361673:A26V;ENSP00000401016:A26V;ENSP00000309515:A26V;ENSP00000390568:A26V;ENSP00000340945:A26V;ENSP00000412377:A26V;ENSP00000409928:A26V	ENSP00000309515:A26V	A	+	2	0	PHYHD1	130729181	0.016000	0.18221	0.005000	0.12908	0.596000	0.36781	0.951000	0.29135	0.039000	0.15632	-0.182000	0.12963	GCG		0.542	PHYHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054506.2	NM_174933	
DOLK	22845	broad.mit.edu	37	9	131709023	131709023	+	Missense_Mutation	SNP	C	C	T	rs377658203		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:131709023C>T	ENST00000372586.3	-	1	875	c.560G>A	c.(559-561)cGc>cAc	p.R187H	NUP188_ENST00000372577.2_5'Flank|RP11-101E3.5_ENST00000482796.1_Intron	NM_014908.3	NP_055723.1	Q9UPQ8	DOLK_HUMAN	dolichol kinase	187					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.R187H(1)		breast(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	11						GGTGAAGCAGCGGGGCAGCAG	0.542																																					p.R187H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G560A	9						.						83.0	81.0	82.0					9																	131709023		2203	4300	6503	130748844	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.560G>A	9.37:g.131709023C>T	ENSP00000361667:p.Arg187His	Somatic		Capture	Illumina HiSeq	Phase_I	130748844	NM_014908	Q5SRE6	Missense_Mutation	SNP	ENST00000372586.3	37	CCDS6915.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.375916	0.82682	.	.	ENSG00000175283	ENST00000372586;ENST00000515348	D	0.90620	-2.7	5.07	5.07	0.68467	.	0.000000	0.64402	D	0.000005	D	0.94430	0.8208	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.93720	0.7032	10	0.38643	T	0.18	-0.0738	17.4448	0.87575	0.0:1.0:0.0:0.0	.	187	Q9UPQ8	DOLK_HUMAN	H	187	ENSP00000361667:R187H	ENSP00000361667:R187H	R	-	2	0	DOLK	130748844	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.487000	0.81328	2.327000	0.79052	0.462000	0.41574	CGC		0.542	DOLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054515.1	NM_014908	
FAM73B	84895	broad.mit.edu	37	9	131830103	131830103	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:131830103C>T	ENST00000358369.4	+	12	1448	c.1222C>T	c.(1222-1224)Cgg>Tgg	p.R408W	FAM73B_ENST00000406926.2_3'UTR|FAM73B_ENST00000277475.5_3'UTR	NM_032809.2	NP_116198.2	Q7L4E1	FA73B_HUMAN	family with sequence similarity 73, member B	408					bone development (GO:0060348)	integral component of membrane (GO:0016021)		p.R408W(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)	13						CTATGCCCTGCGGCCCGAGAC	0.637																																					p.R408W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1222T	9						.						47.0	41.0	43.0					9																	131830103		2202	4300	6502	130869924	SO:0001583	missense	84895	exon12			AK074127	CCDS6917.1	9q34.13	2008-02-05	2005-08-11	2005-08-11	ENSG00000148343	ENSG00000148343			23621	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 54"""	C9orf54			Standard	NM_032809		Approved	FLJ14596, FLJ00199	uc004bxa.3	Q7L4E1	OTTHUMG00000020770	ENST00000358369.4:c.1222C>T	9.37:g.131830103C>T	ENSP00000351138:p.Arg408Trp	Somatic		Capture	Illumina HiSeq	Phase_I	130869924	NM_032809	Q8NBM3|Q8TEJ6|Q969E6	Missense_Mutation	SNP	ENST00000358369.4	37	CCDS6917.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.428710	0.62844	.	.	ENSG00000148343	ENST00000358369	T	0.24538	1.85	5.44	3.39	0.38822	.	0.193788	0.53938	D	0.000052	T	0.44180	0.1281	L	0.57536	1.79	0.80722	D	1	D;D	0.89917	1.0;0.995	D;P	0.68765	0.96;0.773	T	0.36335	-0.9752	10	0.87932	D	0	-20.8946	12.2751	0.54730	0.4694:0.5306:0.0:0.0	.	472;408	B4DZP8;Q7L4E1	.;FA73B_HUMAN	W	408	ENSP00000351138:R408W	ENSP00000351138:R408W	R	+	1	2	FAM73B	130869924	1.000000	0.71417	0.998000	0.56505	0.421000	0.31385	3.465000	0.53064	0.646000	0.30693	0.655000	0.94253	CGG		0.637	FAM73B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054542.7	NM_032809	
ASB6	140459	broad.mit.edu	37	9	132400271	132400271	+	Missense_Mutation	SNP	G	G	A	rs145932765		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:132400271G>A	ENST00000277458.4	-	6	1229	c.1064C>T	c.(1063-1065)gCg>gTg	p.A355V	ASB6_ENST00000450050.2_Missense_Mutation_p.A276V|RP11-483H20.4_ENST00000455074.1_RNA|ASB6_ENST00000277459.4_3'UTR	NM_017873.3	NP_060343.1	Q9NWX5	ASB6_HUMAN	ankyrin repeat and SOCS box containing 6	355					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)		p.A355V(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	15		Ovarian(14;0.00556)				GATCTTTTCCGCCAGGCTGCC	0.592																																					p.A355V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1064T	9						.	G	VAL/ALA,VAL/ALA,	1,4405	2.1+/-5.4	0,1,2202	49.0	47.0	48.0		977,1064,	5.1	1.0	9	dbSNP_134	48	0,8600		0,0,4300	no	missense,missense,utr-3	ASB6	NM_001202403.1,NM_017873.3,NM_177999.2	64,64,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,	326/393,355/422,	132400271	1,13005	2203	4300	6503	131440092	SO:0001583	missense	140459	exon6				CCDS6924.1, CCDS6925.1, CCDS75919.1	9q34.13	2013-01-10	2011-01-25		ENSG00000148331	ENSG00000148331		"""Ankyrin repeat domain containing"""	17181	protein-coding gene	gene with protein product		615051	"""ankyrin repeat and SOCS box-containing 6"""				Standard	NM_017873		Approved		uc004byf.2	Q9NWX5	OTTHUMG00000020787	ENST00000277458.4:c.1064C>T	9.37:g.132400271G>A	ENSP00000277458:p.Ala355Val	Somatic		Capture	Illumina HiSeq	Phase_I	131440092	NM_017873	Q5SZB7|Q9BV15	Missense_Mutation	SNP	ENST00000277458.4	37	CCDS6924.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.318122	0.40996	2.27E-4	0.0	ENSG00000148331	ENST00000277458;ENST00000450050	T;T	0.70869	-0.52;0.77	5.06	5.06	0.68205	.	0.312268	0.33959	N	0.004386	T	0.54481	0.1861	N	0.24115	0.695	0.33220	D	0.554585	B;B;B	0.15473	0.007;0.013;0.013	B;B;B	0.08055	0.002;0.003;0.003	T	0.60520	-0.7247	10	0.46703	T	0.11	-8.3058	9.3642	0.38215	0.0952:0.0:0.9048:0.0	.	276;355;355	B4DRC4;A8K9U2;Q9NWX5	.;.;ASB6_HUMAN	V	355;276	ENSP00000277458:A355V;ENSP00000416172:A276V	ENSP00000277458:A355V	A	-	2	0	ASB6	131440092	0.989000	0.36119	0.957000	0.39632	0.838000	0.47535	2.359000	0.44142	2.635000	0.89317	0.462000	0.41574	GCG		0.592	ASB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054594.1	NM_017873	
ASB6	140459	broad.mit.edu	37	9	132400869	132400869	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:132400869C>T	ENST00000277458.4	-	5	746	c.581G>A	c.(580-582)cGt>cAt	p.R194H	ASB6_ENST00000450050.2_Missense_Mutation_p.R115H|RP11-483H20.4_ENST00000455074.1_RNA|ASB6_ENST00000277459.4_Missense_Mutation_p.V158I	NM_017873.3	NP_060343.1	Q9NWX5	ASB6_HUMAN	ankyrin repeat and SOCS box containing 6	194					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)		p.R194H(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	15		Ovarian(14;0.00556)				CAGTAAGAGACGAATGTTCTC	0.592																																					p.V158I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G472A	9						.						78.0	66.0	70.0					9																	132400869		2203	4300	6503	131440690	SO:0001583	missense	140459	exon4				CCDS6924.1, CCDS6925.1, CCDS75919.1	9q34.13	2013-01-10	2011-01-25		ENSG00000148331	ENSG00000148331		"""Ankyrin repeat domain containing"""	17181	protein-coding gene	gene with protein product		615051	"""ankyrin repeat and SOCS box-containing 6"""				Standard	NM_017873		Approved		uc004byf.2	Q9NWX5	OTTHUMG00000020787	ENST00000277458.4:c.581G>A	9.37:g.132400869C>T	ENSP00000277458:p.Arg194His	Somatic		Capture	Illumina HiSeq	Phase_I	131440690	NM_177999	Q5SZB7|Q9BV15	Missense_Mutation	SNP	ENST00000277458.4	37	CCDS6924.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.32|16.32	3.090111|3.090111	0.55968|0.55968	.|.	.|.	ENSG00000148331|ENSG00000148331	ENST00000277458;ENST00000450050|ENST00000277459	T;T|T	0.65549|0.58210	-0.16;-0.16|0.35	4.69|4.69	4.69|4.69	0.59074|0.59074	Ankyrin repeat-containing domain (4);|.	0.190303|.	0.47455|.	D|.	0.000223|.	T|T	0.31888|0.31888	0.0811|0.0811	.|.	.|.	.|.	0.52501|0.52501	D|D	0.999953|0.999953	D;D|B	0.76494|0.21753	0.999;0.999|0.06	D;D|B	0.69824|0.17433	0.966;0.966|0.018	T|T	0.19257|0.19257	-1.0311|-1.0311	9|8	0.72032|0.02654	D|T	0.01|1	-29.0663|-29.0663	16.7838|16.7838	0.85569|0.85569	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	115;194|158	B4DRC4;Q9NWX5|Q9NWX5-2	.;ASB6_HUMAN|.	H|I	194;115|158	ENSP00000277458:R194H;ENSP00000416172:R115H|ENSP00000277459:V158I	ENSP00000277458:R194H|ENSP00000277459:V158I	R|V	-|-	2|1	0|0	ASB6|ASB6	131440690|131440690	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.398000|0.398000	0.30690|0.30690	2.664000|2.664000	0.46783|0.46783	2.418000|2.418000	0.82041|0.82041	0.561000|0.561000	0.74099|0.74099	CGT|GTC		0.592	ASB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054594.1	NM_017873	
ASS1	445	broad.mit.edu	37	9	133364727	133364727	+	Silent	SNP	C	C	T	rs549085827		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:133364727C>T	ENST00000372394.1	+	13	1327	c.846C>T	c.(844-846)taC>taT	p.Y282Y	ASS1_ENST00000493984.2_3'UTR|ASS1_ENST00000352480.5_Silent_p.Y282Y|ASS1_ENST00000372393.3_Silent_p.Y282Y			P00966	ASSY_HUMAN	argininosuccinate synthase 1	282					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.Y282Y(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)	TAGGTATCTACGAGACCCCAG	0.453													C|||	1	0.000199681	0.0	0.0	5008	,	,		15959	0.001		0.0	False		,,,				2504	0.0				p.Y282Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C846T	9						.						85.0	92.0	90.0					9																	133364727		2203	4300	6503	132354548	SO:0001819	synonymous_variant	445	exon13			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.846C>T	9.37:g.133364727C>T		Somatic		Capture	Illumina HiSeq	Phase_I	132354548	NM_000050	Q6LDL2|Q86UZ0|Q96GT4	Silent	SNP	ENST00000372394.1	37	CCDS6933.1																																																																																				0.453	ASS1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054652.1	NM_000050	
EXOSC2	23404	broad.mit.edu	37	9	133569236	133569236	+	Missense_Mutation	SNP	C	C	A	rs140638723		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:133569236C>A	ENST00000372358.5	+	1	129	c.58C>A	c.(58-60)Cgc>Agc	p.R20S	EXOSC2_ENST00000372352.3_Missense_Mutation_p.R20S|EXOSC2_ENST00000372351.3_Missense_Mutation_p.R20S|EXOSC2_ENST00000546165.1_Missense_Mutation_p.R20S			Q13868	EXOS2_HUMAN	exosome component 2	20					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|7S RNA binding (GO:0008312)	p.R20S(1)		breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(13;0.0588)		OV - Ovarian serous cystadenocarcinoma(145;0.000324)		GAGACTGGGCCGCGACACTAA	0.587																																					p.R20S	Pancreas(134;1683 1824 10118 27928 31640)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C58A	9						.						43.0	42.0	42.0					9																	133569236		2203	4300	6503	132559057	SO:0001583	missense	23404	exon1			AK001916	CCDS6935.1, CCDS65160.1, CCDS65161.1	9q34	2008-02-05			ENSG00000130713	ENSG00000130713			17097	protein-coding gene	gene with protein product	"""homolog of yeast RRP4 (ribosomal RNA processing 4), 3' 5' exoribonuclease (RRP4)"""	602238				8600032, 1538749	Standard	XM_005272176		Approved	hRrp4p, Rrp4p, RRP4, p7	uc004bzu.2	Q13868	OTTHUMG00000020811	ENST00000372358.5:c.58C>A	9.37:g.133569236C>A	ENSP00000361433:p.Arg20Ser	Somatic		Capture	Illumina HiSeq	Phase_I	132559057	NM_014285	A3KFL3|B4DKK6|Q9NUY4	Missense_Mutation	SNP	ENST00000372358.5	37	CCDS6935.1	.	.	.	.	.	.	.	.	.	.	C	5.843	0.339776	0.11069	.	.	ENSG00000130713	ENST00000372358;ENST00000546165;ENST00000372352;ENST00000372351;ENST00000372350;ENST00000495699	.	.	.	6.17	6.17	0.99709	.	0.475764	0.23074	N	0.052224	T	0.24890	0.0604	N	0.01729	-0.75	0.40156	D	0.977006	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.27331	-1.0077	9	0.06494	T	0.89	-34.0061	14.6754	0.68975	0.1449:0.8551:0.0:0.0	.	20;20	B4DKK6;Q13868	.;EXOS2_HUMAN	S	20	.	ENSP00000361425:R20S	R	+	1	0	EXOSC2	132559057	0.001000	0.12720	0.930000	0.37139	0.101000	0.19017	0.304000	0.19228	2.941000	0.99782	0.655000	0.94253	CGC		0.587	EXOSC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054673.1	NM_014285	
LAMC3	10319	broad.mit.edu	37	9	133924508	133924508	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:133924508A>C	ENST00000361069.4	+	9	1754	c.1621A>C	c.(1621-1623)Aca>Cca	p.T541P	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	541	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)	p.T541P(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GGAGGAGCTCACAGCACCAGG	0.612																																					p.T541P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1621C	9						.						21.0	23.0	23.0					9																	133924508		2096	4065	6161	132914329	SO:0001583	missense	10319	exon9			AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.1621A>C	9.37:g.133924508A>C	ENSP00000354360:p.Thr541Pro	Somatic		Capture	Illumina HiSeq	Phase_I	132914329	NM_006059	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	.	.	.	.	.	.	.	.	.	.	A	7.262	0.605389	0.14002	.	.	ENSG00000050555	ENST00000361069;ENST00000355048	T	0.35973	1.28	4.78	-2.37	0.06643	Laminin B type IV (2);	1.073720	0.07004	N	0.823822	T	0.24392	0.0591	L	0.36672	1.1	0.09310	N	1	B	0.06786	0.001	B	0.15052	0.012	T	0.29397	-1.0013	10	0.45353	T	0.12	.	3.3562	0.07169	0.361:0.0:0.1785:0.4605	.	541	Q9Y6N6	LAMC3_HUMAN	P	541	ENSP00000354360:T541P	ENSP00000347156:T541P	T	+	1	0	LAMC3	132914329	0.000000	0.05858	0.017000	0.16124	0.232000	0.25224	0.073000	0.14640	-0.488000	0.06726	0.454000	0.30748	ACA		0.612	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
NUP214	8021	broad.mit.edu	37	9	134073079	134073079	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:134073079C>G	ENST00000359428.5	+	29	4342	c.4198C>G	c.(4198-4200)Cca>Gca	p.P1400A	NUP214_ENST00000411637.2_Missense_Mutation_p.P1390A|NUP214_ENST00000483497.2_Missense_Mutation_p.P226A|NUP214_ENST00000451030.1_Missense_Mutation_p.P1401A|NUP214_ENST00000465486.2_3'UTR			P35658	NU214_HUMAN	nucleoporin 214kDa	1400	11 X 5 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|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)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)	p.P1400A(1)		NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		AGTAGCACCACCAGCAGCCAC	0.572			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																p.P1400A	Pancreas(4;24 48 25510 30394 32571)		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4198G	9						.						68.0	67.0	67.0					9																	134073079		2203	4300	6503	133062900	SO:0001583	missense	8021	exon29			X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.4198C>G	9.37:g.134073079C>G	ENSP00000352400:p.Pro1400Ala	Somatic		Capture	Illumina HiSeq	Phase_I	133062900	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	C	4.969	0.179915	0.09443	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605;ENST00000483497;ENST00000531600;ENST00000541688	T;T;T;T;T	0.38887	1.59;1.59;1.59;1.11;1.12	4.82	-4.12	0.03916	.	1.011940	0.07947	N	0.980334	T	0.14313	0.0346	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.19331	0.0;0.035;0.0;0.0;0.0	B;B;B;B;B	0.19946	0.002;0.027;0.001;0.001;0.003	T	0.30090	-0.9990	10	0.02654	T	1	0.6306	2.4092	0.04420	0.2007:0.2386:0.4172:0.1435	.	226;829;994;1390;1400	B7ZAV2;F5H131;Q5JUP9;P35658-4;P35658	.;.;.;.;NU214_HUMAN	A	1400;1390;1401;1379;994;829;226;177;177	ENSP00000352400:P1400A;ENSP00000396576:P1390A;ENSP00000405014:P1401A;ENSP00000436793:P226A;ENSP00000435364:P177A	ENSP00000352400:P1400A	P	+	1	0	NUP214	133062900	0.000000	0.05858	0.000000	0.03702	0.476000	0.33039	-0.699000	0.05087	-0.352000	0.08237	0.491000	0.48974	CCA		0.572	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
NUP214	8021	broad.mit.edu	37	9	134098223	134098223	+	Silent	SNP	G	G	A	rs553934312		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:134098223G>A	ENST00000359428.5	+	32	5952	c.5808G>A	c.(5806-5808)tcG>tcA	p.S1936S	NUP214_ENST00000411637.2_Silent_p.S1926S|NUP214_ENST00000483497.2_Silent_p.S762S|NUP214_ENST00000451030.1_Silent_p.S1937S			P35658	NU214_HUMAN	nucleoporin 214kDa	1936	11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|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)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)	p.S1936S(1)		NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		TTGCCAGCTCGTCGTTTGGAG	0.493			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""								G|||	1	0.000199681	0.0	0.0	5008	,	,		17521	0.0		0.0	False		,,,				2504	0.001				p.S1936S	Pancreas(4;24 48 25510 30394 32571)		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G5808A	9						.						140.0	126.0	130.0					9																	134098223		2203	4300	6503	133088044	SO:0001819	synonymous_variant	8021	exon32			X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.5808G>A	9.37:g.134098223G>A		Somatic		Capture	Illumina HiSeq	Phase_I	133088044	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Silent	SNP	ENST00000359428.5	37	CCDS6940.1																																																																																				0.493	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
RAPGEF1	2889	broad.mit.edu	37	9	134477492	134477492	+	Silent	SNP	C	C	T	rs549201601		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:134477492C>T	ENST00000372189.3	-	12	2022	c.1899G>A	c.(1897-1899)gcG>gcA	p.A633A	RAPGEF1_ENST00000372195.1_Silent_p.A650A|RAPGEF1_ENST00000372190.3_Silent_p.A651A	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	633					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)	p.A651A(1)		NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		CGCCGCTGACCGCTGAGGGAT	0.647													C|||	1	0.000199681	0.0	0.0	5008	,	,		13289	0.001		0.0	False		,,,				2504	0.0				p.A651A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1953A	9						.						30.0	34.0	33.0					9																	134477492		1977	4143	6120	133467313	SO:0001819	synonymous_variant	2889	exon12			BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"""guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"""	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.1899G>A	9.37:g.134477492C>T		Somatic		Capture	Illumina HiSeq	Phase_I	133467313	NM_198679	Q5JUE4|Q8IV73	Silent	SNP	ENST00000372189.3	37	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	C	5.792	0.330383	0.10956	.	.	ENSG00000107263	ENST00000414781	.	.	.	4.8	-9.4	0.00616	.	.	.	.	.	T	0.30885	0.0779	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.39210	-0.9625	4	.	.	.	.	13.0498	0.58948	0.0981:0.6461:0.0:0.2558	.	.	.	.	S	61	.	.	G	-	1	0	RAPGEF1	133467313	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-2.399000	0.01050	-2.727000	0.00386	-2.069000	0.00389	GGT		0.647	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312	
RAPGEF1	2889	broad.mit.edu	37	9	134518699	134518699	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:134518699G>A	ENST00000372189.3	-	4	493	c.370C>T	c.(370-372)Ctt>Ttt	p.L124F	RAPGEF1_ENST00000372195.1_Missense_Mutation_p.L141F|RAPGEF1_ENST00000372190.3_Missense_Mutation_p.L142F|RAPGEF1_ENST00000481260.1_5'UTR	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	124					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)	p.L142F(1)		NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		GACCCTGGAAGCATCTCCAGT	0.517																																					p.L142F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C424T	9						.						60.0	59.0	60.0					9																	134518699		1966	4168	6134	133508520	SO:0001583	missense	2889	exon4			BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"""guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"""	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.370C>T	9.37:g.134518699G>A	ENSP00000361263:p.Leu124Phe	Somatic		Capture	Illumina HiSeq	Phase_I	133508520	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	37	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	G	32	5.144085	0.94603	.	.	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000357686;ENST00000438647;ENST00000427994	T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07	5.86	5.86	0.93980	.	0.583075	0.18903	N	0.127966	T	0.67813	0.2933	M	0.74881	2.28	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.67891	-0.5553	10	0.87932	D	0	.	19.5509	0.95319	0.0:0.0:1.0:0.0	.	141;124;142	Q68DL3;Q13905;Q13905-3	.;RPGF1_HUMAN;.	F	124;141;18;124;142;104;50;141;103;142	ENSP00000361269:L141F;ENSP00000361263:L124F;ENSP00000361264:L142F;ENSP00000410640:L103F;ENSP00000402174:L142F	ENSP00000266110:L124F	L	-	1	0	RAPGEF1	133508520	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	6.218000	0.72224	2.937000	0.99478	0.650000	0.86243	CTT		0.517	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312	
NTNG2	84628	broad.mit.edu	37	9	135042236	135042236	+	Silent	SNP	G	G	A	rs530408603		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:135042236G>A	ENST00000393229.3	+	2	794	c.18G>A	c.(16-18)gcG>gcA	p.A6A	NTNG2_ENST00000360670.3_Silent_p.A6A|NTNG2_ENST00000372179.3_Silent_p.A6A|NTNG2_ENST00000393228.4_Silent_p.A6A	NM_032536.2	NP_115925.2	Q96CW9	NTNG2_HUMAN	netrin G2	6					axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)|axon (GO:0030424)		p.A6A(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	29				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		ATCTGCTGGCGCTCTTCCTGC	0.657													G|||	1	0.000199681	0.0	0.0	5008	,	,		17985	0.0		0.0	False		,,,				2504	0.001				p.A6A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G18A	9						.						84.0	88.0	87.0					9																	135042236		2203	4300	6503	134032057	SO:0001819	synonymous_variant	84628	exon2			AB058760	CCDS6946.1	9q34	2013-03-01	2003-12-02	2003-12-03	ENSG00000196358	ENSG00000196358		"""Netrins"""	14288	protein-coding gene	gene with protein product	"""Netrin-G2"""		"""netrin G1"""	NTNG1			Standard	NM_032536		Approved	KIAA1857, Lmnt2	uc004cbh.2	Q96CW9	OTTHUMG00000020835	ENST00000393229.3:c.18G>A	9.37:g.135042236G>A		Somatic		Capture	Illumina HiSeq	Phase_I	134032057	NM_032536	Q5JUJ2|Q6UXY0|Q96JH0	Silent	SNP	ENST00000393229.3	37	CCDS6946.1																																																																																				0.657	NTNG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054779.1	NM_032536	
GFI1B	8328	broad.mit.edu	37	9	135866388	135866388	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:135866388G>A	ENST00000339463.3	+	11	1763	c.944G>A	c.(943-945)cGc>cAc	p.R315H	GFI1B_ENST00000372122.1_Missense_Mutation_p.R315H|GFI1B_ENST00000372123.1_Missense_Mutation_p.R269H|GFI1B_ENST00000450530.1_Missense_Mutation_p.R315H|GFI1B_ENST00000372124.1_Missense_Mutation_p.R269H|GFI1B_ENST00000534944.1_Missense_Mutation_p.R269H			Q5VTD9	GFI1B_HUMAN	growth factor independent 1B transcription repressor	315	Interaction with ARIH2.|Mediates interaction with GATA1.				cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K9 methylation (GO:0051574)|regulation of erythrocyte differentiation (GO:0045646)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II transcription factor binding (GO:0001085)	p.R315H(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;9.04e-07)|Epithelial(140;1.17e-05)		GGCTTCCAGCGCAAGGTGGAC	0.647																																					p.R269H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G806A	9						.						91.0	77.0	82.0					9																	135866388		2203	4300	6503	134856209	SO:0001583	missense	8328	exon6			AF081946	CCDS6957.1, CCDS48049.1	9q34.13	2014-09-17	2007-10-04		ENSG00000165702	ENSG00000165702		"""Zinc fingers, C2H2-type"""	4238	protein-coding gene	gene with protein product		604383	"""growth factor independent 1B (potential regulator of CDKN1A, translocated in CML)"""			9878267	Standard	NM_001135031		Approved		uc004ccg.3	Q5VTD9	OTTHUMG00000020848	ENST00000339463.3:c.944G>A	9.37:g.135866388G>A	ENSP00000344782:p.Arg315His	Somatic		Capture	Illumina HiSeq	Phase_I	134856209	NM_001135031	O95270|Q5VTD8|Q6FHZ2|Q6T888	Missense_Mutation	SNP	ENST00000339463.3	37	CCDS6957.1	.	.	.	.	.	.	.	.	.	.	G	33	5.203501	0.95033	.	.	ENSG00000165702	ENST00000372124;ENST00000339463;ENST00000450530;ENST00000534944;ENST00000372123;ENST00000372122	T;T;T;T;T;T	0.36157	1.27;2.84;2.84;1.27;1.27;2.84	4.9	4.9	0.64082	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	0.51991	0.1707	L	0.41632	1.29	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.48822	-0.9001	10	0.42905	T	0.14	-52.9022	17.4238	0.87521	0.0:0.0:1.0:0.0	.	269;315	Q5VTD9-2;Q5VTD9	.;GFI1B_HUMAN	H	269;315;315;269;269;315	ENSP00000361197:R269H;ENSP00000344782:R315H;ENSP00000409546:R315H;ENSP00000446134:R269H;ENSP00000361196:R269H;ENSP00000361195:R315H	ENSP00000344782:R315H	R	+	2	0	GFI1B	134856209	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	8.009000	0.88606	2.425000	0.82216	0.462000	0.41574	CGC		0.647	GFI1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393840.1	NM_004188	
ABO	28	broad.mit.edu	37	9	136131229	136131229	+	RNA	SNP	C	C	T	rs370138477		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:136131229C>T	ENST00000453660.2	-	0	899				RP11-430N14.4_ENST00000606717.1_RNA			P16442	BGAT_HUMAN	ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase; transferase B, alpha 1-3-galactosyltransferase)						protein glycosylation (GO:0006486)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	fucosylgalactoside 3-alpha-galactosyltransferase activity (GO:0004381)|glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity (GO:0004380)|metal ion binding (GO:0046872)	p.E296K(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(2)|prostate(1)|stomach(2)	11				OV - Ovarian serous cystadenocarcinoma(145;5.82e-06)|Epithelial(140;3.45e-05)		CACACGGCCTCGATGCCGTTG	0.647																																					p.S296S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G888A	9						.	C	LYS/GLU	1,4235		0,1,2117	55.0	64.0	61.0		888	4.4	0.9	9		61	0,8450		0,0,4225	no	missense	ABO	NM_020469.2	56	0,1,6342	TT,TC,CC		0.0,0.0236,0.0079	probably-damaging	297/355	136131229	1,12685	2118	4225	6343	135121050			28	exon7			AF134415		9q34.2	2014-07-19			ENSG00000175164	ENSG00000175164	2.4.1.40, 2.4.1.37	"""Blood group antigens"", ""Glycosyltransferase family 6 domain containing"""	79	protein-coding gene	gene with protein product		110300				184030	Standard	NM_020469		Approved	A3GALNT, A3GALT1	uc004cda.1	P16442	OTTHUMG00000020872		9.37:g.136131229C>T		Somatic		Capture	Illumina HiSeq	Phase_I	135121050	NM_020469	B0JDB9|O14758|Q14490|Q53I57|Q6ISD4|Q6KFZ2|Q70V27|Q99484|Q99485|Q9NY01|Q9UQ68|Q9UQ69	Missense_Mutation	SNP	ENST00000453660.2	37																																																																																					0.647	ABO-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000054907.4	NM_020469	
ABO	28	broad.mit.edu	37	9	136132805	136132805	+	RNA	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:136132805G>T	ENST00000453660.2	-	0	375				RP11-430N14.4_ENST00000606717.1_RNA			P16442	BGAT_HUMAN	ABO blood group (transferase A, alpha 1-3-N-acetylgalactosaminyltransferase; transferase B, alpha 1-3-galactosyltransferase)						protein glycosylation (GO:0006486)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	fucosylgalactoside 3-alpha-galactosyltransferase activity (GO:0004381)|glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity (GO:0004380)|metal ion binding (GO:0046872)	p.A121D(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(2)|prostate(1)|stomach(2)	11				OV - Ovarian serous cystadenocarcinoma(145;5.82e-06)|Epithelial(140;3.45e-05)		CTTCTTGATGGCAAACACAGT	0.537																																					p.P122T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C364A	9						.						137.0	152.0	147.0					9																	136132805		2142	4246	6388	135122626			28	exon6			AF134415		9q34.2	2014-07-19			ENSG00000175164	ENSG00000175164	2.4.1.40, 2.4.1.37	"""Blood group antigens"", ""Glycosyltransferase family 6 domain containing"""	79	protein-coding gene	gene with protein product		110300				184030	Standard	NM_020469		Approved	A3GALNT, A3GALT1	uc004cda.1	P16442	OTTHUMG00000020872		9.37:g.136132805G>T		Somatic		Capture	Illumina HiSeq	Phase_I	135122626	NM_020469	B0JDB9|O14758|Q14490|Q53I57|Q6ISD4|Q6KFZ2|Q70V27|Q99484|Q99485|Q9NY01|Q9UQ68|Q9UQ69	Missense_Mutation	SNP	ENST00000453660.2	37																																																																																					0.537	ABO-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000054907.4	NM_020469	
SURF6	6838	broad.mit.edu	37	9	136199079	136199079	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:136199079G>A	ENST00000372022.4	-	5	977	c.712C>T	c.(712-714)Cag>Tag	p.Q238*	SURF6_ENST00000468290.1_5'UTR	NM_006753.4	NP_006744.2	O75683	SURF6_HUMAN	surfeit 6	238					ribosome biogenesis (GO:0042254)	granular component (GO:0001652)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.Q238*(1)		endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	12				OV - Ovarian serous cystadenocarcinoma(145;1.16e-06)|Epithelial(140;8.34e-06)|all cancers(34;7.08e-05)		TCCAGCAGCTGCCGGTAGTTC	0.672																																					p.Q238X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C712T	9						.						46.0	52.0	50.0					9																	136199079		2203	4298	6501	135188900	SO:0001587	stop_gained	6838	exon5			AF186772	CCDS6962.1	9q33-q34	2010-07-06			ENSG00000148296	ENSG00000148296			11478	protein-coding gene	gene with protein product	"""surfeit locus protein 6"""	185642				9740673, 15629442	Standard	NM_006753		Approved	FLJ30322, RRP14	uc004cdb.4	O75683	OTTHUMG00000020871	ENST00000372022.4:c.712C>T	9.37:g.136199079G>A	ENSP00000361092:p.Gln238*	Somatic		Capture	Illumina HiSeq	Phase_I	135188900	NM_006753	Q5T8U1|Q9BRK9|Q9BTZ5|Q9UK24	Nonsense_Mutation	SNP	ENST00000372022.4	37	CCDS6962.1	.	.	.	.	.	.	.	.	.	.	G	39	7.309926	0.98203	.	.	ENSG00000148296	ENST00000372022	.	.	.	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	-30.8762	17.4538	0.87600	0.0:0.0:1.0:0.0	.	.	.	.	X	238	.	ENSP00000361092:Q238X	Q	-	1	0	SURF6	135188900	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.159000	0.94728	2.351000	0.79841	0.467000	0.42956	CAG		0.672	SURF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054905.1	NM_006753	
ADAMTS13	11093	broad.mit.edu	37	9	136291111	136291111	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:136291111G>A	ENST00000371929.3	+	5	912	c.468G>A	c.(466-468)ggG>ggA	p.G156G	ADAMTS13_ENST00000536611.1_5'Flank|ADAMTS13_ENST00000355699.2_Silent_p.G156G|ADAMTS13_ENST00000371916.1_Silent_p.G156G|ADAMTS13_ENST00000356589.2_Silent_p.G156G|ADAMTS13_ENST00000371911.3_Silent_p.G156G|ADAMTS13_ENST00000485925.1_3'UTR	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	156	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.G156G(1)		central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		GCGTCTGTGGGTGGAGCCAGA	0.592																																					p.G156G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G468A	9						.						117.0	90.0	99.0					9																	136291111		2203	4300	6503	135280932	SO:0001819	synonymous_variant	11093	exon5			AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.468G>A	9.37:g.136291111G>A		Somatic		Capture	Illumina HiSeq	Phase_I	135280932	NM_139025	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	De_novo_Start_OutOfFrame	SNP	ENST00000371929.3	37	CCDS6970.1																																																																																				0.592	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
SLC2A6	11182	broad.mit.edu	37	9	136337202	136337202	+	Missense_Mutation	SNP	G	G	A	rs267602153		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:136337202G>A	ENST00000371899.4	-	10	1542	c.1465C>T	c.(1465-1467)Cgg>Tgg	p.R489W	SLC2A6_ENST00000371897.4_Missense_Mutation_p.R427W|SLC2A6_ENST00000485978.1_5'UTR	NM_017585.3	NP_060055.2	Q9UGQ3	GTR6_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 6	489					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)	p.R489W(1)		cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;8.47e-08)|Epithelial(140;9.37e-07)|all cancers(34;1.03e-05)		TCCAGGGACCGTCCCTTGGTC	0.632																																					p.R427W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1279T	9						.						104.0	96.0	99.0					9																	136337202		2203	4300	6503	135327023	SO:0001583	missense	11182	exon9			AJ011372	CCDS6975.1, CCDS48052.1	9q34	2013-05-22			ENSG00000160326	ENSG00000160326		"""Solute carriers"""	11011	protein-coding gene	gene with protein product		606813				10970791	Standard	NM_001145099		Approved	GLUT9, GLUT6, HSA011372	uc004cee.3	Q9UGQ3	OTTHUMG00000020874	ENST00000371899.4:c.1465C>T	9.37:g.136337202G>A	ENSP00000360966:p.Arg489Trp	Somatic		Capture	Illumina HiSeq	Phase_I	135327023	NM_001145099	A6NNU6|Q5SXD7|Q8NCC2	Missense_Mutation	SNP	ENST00000371899.4	37	CCDS6975.1	.	.	.	.	.	.	.	.	.	.	G	19.38	3.817404	0.70912	.	.	ENSG00000160326	ENST00000371897;ENST00000371899	T;T	0.61392	0.11;0.11	4.78	4.78	0.61160	Major facilitator superfamily domain, general substrate transporter (1);	0.056644	0.64402	D	0.000001	T	0.80127	0.4566	M	0.93550	3.43	0.45883	D	0.998732	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.84038	0.0363	10	0.87932	D	0	.	10.6706	0.45755	0.0:0.0:0.7008:0.2992	.	427;489	Q9UGQ3-2;Q9UGQ3	.;GTR6_HUMAN	W	427;489	ENSP00000360964:R427W;ENSP00000360966:R489W	ENSP00000360964:R427W	R	-	1	2	SLC2A6	135327023	1.000000	0.71417	0.999000	0.59377	0.803000	0.45373	2.080000	0.41586	2.514000	0.84764	0.650000	0.86243	CGG		0.632	SLC2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054909.1	NM_017585	
SARDH	1757	broad.mit.edu	37	9	136582541	136582541	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:136582541C>A	ENST00000371872.4	-	8	1314	c.1057G>T	c.(1057-1059)Gac>Tac	p.D353Y	SARDH_ENST00000422262.2_Missense_Mutation_p.D185Y|SARDH_ENST00000439388.1_Missense_Mutation_p.D353Y	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	353					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)	p.D353Y(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		ACCTCCCAGTCCAGGTCAAAG	0.592																																					p.D353Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1057T	9						.						94.0	81.0	86.0					9																	136582541		2203	4300	6503	135572362	SO:0001583	missense	1757	exon8				CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1057G>T	9.37:g.136582541C>A	ENSP00000360938:p.Asp353Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	135572362	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Missense_Mutation	SNP	ENST00000371872.4	37	CCDS6978.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.273672	0.80580	.	.	ENSG00000123453	ENST00000371872;ENST00000439388;ENST00000422262;ENST00000427237;ENST00000539227;ENST00000535281	T;T;T	0.39056	1.1;1.1;1.1	3.95	3.95	0.45737	FAD dependent oxidoreductase (1);	0.116847	0.56097	D	0.000036	T	0.75125	0.3807	H	0.95950	3.745	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.85139	0.0979	10	0.87932	D	0	-37.7887	16.0188	0.80464	0.0:1.0:0.0:0.0	.	353	Q9UL12	SARDH_HUMAN	Y	353;353;185;353;353;353	ENSP00000360938:D353Y;ENSP00000403084:D353Y;ENSP00000415537:D185Y	ENSP00000360938:D353Y	D	-	1	0	SARDH	135572362	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.704000	0.84595	1.760000	0.52011	0.462000	0.41574	GAC		0.592	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
WDR5	11091	broad.mit.edu	37	9	137013455	137013455	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:137013455G>A	ENST00000358625.3	+	8	745	c.574G>A	c.(574-576)Gat>Aat	p.D192N	WDR5_ENST00000425041.1_Missense_Mutation_p.D192N	NM_017588.2	NP_060058.1	P61964	WDR5_HUMAN	WD repeat domain 5	192					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|histone H3-K4 methylation (GO:0051568)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|positive regulation of gluconeogenesis (GO:0045722)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|histone acetyltransferase complex (GO:0000123)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)		p.D192N(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9		Myeloproliferative disorder(178;0.0255)|Medulloblastoma(224;0.123)		Epithelial(140;6.61e-13)|all cancers(34;5.66e-12)|OV - Ovarian serous cystadenocarcinoma(145;3.93e-08)|GBM - Glioblastoma multiforme(294;0.00326)|READ - Rectum adenocarcinoma(205;0.154)		AAGTAGCTATGATGGTCTCTG	0.423																																					p.D192N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G574A	9						.						218.0	202.0	207.0					9																	137013455		2203	4300	6503	136003276	SO:0001583	missense	11091	exon8			AJ011376	CCDS6981.1	9q34	2014-09-03			ENSG00000196363	ENSG00000196363		"""WD repeat domain containing"""	12757	protein-coding gene	gene with protein product	"""SWD3, Set1c WD40 repeat protein, homolog (S. cerevisiae)"", ""cilia and flagella associated protein 89"""	609012				11551928	Standard	XM_005272163		Approved	SWD3, CFAP89	uc004cey.3	P61964	OTTHUMG00000131707	ENST00000358625.3:c.574G>A	9.37:g.137013455G>A	ENSP00000351446:p.Asp192Asn	Somatic		Capture	Illumina HiSeq	Phase_I	136003276	NM_017588	Q91VA5|Q9NWX7|Q9UGP9	Missense_Mutation	SNP	ENST00000358625.3	37	CCDS6981.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.521173	0.85600	.	.	ENSG00000196363	ENST00000358625;ENST00000425041	D;D	0.88975	-2.45;-2.45	3.54	3.54	0.40534	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.93762	0.8006	M	0.79011	2.435	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94584	0.7782	10	0.87932	D	0	.	14.047	0.64710	0.0:0.0:1.0:0.0	.	192	P61964	WDR5_HUMAN	N	192	ENSP00000351446:D192N;ENSP00000401889:D192N	ENSP00000351446:D192N	D	+	1	0	WDR5	136003276	1.000000	0.71417	0.995000	0.50966	0.968000	0.65278	8.778000	0.91785	1.712000	0.51347	0.543000	0.68304	GAT		0.423	WDR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254621.1	NM_052821	
GLT6D1	360203	broad.mit.edu	37	9	138516139	138516139	+	Missense_Mutation	SNP	G	G	A	rs370842340		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:138516139G>A	ENST00000371763.1	-	5	888	c.635C>T	c.(634-636)cCg>cTg	p.P212L		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	212					carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)	p.P212L(1)		endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		TGCTGAGGTCGGCCTCCTCTC	0.512																																					p.P212L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C635T	9						.	A	LEU/PRO	1,3849		0,1,1924	94.0	93.0	94.0		635	-5.1	0.0	9		94	0,8266		0,0,4133	no	missense	GLT6D1	NM_182974.2	98	0,1,6057	AA,AG,GG		0.0,0.026,0.0083	possibly-damaging	212/277	138516139	1,12115	1925	4133	6058	137655960	SO:0001583	missense	360203	exon5			AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"""Glycosyltransferase family 6 domain containing"""	23671	protein-coding gene	gene with protein product		613699	"""galactosyltransferase family 6 domain containing 1"""	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.635C>T	9.37:g.138516139G>A	ENSP00000360829:p.Pro212Leu	Somatic		Capture	Illumina HiSeq	Phase_I	137655960	NM_182974		Missense_Mutation	SNP	ENST00000371763.1	37	CCDS43900.1	.	.	.	.	.	.	.	.	.	.	g	10.56	1.384530	0.25031	2.6E-4	0.0	ENSG00000204007	ENST00000371763	T	0.01240	5.12	3.49	-5.05	0.02955	.	2.109200	0.01764	N	0.030728	T	0.02418	0.0074	M	0.78285	2.405	0.09310	N	1	P	0.50443	0.935	B	0.42959	0.403	T	0.41431	-0.9509	10	0.54805	T	0.06	-0.1733	0.6542	0.00832	0.243:0.2277:0.3235:0.2058	.	212	Q7Z4J2	GL6D1_HUMAN	L	212	ENSP00000360829:P212L	ENSP00000360829:P212L	P	-	2	0	GLT6D1	137655960	0.100000	0.21855	0.000000	0.03702	0.000000	0.00434	0.580000	0.23803	-1.232000	0.02554	-0.808000	0.03180	CCG		0.512	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974	
AGPAT2	10555	broad.mit.edu	37	9	139571064	139571064	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:139571064G>A	ENST00000371696.2	-	4	626	c.561C>T	c.(559-561)ggC>ggT	p.G187G	AGPAT2_ENST00000538402.1_Silent_p.G187G|AGPAT2_ENST00000371694.3_Intron	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	187					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|epidermis development (GO:0008544)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|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)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)	p.G187G(2)		endometrium(1)|large_intestine(1)|lung(2)|prostate(2)	6	all_cancers(76;0.0893)|all_epithelial(76;0.231)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		GGTAGAAGGCGCCCTTCTTAA	0.627																																					p.G187G												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C561T	9						.						112.0	99.0	104.0					9																	139571064		2203	4300	6503	138690885	SO:0001819	synonymous_variant	10555	exon4			AF000237	CCDS7003.1, CCDS35181.1	9q34.3	2013-02-05	2013-02-05		ENSG00000169692	ENSG00000169692	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	325	protein-coding gene	gene with protein product	"""LPAAT-beta"", ""lysophosphatidic acid acyltransferase, beta"""	603100	"""Berardinelli-Seip congenital lipodystrophy"", ""1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)"""	BSCL		9242711, 9212163	Standard	NM_006412		Approved		uc004cii.1	O15120	OTTHUMG00000020936	ENST00000371696.2:c.561C>T	9.37:g.139571064G>A		Somatic		Capture	Illumina HiSeq	Phase_I	138690885	NM_006412	O00516|O15106|Q5VUD3|Q5VUD4|Q9BSV7|Q9BWR7	Silent	SNP	ENST00000371696.2	37	CCDS7003.1																																																																																				0.627	AGPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055090.1	NM_006412	
FAM69B	138311	broad.mit.edu	37	9	139616674	139616674	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:139616674G>A	ENST00000371692.4	+	4	500	c.404G>A	c.(403-405)cGg>cAg	p.R135Q	SNHG7_ENST00000436596.1_RNA|FAM69B_ENST00000371691.1_Missense_Mutation_p.R48Q|SNHG7_ENST00000416970.1_RNA|SNHG7_ENST00000414282.1_RNA	NM_152421.3	NP_689634.2	Q5VUD6	FA69B_HUMAN	family with sequence similarity 69, member B	135						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.R135Q(1)		NS(1)|endometrium(3)|large_intestine(2)|lung(1)|prostate(1)	8	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.03e-05)|Epithelial(140;0.00013)		GCCCCCCGGCGGGAGCTGGTA	0.627																																					p.R135Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G404A	9						.						44.0	48.0	47.0					9																	139616674		2203	4300	6503	138736495	SO:0001583	missense	138311	exon4				CCDS7004.1	9q34.3	2012-08-03			ENSG00000165716	ENSG00000165716			28290	protein-coding gene	gene with protein product		614543				21334309	Standard	NM_152421		Approved	MGC20262, C9orf136	uc004cik.3	Q5VUD6	OTTHUMG00000020940	ENST00000371692.4:c.404G>A	9.37:g.139616674G>A	ENSP00000360757:p.Arg135Gln	Somatic		Capture	Illumina HiSeq	Phase_I	138736495	NM_152421	Q5VUD7|Q8N5N0|Q8WYU5	Missense_Mutation	SNP	ENST00000371692.4	37	CCDS7004.1	.	.	.	.	.	.	.	.	.	.	g	13.48	2.249141	0.39797	.	.	ENSG00000165716	ENST00000371692;ENST00000371691	T;T	0.41065	1.01;1.01	4.28	1.14	0.20703	.	0.242826	0.40908	N	0.000992	T	0.24967	0.0606	L	0.31845	0.965	0.30706	N	0.749804	B	0.13145	0.007	B	0.06405	0.002	T	0.17776	-1.0358	10	0.19590	T	0.45	-23.2328	5.8744	0.18820	0.1901:0.1557:0.6542:0.0	.	135	Q5VUD6	FA69B_HUMAN	Q	135;48	ENSP00000360757:R135Q;ENSP00000360756:R48Q	ENSP00000360756:R48Q	R	+	2	0	FAM69B	138736495	1.000000	0.71417	0.996000	0.52242	0.757000	0.42996	1.197000	0.32211	-0.060000	0.13132	0.478000	0.44815	CGG		0.627	FAM69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055102.1	NM_152421	
C9orf172	389813	broad.mit.edu	37	9	139738905	139738905	+	Silent	SNP	C	C	T	rs376566490		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:139738905C>T	ENST00000436881.1	+	1	39	c.39C>T	c.(37-39)acC>acT	p.T13T		NM_001080482.2	NP_001073951.2	C9J069	CI172_HUMAN	chromosome 9 open reading frame 172	13								p.T13T(1)		endometrium(2)|large_intestine(1)|lung(6)	9						TGGTGTCGACCGTGTACCAGG	0.657																																					p.T13T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C39T	9						.	C		0,4160		0,0,2080	25.0	29.0	28.0		39	3.0	1.0	9		28	1,8399		0,1,4199	no	coding-synonymous	C9orf172	NM_001080482.2		0,1,6279	TT,TC,CC		0.0119,0.0,0.0080		13/977	139738905	1,12559	2080	4200	6280	138858726	SO:0001819	synonymous_variant	389813	exon1				CCDS48059.1	9q34.3	2012-04-03			ENSG00000232434	ENSG00000232434			37284	protein-coding gene	gene with protein product							Standard	NM_001080482		Approved		uc011meh.2	C9J069		ENST00000436881.1:c.39C>T	9.37:g.139738905C>T		Somatic		Capture	Illumina HiSeq	Phase_I	138858726	NM_001080482		Silent	SNP	ENST00000436881.1	37	CCDS48059.1																																																																																				0.657	C9orf172-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080482	
PNPLA7	375775	broad.mit.edu	37	9	140437196	140437196	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:140437196A>G	ENST00000277531.4	-	6	675	c.489T>C	c.(487-489)ttT>ttC	p.F163F	PNPLA7_ENST00000406427.1_Silent_p.F188F	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	163					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.F163F(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)		GCAGCTGCACAAAGACGATGT	0.632																																					p.F163F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T489C	9						.						76.0	70.0	72.0					9																	140437196		2203	4300	6503	139557017	SO:0001819	synonymous_variant	375775	exon6			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.489T>C	9.37:g.140437196A>G		Somatic		Capture	Illumina HiSeq	Phase_I	139557017	NM_152286	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Silent	SNP	ENST00000277531.4	37	CCDS7045.1																																																																																				0.632	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
CACNA1B	774	broad.mit.edu	37	9	140772602	140772602	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:140772602C>T	ENST00000371372.1	+	1	362	c.217C>T	c.(217-219)Cgc>Tgc	p.R73C	RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000371363.1_Missense_Mutation_p.R73C|CACNA1B_ENST00000371355.4_Missense_Mutation_p.R73C|CACNA1B_ENST00000371357.1_Missense_Mutation_p.R73C|CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000277551.2_Missense_Mutation_p.R73C	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	73					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.R73C(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	CACCGTCAACCGCTCGCTCTT	0.667																																					p.R73C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C217T	9						.						29.0	35.0	33.0					9																	140772602		2078	4213	6291	139892423	SO:0001583	missense	774	exon1			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.217C>T	9.37:g.140772602C>T	ENSP00000360423:p.Arg73Cys	Somatic		Capture	Illumina HiSeq	Phase_I	139892423	NM_000718	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.216760	0.79352	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55	3.46	3.46	0.39613	.	0.300780	0.25380	U	0.031094	T	0.70159	0.3192	M	0.92367	3.3	0.80722	D	1	D	0.89917	1.0	P	0.54346	0.749	T	0.77335	-0.2626	10	0.87932	D	0	.	10.1613	0.42853	0.2156:0.7844:0.0:0.0	.	73	B1AQK6	.	C	73	ENSP00000360423:R73C;ENSP00000277551:R73C;ENSP00000360414:R73C;ENSP00000360408:R73C;ENSP00000360406:R73C	ENSP00000277551:R73C	R	+	1	0	CACNA1B	139892423	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	1.695000	0.37763	1.497000	0.48584	0.298000	0.19748	CGC		0.667	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
KANK1	23189	broad.mit.edu	37	9	711557	711557	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:711557G>A	ENST00000382303.1	+	7	1443	c.791G>A	c.(790-792)cGc>cAc	p.R264H	KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382293.3_Missense_Mutation_p.R106H|KANK1_ENST00000382297.2_Missense_Mutation_p.R264H	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	264					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)	p.R106H(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		CAGCACATCCGCGAGCAGATG	0.597																																					p.R106H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G317A	9						.						68.0	66.0	67.0					9																	711557		2203	4300	6503	701557	SO:0001583	missense	23189	exon2			AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.791G>A	9.37:g.711557G>A	ENSP00000371740:p.Arg264His	Somatic		Capture	Illumina HiSeq	Phase_I	701557	NM_153186	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.880801	0.91740	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.00966	5.49;5.49;5.49	5.82	5.82	0.92795	.	0.000000	0.53938	D	0.000053	T	0.07458	0.0188	M	0.83953	2.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00677	-1.1614	10	0.87932	D	0	-3.5415	20.0953	0.97838	0.0:0.0:1.0:0.0	.	264;264	Q5W0W1;Q14678	.;KANK1_HUMAN	H	264;264;264;106	ENSP00000371740:R264H;ENSP00000371734:R264H;ENSP00000371730:R106H	ENSP00000346479:R264H	R	+	2	0	KANK1	701557	1.000000	0.71417	0.967000	0.41034	0.976000	0.68499	9.363000	0.97131	2.767000	0.95098	0.655000	0.94253	CGC		0.597	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
SMARCA2	6595	broad.mit.edu	37	9	2056700	2056700	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:2056700G>A	ENST00000382203.1	+	7	1411	c.1202G>A	c.(1201-1203)cGc>cAc	p.R401H	SMARCA2_ENST00000382194.1_Missense_Mutation_p.R401H|SMARCA2_ENST00000357248.2_Missense_Mutation_p.R401H|SMARCA2_ENST00000349721.2_Missense_Mutation_p.R401H			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	401					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|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)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)	p.R397H(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		GCCTGCATGCGCAGGGACACG	0.567																																					p.R401H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1202A	9						.						49.0	47.0	47.0					9																	2056700		2203	4300	6503	2046700	SO:0001583	missense	6595	exon7			D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.1202G>A	9.37:g.2056700G>A	ENSP00000371638:p.Arg401His	Somatic		Capture	Illumina HiSeq	Phase_I	2046700	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	37	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	G	34	5.292594	0.95546	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000450198;ENST00000382203;ENST00000382194	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.58935	0.2157	L	0.48362	1.52	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.998	D;D;D	0.80764	0.941;0.994;0.976	T	0.58521	-0.7622	10	0.45353	T	0.12	-15.7933	18.2171	0.89889	0.0:0.0:1.0:0.0	.	2;401;401	B4DK35;P51531-2;P51531	.;.;SMCA2_HUMAN	H	401	ENSP00000265773:R401H;ENSP00000349788:R401H;ENSP00000392081:R401H;ENSP00000371638:R401H;ENSP00000371629:R401H	ENSP00000265773:R401H	R	+	2	0	SMARCA2	2046700	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	9.832000	0.99423	2.292000	0.77174	0.655000	0.94253	CGC		0.567	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
KIAA0020	9933	broad.mit.edu	37	9	2824723	2824723	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:2824723C>T	ENST00000397885.2	-	11	1334	c.1128G>A	c.(1126-1128)acG>acA	p.T376T		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	376	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.T376T(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)		TTACCTTGGGCGTGCCATGCC	0.532																																					p.T376T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1128A	9						.						52.0	38.0	43.0					9																	2824723		2203	4300	6503	2814723	SO:0001819	synonymous_variant	9933	exon11			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.1128G>A	9.37:g.2824723C>T		Somatic		Capture	Illumina HiSeq	Phase_I	2814723	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Silent	SNP	ENST00000397885.2	37	CCDS6448.2																																																																																				0.532	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
ERMP1	79956	broad.mit.edu	37	9	5810164	5810164	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:5810164A>G	ENST00000339450.5	-	8	1484	c.1395T>C	c.(1393-1395)ctT>ctC	p.L465L	ERMP1_ENST00000381506.3_Silent_p.L241L|ERMP1_ENST00000543230.1_Silent_p.L43L|ERMP1_ENST00000214893.5_5'UTR	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	465						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)	p.L465L(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		GAACGGTAACAAGGCTAGTGA	0.408																																					p.L465L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1395C	9						.						175.0	154.0	161.0					9																	5810164		2203	4300	6503	5800164	SO:0001819	synonymous_variant	79956	exon8			AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"""Felix-ina"""	611156	"""KIAA1815"""	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.1395T>C	9.37:g.5810164A>G		Somatic		Capture	Illumina HiSeq	Phase_I	5800164	NM_024896	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Silent	SNP	ENST00000339450.5	37	CCDS34983.1																																																																																				0.408	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896	
GLDC	2731	broad.mit.edu	37	9	6604710	6604710	+	Silent	SNP	G	G	A	rs79057118	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:6604710G>A	ENST00000321612.6	-	7	1086	c.936C>T	c.(934-936)atC>atT	p.I312I		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	312					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)	p.I312I(1)		cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	TGCCCAGGGCGATGTCTACCC	0.527													G|||	17	0.00339457	0.0	0.0014	5008	,	,		18317	0.0159		0.0	False		,,,				2504	0.0				p.I312I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C936T	9						.	G		0,4406		0,0,2203	94.0	93.0	93.0		936	-10.7	0.3	9	dbSNP_133	93	1,8599		0,1,4299	no	coding-synonymous	GLDC	NM_000170.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		312/1021	6604710	1,13005	2203	4300	6503	6594710	SO:0001819	synonymous_variant	2731	exon7			D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"""glycine cleavage system protein P"", ""glycine decarboxylase"""	238300	"""glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"""			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.936C>T	9.37:g.6604710G>A		Somatic		Capture	Illumina HiSeq	Phase_I	6594710	NM_000170	Q2M2F8	Silent	SNP	ENST00000321612.6	37	CCDS34987.1																																																																																				0.527	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170	
TTC39B	158219	broad.mit.edu	37	9	15189768	15189768	+	Silent	SNP	C	C	T	rs376726304		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:15189768C>T	ENST00000512701.2	-	12	1164	c.1128G>A	c.(1126-1128)gcG>gcA	p.A376A	TTC39B_ENST00000507993.1_Silent_p.A211A|TTC39B_ENST00000297615.5_Silent_p.A307A|TTC39B_ENST00000380850.4_Silent_p.A376A|TTC39B_ENST00000355694.2_Silent_p.A310A|TTC39B_ENST00000507285.1_Silent_p.A211A			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	376								p.A310A(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						GCTCTGCTTCCGCAACATTCA	0.408													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17369	0.0		0.0	False		,,,				2504	0.0				p.A376A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1128A	9						.	C	,,,,	1,4405	2.1+/-5.4	0,1,2202	75.0	69.0	71.0		1122,1128,921,633,1128	3.9	1.0	9		71	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTC39B	NM_001168339.1,NM_001168340.1,NM_001168341.1,NM_001168342.1,NM_152574.2	,,,,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,,	374/681,376/670,307/614,211/518,376/683	15189768	1,13005	2203	4300	6503	15179768	SO:0001819	synonymous_variant	158219	exon12			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.1128G>A	9.37:g.15189768C>T		Somatic		Capture	Illumina HiSeq	Phase_I	15179768	NM_001168340	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Silent	SNP	ENST00000512701.2	37	CCDS6477.2																																																																																				0.408	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574	
SNAPC3	6619	broad.mit.edu	37	9	15433622	15433622	+	Silent	SNP	C	C	T	rs199814272		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:15433622C>T	ENST00000380821.3	+	3	641	c.465C>T	c.(463-465)ttC>ttT	p.F155F	SNAPC3_ENST00000461041.1_3'UTR|RNU6-319P_ENST00000516025.1_RNA	NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	155					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.F155F(1)		breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		AAGAAACATTCGTTTATGAGA	0.363													C|||	1	0.000199681	0.0	0.0	5008	,	,		18020	0.001		0.0	False		,,,				2504	0.0				p.F155F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C465T	9						.						137.0	133.0	135.0					9																	15433622		2203	4300	6503	15423622	SO:0001819	synonymous_variant	6619	exon3			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.465C>T	9.37:g.15433622C>T		Somatic		Capture	Illumina HiSeq	Phase_I	15423622	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Silent	SNP	ENST00000380821.3	37	CCDS6478.1																																																																																				0.363	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697	
BNC2	54796	broad.mit.edu	37	9	16727881	16727881	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:16727881C>T	ENST00000380672.4	-	3	301	c.244G>A	c.(244-246)Gga>Aga	p.G82R	RP11-62F24.2_ENST00000450445.1_RNA|BNC2_ENST00000545497.1_Intron|BNC2_ENST00000380667.2_Intron|BNC2_ENST00000380666.2_Missense_Mutation_p.G82R	NM_017637.5	NP_060107.3			basonuclin 2									p.G82R(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		GTTCTGGTTCCGAACTGCATG	0.468																																					p.G82R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G244A	9						.						263.0	233.0	243.0					9																	16727881		2203	4300	6503	16717881	SO:0001583	missense	54796	exon3			AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"""Zinc fingers, C2H2-type"""	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.244G>A	9.37:g.16727881C>T	ENSP00000370047:p.Gly82Arg	Somatic		Capture	Illumina HiSeq	Phase_I	16717881	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	37	CCDS6482.2	.	.	.	.	.	.	.	.	.	.	C	20.9	4.060046	0.76074	.	.	ENSG00000173068	ENST00000380672;ENST00000418777;ENST00000456672;ENST00000436939;ENST00000380666;ENST00000540340	T;T;T	0.08896	3.04;3.04;3.04	6.17	6.17	0.99709	.	0.078788	0.52532	D	0.000066	T	0.14485	0.0350	N	0.08118	0	0.46396	D	0.999023	D;D;D;P	0.76494	0.999;0.989;0.982;0.784	P;P;P;B	0.62649	0.905;0.8;0.537;0.203	T	0.22208	-1.0223	10	0.87932	D	0	-7.8383	20.8794	0.99867	0.0:1.0:0.0:0.0	.	82;82;40;82	Q06HC4;Q6ZN30-2;Q5H9S4;Q6ZN30	.;.;.;BNC2_HUMAN	R	82;39;82;82;82;82	ENSP00000370047:G82R;ENSP00000408370:G39R;ENSP00000370041:G82R	ENSP00000370041:G82R	G	-	1	0	BNC2	16717881	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.347000	0.65998	2.941000	0.99782	0.655000	0.94253	GGA		0.468	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637	
HAUS6	54801	broad.mit.edu	37	9	19096745	19096745	+	Missense_Mutation	SNP	G	G	A	rs539387980		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:19096745G>A	ENST00000380502.3	-	2	618	c.151C>T	c.(151-153)Cgt>Tgt	p.R51C		NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	51					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)		p.R51C(2)		autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						AAGGCATCACGGTTCAGCTTG	0.299													G|||	1	0.000199681	0.0	0.0014	5008	,	,		16267	0.0		0.0	False		,,,				2504	0.0				p.R51C												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C151T	9						.						46.0	51.0	49.0					9																	19096745		2203	4298	6501	19086745	SO:0001583	missense	54801	exon2			AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"""HAUS augmin-like complex subunits"""	25948	protein-coding gene	gene with protein product		613433	"""family with sequence similarity 29, member A"""	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.151C>T	9.37:g.19096745G>A	ENSP00000369871:p.Arg51Cys	Somatic		Capture	Illumina HiSeq	Phase_I	19086745	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	37	CCDS6489.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.648439	0.67358	.	.	ENSG00000147874	ENST00000380502	T	0.24350	1.86	5.25	4.23	0.50019	.	0.265582	0.41712	D	0.000830	T	0.40979	0.1139	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.65010	0.931	T	0.27706	-1.0066	10	0.62326	D	0.03	-12.1386	5.8937	0.18927	0.095:0.0:0.5835:0.3215	.	51	Q7Z4H7	HAUS6_HUMAN	C	51	ENSP00000369871:R51C	ENSP00000369871:R51C	R	-	1	0	HAUS6	19086745	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.368000	0.59505	2.604000	0.88044	0.650000	0.86243	CGT		0.299	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
MLLT3	4300	broad.mit.edu	37	9	20414379	20414379	+	Silent	SNP	G	G	A	rs373338988		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:20414379G>A	ENST00000380338.4	-	5	751	c.465C>T	c.(463-465)agC>agT	p.S155S	MLLT3_ENST00000429426.2_Silent_p.S152S|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	155	Poly-Ser.				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.S155S(4)		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)		tgctgctactgctgctgctgc	0.532			T	MLL	ALL																																p.S155S			Dom	yes		9	9p22	4300	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""		L	.	.	4	Substitution - coding silent(4)	urinary_tract(1)|large_intestine(1)|lung(1)|kidney(1)	c.C465T	9						.						10.0	15.0	14.0					9																	20414379		1871	3851	5722	20404379	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.465C>T	9.37:g.20414379G>A		Somatic		Capture	Illumina HiSeq	Phase_I	20404379	NM_004529	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	CCDS6494.1																																																																																				0.532	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529	
FOCAD	54914	broad.mit.edu	37	9	20981436	20981436	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:20981436G>C	ENST00000380249.1	+	40	4753	c.4389G>C	c.(4387-4389)aaG>aaC	p.K1463N	FOCAD_ENST00000338382.6_Missense_Mutation_p.K1463N|FOCAD_ENST00000605086.1_Missense_Mutation_p.K899N	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1463						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)		p.K1463N(1)									TGAATACCAAGAGATATCTCC	0.398																																					p.K1463N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4389C	9						.						154.0	151.0	152.0					9																	20981436		2203	4300	6503	20971436	SO:0001583	missense	54914	exon40			AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.4389G>C	9.37:g.20981436G>C	ENSP00000369599:p.Lys1463Asn	Somatic		Capture	Illumina HiSeq	Phase_I	20971436	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	.	.	.	.	.	.	.	.	.	.	G	10.58	1.389317	0.25118	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.25250	1.81;1.81	5.96	0.843	0.18935	.	0.265954	0.38272	N	0.001750	T	0.30262	0.0759	L	0.54323	1.7	0.28560	N	0.911199	P	0.43231	0.801	P	0.49012	0.598	T	0.14364	-1.0475	10	0.66056	D	0.02	-15.3916	8.7337	0.34514	0.2413:0.1044:0.6542:0.0	.	1463	Q5VW36	K1797_HUMAN	N	1463	ENSP00000369599:K1463N;ENSP00000344307:K1463N	ENSP00000344307:K1463N	K	+	3	2	KIAA1797	20971436	1.000000	0.71417	0.998000	0.56505	0.067000	0.16453	2.091000	0.41691	0.116000	0.18110	-0.797000	0.03246	AAG		0.398	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
TOPORS	10210	broad.mit.edu	37	9	32542177	32542177	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:32542177G>A	ENST00000360538.2	-	3	2462	c.2346C>T	c.(2344-2346)acC>acT	p.T782T	TOPORS_ENST00000379858.1_Silent_p.T717T	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	782	Arg-rich.|Interaction with TOP1.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T782T(1)		large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		GGTCAGTCCCGGTAGATGCAG	0.443																																					p.T717T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2151T	9						.						104.0	103.0	103.0					9																	32542177		2203	4300	6503	32532177	SO:0001819	synonymous_variant	10210	exon2			AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"""RING-type (C3HC4) zinc fingers"""	21653	protein-coding gene	gene with protein product		609507	"""retinitis pigmentosa 31 (autosomal dominant)"", ""topoisomerase I binding, arginine/serine-rich"""	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.2346C>T	9.37:g.32542177G>A		Somatic		Capture	Illumina HiSeq	Phase_I	32532177	NM_001195622	O43273|Q6P987|Q9NS55|Q9UNR9	Silent	SNP	ENST00000360538.2	37	CCDS6527.1																																																																																				0.443	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802	
TAF1L	138474	broad.mit.edu	37	9	32631937	32631937	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:32631937A>G	ENST00000242310.4	-	1	3730	c.3641T>C	c.(3640-3642)gTg>gCg	p.V1214A	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1214					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.V1214A(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CCGTATGCGCACATAGGCATC	0.433																																					p.V1214A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3641C	9						.						174.0	154.0	161.0					9																	32631937		2203	4300	6503	32621937	SO:0001583	missense	138474	exon1			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.3641T>C	9.37:g.32631937A>G	ENSP00000418379:p.Val1214Ala	Somatic		Capture	Illumina HiSeq	Phase_I	32621937	NM_153809	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	A	11.29	1.595929	0.28445	.	.	ENSG00000122728	ENST00000242310	T	0.62232	0.04	0.479	0.479	0.16796	.	0.479063	0.23197	N	0.050832	T	0.47930	0.1472	L	0.49350	1.555	0.24250	N	0.995328	B	0.22346	0.068	B	0.22601	0.04	T	0.38564	-0.9655	10	0.48119	T	0.1	.	3.2606	0.06848	0.5508:0.449:0.0:1.0E-4	.	1214	Q8IZX4	TAF1L_HUMAN	A	1214	ENSP00000418379:V1214A	ENSP00000418379:V1214A	V	-	2	0	TAF1L	32621937	1.000000	0.71417	0.976000	0.42696	0.527000	0.34593	1.400000	0.34577	0.426000	0.26116	0.164000	0.16699	GTG		0.433	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
DNAI1	27019	broad.mit.edu	37	9	34514692	34514692	+	Silent	SNP	G	G	A	rs547499630		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:34514692G>A	ENST00000242317.4	+	18	1944	c.1773G>A	c.(1771-1773)gcG>gcA	p.A591A		NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	591					cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)	p.A591A(2)		autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		TGGCCTGGGCGCCATACTCTT	0.567									Kartagener syndrome																												p.A591A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1773A	9						.						158.0	144.0	149.0					9																	34514692		2203	4300	6503	34504692	SO:0001819	synonymous_variant	27019	exon18	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"""Axonemal dyneins"", ""WD repeat domain containing"""	2954	protein-coding gene	gene with protein product		604366	"""dynein, axonemal, intermediate polypeptide 1"""			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	ENST00000242317.4:c.1773G>A	9.37:g.34514692G>A		Somatic		Capture	Illumina HiSeq	Phase_I	34504692	NM_012144	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Silent	SNP	ENST00000242317.4	37	CCDS6557.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.273333	0.23221	.	.	ENSG00000122735	ENST00000442556	.	.	.	5.14	-2.15	0.07102	.	.	.	.	.	T	0.38825	0.1055	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31503	-0.9941	4	.	.	.	.	1.1668	0.01817	0.3651:0.3184:0.1764:0.1401	.	.	.	.	H	95	.	.	R	+	2	0	DNAI1	34504692	0.017000	0.18338	0.997000	0.53966	0.991000	0.79684	-1.062000	0.03468	-0.170000	0.10816	-0.340000	0.08031	CGC		0.567	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1		
RUSC2	9853	broad.mit.edu	37	9	35547198	35547198	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:35547198A>G	ENST00000455600.1	+	2	1249	c.680A>G	c.(679-681)cAg>cGg	p.Q227R	RUSC2_ENST00000468041.1_3'UTR	NM_001135999.1	NP_001129471	Q8N2Y8	RUSC2_HUMAN	RUN and SH3 domain containing 2	227						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)	Rab GTPase binding (GO:0017137)	p.Q227R(1)		NS(1)|breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(4)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32			Lung(28;0.000837)|LUSC - Lung squamous cell carcinoma(32;0.00109)|STAD - Stomach adenocarcinoma(86;0.194)			TCCTTTGACCAGGAATGGAAG	0.592																																					p.Q227R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A680G	9						.						76.0	74.0	74.0					9																	35547198		2203	4300	6503	35537198	SO:0001583	missense	9853	exon2			AB002373	CCDS35008.1	9p13.2	2003-12-02			ENSG00000198853	ENSG00000198853			23625	protein-coding gene	gene with protein product		611053				9205841	Standard	NM_001135999		Approved	KIAA0375	uc003zww.3	Q8N2Y8	OTTHUMG00000019861	ENST00000455600.1:c.680A>G	9.37:g.35547198A>G	ENSP00000393922:p.Gln227Arg	Somatic		Capture	Illumina HiSeq	Phase_I	35537198	NM_014806	A2RU62|A7E2A9|O15080|Q5W134|Q641Q6|Q6P1W7	Missense_Mutation	SNP	ENST00000455600.1	37	CCDS35008.1	.	.	.	.	.	.	.	.	.	.	A	10.04	1.241139	0.22711	.	.	ENSG00000198853	ENST00000361226;ENST00000455600;ENST00000543478	T;T	0.25414	1.8;1.8	5.36	4.23	0.50019	.	0.138161	0.49305	D	0.000145	T	0.13372	0.0324	N	0.17082	0.46	0.34211	D	0.674289	B	0.26635	0.155	B	0.24155	0.051	T	0.11817	-1.0572	10	0.38643	T	0.18	-4.4054	5.3898	0.16237	0.7622:0.0:0.0822:0.1556	.	227	Q8N2Y8	RUSC2_HUMAN	R	227	ENSP00000355177:Q227R;ENSP00000393922:Q227R	ENSP00000355177:Q227R	Q	+	2	0	RUSC2	35537198	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.806000	0.47947	2.039000	0.60335	0.459000	0.35465	CAG		0.592	RUSC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052309.1	XM_048462	
ZBTB5	9925	broad.mit.edu	37	9	37442005	37442005	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:37442005G>A	ENST00000307750.4	-	2	732	c.544C>T	c.(544-546)Cgc>Tgc	p.R182C		NM_014872.2	NP_055687.1	O15062	ZBTB5_HUMAN	zinc finger and BTB domain containing 5	182					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.R182C(1)		NS(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8				GBM - Glioblastoma multiforme(29;0.00733)|Lung(182;0.226)		AAGGGCGTGCGCTGATCCAGG	0.607																																					p.R182C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C544T	9						.						55.0	56.0	56.0					9																	37442005		2203	4299	6502	37432005	SO:0001583	missense	9925	exon2			AB002352	CCDS6610.1	9p13.1	2013-01-09			ENSG00000168795	ENSG00000168795		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	23836	protein-coding gene	gene with protein product						9205841	Standard	NM_014872		Approved	KIAA0354	uc003zzx.3	O15062	OTTHUMG00000019918	ENST00000307750.4:c.544C>T	9.37:g.37442005G>A	ENSP00000307604:p.Arg182Cys	Somatic		Capture	Illumina HiSeq	Phase_I	37432005	NM_014872		Missense_Mutation	SNP	ENST00000307750.4	37	CCDS6610.1	.	.	.	.	.	.	.	.	.	.	G	15.71	2.914660	0.52546	.	.	ENSG00000168795	ENST00000307750	T	0.10477	2.87	5.54	4.64	0.57946	.	0.000000	0.85682	D	0.000000	T	0.18002	0.0432	L	0.27053	0.805	0.58432	D	0.999995	D	0.89917	1.0	D	0.63192	0.912	T	0.02208	-1.1195	10	0.41790	T	0.15	.	13.391	0.60825	0.0:0.0:0.5991:0.4009	.	182	O15062	ZBTB5_HUMAN	C	182	ENSP00000307604:R182C	ENSP00000307604:R182C	R	-	1	0	ZBTB5	37432005	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.881000	0.48538	1.566000	0.49654	-0.169000	0.13324	CGC		0.607	ZBTB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052462.1	NM_014872	
POLR1E	64425	broad.mit.edu	37	9	37501827	37501827	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:37501827G>A	ENST00000377798.4	+	11	1199	c.1086G>A	c.(1084-1086)aaG>aaA	p.K362K	POLR1E_ENST00000377792.3_Silent_p.K424K|POLR1E_ENST00000442009.2_Silent_p.K292K	NM_022490.1	NP_071935.1	O15160	RPAC1_HUMAN	polymerase (RNA) I polypeptide E, 53kDa	0					gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.K362K(1)		autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	12				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)		GGGACTTGAAGCTCAGTGAGA	0.458																																					p.K362K	Ovarian(116;843 1620 18506 32459 34463)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1086A	9						.						108.0	97.0	101.0					9																	37501827		2203	4300	6503	37491827	SO:0001819	synonymous_variant	64425	exon11			AK091294	CCDS6611.1	9p13.1	2013-01-21	2006-03-09	2006-03-09	ENSG00000137054	ENSG00000137054		"""RNA polymerase subunits"""	17631	protein-coding gene	gene with protein product	"""RNA polymerase I associated factor 53"""		"""polymerase (RNA) I associated factor 1"""	PRAF1		8641287	Standard	XM_005251547		Approved	FLJ13390, PAF53, FLJ13970	uc003zzy.1	Q9GZS1	OTTHUMG00000019920	ENST00000377798.4:c.1086G>A	9.37:g.37501827G>A		Somatic		Capture	Illumina HiSeq	Phase_I	37491827	NM_022490	O75395|Q5JTE3	Silent	SNP	ENST00000377798.4	37	CCDS6611.1																																																																																				0.458	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052464.1	NM_022490	
FBXO10	26267	broad.mit.edu	37	9	37525117	37525117	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:37525117C>T	ENST00000432825.2	-	6	1807	c.1759G>A	c.(1759-1761)Ggc>Agc	p.G587S	FBXO10_ENST00000543968.1_5'UTR|RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000541829.1_Missense_Mutation_p.G112S	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	587					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.G587S(1)		breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		AGGCCTTTGCCGTTCTCATTC	0.582																																					p.G587S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1759A	9						.						37.0	37.0	37.0					9																	37525117		2015	4157	6172	37515117	SO:0001583	missense	26267	exon6			AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"""F-boxes /  ""other"""""	13589	protein-coding gene	gene with protein product		609092	"""F-box only protein 10"""			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.1759G>A	9.37:g.37525117C>T	ENSP00000403802:p.Gly587Ser	Somatic		Capture	Illumina HiSeq	Phase_I	37515117	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	37	CCDS47966.1	.	.	.	.	.	.	.	.	.	.	C	33	5.284733	0.95517	.	.	ENSG00000147912	ENST00000432825;ENST00000541829	T;T	0.38401	1.14;1.14	4.96	4.96	0.65561	Pectin lyase fold/virulence factor (1);Carbohydrate-binding/sugar hydrolysis domain (1);	0.000000	0.85682	D	0.000000	T	0.63141	0.2486	M	0.79926	2.475	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.991;0.994;1.0	T	0.67189	-0.5733	10	0.52906	T	0.07	-28.6805	17.0096	0.86401	0.0:1.0:0.0:0.0	.	466;112;587	Q59F51;Q08AL4;Q9UK96	.;.;FBX10_HUMAN	S	587;112	ENSP00000403802:G587S;ENSP00000441307:G112S	ENSP00000403802:G587S	G	-	1	0	FBXO10	37515117	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.723000	0.68492	2.290000	0.77057	0.655000	0.94253	GGC		0.582	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3		
PGM5	5239	broad.mit.edu	37	9	71098936	71098936	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:71098936C>T	ENST00000396396.1	+	9	1680	c.1451C>T	c.(1450-1452)cCt>cTt	p.P484L		NM_021965.3	NP_068800.2	Q15124	PGM5_HUMAN	phosphoglucomutase 5	484					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)	cell-cell adherens junction (GO:0005913)|costamere (GO:0043034)|cytoplasmic side of plasma membrane (GO:0009898)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|sarcolemma (GO:0042383)|spot adherens junction (GO:0005914)|stress fiber (GO:0001725)|Z disc (GO:0030018)	intramolecular transferase activity, phosphotransferases (GO:0016868)|magnesium ion binding (GO:0000287)|structural molecule activity (GO:0005198)	p.P484L(1)		endometrium(5)|kidney(1)|large_intestine(5)|liver(2)|lung(15)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	34						TACGTGGACCCTGTGGATGGC	0.512																																					p.P484L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1451T	9						.						161.0	136.0	145.0					9																	71098936		2203	4300	6503	70288756	SO:0001583	missense	5239	exon9			L40933	CCDS6622.2	9q13	2008-02-05			ENSG00000154330	ENSG00000154330			8908	protein-coding gene	gene with protein product	"""phosphoglucomutase-related protein"""	600981				8586438, 8631316	Standard	NM_021965		Approved	PGMRP	uc004agr.3	Q15124	OTTHUMG00000019966	ENST00000396396.1:c.1451C>T	9.37:g.71098936C>T	ENSP00000379678:p.Pro484Leu	Somatic		Capture	Illumina HiSeq	Phase_I	70288756	NM_021965	B1AM46|B4DLQ6|Q5VYV3|Q8N527|Q9UDH4	Missense_Mutation	SNP	ENST00000396396.1	37	CCDS6622.2	.	.	.	.	.	.	.	.	.	.	C	34	5.411697	0.96072	.	.	ENSG00000154330	ENST00000396396	T	0.55760	0.5	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.78935	0.4362	M	0.89658	3.05	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82131	-0.0609	10	0.62326	D	0.03	.	18.7313	0.91736	0.0:1.0:0.0:0.0	.	484	Q15124	PGM5_HUMAN	L	484	ENSP00000379678:P484L	ENSP00000379678:P484L	P	+	2	0	PGM5	70288756	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	7.647000	0.83462	2.716000	0.92895	0.655000	0.94253	CCT		0.512	PGM5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052548.2	NM_021965	
PIP5K1B	8395	broad.mit.edu	37	9	71509353	71509353	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:71509353C>T	ENST00000265382.3	+	8	875	c.570C>T	c.(568-570)aaC>aaT	p.N190N	PIP5K1B_ENST00000541509.1_Silent_p.N190N	NM_003558.2	NP_003549.1	O14986	PI51B_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, beta	190	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)	p.N190N(1)		breast(1)|large_intestine(2)|stomach(1)	4				Lung(182;0.133)		TGATGAACAACGTTTTGCCAC	0.408																																					p.N190N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C570T	9						.						98.0	88.0	92.0					9																	71509353		2203	4300	6503	70699173	SO:0001819	synonymous_variant	8395	exon8			U78579	CCDS6624.1, CCDS65063.1	9q13	2008-02-05			ENSG00000107242	ENSG00000107242			8995	protein-coding gene	gene with protein product		602745				9177790, 8841185	Standard	NM_003558		Approved	STM7, MSS4	uc004agu.4	O14986	OTTHUMG00000019976	ENST00000265382.3:c.570C>T	9.37:g.71509353C>T		Somatic		Capture	Illumina HiSeq	Phase_I	70699173	NM_003558	A8K9L9|B4DIG7|P78518|P78519|Q5T5K6|Q5T5K8|Q5T5K9|Q5VZ00|Q7KYT5|Q8NHQ5|Q92749	Silent	SNP	ENST00000265382.3	37	CCDS6624.1																																																																																				0.408	PIP5K1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052561.2	NM_003558	
PRKACG	5568	broad.mit.edu	37	9	71628114	71628114	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:71628114C>T	ENST00000377276.2	-	1	925	c.895G>A	c.(895-897)Gcc>Acc	p.A299T		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	299	AGC-kinase C-terminal.				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.A299T(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						CTGGTTGTGGCGAACCACTTG	0.567																																					p.A299T	Esophageal Squamous(110;2236 2623 32146)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G895A	9						.						105.0	98.0	100.0					9																	71628114		2203	4300	6503	70817934	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.895G>A	9.37:g.71628114C>T	ENSP00000366488:p.Ala299Thr	Somatic		Capture	Illumina HiSeq	Phase_I	70817934	NM_002732	O60850|Q5VZ02|Q86YI1	Missense_Mutation	SNP	ENST00000377276.2	37	CCDS6625.1	.	.	.	.	.	.	.	.	.	.	C	7.301	0.613130	0.14066	.	.	ENSG00000165059	ENST00000377276	T	0.07688	3.17	1.18	-2.36	0.06663	AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	.	.	.	.	T	0.09423	0.0232	M	0.76002	2.32	0.23150	N	0.998217	B	0.15719	0.014	B	0.10450	0.005	T	0.33954	-0.9848	9	0.59425	D	0.04	.	2.6244	0.04925	0.3511:0.1844:0.0:0.4644	.	299	P22612	KAPCG_HUMAN	T	299	ENSP00000366488:A299T	ENSP00000366488:A299T	A	-	1	0	PRKACG	70817934	0.894000	0.30519	0.000000	0.03702	0.000000	0.00434	0.719000	0.25881	-1.557000	0.01692	-1.516000	0.00938	GCC		0.567	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1		
TJP2	9414	broad.mit.edu	37	9	71789326	71789326	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:71789326G>A	ENST00000377245.4	+	1	246	c.38G>A	c.(37-39)cGg>cAg	p.R13Q	TJP2_ENST00000453658.2_Intron|TJP2_ENST00000265384.7_Missense_Mutation_p.R13Q|TJP2_ENST00000348208.4_Missense_Mutation_p.R13Q|TJP2_ENST00000377259.1_Intron	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	13					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)	p.R13Q(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						CCACCCCGGCGGGAGCTGTCA	0.701																																					p.R13Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G38A	9						.						25.0	27.0	26.0					9																	71789326		2094	4082	6176	70979146	SO:0001583	missense	9414	exon1			L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.38G>A	9.37:g.71789326G>A	ENSP00000366453:p.Arg13Gln	Somatic		Capture	Illumina HiSeq	Phase_I	70979146	NM_201629	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	37	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.998704	0.74818	.	.	ENSG00000119139	ENST00000377245;ENST00000348208;ENST00000265384	T;T;T	0.08807	3.06;3.07;3.05	5.27	4.38	0.52667	PDZ/DHR/GLGF (1);	0.227147	0.24793	N	0.035542	T	0.04679	0.0127	N	0.08118	0	0.80722	D	1	B;B;B	0.24132	0.098;0.059;0.098	B;B;B	0.14578	0.011;0.005;0.011	T	0.38457	-0.9660	10	0.62326	D	0.03	.	9.8451	0.41021	0.0951:0.0:0.9049:0.0	.	13;13;13	Q9UDY2-2;Q9UDY2;Q9UDY2-5	.;ZO2_HUMAN;.	Q	13	ENSP00000366453:R13Q;ENSP00000345893:R13Q;ENSP00000265384:R13Q	ENSP00000265384:R13Q	R	+	2	0	TJP2	70979146	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	4.223000	0.58587	1.210000	0.43336	0.467000	0.42956	CGG		0.701	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
APBA1	320	broad.mit.edu	37	9	72132105	72132105	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:72132105C>T	ENST00000265381.4	-	2	244	c.22G>A	c.(22-24)Gcg>Acg	p.A8T		NM_001163.3	NP_001154.2	Q02410	APBA1_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 1	8					axon cargo transport (GO:0008088)|cell adhesion (GO:0007155)|gamma-aminobutyric acid secretion (GO:0014051)|glutamate secretion (GO:0014047)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein complex assembly (GO:0006461)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	beta-amyloid binding (GO:0001540)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.A8T(1)		endometrium(4)|kidney(2)|large_intestine(12)|lung(13)|prostate(3)|skin(3)	37						TCCACCTCCGCAGACCCCTCC	0.642																																					p.A8T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G22A	9						.						12.0	9.0	10.0					9																	72132105		2178	4272	6450	71321925	SO:0001583	missense	320	exon2			AF029106	CCDS6630.1	9q13-q21	2008-07-18	2008-07-18		ENSG00000107282	ENSG00000107282			578	protein-coding gene	gene with protein product		602414		MINT1		7678331, 7719031	Standard	NM_001163		Approved	D9S411E, X11	uc004ahh.2	Q02410	OTTHUMG00000019984	ENST00000265381.4:c.22G>A	9.37:g.72132105C>T	ENSP00000265381:p.Ala8Thr	Somatic		Capture	Illumina HiSeq	Phase_I	71321925	NM_001163	O14914|O60570|Q5VYR8	Missense_Mutation	SNP	ENST00000265381.4	37	CCDS6630.1	.	.	.	.	.	.	.	.	.	.	C	9.994	1.231634	0.22626	.	.	ENSG00000107282	ENST00000265381	T	0.04234	3.67	5.09	3.16	0.36331	.	0.470782	0.20287	N	0.095338	T	0.02610	0.0079	N	0.08118	0	0.27008	N	0.964761	B	0.06786	0.001	B	0.04013	0.001	T	0.41179	-0.9523	10	0.30854	T	0.27	.	8.0577	0.30614	0.0:0.5034:0.3937:0.1029	.	8	Q02410	APBA1_HUMAN	T	8	ENSP00000265381:A8T	ENSP00000265381:A8T	A	-	1	0	APBA1	71321925	0.765000	0.28485	1.000000	0.80357	0.992000	0.81027	0.537000	0.23144	1.127000	0.42034	0.655000	0.94253	GCG		0.642	APBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052589.2	NM_001163	
C9orf135	138255	broad.mit.edu	37	9	72472895	72472895	+	Splice_Site	SNP	T	T	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:72472895T>A	ENST00000377197.3	+	4	536		c.e4+2		C9orf135_ENST00000466872.2_Splice_Site|C9orf135_ENST00000527647.1_Splice_Site	NM_001010940.1	NP_001010940.1	Q5VTT2	CI135_HUMAN	chromosome 9 open reading frame 135							integral component of membrane (GO:0016021)		p.?(1)		endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7						GAGCAAAATGTTAGTAGTCCC	0.423																																					.												.	.	1	Unknown(1)	large_intestine(1)	.	9						.						95.0	87.0	90.0					9																	72472895		2203	4300	6503	71662715	SO:0001630	splice_region_variant	138255	.				CCDS35041.1	9q21.11	2013-06-07	2013-06-07	2013-06-07	ENSG00000204711	ENSG00000204711			31422	protein-coding gene	gene with protein product							Standard	XM_005251705		Approved		uc004ahl.3	Q5VTT2	OTTHUMG00000019985	ENST00000377197.3:c.449+2T>A	9.37:g.72472895T>A		Somatic		Capture	Illumina HiSeq	Phase_I	71662715	.	A7E2U4|B2RN61	Splice_Site	SNP	ENST00000377197.3	37	CCDS35041.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.95|12.95	2.090545|2.090545	0.36855|0.36855	.|.	.|.	ENSG00000204711|ENSG00000204711	ENST00000377197;ENST00000527647|ENST00000480564	.|.	.|.	.|.	5.21|5.21	5.21|5.21	0.72293|0.72293	.|.	.|.	.|.	.|.	.|.	.|T	.|0.63710	.|0.2534	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.62751	.|-0.6788	.|4	.|.	.|.	.|.	.|.	11.7761|11.7761	0.51987|0.51987	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	.|D	-1|124	.|.	.|.	.|V	+|+	.|2	.|0	C9orf135|C9orf135	71662715|71662715	1.000000|1.000000	0.71417|0.71417	0.921000|0.921000	0.36526|0.36526	0.268000|0.268000	0.26511|0.26511	3.875000|3.875000	0.56108|0.56108	2.102000|2.102000	0.63906|0.63906	0.448000|0.448000	0.29417|0.29417	.|GTT		0.423	C9orf135-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052591.1	NM_001010940	Intron
PRUNE2	158471	broad.mit.edu	37	9	79253134	79253134	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:79253134C>T	ENST00000376718.3	-	13	8922	c.8799G>A	c.(8797-8799)gcG>gcA	p.A2933A	PRUNE2_ENST00000443509.2_Silent_p.A182A|PRUNE2_ENST00000428286.1_Silent_p.A2575A|PRUNE2_ENST00000223609.6_Silent_p.A198A|PRUNE2_ENST00000466266.2_5'UTR	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2933	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.A2933A(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						AGTGGTAATCCGCCCGACTGC	0.448																																					p.A2933A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G8799A	9						.						65.0	60.0	62.0					9																	79253134		1568	3582	5150	78442954	SO:0001819	synonymous_variant	158471	exon13			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.8799G>A	9.37:g.79253134C>T		Somatic		Capture	Illumina HiSeq	Phase_I	78442954	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	C	9.861	1.196428	0.22037	.	.	ENSG00000106772	ENST00000426088	.	.	.	5.46	3.48	0.39840	.	.	.	.	.	T	0.45915	0.1366	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42666	-0.9438	4	.	.	.	-11.7734	3.1492	0.06481	0.2646:0.5168:0.1252:0.0934	.	.	.	.	R	2258	.	.	G	-	1	0	PRUNE2	78442954	0.996000	0.38824	1.000000	0.80357	0.997000	0.91878	0.394000	0.20834	2.584000	0.87258	0.555000	0.69702	GGA		0.448	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
PRUNE2	158471	broad.mit.edu	37	9	79322113	79322113	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:79322113C>T	ENST00000376718.3	-	8	5200	c.5077G>A	c.(5077-5079)Ggt>Agt	p.G1693S	PRUNE2_ENST00000428286.1_Missense_Mutation_p.G1334S	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1693					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.G1693S(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						TCTTCACCACCGACACTGTCA	0.458																																					p.G1693S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5077A	9						.						80.0	68.0	72.0					9																	79322113		1568	3582	5150	78511933	SO:0001583	missense	158471	exon8			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.5077G>A	9.37:g.79322113C>T	ENSP00000365908:p.Gly1693Ser	Somatic		Capture	Illumina HiSeq	Phase_I	78511933	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	5.278|5.278	0.236657|0.236657	0.10023|0.10023	.|.	.|.	ENSG00000106772|ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033|ENST00000426088	T;T|.	0.46819|.	0.86;0.87|.	5.43|5.43	1.35|1.35	0.21983|0.21983	.|.	0.403035|.	0.21219|.	N|.	0.078168|.	T|T	0.40815|0.40815	0.1132|0.1132	L|L	0.54323|0.54323	1.7|1.7	0.09310|0.09310	N|N	1|1	D|.	0.52996|.	0.957|.	B|.	0.36378|.	0.223|.	T|T	0.29882|0.29882	-0.9997|-0.9997	10|5	0.54805|.	T|.	0.06|.	-0.8884|-0.8884	6.6281|6.6281	0.22841|0.22841	0.0:0.6437:0.1307:0.2256|0.0:0.6437:0.1307:0.2256	.|.	1693|.	Q8WUY3|.	PRUN2_HUMAN|.	S|Q	1693;1334;1692|1014	ENSP00000365908:G1693S;ENSP00000397425:G1334S|.	ENSP00000365908:G1693S|.	G|R	-|-	1|2	0|0	PRUNE2|PRUNE2	78511933|78511933	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.072000|0.072000	0.16883|0.16883	0.827000|0.827000	0.27421|0.27421	0.684000|0.684000	0.31448|0.31448	-0.213000|-0.213000	0.12676|0.12676	GGT|CGG		0.458	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
TLE4	7091	broad.mit.edu	37	9	82267619	82267619	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:82267619G>A	ENST00000376552.2	+	7	1520	c.502G>A	c.(502-504)Ggg>Agg	p.G168R	TLE4_ENST00000376544.3_Missense_Mutation_p.G168R|TLE4_ENST00000376537.4_Missense_Mutation_p.G168R|TLE4_ENST00000376534.4_5'UTR|TLE4_ENST00000455913.1_3'UTR|TLE4_ENST00000265284.6_Missense_Mutation_p.G143R|TLE4_ENST00000376520.4_Missense_Mutation_p.G168R	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	168	Gly/Pro-rich (GP domain).				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription corepressor activity (GO:0003714)	p.G168R(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						TAGCAGTGCCGGGCTTCTGGC	0.547																																					p.G168R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G502A	9						.						96.0	99.0	98.0					9																	82267619		1951	4136	6087	81457439	SO:0001583	missense	7091	exon7			M99439	CCDS43837.1, CCDS65069.1, CCDS65070.1, CCDS75851.1	9q21.32	2014-03-07	2014-03-07		ENSG00000106829	ENSG00000106829		"""WD repeat domain containing"""	11840	protein-coding gene	gene with protein product		605132	"""transducin-like enhancer of split 4, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005252167		Approved	E(spI), ESG, GRG4	uc004alc.3	Q04727	OTTHUMG00000020072	ENST00000376552.2:c.502G>A	9.37:g.82267619G>A	ENSP00000365735:p.Gly168Arg	Somatic		Capture	Illumina HiSeq	Phase_I	81457439	NM_007005	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	37	CCDS43837.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.357244	0.82243	.	.	ENSG00000106829	ENST00000376552;ENST00000376544;ENST00000376520;ENST00000399288;ENST00000435650;ENST00000376537;ENST00000265284;ENST00000425506;ENST00000428713;ENST00000490347	T;T;T;T;T;T;T;T;T	0.60171	0.4;0.21;0.4;0.39;0.4;0.35;0.41;1.12;0.65	6.04	5.15	0.70609	.	0.151060	0.64402	D	0.000012	T	0.77329	0.4114	M	0.86268	2.805	0.80722	D	1	D;P;D;P	0.71674	0.998;0.941;0.997;0.859	D;B;D;D	0.69307	0.963;0.348;0.931;0.918	T	0.79792	-0.1654	10	0.44086	T	0.13	-15.9282	15.4459	0.75228	0.0663:0.0:0.9337:0.0	.	143;168;168;168	F8W6T6;Q04727-2;Q04727-3;Q04727	.;.;.;TLE4_HUMAN	R	168;168;168;182;182;168;143;166;153;38	ENSP00000365735:G168R;ENSP00000365727:G168R;ENSP00000365703:G168R;ENSP00000415423:G182R;ENSP00000365720:G168R;ENSP00000265284:G143R;ENSP00000412567:G166R;ENSP00000409313:G153R;ENSP00000417844:G38R	ENSP00000265284:G143R	G	+	1	0	TLE4	81457439	1.000000	0.71417	0.454000	0.27019	0.611000	0.37282	4.285000	0.58989	1.566000	0.49654	0.563000	0.77884	GGG		0.547	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237	
UBQLN1	29979	broad.mit.edu	37	9	86292715	86292715	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:86292715G>A	ENST00000376395.4	-	6	1555	c.1032C>T	c.(1030-1032)ggC>ggT	p.G344G	UBQLN1_ENST00000257468.7_Silent_p.G344G	NM_013438.4|NM_053067.2	NP_038466.2|NP_444295.1	Q9UMX0	UBQL1_HUMAN	ubiquilin 1	344					cellular response to hypoxia (GO:0071456)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|regulation of protein ubiquitination (GO:0031396)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|protein complex (GO:0043234)	kinase binding (GO:0019900)	p.G344G(1)		breast(4)|endometrium(2)|kidney(4)|large_intestine(6)|lung(10)|prostate(1)	27						TACCAGTAGTGCCACCCACAG	0.517																																					p.G344G	Melanoma(186;1284 2073 12755 14558 18426)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1032T	9						.						79.0	72.0	74.0					9																	86292715		2203	4300	6503	85482535	SO:0001819	synonymous_variant	29979	exon6			AF176069	CCDS6663.1, CCDS6664.1	9q22	2013-02-12			ENSG00000135018	ENSG00000135018		"""Ubiquilin family"""	12508	protein-coding gene	gene with protein product		605046				9303440, 10807547	Standard	NM_013438		Approved	DSK2, PLIC-1, XDRP1, DA41	uc004amv.3	Q9UMX0	OTTHUMG00000020104	ENST00000376395.4:c.1032C>T	9.37:g.86292715G>A		Somatic		Capture	Illumina HiSeq	Phase_I	85482535	NM_053067	Q5T6J5|Q5T6J9|Q8IXS9|Q8N2Q3|Q9H0T8|Q9H3R4|Q9HAZ5	Silent	SNP	ENST00000376395.4	37	CCDS6663.1																																																																																				0.517	UBQLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052834.1	NM_013438	
HNRNPK	3190	broad.mit.edu	37	9	86586631	86586631	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:86586631C>T	ENST00000376264.2	-	12	1222	c.964G>A	c.(964-966)Gcc>Acc	p.A322T	HNRNPK_ENST00000351839.3_Missense_Mutation_p.A322T|RP11-575L7.8_ENST00000448389.1_RNA|HNRNPK_ENST00000376281.4_Missense_Mutation_p.A322T|HNRNPK_ENST00000376263.3_Missense_Mutation_p.A322T|MIR7-1_ENST00000384871.1_RNA|HNRNPK_ENST00000360384.5_Missense_Mutation_p.A322T	NM_002140.3|NM_031262.2	NP_002131.2|NP_112552.1	P61978	HNRPK_HUMAN	heterogeneous nuclear ribonucleoprotein K	322	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}.				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.A322T(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|stomach(1)	19						CTGTCATAGGCCATGAGGTCT	0.448																																					p.A322T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G964A	9						.						187.0	166.0	173.0					9																	86586631		2203	4300	6503	85776451	SO:0001583	missense	3190	exon12				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.964G>A	9.37:g.86586631C>T	ENSP00000365440:p.Ala322Thr	Somatic		Capture	Illumina HiSeq	Phase_I	85776451	NM_002140	Q07244|Q15671|Q59F98|Q5T6W4|Q60577|Q922Y7|Q96J62	Missense_Mutation	SNP	ENST00000376264.2	37	CCDS6667.1	.	.	.	.	.	.	.	.	.	.	C	10.05	1.245362	0.22796	.	.	ENSG00000165119	ENST00000376281;ENST00000376264;ENST00000376263;ENST00000376268;ENST00000351839;ENST00000435158;ENST00000360384;ENST00000376258;ENST00000457156;ENST00000376256	T;T;T;T;T	0.45668	0.9;0.89;0.9;0.89;0.89	5.82	5.82	0.92795	.	0.391625	0.26092	N	0.026397	T	0.24275	0.0588	N	0.08118	0	0.32936	D	0.517706	B;B;B;B;B;B;B;B	0.18013	0.001;0.025;0.006;0.004;0.006;0.002;0.001;0.004	B;B;B;B;B;B;B;B	0.18263	0.002;0.021;0.002;0.004;0.004;0.005;0.002;0.002	T	0.23940	-1.0174	10	0.28530	T	0.3	-3.5861	12.8526	0.57867	0.2036:0.7964:0.0:0.0	.	298;287;322;317;322;298;322;322	B4DUQ1;Q5T6W5;Q5EC54;B4DFF1;P61978-2;P61978-3;P61978;Q6IBN1	.;.;.;.;.;.;HNRPK_HUMAN;.	T	322;322;322;322;322;287;322;317;298;253	ENSP00000365458:A322T;ENSP00000365440:A322T;ENSP00000365439:A322T;ENSP00000317788:A322T;ENSP00000353552:A322T	ENSP00000317788:A322T	A	-	1	0	HNRNPK	85776451	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.765000	0.47621	2.760000	0.94817	0.655000	0.94253	GCC		0.448	HNRNPK-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052846.2		
DAPK1	1612	broad.mit.edu	37	9	90296516	90296516	+	Silent	SNP	T	T	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:90296516T>A	ENST00000408954.3	+	20	2534	c.2199T>A	c.(2197-2199)ccT>ccA	p.P733P	DAPK1_ENST00000469640.2_Silent_p.P733P|DAPK1_ENST00000472284.1_Silent_p.P733P|DAPK1_ENST00000491893.1_Silent_p.P733P|DAPK1_ENST00000358077.5_Silent_p.P733P	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	733					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.P734P(1)|p.P733P(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						GGTTCCCACCTTCACCCCTGG	0.572									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.P733P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T2199A	9						.						34.0	36.0	36.0					9																	90296516		1923	4107	6030	89486336	SO:0001819	synonymous_variant	1612	exon20	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.2199T>A	9.37:g.90296516T>A		Somatic		Capture	Illumina HiSeq	Phase_I	89486336	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																				0.572	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	90321349	90321349	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:90321349C>T	ENST00000408954.3	+	26	3698	c.3363C>T	c.(3361-3363)gaC>gaT	p.D1121D	DAPK1_ENST00000469640.2_Silent_p.D1146D|DAPK1_ENST00000472284.1_Silent_p.D1121D|DAPK1_ENST00000491893.1_Silent_p.D1055D|DAPK1_ENST00000358077.5_Silent_p.D1121D	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1121					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.D1122D(1)|p.D1121D(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						ATGAGGAGGACGAGGTGATGG	0.622									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.D1121D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C3363T	9						.						101.0	113.0	109.0					9																	90321349		2196	4290	6486	89511169	SO:0001819	synonymous_variant	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.3363C>T	9.37:g.90321349C>T		Somatic		Capture	Illumina HiSeq	Phase_I	89511169	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																				0.622	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	90502608	90502608	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:90502608C>T	ENST00000325643.5	+	4	3272	c.3206C>T	c.(3205-3207)gCt>gTt	p.A1069V		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	1069					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.A1069V(1)									AGCACAGGGGCTCTGGGGACC	0.587																																					p.A1069V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3206T	9						.						91.0	86.0	88.0					9																	90502608		2203	4300	6503	89692428	SO:0001583	missense	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.3206C>T	9.37:g.90502608C>T	ENSP00000322640:p.Ala1069Val	Somatic		Capture	Illumina HiSeq	Phase_I	89692428	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	c	9.182	1.023757	0.19433	.	.	ENSG00000177992	ENST00000325643	T	0.04275	3.66	2.58	-0.377	0.12501	.	3.264500	0.01078	N	0.004920	T	0.04272	0.0118	N	0.19112	0.55	0.09310	N	1	B	0.26400	0.148	B	0.24394	0.053	T	0.40136	-0.9579	10	0.72032	D	0.01	.	5.1073	0.14790	0.0:0.5458:0.0:0.4542	.	1069	Q6ZUB1	CI079_HUMAN	V	1069	ENSP00000322640:A1069V	ENSP00000322640:A1069V	A	+	2	0	C9orf79	89692428	0.002000	0.14202	0.002000	0.10522	0.056000	0.15407	1.145000	0.31577	-0.086000	0.12550	-0.253000	0.11424	GCT		0.587	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
SPIN1	10927	broad.mit.edu	37	9	91083431	91083431	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:91083431A>G	ENST00000375859.3	+	5	778	c.500A>G	c.(499-501)tAc>tGc	p.Y167C	SPIN1_ENST00000469017.2_3'UTR|SPIN1_ENST00000541629.1_Missense_Mutation_p.Y167C	NM_006717.2	NP_006708.2	Q9Y657	SPIN1_HUMAN	spindlin 1	167	Tudor-like domain 2.				chromatin modification (GO:0016568)|gamete generation (GO:0007276)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|positive regulation of Wnt signaling pathway (GO:0030177)|rRNA transcription (GO:0009303)|Wnt signaling pathway (GO:0016055)	nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle (GO:0005819)	methylated histone binding (GO:0035064)	p.Y167C(1)		endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4						ACATGGTTTTACATTACCTAT	0.423																																					p.Y167C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A500G	9						.						201.0	194.0	196.0					9																	91083431		2170	4290	6460	90273251	SO:0001583	missense	10927	exon5			AF317228	CCDS43843.1	9q22.1	2008-02-05	2007-01-03	2007-01-03	ENSG00000106723	ENSG00000106723			11243	protein-coding gene	gene with protein product		609936	"""spindlin"""	SPIN		16098913	Standard	NM_006717		Approved		uc004apy.3	Q9Y657	OTTHUMG00000020168	ENST00000375859.3:c.500A>G	9.37:g.91083431A>G	ENSP00000365019:p.Tyr167Cys	Somatic		Capture	Illumina HiSeq	Phase_I	90273251	NM_006717	A8K0X6|B3KRQ4|Q7KZJ8|Q9GZT2|Q9H0N7	Missense_Mutation	SNP	ENST00000375859.3	37	CCDS43843.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.446244	0.84101	.	.	ENSG00000106723	ENST00000375859;ENST00000541629	T;T	0.52295	0.67;0.67	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.68220	0.2977	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.73059	-0.4102	10	0.87932	D	0	-11.7349	14.6179	0.68562	1.0:0.0:0.0:0.0	.	167	Q9Y657	SPIN1_HUMAN	C	167	ENSP00000365019:Y167C;ENSP00000441864:Y167C	ENSP00000365019:Y167C	Y	+	2	0	SPIN1	90273251	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.726000	0.74758	2.037000	0.60232	0.533000	0.62120	TAC		0.423	SPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052967.1	NM_006717	
SEMA4D	10507	broad.mit.edu	37	9	92002512	92002512	+	Silent	SNP	G	G	A	rs529247702		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:92002512G>A	ENST00000450295.1	-	12	1895	c.1119C>T	c.(1117-1119)agC>agT	p.S373S	SEMA4D_ENST00000422704.2_Silent_p.S373S|SEMA4D_ENST00000420987.1_Silent_p.S373S|SEMA4D_ENST00000339861.4_Silent_p.S373S|SEMA4D_ENST00000343780.4_Silent_p.S373S|SEMA4D_ENST00000455551.2_Silent_p.S373S|SEMA4D_ENST00000356444.2_Silent_p.S373S|SEMA4D_ENST00000438547.2_Silent_p.S373S			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	373	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.S373S(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						CCCGTGCCTCGCTGTCGATGC	0.582													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19335	0.0		0.0	False		,,,				2504	0.0				p.S373S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1119T	9						.						110.0	116.0	114.0					9																	92002512		2203	4300	6503	91192332	SO:0001819	synonymous_variant	10507	exon14			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.1119C>T	9.37:g.92002512G>A		Somatic		Capture	Illumina HiSeq	Phase_I	91192332	NM_001142287	B2RPM6|Q7Z5S4|Q8N8B0	Silent	SNP	ENST00000450295.1	37	CCDS6685.1																																																																																				0.582	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378	
AUH	549	broad.mit.edu	37	9	93983174	93983174	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:93983174G>A	ENST00000375731.4	-	7	779	c.756C>T	c.(754-756)ggC>ggT	p.G252G	AUH_ENST00000303617.5_Silent_p.G223G	NM_001698.2	NP_001689.1	Q13825	AUHM_HUMAN	AU RNA binding protein/enoyl-CoA hydratase	252					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enoyl-CoA hydratase activity (GO:0004300)|methylglutaconyl-CoA hydratase activity (GO:0004490)|mRNA 3'-UTR binding (GO:0003730)	p.G252G(1)		endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	11						GGCTGATTAAGCCCACTGCTT	0.552																																					p.G252G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C756T	9						.						104.0	94.0	97.0					9																	93983174		2203	4300	6503	93022995	SO:0001819	synonymous_variant	549	exon7			X79888	CCDS6689.1	9q22	2014-09-17	2010-04-30		ENSG00000148090	ENSG00000148090			890	protein-coding gene	gene with protein product		600529	"""AU RNA-binding protein/enoyl-Coenzyme A hydratase"", ""AU RNA binding protein/enoyl-Coenzyme A hydratase"""			7892223	Standard	NM_001698		Approved		uc004arf.4	Q13825	OTTHUMG00000020207	ENST00000375731.4:c.756C>T	9.37:g.93983174G>A		Somatic		Capture	Illumina HiSeq	Phase_I	93022995	NM_001698	B1ALV7|B1ALV8|Q8WUE4	Silent	SNP	ENST00000375731.4	37	CCDS6689.1																																																																																				0.552	AUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053032.1		
ROR2	4920	broad.mit.edu	37	9	94486394	94486394	+	Silent	SNP	C	C	T	rs532042443	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:94486394C>T	ENST00000375708.3	-	9	2580	c.2382G>A	c.(2380-2382)ccG>ccA	p.P794P	ROR2_ENST00000375715.1_Intron|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	794	Pro-rich.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)	p.P794P(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GTGGGAAGGGCGGGGCCTTCT	0.677													C|||	2	0.000399361	0.0	0.0	5008	,	,		15381	0.0		0.0	False		,,,				2504	0.002				p.P794P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2382A	9						.						48.0	55.0	53.0					9																	94486394		2203	4300	6503	93526215	SO:0001819	synonymous_variant	4920	exon9			M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.2382G>A	9.37:g.94486394C>T		Somatic		Capture	Illumina HiSeq	Phase_I	93526215	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Silent	SNP	ENST00000375708.3	37	CCDS6691.1																																																																																				0.677	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1		
IPPK	64768	broad.mit.edu	37	9	95411776	95411776	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:95411776G>A	ENST00000287996.3	-	5	649	c.373C>T	c.(373-375)Cgc>Tgc	p.R125C		NM_022755.5	NP_073592.1	Q9H8X2	IPPK_HUMAN	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	125					inositol phosphate metabolic process (GO:0043647)|inositol phosphorylation (GO:0052746)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|inositol pentakisphosphate 2-kinase activity (GO:0035299)	p.R125C(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(2)|urinary_tract(1)	15						TCTGCAAAGCGGTAGGTTTGG	0.507																																					p.R125C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C373T	9						.						162.0	125.0	138.0					9																	95411776		2203	4300	6503	94451597	SO:0001583	missense	64768	exon5			AK023225	CCDS6699.1	9q22.31	2010-12-02	2005-10-20	2005-10-20	ENSG00000127080	ENSG00000127080			14645	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 12"""	C9orf12		12084730	Standard	NM_022755		Approved	INSP5K2, FLJ13163, IP5K, IPK1	uc004asl.1	Q9H8X2	OTTHUMG00000020231	ENST00000287996.3:c.373C>T	9.37:g.95411776G>A	ENSP00000287996:p.Arg125Cys	Somatic		Capture	Illumina HiSeq	Phase_I	94451597	NM_022755	Q5T9F7|Q9H7V8	Missense_Mutation	SNP	ENST00000287996.3	37	CCDS6699.1	.	.	.	.	.	.	.	.	.	.	G	14.28	2.489247	0.44249	.	.	ENSG00000127080	ENST00000287996	T	0.29655	1.56	4.9	3.05	0.35203	.	0.576805	0.20880	N	0.084013	T	0.21674	0.0522	L	0.29908	0.895	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.04103	-1.0977	10	0.48119	T	0.1	-0.3547	9.7939	0.40722	0.1748:0.0:0.8252:0.0	.	125	Q9H8X2	IPPK_HUMAN	C	125	ENSP00000287996:R125C	ENSP00000287996:R125C	R	-	1	0	IPPK	94451597	0.998000	0.40836	0.846000	0.33378	0.931000	0.56810	2.187000	0.42602	0.743000	0.32719	0.557000	0.71058	CGC		0.507	IPPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053101.1	NM_022755	
BICD2	23299	broad.mit.edu	37	9	95480987	95480987	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:95480987C>T	ENST00000375512.3	-	5	2007	c.1940G>A	c.(1939-1941)cGc>cAc	p.R647H	BICD2_ENST00000356884.6_Missense_Mutation_p.R647H	NM_015250.3	NP_056065.1	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 (Drosophila)	647					cell death (GO:0008219)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase binding (GO:0017137)	p.R647H(1)		cervix(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23						CTCCGTGGTGCGGTCCACGGC	0.612																																					p.R647H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1940A	9						.						149.0	143.0	145.0					9																	95480987		2203	4300	6503	94520808	SO:0001583	missense	23299	exon5			AB014599	CCDS6700.1, CCDS35064.1	9q22.32	2008-02-05			ENSG00000185963	ENSG00000185963			17208	protein-coding gene	gene with protein product		609797				9734811	Standard	NM_001003800		Approved	KIAA0699	uc004asp.1	Q8TD16	OTTHUMG00000021036	ENST00000375512.3:c.1940G>A	9.37:g.95480987C>T	ENSP00000364662:p.Arg647His	Somatic		Capture	Illumina HiSeq	Phase_I	94520808	NM_015250	O75181|Q5TBQ2|Q5TBQ3|Q96LH2|Q9BT84|Q9H561	Missense_Mutation	SNP	ENST00000375512.3	37	CCDS6700.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.860427	0.91433	.	.	ENSG00000185963	ENST00000356884;ENST00000375512	T;T	0.53857	0.6;0.6	5.39	5.39	0.77823	.	0.169615	0.49916	N	0.000133	T	0.62478	0.2431	L	0.35288	1.05	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.57087	-0.7871	10	0.30078	T	0.28	-24.0069	17.0121	0.86409	0.0:1.0:0.0:0.0	.	647;647	Q8TD16-2;Q8TD16	.;BICD2_HUMAN	H	647	ENSP00000349351:R647H;ENSP00000364662:R647H	ENSP00000349351:R647H	R	-	2	0	BICD2	94520808	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.473000	0.81007	2.707000	0.92482	0.561000	0.74099	CGC		0.612	BICD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055508.1	NM_015250	
BICD2	23299	broad.mit.edu	37	9	95482594	95482594	+	Silent	SNP	C	C	T	rs368860496		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:95482594C>T	ENST00000375512.3	-	4	1117	c.1050G>A	c.(1048-1050)caG>caA	p.Q350Q	BICD2_ENST00000356884.6_Silent_p.Q350Q	NM_015250.3	NP_056065.1	Q8TD16	BICD2_HUMAN	bicaudal D homolog 2 (Drosophila)	350					cell death (GO:0008219)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase binding (GO:0017137)			cervix(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23						GCATCAGCTGCTGCTTCAGCT	0.632																																					p.Q350Q												.	.	0			c.G1050A	9						.	C	,	0,4406		0,0,2203	50.0	48.0	49.0		1050,1050	3.2	1.0	9		49	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	BICD2	NM_001003800.1,NM_015250.3	,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,	350/856,350/825	95482594	2,13004	2203	4300	6503	94522415	SO:0001819	synonymous_variant	23299	exon4			AB014599	CCDS6700.1, CCDS35064.1	9q22.32	2008-02-05			ENSG00000185963	ENSG00000185963			17208	protein-coding gene	gene with protein product		609797				9734811	Standard	NM_001003800		Approved	KIAA0699	uc004asp.1	Q8TD16	OTTHUMG00000021036	ENST00000375512.3:c.1050G>A	9.37:g.95482594C>T		Germline		Capture	Illumina HiSeq	Phase_I	94522415	NM_015250	O75181|Q5TBQ2|Q5TBQ3|Q96LH2|Q9BT84|Q9H561	Silent	SNP	ENST00000375512.3	37	CCDS6700.1																																																																																				0.632	BICD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055508.1	NM_015250	
ZNF484	83744	broad.mit.edu	37	9	95609315	95609315	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:95609315C>A	ENST00000375495.3	-	5	1902	c.1754G>T	c.(1753-1755)tGt>tTt	p.C585F	ZNF484_ENST00000395505.2_Missense_Mutation_p.C549F|ZNF484_ENST00000395506.3_Missense_Mutation_p.C587F|ZNF484_ENST00000332591.6_Missense_Mutation_p.C549F|ANKRD19P_ENST00000473204.1_RNA	NM_031486.2	NP_113674.1	Q5JVG2	ZN484_HUMAN	zinc finger protein 484	585					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.C585F(1)		NS(1)|breast(1)|cervix(1)|kidney(8)|large_intestine(10)|lung(10)|prostate(2)	33						GGCCTTACCACATTCAGTGCA	0.383																																					p.C549F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1646T	9						.						129.0	128.0	128.0					9																	95609315		2203	4300	6503	94649136	SO:0001583	missense	83744	exon4			AK091203	CCDS35066.1, CCDS35067.1, CCDS59136.1	9q22.32	2013-01-08			ENSG00000127081	ENSG00000127081		"""Zinc fingers, C2H2-type"", ""-"""	23385	protein-coding gene	gene with protein product							Standard	NM_001007101		Approved	BA526D8.4, FLJ33884	uc004asu.2	Q5JVG2	OTTHUMG00000020236	ENST00000375495.3:c.1754G>T	9.37:g.95609315C>A	ENSP00000364645:p.Cys585Phe	Somatic		Capture	Illumina HiSeq	Phase_I	94649136	NM_001007101	B1AL89|B4DRI2	Missense_Mutation	SNP	ENST00000375495.3	37	CCDS35066.1	.	.	.	.	.	.	.	.	.	.	.	15.56	2.869404	0.51588	.	.	ENSG00000127081	ENST00000395505;ENST00000395506;ENST00000375495;ENST00000332591	D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04	2.21	2.21	0.28008	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94817	0.8326	H	0.98849	4.35	0.40318	D	0.97879	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.94993	0.8136	9	0.66056	D	0.02	.	10.5057	0.44832	0.0:1.0:0.0:0.0	.	587;585	B4DRI2;Q5JVG2	.;ZN484_HUMAN	F	549;587;585;549	ENSP00000378881:C549F;ENSP00000378882:C587F;ENSP00000364645:C585F;ENSP00000364646:C549F	ENSP00000364646:C549F	C	-	2	0	ZNF484	94649136	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.394000	0.73223	1.547000	0.49401	0.551000	0.68910	TGT		0.383	ZNF484-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000053111.2	XM_046861	
SUSD3	203328	broad.mit.edu	37	9	95838089	95838089	+	Missense_Mutation	SNP	C	C	A	rs201778335		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:95838089C>A	ENST00000375472.3	+	2	148	c.112C>A	c.(112-114)Ccc>Acc	p.P38T	SUSD3_ENST00000375469.1_Missense_Mutation_p.P25T	NM_145006.2	NP_659443.1	Q96L08	SUSD3_HUMAN	sushi domain containing 3	38	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.P38T(1)		NS(1)|autonomic_ganglia(1)|breast(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	13						GCTGCGGCTACCCCCGCAAGC	0.682																																					p.P38T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C112A	9						.						66.0	52.0	57.0					9																	95838089		2203	4300	6503	94877910	SO:0001583	missense	203328	exon2			AK128289	CCDS6701.1, CCDS69620.1, CCDS75857.1	9q22.32	2004-01-29			ENSG00000157303	ENSG00000157303			28391	protein-coding gene	gene with protein product						12975309	Standard	NM_001287007		Approved	MGC26847	uc004atb.3	Q96L08	OTTHUMG00000020241	ENST00000375472.3:c.112C>A	9.37:g.95838089C>A	ENSP00000364621:p.Pro38Thr	Somatic		Capture	Illumina HiSeq	Phase_I	94877910	NM_145006	Q49AA6|Q6UXV7	Missense_Mutation	SNP	ENST00000375472.3	37	CCDS6701.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.221432	0.58560	.	.	ENSG00000157303	ENST00000375472;ENST00000375469	T;T	0.64803	-0.12;-0.12	5.25	3.42	0.39159	Complement control module (2);Sushi/SCR/CCP (3);	0.113084	0.64402	D	0.000008	T	0.72036	0.3411	M	0.73962	2.25	0.39448	D	0.967367	D;D	0.57899	0.976;0.981	P;P	0.58077	0.741;0.832	T	0.74780	-0.3549	10	0.87932	D	0	-30.6266	9.6021	0.39609	0.0:0.8288:0.0:0.1712	.	25;38	Q96L08-2;Q96L08	.;SUSD3_HUMAN	T	38;25	ENSP00000364621:P38T;ENSP00000364618:P25T	ENSP00000364618:P25T	P	+	1	0	SUSD3	94877910	0.599000	0.26891	0.030000	0.17652	0.053000	0.15095	2.616000	0.46376	0.730000	0.32425	0.561000	0.74099	CCC		0.682	SUSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053120.1	NM_145006	
WNK2	65268	broad.mit.edu	37	9	96026308	96026308	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:96026308C>T	ENST00000297954.4	+	15	3689	c.3689C>T	c.(3688-3690)aCg>aTg	p.T1230M	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000349097.3_Missense_Mutation_p.T842M|WNK2_ENST00000395477.2_Missense_Mutation_p.T1230M|WNK2_ENST00000427277.2_Missense_Mutation_p.T842M|WNK2_ENST00000395475.2_3'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1230					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.T1230M(1)|p.T1216M(1)		breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						GAAATTGCCACGTATATGGTG	0.592																																					p.T1230M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3689T	9						.						98.0	73.0	81.0					9																	96026308		2203	4299	6502	95066129	SO:0001583	missense	65268	exon15			AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.3689C>T	9.37:g.96026308C>T	ENSP00000297954:p.Thr1230Met	Somatic		Capture	Illumina HiSeq	Phase_I	95066129	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.76|15.76	2.929704|2.929704	0.52759|0.52759	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000432730;ENST00000448251|ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277	.|T;T;T;T	.|0.32988	.|1.43;1.43;1.43;1.43	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.55513|0.55513	0.1925|0.1925	M|M	0.63843|0.63843	1.955|1.955	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	.|0.91635	.|0.999;0.994;0.997;0.996	T|T	0.58081|0.58081	-0.7699|-0.7699	5|10	.|0.87932	.|D	.|0	.|.	18.9908|18.9908	0.92791|0.92791	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1230;833;1230;1230	.|Q9Y3S1-2;A6PVR4;F8W9F9;Q9Y3S1	.|.;.;.;WNK2_HUMAN	C|M	1226;27|1230;1230;842;842	.|ENSP00000297954:T1230M;ENSP00000378860:T1230M;ENSP00000297876:T842M;ENSP00000411181:T842M	.|ENSP00000297954:T1230M	R|T	+|+	1|2	0|0	WNK2|WNK2	95066129|95066129	0.974000|0.974000	0.33945|0.33945	0.979000|0.979000	0.43373|0.43373	0.018000|0.018000	0.09664|0.09664	2.429000|2.429000	0.44758|0.44758	2.562000|2.562000	0.86427|0.86427	0.563000|0.563000	0.77884|0.77884	CGT|ACG		0.592	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
ZNF169	169841	broad.mit.edu	37	9	97062823	97062823	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:97062823G>A	ENST00000395395.2	+	5	1073	c.983G>A	c.(982-984)cGc>cAc	p.R328H	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	328					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.R328H(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				CGAGGCTTTCGCCAGAAGATA	0.547																																					p.R328H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G983A	9						.						99.0	93.0	95.0					9																	97062823		2203	4300	6503	96102644	SO:0001583	missense	169841	exon5			U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"""Zinc fingers, C2H2-type"", ""-"""	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.983G>A	9.37:g.97062823G>A	ENSP00000378792:p.Arg328His	Somatic		Capture	Illumina HiSeq	Phase_I	96102644	NM_194320	A2AGP5|A8K127|Q6PI28	Missense_Mutation	SNP	ENST00000395395.2	37	CCDS6709.2	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990356	0.35131	.	.	ENSG00000175787	ENST00000395395;ENST00000340911	T	0.36157	1.27	2.83	0.858	0.19030	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32615	0.0835	N	0.13371	0.34	0.09310	N	1	D	0.76494	0.999	D	0.70716	0.97	T	0.11470	-1.0586	9	0.41790	T	0.15	.	1.4715	0.02417	0.1316:0.2157:0.4324:0.2203	.	328	Q14929	ZN169_HUMAN	H	328;137	ENSP00000378792:R328H	ENSP00000340711:R137H	R	+	2	0	ZNF169	96102644	0.000000	0.05858	0.257000	0.24404	0.566000	0.35808	-0.410000	0.07151	0.235000	0.21160	0.603000	0.83216	CGC		0.547	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320	
ZNF169	169841	broad.mit.edu	37	9	97063149	97063149	+	Missense_Mutation	SNP	C	C	T	rs377137736		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:97063149C>T	ENST00000395395.2	+	5	1399	c.1309C>T	c.(1309-1311)Cgg>Tgg	p.R437W	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	437					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.R437W(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				CCAGTGTGGGCGGGGTTTTAG	0.582																																					p.R437W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1309T	9						.	C	TRP/ARG	0,4406		0,0,2203	62.0	60.0	61.0		1309	-0.1	0.0	9		61	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF169	NM_194320.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	437/604	97063149	1,13005	2203	4300	6503	96102970	SO:0001583	missense	169841	exon5			U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"""Zinc fingers, C2H2-type"", ""-"""	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.1309C>T	9.37:g.97063149C>T	ENSP00000378792:p.Arg437Trp	Somatic		Capture	Illumina HiSeq	Phase_I	96102970	NM_194320	A2AGP5|A8K127|Q6PI28	Missense_Mutation	SNP	ENST00000395395.2	37	CCDS6709.2	.	.	.	.	.	.	.	.	.	.	C	10.22	1.290320	0.23478	0.0	1.16E-4	ENSG00000175787	ENST00000395395;ENST00000340911	T	0.19806	2.12	2.83	-0.124	0.13523	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30665	0.0772	M	0.79805	2.47	0.19300	N	0.99998	P	0.50943	0.94	P	0.51193	0.662	T	0.19647	-1.0299	9	0.87932	D	0	.	2.5923	0.04846	0.218:0.3677:0.0:0.4142	.	437	Q14929	ZN169_HUMAN	W	437;246	ENSP00000378792:R437W	ENSP00000340711:R246W	R	+	1	2	ZNF169	96102970	0.020000	0.18652	0.022000	0.16811	0.450000	0.32258	0.597000	0.24059	-0.027000	0.13873	-0.199000	0.12753	CGG		0.582	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320	
FANCC	2176	broad.mit.edu	37	9	97873912	97873912	+	Missense_Mutation	SNP	C	C	T	rs371897078		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:97873912C>T	ENST00000289081.3	-	13	1416	c.1162G>A	c.(1162-1164)Gga>Aga	p.G388R	RP11-80I15.4_ENST00000423075.1_RNA|FANCC_ENST00000375305.1_Missense_Mutation_p.G388R|FANCC_ENST00000464653.1_5'Flank	NM_000136.2	NP_000127.2	Q00597	FANCC_HUMAN	Fanconi anemia, complementation group C	388					DNA repair (GO:0006281)|germ cell development (GO:0007281)|myeloid cell homeostasis (GO:0002262)|nucleotide-excision repair (GO:0006289)|protein complex assembly (GO:0006461)|removal of superoxide radicals (GO:0019430)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.G388R(1)		kidney(1)|skin(1)|upper_aerodigestive_tract(1)	3		Acute lymphoblastic leukemia(62;0.138)				AAGGGACCTCCGCAGGACCTG	0.517			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.G388R		yes	Rec		Fanconi anaemia C	9	9q22.3	2176	"""Fanconi anemia, complementation group C"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1162A	9						.	C	ARG/GLY	2,4404	4.2+/-10.8	0,2,2201	94.0	90.0	91.0		1162	-1.6	0.0	9		91	0,8600		0,0,4300	no	missense	FANCC	NM_000136.2	125	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	388/559	97873912	2,13004	2203	4300	6503	96913733	SO:0001583	missense	2176	exon13	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	BC006303	CCDS35071.1, CCDS75861.1	9q22.3	2014-09-17			ENSG00000158169	ENSG00000158169		"""Fanconi anemia, complementation groups"""	3584	protein-coding gene	gene with protein product		613899		FACC		1303234	Standard	NM_001243743		Approved	FAC, FA3	uc004avh.3	Q00597	OTTHUMG00000020279	ENST00000289081.3:c.1162G>A	9.37:g.97873912C>T	ENSP00000289081:p.Gly388Arg	Somatic		Capture	Illumina HiSeq	Phase_I	96913733	NM_000136	B1ALR8	Missense_Mutation	SNP	ENST00000289081.3	37	CCDS35071.1	.	.	.	.	.	.	.	.	.	.	C	0.341	-0.950672	0.02285	4.54E-4	0.0	ENSG00000158169	ENST00000289081;ENST00000375305	T;T	0.46819	0.86;0.86	5.53	-1.59	0.08453	.	0.733149	0.14120	N	0.340137	T	0.27524	0.0676	L	0.40543	1.245	0.09310	N	1	B	0.16603	0.018	B	0.15052	0.012	T	0.23119	-1.0197	10	0.11485	T	0.65	-3.6172	2.6836	0.05101	0.1107:0.4547:0.2261:0.2085	.	388	Q00597	FANCC_HUMAN	R	388	ENSP00000289081:G388R;ENSP00000364454:G388R	ENSP00000289081:G388R	G	-	1	0	FANCC	96913733	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.501000	0.06398	-0.455000	0.07054	-0.137000	0.14449	GGA		0.517	FANCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053219.1	NM_000136	
PTCH1	5727	broad.mit.edu	37	9	98218623	98218623	+	Missense_Mutation	SNP	C	C	T	rs587778629		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:98218623C>T	ENST00000331920.6	-	19	3540	c.3241G>A	c.(3241-3243)Gtg>Atg	p.V1081M	PTCH1_ENST00000430669.2_Missense_Mutation_p.V1015M|PTCH1_ENST00000375274.2_Missense_Mutation_p.V1080M|PTCH1_ENST00000418258.1_Missense_Mutation_p.V930M|PTCH1_ENST00000429896.2_Missense_Mutation_p.V930M|PTCH1_ENST00000421141.1_Missense_Mutation_p.V930M|PTCH1_ENST00000437951.1_Missense_Mutation_p.V1015M	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	1081					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.V1081M(2)|p.V1080M(1)|p.V1057_L1102del(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)				ACCACGGGCACGGCACTGAGC	0.542																																					p.V930M												.	.	4	Substitution - Missense(3)|Deletion - In frame(1)	large_intestine(3)|central_nervous_system(1)	c.G2788A	9						.						144.0	108.0	120.0					9																	98218623		2203	4300	6503	97258444	SO:0001583	missense	5727	exon19			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	ENST00000331920.6:c.3241G>A	9.37:g.98218623C>T	ENSP00000332353:p.Val1081Met	Somatic		Capture	Illumina HiSeq	Phase_I	97258444	NM_001083605	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.746836	0.89663	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000375275;ENST00000430669;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.88201	-2.35;-2.35;-2.35;-2.35;-2.35;-2.35;-2.35	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	D	0.93475	0.7918	L	0.59436	1.845	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.991	D;D;P	0.77557	0.99;0.975;0.782	D	0.93798	0.7098	10	0.66056	D	0.02	-23.0627	18.9905	0.92789	0.0:1.0:0.0:0.0	.	1015;1080;1081	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	M	1081;1015;930;930;517;1015;930;1080	ENSP00000332353:V1081M;ENSP00000389744:V1015M;ENSP00000399981:V930M;ENSP00000396135:V930M;ENSP00000410287:V1015M;ENSP00000414823:V930M;ENSP00000364423:V1080M	ENSP00000332353:V1081M	V	-	1	0	PTCH1	97258444	1.000000	0.71417	0.966000	0.40874	0.786000	0.44442	5.771000	0.68881	2.505000	0.84491	0.561000	0.74099	GTG		0.542	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
ZNF782	158431	broad.mit.edu	37	9	99581045	99581045	+	Missense_Mutation	SNP	T	T	G	rs368899631		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:99581045T>G	ENST00000481138.1	-	6	1921	c.1260A>C	c.(1258-1260)aaA>aaC	p.K420N	ZNF782_ENST00000466833.1_5'Flank|ZNF782_ENST00000535338.1_Missense_Mutation_p.K288N	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	420					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.K420N(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				ATTTGTATGGTTTCTCTCCCG	0.468																																					p.K420N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1260C	9						.						136.0	134.0	135.0					9																	99581045		2203	4300	6503	98620866	SO:0001583	missense	158431	exon6			AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"""Zinc fingers, C2H2-type"", ""-"""	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.1260A>C	9.37:g.99581045T>G	ENSP00000419397:p.Lys420Asn	Somatic		Capture	Illumina HiSeq	Phase_I	98620866	NM_001001662	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.29|16.29	3.081096|3.081096	0.55753|0.55753	.|.	.|.	ENSG00000196597|ENSG00000196597	ENST00000481138;ENST00000535338|ENST00000289032	T;T|.	0.26067|.	1.76;1.76|.	2.93|2.93	1.16|1.16	0.20824|0.20824	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);|.	0.000000|.	0.35525|.	N|.	0.003143|.	T|T	0.52741|0.52741	0.1753|0.1753	M|M	0.79011|0.79011	2.435|2.435	0.23309|0.23309	N|N	0.997939|0.997939	D|.	0.89917|.	1.0|.	D|.	0.85130|.	0.997|.	T|T	0.46414|0.46414	-0.9193|-0.9193	10|5	0.66056|.	D|.	0.02|.	.|.	5.5594|5.5594	0.17135|0.17135	0.0:0.2326:0.0:0.7674|0.0:0.2326:0.0:0.7674	.|.	420|.	Q6ZMW2|.	ZN782_HUMAN|.	N|P	420;288|409	ENSP00000419397:K420N;ENSP00000440624:K288N|.	ENSP00000419397:K420N|.	K|T	-|-	3|1	2|0	ZNF782|ZNF782	98620866|98620866	0.921000|0.921000	0.31238|0.31238	1.000000|1.000000	0.80357|0.80357	0.963000|0.963000	0.63663|0.63663	0.088000|0.088000	0.14979|0.14979	0.238000|0.238000	0.21222|0.21222	0.533000|0.533000	0.62120|0.62120	AAA|ACC		0.468	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662	
CTSV	1515	broad.mit.edu	37	9	99797895	99797895	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:99797895C>T	ENST00000259470.5	-	6	951	c.702G>A	c.(700-702)aaG>aaA	p.K234K	CTSV_ENST00000538255.1_Silent_p.K234K|CTSV_ENST00000479932.1_5'Flank	NM_001333.3	NP_001324.2	O60911	CATL2_HUMAN	cathepsin V	234					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|autophagic cell death (GO:0048102)|catagen (GO:0042637)|cellular response to starvation (GO:0009267)|decidualization (GO:0046697)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|multicellular organismal aging (GO:0010259)|negative regulation of keratinocyte proliferation (GO:0010839)|nerve development (GO:0021675)|protein autoprocessing (GO:0016540)|regulation of actin cytoskeleton reorganization (GO:2000249)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to gonadotropin (GO:0034698)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|perikaryon (GO:0043204)	aminopeptidase activity (GO:0004177)|cysteine-type carboxypeptidase activity (GO:0016807)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptide binding (GO:0042277)	p.K234K(1)									TCATCAGGGCCTTCTCCTTTC	0.468																																					p.K234K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G702A	9						.						86.0	76.0	80.0					9																	99797895		2203	4300	6503	98837716	SO:0001819	synonymous_variant	1515	exon6			Y14734	CCDS6723.1	9q22.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000136943	ENSG00000136943		"""Cathepsins"""	2538	protein-coding gene	gene with protein product		603308	"""cathepsin L2"""	CTSL2		9563472, 10029531	Standard	NM_001201575		Approved	CTSU	uc004awt.3	O60911	OTTHUMG00000020314	ENST00000259470.5:c.702G>A	9.37:g.99797895C>T		Somatic		Capture	Illumina HiSeq	Phase_I	98837716	NM_001333	O60233|Q2TB86|Q5T1U0	Silent	SNP	ENST00000259470.5	37	CCDS6723.1																																																																																				0.468	CTSV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053301.2	NM_001333	
SMC2	10592	broad.mit.edu	37	9	106885501	106885501	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:106885501delA	ENST00000286398.7	+	17	2533	c.2245delA	c.(2245-2247)aaafs	p.K750fs	SMC2_ENST00000303219.8_Frame_Shift_Del_p.K750fs|SMC2_ENST00000374793.3_Frame_Shift_Del_p.K750fs|SMC2_ENST00000374787.3_Frame_Shift_Del_p.K750fs	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	750					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)	p.T751fs*9(1)		breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						AGATGCCCTTAAAAAAACCAT	0.368																																					p.K749fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2245delA	9						.						95.0	89.0	91.0					9																	106885501		2203	4300	6503	105925322	SO:0001589	frameshift_variant	10592	exon17			AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"""Structural maintenance of chromosomes proteins"""	14011	protein-coding gene	gene with protein product		605576	"""SMC2 (structural maintenance of chromosomes 2, yeast)-like 1"", ""SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"""	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.2245delA	9.37:g.106885501delA	ENSP00000286398:p.Lys750fs	Somatic		Capture	Illumina HiSeq	Phase_I	105925322	NM_006444	Q6IEE0|Q9P1P2	Frame_Shift_Del	DEL	ENST00000286398.7	37	CCDS35086.1																																																																																				0.368	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1		
CACNA1B	774	broad.mit.edu	37	9	140866022	140866022	+	Silent	SNP	G	G	A	rs199721953		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chr9:140866022G>A	ENST00000371372.1	+	11	1666	c.1521G>A	c.(1519-1521)ccG>ccA	p.P507P	CACNA1B_ENST00000371363.1_Silent_p.P507P|CACNA1B_ENST00000371355.4_Silent_p.P508P|CACNA1B_ENST00000371357.1_Silent_p.P508P|CACNA1B_ENST00000277549.5_5'UTR|CACNA1B_ENST00000277551.2_Silent_p.P507P	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	507					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.P507P(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	ACAACCAGCCGCGGCGGCTTA	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		17085	0.0		0.001	False		,,,				2504	0.0				p.P507P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1521A	9						.						80.0	92.0	88.0					9																	140866022		2157	4246	6403	139985843	SO:0001819	synonymous_variant	774	exon11			AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.1521G>A	9.37:g.140866022G>A		Somatic		Capture	Illumina HiSeq	Phase_I	139985843	NM_000718	B1AQK5	Silent	SNP	ENST00000371372.1	37	CCDS59522.1																																																																																				0.602	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
USP9X	8239	broad.mit.edu	37	X	41089034	41089035	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:41089034_41089035insA	ENST00000324545.8	+	43	8066_8067	c.7433_7434insA	c.(7432-7437)gtaaaafs	p.VK2478fs	USP9X_ENST00000378308.2_Splice_Site	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	2478					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.?(2)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CCAGAGGAGGTAAAAAAAGCCA	0.371														1	0.000264901	0.0	0.0014	3775	,	,		12931	0.0		0.0	False		,,,				2504	0.0				p.V2478fs	Ovarian(172;1807 2695 35459 49286)											.	.	2	Unknown(2)	large_intestine(2)	c.7433_7434insA	X						.																																			40973979	SO:0001589	frameshift_variant	8239	exon43			X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.7440dupA	X.37:g.41089041_41089041dupA	ENSP00000316357:p.Val2478fs	Somatic		Capture	Illumina HiSeq	Phase_I	40973978	NM_001039590	O75550|Q8WWT3|Q8WX12	Frame_Shift_Ins	INS	ENST00000324545.8	37	CCDS43930.1																																																																																				0.371	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652	
WWC3	55841	broad.mit.edu	37	X	10085433	10085433	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:10085433C>T	ENST00000380861.4	+	11	1725	c.1334C>T	c.(1333-1335)aCg>aTg	p.T445M	WWC3_ENST00000454666.1_Missense_Mutation_p.T445M	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	445	Ser-rich.				negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)	p.T445M(1)		NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						TCCCTGGACACGCCCCAGTCC	0.682																																					p.T445M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1334T	X						.						40.0	41.0	41.0					X																	10085433		2203	4300	6503	10045433	SO:0001583	missense	55841	exon11			AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1334C>T	X.37:g.10085433C>T	ENSP00000370242:p.Thr445Met	Somatic		Capture	Illumina HiSeq	Phase_I	10045433	NM_015691	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	C	17.44	3.389890	0.61956	.	.	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543293;ENST00000398613	T;T	0.06528	3.29;3.29	5.43	4.54	0.55810	.	0.363954	0.31461	N	0.007618	T	0.26484	0.0647	M	0.80422	2.495	0.45995	D	0.998805	D	0.89917	1.0	D	0.91635	0.999	T	0.01734	-1.1285	10	0.49607	T	0.09	-11.5638	14.6974	0.69132	0.1462:0.8538:0.0:0.0	.	445	Q9ULE0	WWC3_HUMAN	M	445;445;109;445	ENSP00000370242:T445M;ENSP00000399584:T445M	ENSP00000370242:T445M	T	+	2	0	WWC3	10045433	1.000000	0.71417	0.141000	0.22245	0.558000	0.35554	7.623000	0.83113	1.039000	0.40074	0.464000	0.42555	ACG		0.682	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
CLCN4	1183	broad.mit.edu	37	X	10153087	10153087	+	Silent	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:10153087A>G	ENST00000380833.4	+	3	406	c.15A>G	c.(13-15)ggA>ggG	p.G5G	CLCN4_ENST00000380829.1_Silent_p.G5G|CLCN4_ENST00000421085.2_Intron	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	5					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.G5G(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						TCAATGCGGGAGCGATGAGTG	0.517																																					p.G5G	Melanoma(74;1050 1296 1576 30544 38374)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A15G	X						.						171.0	137.0	148.0					X																	10153087		2203	4300	6503	10113087	SO:0001819	synonymous_variant	1183	exon3			X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"""Ion channels / Chloride channels : Voltage-sensitive"""	2022	protein-coding gene	gene with protein product		302910	"""chloride channel 4"""			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.15A>G	X.37:g.10153087A>G		Somatic		Capture	Illumina HiSeq	Phase_I	10113087	NM_001830	A1L3U1|B7Z5Z4|Q9UBU1	Silent	SNP	ENST00000380833.4	37	CCDS14137.1																																																																																				0.517	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1		
DRP2	1821	broad.mit.edu	37	X	100513418	100513418	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:100513418C>T	ENST00000395209.3	+	22	3038	c.2511C>T	c.(2509-2511)gcC>gcT	p.A837A	DRP2_ENST00000541709.1_Silent_p.A759A|DRP2_ENST00000402866.1_Silent_p.A837A|DRP2_ENST00000538510.1_Silent_p.A837A	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	837					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)	p.A834A(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						AGCTTCTGGCCGAGGCCCGTA	0.612																																					p.A837A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2511T	X						.						34.0	31.0	32.0					X																	100513418		2202	4297	6499	100400074	SO:0001819	synonymous_variant	1821	exon22			U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.2511C>T	X.37:g.100513418C>T		Somatic		Capture	Illumina HiSeq	Phase_I	100400074	NM_001939	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Silent	SNP	ENST00000395209.3	37	CCDS14480.2																																																																																				0.612	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939	
SLC25A53	401612	broad.mit.edu	37	X	103349504	103349504	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:103349504C>T	ENST00000357421.4	-	2	617	c.437G>A	c.(436-438)cGc>cAc	p.R146H		NM_001012755.3	NP_001012773.2	Q5H9E4	S2553_HUMAN	solute carrier family 25, member 53	146					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.R146H(1)									AGCTTGCTTGCGACCATCCTG	0.587																																					p.R146H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G437A	X						.						100.0	105.0	103.0					X																	103349504		2203	4300	6503	103236160	SO:0001583	missense	401612	exon2				CCDS35363.1	Xq22.2	2013-05-22	2012-03-29	2012-03-29	ENSG00000176274	ENSG00000269743		"""Solute carriers"""	31894	protein-coding gene	gene with protein product			"""mitochondrial carrier triple repeat 6"""	MCART6			Standard	NM_001012755		Approved		uc004elu.3	Q5H9E4	OTTHUMG00000022124	ENST00000357421.4:c.437G>A	X.37:g.103349504C>T	ENSP00000361681:p.Arg146His	Somatic		Capture	Illumina HiSeq	Phase_I	103236160	NM_001012755	B2RTT9	Missense_Mutation	SNP	ENST00000357421.4	37	CCDS35363.1	.	.	.	.	.	.	.	.	.	.	c	15.24	2.774540	0.49786	.	.	ENSG00000176274	ENST00000357421	T	0.79554	-1.28	4.18	4.18	0.49190	Mitochondrial carrier domain (2);	0.144296	0.48286	D	0.000186	D	0.85221	0.5647	L	0.48986	1.54	0.41923	D	0.990521	D	0.89917	1.0	D	0.68353	0.957	D	0.85792	0.1368	10	0.49607	T	0.09	-17.9312	13.1831	0.59666	0.0:1.0:0.0:0.0	.	146	Q5H9E4	MCAR6_HUMAN	H	146	ENSP00000361681:R146H	ENSP00000361681:R146H	R	-	2	0	MCART6	103236160	0.993000	0.37304	0.999000	0.59377	0.985000	0.73830	1.373000	0.34272	2.061000	0.61500	0.594000	0.82650	CGC		0.587	SLC25A53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057761.1	NM_001012755	
MORC4	79710	broad.mit.edu	37	X	106185855	106185855	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:106185855C>T	ENST00000355610.4	-	15	2540	c.2266G>A	c.(2266-2268)Gaa>Aaa	p.E756K	MORC4_ENST00000255495.7_Missense_Mutation_p.E756K|MORC4_ENST00000535534.1_Missense_Mutation_p.E504K	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	756						nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.E579K(1)		endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	28						TTATGACCTTCGCTCTCCTCA	0.458																																					p.E756K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2266A	X						.						151.0	143.0	146.0					X																	106185855		2203	4300	6503	106072511	SO:0001583	missense	79710	exon15			AK021627	CCDS14525.2, CCDS48146.1	Xq22.3	2008-02-05	2005-06-15	2005-06-15	ENSG00000133131	ENSG00000133131			23485	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 2"", ""zinc finger, CW type with coiled-coil domain 2"""	ZCWCC2		14607086	Standard	NM_024657		Approved	ZCW4, FLJ11565	uc004emp.4	Q8TE76	OTTHUMG00000022155	ENST00000355610.4:c.2266G>A	X.37:g.106185855C>T	ENSP00000347821:p.Glu756Lys	Somatic		Capture	Illumina HiSeq	Phase_I	106072511	NM_001085354	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	37	CCDS14525.2	.	.	.	.	.	.	.	.	.	.	c	0.020	-1.438587	0.01098	.	.	ENSG00000133131	ENST00000355610;ENST00000535534;ENST00000255495	T;T;T	0.32515	2.73;1.45;2.69	5.34	3.55	0.40652	.	0.848621	0.09868	N	0.745309	T	0.18087	0.0434	N	0.22421	0.69	0.09310	N	1	B;B;B	0.20780	0.048;0.048;0.048	B;B;B	0.09377	0.004;0.004;0.004	T	0.34625	-0.9821	10	0.11485	T	0.65	-0.2858	7.1087	0.25378	0.0:0.7838:0.0:0.2162	.	504;756;756	A1YR24;A1YR23;Q8TE76	.;.;MORC4_HUMAN	K	756;504;756	ENSP00000347821:E756K;ENSP00000440359:E504K;ENSP00000255495:E756K	ENSP00000255495:E756K	E	-	1	0	MORC4	106072511	0.000000	0.05858	0.001000	0.08648	0.039000	0.13416	-0.446000	0.06837	0.452000	0.26830	0.525000	0.51046	GAA		0.458	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657	
COL4A5	1287	broad.mit.edu	37	X	107929332	107929332	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:107929332G>T	ENST00000361603.2	+	46	4514	c.4270G>T	c.(4270-4272)Gga>Tga	p.G1424*	COL4A5_ENST00000328300.6_Nonsense_Mutation_p.G1430*	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1424	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)	p.G1424*(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						AGGGCGCAAAGGAGACCCAGG	0.532									Alport syndrome with Diffuse Leiomyomatosis																												p.G1424X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G4270T	X						.						81.0	63.0	69.0					X																	107929332		2203	4300	6503	107815988	SO:0001587	stop_gained	1287	exon46	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"""Collagens"""	2207	protein-coding gene	gene with protein product		303630	"""Alport syndrome"""	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.4270G>T	X.37:g.107929332G>T	ENSP00000354505:p.Gly1424*	Somatic		Capture	Illumina HiSeq	Phase_I	107815988	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Nonsense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	46|46	12.486414|12.486414	0.99671|0.99671	.|.	.|.	ENSG00000188153|ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186|ENST00000515658	.|D	.|0.95885	.|-3.84	5.24|5.24	5.24|5.24	0.73138|0.73138	.|.	0.059862|.	0.64402|.	D|.	0.000003|.	.|D	.|0.97247	.|0.9100	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|D	.|0.97292	.|0.9925	.|5	0.87932|0.49607	D|T	0|0.09	.|.	18.1848|18.1848	0.89789|0.89789	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|N	1430;1424;1430|28	.|ENSP00000423520:K28N	ENSP00000331902:G1430X|ENSP00000423520:K28N	G|K	+|+	1|3	0|2	COL4A5|COL4A5	107815988|107815988	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.507000|9.507000	0.97996|0.97996	2.318000|2.318000	0.78349|0.78349	0.600000|0.600000	0.82982|0.82982	GGA|AAG		0.532	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2		
GUCY2F	2986	broad.mit.edu	37	X	108708574	108708574	+	Missense_Mutation	SNP	C	C	T	rs568281158		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:108708574C>T	ENST00000218006.2	-	3	1120	c.829G>A	c.(829-831)Gtc>Atc	p.V277I		NM_001522.2	NP_001513.2	P51841	GUC2F_HUMAN	guanylate cyclase 2F, retinal	277					intracellular signal transduction (GO:0035556)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|nuclear outer membrane (GO:0005640)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)	p.V277I(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(6)|large_intestine(14)|lung(33)|prostate(3)|skin(1)	67						GGAACAAAGACGTAGGTTCCA	0.463																																					p.V277I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G829A	X						.						178.0	140.0	153.0					X																	108708574		2203	4300	6503	108595230	SO:0001583	missense	2986	exon3			L37378	CCDS14545.1	Xq22	2008-08-01			ENSG00000101890	ENSG00000101890			4691	protein-coding gene	gene with protein product	"""guanylate cyclase 2D-like, membrane (retina-specific)"""	300041				8838319, 7777544	Standard	NM_001522		Approved	GUC2DL, GC-F, RetGC-2, ROS-GC2, CYGF	uc004eod.4	P51841	OTTHUMG00000022184	ENST00000218006.2:c.829G>A	X.37:g.108708574C>T	ENSP00000218006:p.Val277Ile	Somatic		Capture	Illumina HiSeq	Phase_I	108595230	NM_001522	Q9UJF1	Missense_Mutation	SNP	ENST00000218006.2	37	CCDS14545.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.086968	0.76642	.	.	ENSG00000101890	ENST00000218006	D	0.85861	-2.04	4.04	4.04	0.47022	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.86585	0.5968	L	0.59912	1.85	0.50171	D	0.999855	D	0.60160	0.987	P	0.53224	0.721	D	0.86127	0.1572	10	0.40728	T	0.16	.	13.1168	0.59305	0.0:1.0:0.0:0.0	.	277	P51841	GUC2F_HUMAN	I	277	ENSP00000218006:V277I	ENSP00000218006:V277I	V	-	1	0	GUCY2F	108595230	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	2.849000	0.48286	2.255000	0.74692	0.600000	0.82982	GTC		0.463	GUCY2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057884.1	NM_001522	
CT83	203413	broad.mit.edu	37	X	115592987	115592987	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:115592987T>C	ENST00000371894.4	-	2	409	c.263A>G	c.(262-264)gAa>gGa	p.E88G		NM_001017978.2	NP_001017978.1	Q5H943	KKLC1_HUMAN		88						integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.E88G(1)		breast(1)|large_intestine(3)|lung(8)	12						CAGCTTGTTTTCCACCATACT	0.438																																					p.E88G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A263G	X						.						191.0	161.0	171.0					X																	115592987		2203	4300	6503	115507015	SO:0001583	missense	203413	exon2																														ENST00000371894.4:c.263A>G	X.37:g.115592987T>C	ENSP00000360961:p.Glu88Gly	Somatic		Capture	Illumina HiSeq	Phase_I	115507015	NM_001017978		Missense_Mutation	SNP	ENST00000371894.4	37	CCDS35372.1	.	.	.	.	.	.	.	.	.	.	T	14.26	2.481735	0.44147	.	.	ENSG00000204019	ENST00000371894	.	.	.	5.2	5.2	0.72013	.	0.164042	0.28933	N	0.013676	T	0.36082	0.0954	L	0.27053	0.805	0.09310	N	1	D	0.57571	0.98	P	0.52957	0.714	T	0.21245	-1.0251	9	0.72032	D	0.01	-5.461	10.1985	0.43069	0.0:0.0:0.0:1.0	.	88	Q5H943	KKLC1_HUMAN	G	88	.	ENSP00000360961:E88G	E	-	2	0	CXorf61	115507015	0.106000	0.21978	0.062000	0.19696	0.242000	0.25591	3.272000	0.51616	1.933000	0.56026	0.434000	0.28630	GAA		0.438	CXorf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057985.1		
DOCK11	139818	broad.mit.edu	37	X	117712534	117712534	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:117712534C>T	ENST00000276202.7	+	13	1499	c.1436C>T	c.(1435-1437)gCc>gTc	p.A479V	DOCK11_ENST00000276204.6_Missense_Mutation_p.A479V	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	479					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A479V(1)		breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TTTCTAGTTGCCAGAATTGAA	0.353																																					p.A479V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1436T	X						.						81.0	75.0	77.0					X																	117712534		2203	4300	6503	117596562	SO:0001583	missense	139818	exon13			AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"""Pleckstrin homology (PH) domain containing"""	23483	protein-coding gene	gene with protein product	"""zizimin2"""	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.1436C>T	X.37:g.117712534C>T	ENSP00000276202:p.Ala479Val	Somatic		Capture	Illumina HiSeq	Phase_I	117596562	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	37	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	C	14.95	2.687423	0.48097	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	T;T	0.04551	3.6;3.6	6.05	5.18	0.71444	.	0.049389	0.85682	N	0.000000	T	0.05823	0.0152	L	0.28458	0.855	0.49483	D	0.999795	P;P	0.50066	0.931;0.855	P;P	0.49665	0.618;0.474	T	0.23368	-1.0190	10	0.02654	T	1	-1.1767	12.4288	0.55563	0.0:0.9163:0.0:0.0837	.	479;479	A6NIW2;Q5JSL3	.;DOC11_HUMAN	V	479	ENSP00000276204:A479V;ENSP00000276202:A479V	ENSP00000276202:A479V	A	+	2	0	DOCK11	117596562	1.000000	0.71417	0.729000	0.30791	0.426000	0.31534	4.637000	0.61346	1.282000	0.44496	0.594000	0.82650	GCC		0.353	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
RHOXF2	84528	broad.mit.edu	37	X	119293136	119293136	+	Missense_Mutation	SNP	G	G	A	rs150161751		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:119293136G>A	ENST00000371388.3	+	2	485	c.295G>A	c.(295-297)Ggc>Agc	p.G99S		NM_032498.1	NP_115887.1	Q9BQY4	RHXF2_HUMAN	Rhox homeobox family, member 2	99					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.G99S(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(2)	8						GGGCACCAGCGGCAGCGATGG	0.647																																					p.G99S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G295A	X						.	C	SER/GLY	1,3788		0,1,1622,543	40.0	45.0	44.0		295	-4.0	0.0	X	dbSNP_134	44	0,6714		0,0,2427,1860	no	missense	RHOXF2	NM_032498.1	56	0,1,4049,2403	AA,AG,GG,G		0.0,0.0264,0.0095	benign	99/289	119293136	1,10502	2166	4287	6453	119177164	SO:0001583	missense	727940	exon2				CCDS14594.1	Xq24	2012-12-20			ENSG00000131721	ENSG00000131721		"""Homeoboxes / PRD class"""	30011	protein-coding gene	gene with protein product	"""cancer/testis antigen 107"""	300447				12490318	Standard	NM_032498		Approved	THG1, PEPP-2, PEPP2, CT107		Q9BQY4	OTTHUMG00000022296	ENST00000371388.3:c.295G>A	X.37:g.119293136G>A	ENSP00000360441:p.Gly99Ser	Somatic		Capture	Illumina HiSeq	Phase_I	119177164	NM_032498	Q9BR00	Missense_Mutation	SNP	ENST00000371388.3	37	CCDS14594.1	.	.	.	.	.	.	.	.	.	.	g	0.861	-0.735241	0.03111	2.64E-4	0.0	ENSG00000131721	ENST00000371388	D	0.92397	-3.03	1.98	-3.96	0.04106	.	.	.	.	.	T	0.74951	0.3784	N	0.08118	0	0.09310	N	1	B	0.21381	0.055	B	0.13407	0.009	T	0.66244	-0.5972	9	0.02654	T	1	0.8519	4.9515	0.14017	0.2823:0.487:0.2308:0.0	.	99	Q9BQY4	RHXF2_HUMAN	S	99	ENSP00000360441:G99S	ENSP00000360441:G99S	G	+	1	0	RHOXF2	119177164	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.893000	0.04127	-1.500000	0.01819	-1.857000	0.00563	GGC		0.647	RHOXF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411977.1	NM_032498	
TENM1	10178	broad.mit.edu	37	X	123540294	123540294	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:123540294T>C	ENST00000371130.3	-	25	5070	c.5007A>G	c.(5005-5007)ggA>ggG	p.G1669G	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Silent_p.G1676G	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1669					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G1671G(1)									TGCTGACCTCTCCAGTGGGAA	0.507																																					p.G1669G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A5007G	X						.						155.0	138.0	144.0					X																	123540294		2203	4300	6503	123367975	SO:0001819	synonymous_variant	10178	exon25			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.5007A>G	X.37:g.123540294T>C		Somatic		Capture	Illumina HiSeq	Phase_I	123367975	NM_014253	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																				0.507	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
BCORL1	63035	broad.mit.edu	37	X	129162722	129162722	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:129162722C>T	ENST00000218147.7	+	8	4388	c.4191C>T	c.(4189-4191)aaC>aaT	p.N1397N	BCORL1_ENST00000540052.1_Silent_p.N1397N|BCORL1_ENST00000303743.5_Silent_p.N1397N|BCORL1_ENST00000359304.2_Silent_p.N1267N			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	1397					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.N1397N(1)		breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						ATTCACCAAACGGTTTCCTCC	0.502											OREG0019921	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N1397N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4191T	X						.						103.0	101.0	102.0					X																	129162722		2203	4300	6503	128990403	SO:0001819	synonymous_variant	63035	exon7			AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"""Ankyrin repeat domain containing"""	25657	protein-coding gene	gene with protein product		300688	"""chromosome X open reading frame 10"", ""BCL6 co-repressor-like 1"""	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.4191C>T	X.37:g.129162722C>T		Somatic	1570	Capture	Illumina HiSeq	Phase_I	128990403	NM_021946	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Silent	SNP	ENST00000218147.7	37	CCDS14616.1	.	.	.	.	.	.	.	.	.	.	C	8.809	0.934804	0.18206	.	.	ENSG00000085185	ENST00000441294	.	.	.	5.89	0.211	0.15236	.	.	.	.	.	T	0.57095	0.2030	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50242	-0.8851	4	.	.	.	-14.03	9.471	0.38842	0.0:0.3487:0.0:0.6513	.	.	.	.	W	703	.	.	R	+	1	2	BCORL1	128990403	0.983000	0.35010	0.999000	0.59377	0.993000	0.82548	-0.047000	0.11963	-0.049000	0.13379	-0.296000	0.09543	CGG		0.502	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946	
USP26	83844	broad.mit.edu	37	X	132159667	132159667	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:132159667C>T	ENST00000511190.1	-	6	3051	c.2582G>A	c.(2581-2583)cGg>cAg	p.R861Q	USP26_ENST00000370832.1_Missense_Mutation_p.R861Q|USP26_ENST00000406273.1_Missense_Mutation_p.R861Q	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	861	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.R861Q(2)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					ACCTAACACCCGCATATCATC	0.438																																					p.R861Q	NSCLC(104;342 1621 36940 47097 52632)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2582A	X						.						139.0	117.0	125.0					X																	132159667		2203	4300	6503	131987333	SO:0001583	missense	83844	exon1			AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"""Ubiquitin-specific peptidases"""	13485	protein-coding gene	gene with protein product		300309	"""ubiquitin specific protease 26"""			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.2582G>A	X.37:g.132159667C>T	ENSP00000423390:p.Arg861Gln	Somatic		Capture	Illumina HiSeq	Phase_I	131987333	NM_031907	B9WRT6|Q5H9H4	Missense_Mutation	SNP	ENST00000511190.1	37	CCDS14635.1	.	.	.	.	.	.	.	.	.	.	T	4.834	0.154967	0.09236	.	.	ENSG00000134588	ENST00000370832;ENST00000511190;ENST00000406273	T;T;T	0.31510	1.49;1.49;1.49	3.64	1.08	0.20341	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	1.646050	0.04079	N	0.309366	T	0.09069	0.0224	N	0.00707	-1.245	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.21827	-1.0234	10	0.13470	T	0.59	5.8655	3.5089	0.07701	0.3452:0.1062:0.0:0.5486	.	861	Q9BXU7	UBP26_HUMAN	Q	861	ENSP00000359869:R861Q;ENSP00000423390:R861Q;ENSP00000384360:R861Q	ENSP00000359869:R861Q	R	-	2	0	USP26	131987333	0.007000	0.16637	0.000000	0.03702	0.224000	0.24922	1.442000	0.35046	-0.159000	0.11021	-0.428000	0.05917	CGG		0.438	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907	
MOSPD2	158747	broad.mit.edu	37	X	14918718	14918718	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:14918718A>T	ENST00000380492.3	+	6	587	c.499A>T	c.(499-501)Atc>Ttc	p.I167F	MOSPD2_ENST00000495110.1_3'UTR|MOSPD2_ENST00000482354.1_Missense_Mutation_p.I167F	NM_001177475.1|NM_152581.3	NP_001170946.1|NP_689794.1	Q8NHP6	MSPD2_HUMAN	motile sperm domain containing 2	167	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	structural molecule activity (GO:0005198)	p.I167F(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	Hepatocellular(33;0.183)					TGTACGCTTTATCATCAACTG	0.284																																					p.I167F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A499T	X						.						73.0	67.0	69.0					X																	14918718		2203	4284	6487	14828639	SO:0001583	missense	158747	exon6			AL834345	CCDS14162.1	Xp22.31	2006-03-16			ENSG00000130150	ENSG00000130150			28381	protein-coding gene	gene with protein product						15533722	Standard	NM_152581		Approved	MGC26706	uc004cwi.3	Q8NHP6	OTTHUMG00000021170	ENST00000380492.3:c.499A>T	X.37:g.14918718A>T	ENSP00000369860:p.Ile167Phe	Somatic		Capture	Illumina HiSeq	Phase_I	14828639	NM_152581	Q8N3H2|Q8NA83	Missense_Mutation	SNP	ENST00000380492.3	37	CCDS14162.1	.	.	.	.	.	.	.	.	.	.	A	19.07	3.755794	0.69648	.	.	ENSG00000130150	ENST00000380492	T	0.77877	-1.13	5.35	4.2	0.49525	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.147766	0.64402	D	0.000011	D	0.85340	0.5674	M	0.81112	2.525	0.80722	D	1	D	0.63880	0.993	D	0.67900	0.954	D	0.85972	0.1477	10	0.72032	D	0.01	.	7.2504	0.26146	0.8281:0.0:0.1719:0.0	.	167	Q8NHP6	MSPD2_HUMAN	F	167	ENSP00000369860:I167F	ENSP00000369860:I167F	I	+	1	0	MOSPD2	14828639	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.658000	0.54482	1.794000	0.52575	0.441000	0.28932	ATC		0.284	MOSPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055837.1	NM_152581	
SLITRK2	84631	broad.mit.edu	37	X	144904883	144904883	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:144904883C>T	ENST00000370490.1	+	1	5195	c.940C>T	c.(940-942)Cga>Tga	p.R314*	SLITRK2_ENST00000434188.2_Nonsense_Mutation_p.R314*|SLITRK2_ENST00000447897.2_Nonsense_Mutation_p.R314*|SLITRK2_ENST00000428560.2_Nonsense_Mutation_p.R314*|SLITRK2_ENST00000413937.2_Nonsense_Mutation_p.R314*			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	314					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.R314*(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					TCCAACTCCTCGAGTGACTGT	0.552																																					p.R314X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C940T	X						.						71.0	64.0	66.0					X																	144904883		2203	4300	6503	144712575	SO:0001587	stop_gained	84631	exon3			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"""slit-like 1 (Drosophila)"""	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.940C>T	X.37:g.144904883C>T	ENSP00000359521:p.Arg314*	Somatic		Capture	Illumina HiSeq	Phase_I	144712575	NM_001144006	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Nonsense_Mutation	SNP	ENST00000370490.1	37	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	C	59	35.493223	0.99982	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	.	.	.	5.67	2.52	0.30459	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	-6.4296	13.1025	0.59228	0.4142:0.5858:0.0:0.0	.	.	.	.	X	314	.	ENSP00000334374:R314X	R	+	1	2	SLITRK2	144712575	0.998000	0.40836	0.969000	0.41365	0.968000	0.65278	3.790000	0.55461	0.506000	0.28125	0.600000	0.82982	CGA		0.552	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
CD99L2	83692	broad.mit.edu	37	X	149937531	149937531	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:149937531C>T	ENST00000370377.3	-	11	882	c.765G>A	c.(763-765)ccG>ccA	p.P255P	CD99L2_ENST00000437787.2_Silent_p.P182P|CD99L2_ENST00000355149.3_Silent_p.P183P|CD99L2_ENST00000346693.4_5'UTR|CD99L2_ENST00000466436.1_Silent_p.P206P	NM_001242614.1|NM_031462.3	NP_001229543.1|NP_113650.2	Q8TCZ2	C99L2_HUMAN	CD99 molecule-like 2	255	Poly-Pro.				cell adhesion (GO:0007155)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P255P(1)		endometrium(4)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					GTTCGGGCGGCGGCGGCGGCT	0.607													C|||	1	0.000264901	0.0	0.0	3775	,	,		10733	0.001		0.0	False		,,,				2504	0.0				p.P206P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G618A	X						.						54.0	64.0	61.0					X																	149937531		2203	4297	6500	149688189	SO:0001819	synonymous_variant	83692	exon9			BC030536	CCDS14697.1, CCDS14698.1, CCDS35427.1, CCDS55527.1, CCDS76044.1	Xq28	2007-12-04	2006-03-28	2003-02-14	ENSG00000102181	ENSG00000102181			18237	protein-coding gene	gene with protein product		300846	"""MIC2 like 1"", ""CD99 antigen-like 2"""	MIC2L1			Standard	NM_001184808		Approved	CD99B	uc004fek.3	Q8TCZ2	OTTHUMG00000024247	ENST00000370377.3:c.765G>A	X.37:g.149937531C>T		Somatic		Capture	Illumina HiSeq	Phase_I	149688189	NM_134446	A8K2D5|A8K5R0|B3KWG2|B4DDL7|E7EMK5|E9PD27|Q8TAW2|Q8TCZ0|Q8TCZ1|Q9BQG9	Silent	SNP	ENST00000370377.3	37	CCDS35427.1																																																																																				0.607	CD99L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000061199.1	NM_031462	
TMEM187	8269	broad.mit.edu	37	X	153248162	153248162	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:153248162T>C	ENST00000369982.4	+	2	1396	c.649T>C	c.(649-651)Tgg>Cgg	p.W217R	MIR3202-1_ENST00000580198.1_RNA	NM_003492.2	NP_003483.1	Q14656	TM187_HUMAN	transmembrane protein 187	217						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)		p.W217R(1)		breast(1)|large_intestine(1)|lung(1)|prostate(2)	5	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GCTCGCACGGTGGCGTCTCTT	0.552																																					p.W217R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T649C	X						.						118.0	97.0	104.0					X																	153248162		2203	4300	6503	152901356	SO:0001583	missense	8269	exon2			X92475	CCDS14739.1	Xq28	2007-03-14	2007-03-14	2007-03-14	ENSG00000177854	ENSG00000177854			13705	protein-coding gene	gene with protein product		300059	"""chromosome X open reading frame 12"""	CXorf12		8661027	Standard	NM_003492		Approved	ITBA1, DXS9878E	uc004fjq.2	Q14656	OTTHUMG00000024220	ENST00000369982.4:c.649T>C	X.37:g.153248162T>C	ENSP00000358999:p.Trp217Arg	Somatic		Capture	Illumina HiSeq	Phase_I	152901356	NM_003492	B2RC47|Q6IAV7	Missense_Mutation	SNP	ENST00000369982.4	37	CCDS14739.1	.	.	.	.	.	.	.	.	.	.	T	15.81	2.943047	0.53079	.	.	ENSG00000177854	ENST00000369982	T	0.23754	1.89	4.35	4.35	0.52113	.	0.309872	0.21825	U	0.068565	T	0.47097	0.1427	M	0.73962	2.25	0.09310	N	1	D	0.61697	0.99	D	0.63192	0.912	T	0.38779	-0.9645	10	0.72032	D	0.01	.	12.0942	0.53744	0.0:0.0:0.0:1.0	.	217	Q14656	TM187_HUMAN	R	217	ENSP00000358999:W217R	ENSP00000358999:W217R	W	+	1	0	TMEM187	152901356	1.000000	0.71417	0.050000	0.19076	0.867000	0.49689	4.456000	0.60081	1.556000	0.49512	0.356000	0.21956	TGG		0.552	TMEM187-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061093.1	NM_003492	
ARSH	347527	broad.mit.edu	37	X	2945494	2945494	+	Missense_Mutation	SNP	G	G	A	rs145391454	byFrequency	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:2945494G>A	ENST00000381130.2	+	7	1177	c.1177G>A	c.(1177-1179)Gga>Aga	p.G393R		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	393					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)|integral component of membrane (GO:0016021)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.G393R(1)		breast(3)|endometrium(8)|kidney(2)|large_intestine(6)|lung(13)|skin(1)|stomach(1)	34		all_cancers(21;9e-05)|all_epithelial(21;6.22e-06)|all_lung(23;0.000597)|Lung NSC(23;0.00901)|Lung SC(21;0.186)				TTATATAGGCGGAGGGATCTT	0.473																																					p.G393R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1177A	X						.	G	ARG/GLY	1,3834		0,1,0,1631,571	123.0	101.0	109.0		1177	3.4	0.1	X	dbSNP_134	109	5,6723		0,4,1,2424,1871	yes	missense	ARSH	NM_001011719.1	125	0,5,1,4055,2442	AA,AG,A,GG,G		0.0743,0.0261,0.0568	probably-damaging	393/563	2945494	6,10557	2203	4300	6503	2955494	SO:0001583	missense	347527	exon7			AY875940	CCDS35198.1	Xp22.33	2013-02-14	2006-03-07		ENSG00000205667	ENSG00000205667		"""Arylsulfatase family"""	32488	protein-coding gene	gene with protein product		300586	"""arylsulfatase H"""			16174644	Standard	NM_001011719		Approved		uc011mhj.2	Q5FYA8	OTTHUMG00000159612	ENST00000381130.2:c.1177G>A	X.37:g.2945494G>A	ENSP00000370522:p.Gly393Arg	Somatic		Capture	Illumina HiSeq	Phase_I	2955494	NM_001011719		Missense_Mutation	SNP	ENST00000381130.2	37	CCDS35198.1	.	.	.	.	.	.	.	.	.	.	G	14.95	2.689364	0.48097	2.61E-4	7.43E-4	ENSG00000205667	ENST00000381130	D	0.97404	-4.37	3.4	3.4	0.38934	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.062133	0.64402	U	0.000005	D	0.98767	0.9585	H	0.96970	3.915	0.48395	D	0.999645	D	0.64830	0.994	P	0.62382	0.901	D	0.99632	1.0986	10	0.87932	D	0	.	14.2922	0.66286	0.0:0.0:1.0:0.0	.	393	Q5FYA8	ARSH_HUMAN	R	393	ENSP00000370522:G393R	ENSP00000370522:G393R	G	+	1	0	ARSH	2955494	1.000000	0.71417	0.090000	0.20809	0.082000	0.17680	3.652000	0.54439	1.328000	0.45358	0.596000	0.82720	GGA		0.473	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719	
ARSF	416	broad.mit.edu	37	X	3002419	3002419	+	Missense_Mutation	SNP	C	C	T	rs182964743		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:3002419C>T	ENST00000381127.1	+	6	763	c.542C>T	c.(541-543)aCg>aTg	p.T181M	ARSF_ENST00000537104.1_Missense_Mutation_p.T181M|ARSF_ENST00000359361.2_Missense_Mutation_p.T181M	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	181					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 vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.T181M(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TCTCGTAACACGGAATTAGCC	0.527													c|||	1	0.000264901	0.0008	0.0	3775	,	,		14101	0.0		0.0	False		,,,				2504	0.0				p.T181M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C542T	X						.						142.0	107.0	119.0					X																	3002419		2203	4300	6503	3012419	SO:0001583	missense	416	exon6			X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"""Arylsulfatase family"""	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.542C>T	X.37:g.3002419C>T	ENSP00000370519:p.Thr181Met	Somatic		Capture	Illumina HiSeq	Phase_I	3012419	NM_004042	Q8TCC5	Missense_Mutation	SNP	ENST00000381127.1	37	CCDS14123.1	1	6.027727546714888E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	6.703	0.498281	0.12762	.	.	ENSG00000062096	ENST00000381127;ENST00000537104;ENST00000359361	D;D;D	0.93604	-3.25;-3.25;-3.25	3.44	0.434	0.16539	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.645007	0.13483	U	0.384558	T	0.80423	0.4620	N	0.02916	-0.46	0.09310	N	1	B	0.06786	0.001	B	0.17098	0.017	T	0.67937	-0.5541	10	0.32370	T	0.25	.	5.8964	0.18941	0.0:0.6522:0.1535:0.1943	.	181	P54793	ARSF_HUMAN	M	181	ENSP00000370519:T181M;ENSP00000445594:T181M;ENSP00000352319:T181M	ENSP00000352319:T181M	T	+	2	0	ARSF	3012419	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.231000	0.09069	-0.442000	0.07190	-0.275000	0.10095	ACG		0.527	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1		
TBL1X	6907	broad.mit.edu	37	X	9679710	9679710	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:9679710C>T	ENST00000217964.7	+	16	2139	c.1499C>T	c.(1498-1500)aCg>aTg	p.T500M	TBL1X_ENST00000424279.1_Missense_Mutation_p.T449M|TBL1X_ENST00000407597.2_Missense_Mutation_p.T500M|TBL1X_ENST00000380961.1_Missense_Mutation_p.T449M|TBL1X_ENST00000536365.1_Missense_Mutation_p.T449M	NM_005647.3	NP_005638.1	O60907	TBL1X_HUMAN	transducin (beta)-like 1X-linked	500					canonical Wnt signaling pathway (GO:0060070)|cellular lipid metabolic process (GO:0044255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|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)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|histone binding (GO:0042393)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.T500M(1)		breast(2)|cervix(1)|endometrium(5)|large_intestine(7)|lung(2)|ovary(1)|skin(2)	20		Hepatocellular(5;0.000888)				TGCACCCACACGCTCACGAAG	0.517																																					p.T449M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1346T	X						.						150.0	102.0	118.0					X																	9679710		2203	4300	6503	9639710	SO:0001583	missense	6907	exon16			Y12781	CCDS14133.1, CCDS48078.1	Xp22.3	2013-01-10	2002-05-22	2002-05-24	ENSG00000101849	ENSG00000101849		"""WD repeat domain containing"""	11585	protein-coding gene	gene with protein product		300196	"""transducin (beta)-like 1"""	TBL1		10330347	Standard	NM_005647		Approved	EBI	uc004csr.3	O60907	OTTHUMG00000021117	ENST00000217964.7:c.1499C>T	X.37:g.9679710C>T	ENSP00000217964:p.Thr500Met	Somatic		Capture	Illumina HiSeq	Phase_I	9639710	NM_001139468	A8K044|A8K4J7|Q86UY2	Missense_Mutation	SNP	ENST00000217964.7	37	CCDS14133.1	.	.	.	.	.	.	.	.	.	.	C	17.36	3.370479	0.61624	.	.	ENSG00000101849	ENST00000407597;ENST00000424279;ENST00000536365;ENST00000380961;ENST00000217964	T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03	4.24	4.24	0.50183	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	0.74943	0.3783	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.74023	0.967;0.982	T	0.78904	-0.2020	10	0.87932	D	0	.	16.6583	0.85234	0.0:1.0:0.0:0.0	.	463;500	Q59F53;O60907	.;TBL1X_HUMAN	M	500;449;449;449;500	ENSP00000385988:T500M;ENSP00000394097:T449M;ENSP00000445317:T449M;ENSP00000370348:T449M;ENSP00000217964:T500M	ENSP00000217964:T500M	T	+	2	0	TBL1X	9639710	1.000000	0.71417	0.798000	0.32154	0.182000	0.23217	6.922000	0.75811	2.042000	0.60477	0.506000	0.49869	ACG		0.517	TBL1X-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055709.1	NM_005647	
RBBP7	5931	broad.mit.edu	37	X	16876898	16876898	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:16876898G>A	ENST00000380087.2	-	4	742	c.382C>T	c.(382-384)Cgt>Tgt	p.R128C	RBBP7_ENST00000404022.1_Missense_Mutation_p.R119C|RBBP7_ENST00000380084.4_Missense_Mutation_p.R172C			Q16576	RBBP7_HUMAN	retinoblastoma binding protein 7	128					cell proliferation (GO:0008283)|cellular heat acclimation (GO:0070370)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	RNA binding (GO:0003723)	p.R128C(1)		biliary_tract(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	25	Hepatocellular(33;0.0997)					TAACGAGCACGGTTTACTTCT	0.388																																					p.R172C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C514T	X						.						240.0	191.0	207.0					X																	16876898		2203	4300	6503	16786819	SO:0001583	missense	5931	exon4			U35143	CCDS14179.1, CCDS56598.1	Xp22.22	2013-01-10	2001-11-28		ENSG00000102054	ENSG00000102054		"""WD repeat domain containing"""	9890	protein-coding gene	gene with protein product	"""G1/S transition control protein-binding protein RbAp46"", ""retinoblastoma-binding protein 7"", ""retinoblastoma-binding protein RbAp46"", ""histone acetyltransferase type B subunit 2"", ""retinoblastoma-binding protein p46"""	300825	"""retinoblastoma-binding protein 7"""			7503932	Standard	NM_002893		Approved	RbAp46	uc004cxs.2	Q16576	OTTHUMG00000021198	ENST00000380087.2:c.382C>T	X.37:g.16876898G>A	ENSP00000369427:p.Arg128Cys	Somatic		Capture	Illumina HiSeq	Phase_I	16786819	NM_001198719	Q5JP00	Missense_Mutation	SNP	ENST00000380087.2	37	CCDS14179.1	.	.	.	.	.	.	.	.	.	.	G	18.11	3.549812	0.65311	.	.	ENSG00000102054	ENST00000380087;ENST00000380084;ENST00000404022;ENST00000416035	T;T;T;T	0.63255	-0.03;-0.03;-0.03;0.15	5.17	4.3	0.51218	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.061137	0.64402	D	0.000003	D	0.82669	0.5087	H	0.94734	3.575	0.80722	D	1	D;P;D	0.76494	0.999;0.944;0.995	D;P;P	0.63793	0.918;0.69;0.69	D	0.87116	0.2188	10	0.87932	D	0	0.8147	13.4437	0.61127	0.0:0.0:0.8421:0.1579	.	119;128;172	E9PC52;Q16576;Q5JP00	.;RBBP7_HUMAN;.	C	128;172;119;48	ENSP00000369427:R128C;ENSP00000369424:R172C;ENSP00000386068:R119C;ENSP00000392714:R48C	ENSP00000369424:R172C	R	-	1	0	RBBP7	16786819	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	3.834000	0.55798	1.056000	0.40484	0.594000	0.82650	CGT		0.388	RBBP7-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055920.2	NM_002893	
NHS	4810	broad.mit.edu	37	X	17739580	17739580	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:17739580A>G	ENST00000380060.3	+	4	1210	c.872A>G	c.(871-873)gAa>gGa	p.E291G	NHS_ENST00000485305.1_3'UTR|NHS_ENST00000398097.3_Missense_Mutation_p.E135G	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	312					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.E291G(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)					CCAGAGGATGAAGATACAGAT	0.438																																					p.E135G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A404G	X						.						124.0	103.0	110.0					X																	17739580		2203	4300	6503	17649501	SO:0001583	missense	4810	exon5				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.872A>G	X.37:g.17739580A>G	ENSP00000369400:p.Glu291Gly	Somatic		Capture	Illumina HiSeq	Phase_I	17649501	NM_001136024	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	37	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.629031	0.87560	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.56611	0.45;0.46	5.88	5.88	0.94601	.	0.095977	0.64402	D	0.000001	T	0.70928	0.3280	M	0.79693	2.465	0.58432	D	0.999997	P;P;P;D	0.69078	0.925;0.925;0.925;0.997	P;P;P;P	0.59357	0.621;0.621;0.621;0.856	T	0.75830	-0.3179	10	0.72032	D	0.01	-22.0187	15.2041	0.73165	1.0:0.0:0.0:0.0	.	312;133;135;291	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	G	291;135;133	ENSP00000369400:E291G;ENSP00000381170:E135G	ENSP00000369397:E133G	E	+	2	0	NHS	17649501	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.353000	0.52247	1.973000	0.57446	0.486000	0.48141	GAA		0.438	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270	
NHS	4810	broad.mit.edu	37	X	17746106	17746106	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:17746106C>T	ENST00000380060.3	+	6	4155	c.3817C>T	c.(3817-3819)Cct>Tct	p.P1273S	NHS_ENST00000398097.3_Missense_Mutation_p.P1117S	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1294					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.P1273S(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)					ACAATATGGACCTGGTCCAGA	0.468																																					p.P1117S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3349T	X						.						71.0	69.0	69.0					X																	17746106		2203	4300	6503	17656027	SO:0001583	missense	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.3817C>T	X.37:g.17746106C>T	ENSP00000369400:p.Pro1273Ser	Somatic		Capture	Illumina HiSeq	Phase_I	17656027	NM_001136024	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	37	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	C	6.175	0.400540	0.11696	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.39229	1.09;1.09	5.79	0.8	0.18672	.	0.802899	0.11280	N	0.580409	T	0.15176	0.0366	N	0.03608	-0.345	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.26643	-1.0097	10	0.14252	T	0.57	0.0307	2.8293	0.05495	0.1303:0.3189:0.3323:0.2186	.	1294;1115;1117;1273	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	S	1273;1117;1115	ENSP00000369400:P1273S;ENSP00000381170:P1117S	ENSP00000369397:P1115S	P	+	1	0	NHS	17656027	0.829000	0.29322	0.289000	0.24876	0.673000	0.39480	0.722000	0.25925	-0.036000	0.13669	-0.255000	0.11280	CCT		0.468	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270	
NHS	4810	broad.mit.edu	37	X	17750148	17750148	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:17750148C>T	ENST00000380060.3	+	8	4795	c.4457C>T	c.(4456-4458)gCc>gTc	p.A1486V	NHS_ENST00000398097.3_Missense_Mutation_p.A1330V	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1507					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.A1486V(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)					TACCGAAATGCCAAAAAGTCC	0.498																																					p.A1330V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3989T	X						.						150.0	130.0	137.0					X																	17750148		2203	4300	6503	17660069	SO:0001583	missense	4810	exon9				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.4457C>T	X.37:g.17750148C>T	ENSP00000369400:p.Ala1486Val	Somatic		Capture	Illumina HiSeq	Phase_I	17660069	NM_001136024	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	37	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	C	16.20	3.056576	0.55325	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.46819	0.86;0.86	5.88	5.88	0.94601	.	0.050389	0.85682	D	0.000000	T	0.50463	0.1617	L	0.47190	1.495	0.58432	D	0.999996	P;P;P;P	0.51537	0.946;0.946;0.946;0.664	P;P;P;P	0.50405	0.586;0.586;0.586;0.64	T	0.39761	-0.9598	10	0.07813	T	0.8	-18.1455	19.2243	0.93812	0.0:1.0:0.0:0.0	.	1507;1328;1330;1486	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	V	1486;1330;1328	ENSP00000369400:A1486V;ENSP00000381170:A1330V	ENSP00000369397:A1328V	A	+	2	0	NHS	17660069	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.664000	0.54525	2.492000	0.84095	0.600000	0.82982	GCC		0.498	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270	
RS1	6247	broad.mit.edu	37	X	18660227	18660227	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:18660227C>T	ENST00000379984.3	-	6	612	c.572G>A	c.(571-573)cGg>cAg	p.R191Q	CDKL5_ENST00000379996.3_Intron|RS1_ENST00000476595.1_5'UTR|CDKL5_ENST00000379989.3_Intron	NM_000330.3	NP_000321.1	O15537	XLRS1_HUMAN	retinoschisin 1	191	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				adaptation of rhodopsin mediated signaling (GO:0016062)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|retina layer formation (GO:0010842)|visual perception (GO:0007601)	extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)	p.R191Q(1)		cervix(1)|endometrium(4)|large_intestine(5)|lung(2)|ovary(2)|skin(1)	15	Hepatocellular(33;0.183)					GATGGGGGGCCGCAGCAGGTT	0.602																																					p.R191Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G572A	X						.						79.0	70.0	73.0					X																	18660227		2203	4300	6503	18570148	SO:0001583	missense	6247	exon6			AF014459	CCDS14187.1	Xp22.2-p22.1	2014-09-17	2008-07-29		ENSG00000102104	ENSG00000102104			10457	protein-coding gene	gene with protein product		300839	"""retinoschisis (X-linked, juvenile) 1"""	RS		9326935, 17804407	Standard	NM_000330		Approved	XLRS1	uc004cyo.3	O15537	OTTHUMG00000021216	ENST00000379984.3:c.572G>A	X.37:g.18660227C>T	ENSP00000369320:p.Arg191Gln	Somatic		Capture	Illumina HiSeq	Phase_I	18570148	NM_000330	Q0QD39	Missense_Mutation	SNP	ENST00000379984.3	37	CCDS14187.1	.	.	.	.	.	.	.	.	.	.	C	35	5.451925	0.96223	.	.	ENSG00000102104	ENST00000379984	D	0.98150	-4.75	5.64	5.64	0.86602	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.97629	0.9223	L	0.37697	1.125	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96607	0.9449	10	0.15499	T	0.54	.	18.6917	0.91585	0.0:1.0:0.0:0.0	.	191	O15537	XLRS1_HUMAN	Q	191	ENSP00000369320:R191Q	ENSP00000369320:R191Q	R	-	2	0	RS1	18570148	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.487000	0.81328	2.358000	0.79984	0.600000	0.82982	CGG		0.602	RS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055949.1		
RS1	6247	broad.mit.edu	37	X	18674837	18674837	+	Silent	SNP	G	G	A	rs62645885		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:18674837G>A	ENST00000379984.3	-	3	160	c.120C>T	c.(118-120)tgC>tgT	p.C40C		NM_000330.3	NP_000321.1	O15537	XLRS1_HUMAN	retinoschisin 1	40					adaptation of rhodopsin mediated signaling (GO:0016062)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|retina layer formation (GO:0010842)|visual perception (GO:0007601)	extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)	p.C40C(1)		cervix(1)|endometrium(4)|large_intestine(5)|lung(2)|ovary(2)|skin(1)	15	Hepatocellular(33;0.183)					CTTGGCAATCGCACTTGCATG	0.552																																					p.C40C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C120T	X	GRCh37	CM971317	RS1	M		.						225.0	171.0	189.0					X																	18674837		2203	4300	6503	18584758	SO:0001819	synonymous_variant	6247	exon3			AF014459	CCDS14187.1	Xp22.2-p22.1	2014-09-17	2008-07-29		ENSG00000102104	ENSG00000102104			10457	protein-coding gene	gene with protein product		300839	"""retinoschisis (X-linked, juvenile) 1"""	RS		9326935, 17804407	Standard	NM_000330		Approved	XLRS1	uc004cyo.3	O15537	OTTHUMG00000021216	ENST00000379984.3:c.120C>T	X.37:g.18674837G>A		Somatic		Capture	Illumina HiSeq	Phase_I	18584758	NM_000330	Q0QD39	Silent	SNP	ENST00000379984.3	37	CCDS14187.1																																																																																				0.552	RS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055949.1		
RS1	6247	broad.mit.edu	37	X	18675769	18675769	+	Silent	SNP	C	C	T	rs281865339		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:18675769C>T	ENST00000379984.3	-	2	109	c.69G>A	c.(67-69)tcG>tcA	p.S23S		NM_000330.3	NP_000321.1	O15537	XLRS1_HUMAN	retinoschisin 1	23					adaptation of rhodopsin mediated signaling (GO:0016062)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|retina layer formation (GO:0010842)|visual perception (GO:0007601)	extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)	p.S23S(1)		cervix(1)|endometrium(4)|large_intestine(5)|lung(2)|ovary(2)|skin(1)	15	Hepatocellular(33;0.183)					CCTCGGTAGACGATAATCCCA	0.343																																					p.S23S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G69A	X						.						114.0	98.0	104.0					X																	18675769		2203	4300	6503	18585690	SO:0001819	synonymous_variant	6247	exon2			AF014459	CCDS14187.1	Xp22.2-p22.1	2014-09-17	2008-07-29		ENSG00000102104	ENSG00000102104			10457	protein-coding gene	gene with protein product		300839	"""retinoschisis (X-linked, juvenile) 1"""	RS		9326935, 17804407	Standard	NM_000330		Approved	XLRS1	uc004cyo.3	O15537	OTTHUMG00000021216	ENST00000379984.3:c.69G>A	X.37:g.18675769C>T		Somatic		Capture	Illumina HiSeq	Phase_I	18585690	NM_000330	Q0QD39	Silent	SNP	ENST00000379984.3	37	CCDS14187.1																																																																																				0.343	RS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055949.1		
ACOT9	23597	broad.mit.edu	37	X	23751331	23751331	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:23751331C>T	ENST00000336430.7	-	3	253	c.122G>A	c.(121-123)cGa>cAa	p.R41Q	ACOT9_ENST00000379295.1_5'UTR|ACOT9_ENST00000379303.5_Missense_Mutation_p.R50Q|ACOT9_ENST00000492081.1_5'UTR	NM_001033583.2	NP_001028755.2	Q9Y305	ACOT9_HUMAN	acyl-CoA thioesterase 9	41					acyl-CoA metabolic process (GO:0006637)	mitochondrion (GO:0005739)	acetyl-CoA hydrolase activity (GO:0003986)|carboxylic ester hydrolase activity (GO:0052689)	p.R41Q(2)		breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(4)|pancreas(1)|skin(1)	15						CAACTTATCTCGAACTGAAAC	0.368																																					p.R50Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G149A	X						.						118.0	99.0	105.0					X																	23751331		2203	4300	6503	23661252	SO:0001583	missense	23597	exon4			AF132950	CCDS35216.1, CCDS43924.1	Xp22.11	2008-02-05			ENSG00000123130	ENSG00000123130		"""Acyl CoA thioesterases"""	17152	protein-coding gene	gene with protein product		300862				10383425, 10810093, 16103133, 16940157	Standard	XM_005274471		Approved	CGI-16, MT-ACT48, ACATE2	uc004dao.3	Q9Y305	OTTHUMG00000021257	ENST00000336430.7:c.122G>A	X.37:g.23751331C>T	ENSP00000336580:p.Arg41Gln	Somatic		Capture	Illumina HiSeq	Phase_I	23661252	NM_001037171	B3KNC9|B7ZM94	Missense_Mutation	SNP	ENST00000336430.7	37	CCDS35216.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364865	0.82463	.	.	ENSG00000123130	ENST00000379303;ENST00000336430	T;T	0.35048	1.34;1.33	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.44350	0.1289	M	0.83118	2.625	0.80722	D	1	B;P	0.40398	0.345;0.716	B;B	0.35770	0.041;0.21	T	0.52298	-0.8594	10	0.41790	T	0.15	-6.5708	18.2181	0.89893	0.0:1.0:0.0:0.0	.	41;50	Q9Y305;Q9Y305-4	ACOT9_HUMAN;.	Q	50;41	ENSP00000368605:R50Q;ENSP00000336580:R41Q	ENSP00000336580:R41Q	R	-	2	0	ACOT9	23661252	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	7.108000	0.77055	2.239000	0.73571	0.600000	0.82982	CGA		0.368	ACOT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056065.1	NM_012332	
USP9X	8239	broad.mit.edu	37	X	41025219	41025219	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:41025219C>T	ENST00000324545.8	+	16	2713	c.2080C>T	c.(2080-2082)Cgt>Tgt	p.R694C	USP9X_ENST00000378308.2_Missense_Mutation_p.R694C	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	694					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)	p.R687C(1)		NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CCTTTGTGATCGTGAAGCCTG	0.393																																					p.R694C	Ovarian(172;1807 2695 35459 49286)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2080T	X						.						145.0	139.0	141.0					X																	41025219		2202	4300	6502	40910163	SO:0001583	missense	8239	exon16			X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.2080C>T	X.37:g.41025219C>T	ENSP00000316357:p.Arg694Cys	Somatic		Capture	Illumina HiSeq	Phase_I	40910163	NM_001039590	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	37	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.041076	0.75732	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.04234	3.67;3.67	4.92	4.92	0.64577	Armadillo-like helical (1);	0.000000	0.85682	D	0.000000	T	0.21631	0.0521	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.00617	-1.1642	10	0.62326	D	0.03	.	17.5479	0.87867	0.0:1.0:0.0:0.0	.	694;694	Q93008-1;Q93008	.;USP9X_HUMAN	C	694	ENSP00000367558:R694C;ENSP00000316357:R694C	ENSP00000316357:R694C	R	+	1	0	USP9X	40910163	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.811000	0.55620	2.159000	0.67721	0.600000	0.82982	CGT		0.393	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652	
CASK	8573	broad.mit.edu	37	X	41437629	41437629	+	Silent	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:41437629C>T	ENST00000378163.1	-	15	1941	c.1467G>A	c.(1465-1467)cgG>cgA	p.R489R	CASK_ENST00000472704.1_5'UTR|CASK_ENST00000378166.4_Silent_p.R489R|CASK_ENST00000378158.1_Silent_p.R489R|CASK_ENST00000378154.1_Silent_p.R489R|CASK_ENST00000318588.9_Silent_p.R489R|CASK_ENST00000361962.4_Silent_p.R489R|CASK_ENST00000421587.2_Silent_p.R483R|CASK_ENST00000442742.2_Silent_p.R489R			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	489	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)	p.R489R(1)		breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						ACTGTACCAGCCGAACTCTGG	0.433																																					p.R489R	NSCLC(42;104 1086 3090 27189 35040)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1467A	X						.						125.0	99.0	108.0					X																	41437629		2203	4300	6503	41322573	SO:0001819	synonymous_variant	8573	exon15			AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044			1497	protein-coding gene	gene with protein product		300172	"""trinucleotide repeat containing 8"""	TNRC8		9722958	Standard	NM_003688		Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000378163.1:c.1467G>A	X.37:g.41437629C>T		Somatic		Capture	Illumina HiSeq	Phase_I	41322573	NM_001126054	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Silent	SNP	ENST00000378163.1	37																																																																																					0.433	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688	
ARAF	369	broad.mit.edu	37	X	47424260	47424260	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:47424260G>A	ENST00000377045.4	+	4	459	c.265G>A	c.(265-267)Gag>Aag	p.E89K	ARAF_ENST00000377039.2_Missense_Mutation_p.E89K|ARAF_ENST00000290277.6_Missense_Mutation_p.E89K	NM_001256196.1|NM_001654.4	NP_001243125.1|NP_001645.1	P10398	ARAF_HUMAN	A-Raf proto-oncogene, serine/threonine kinase	89	RBD. {ECO:0000255|PROSITE- ProRule:PRU00262}.				cellular protein modification process (GO:0006464)|negative regulation of apoptotic process (GO:0043066)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.E89K(1)		biliary_tract(1)|endometrium(4)|large_intestine(7)|liver(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	29					Adenosine triphosphate(DB00171)	GCTCATTGTCGAGGTCCTTGA	0.582																																					p.E89K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G265A	X						.						106.0	58.0	74.0					X																	47424260		2203	4300	6503	47309204	SO:0001583	missense	369	exon4			X04790	CCDS35232.1, CCDS59164.1, CCDS75970.1	Xp11.3-p11.23	2014-06-26	2014-06-26	2005-01-19	ENSG00000078061	ENSG00000078061			646	protein-coding gene	gene with protein product		311010	"""v-raf murine sarcoma 3611 viral oncogene homolog 1"""	ARAF1			Standard	NM_001654		Approved		uc004dic.2	P10398	OTTHUMG00000021446	ENST00000377045.4:c.265G>A	X.37:g.47424260G>A	ENSP00000366244:p.Glu89Lys	Somatic		Capture	Illumina HiSeq	Phase_I	47309204	NM_001654	P07557|Q5H9B2|Q5H9B3	Missense_Mutation	SNP	ENST00000377045.4	37	CCDS35232.1	.	.	.	.	.	.	.	.	.	.	G	32	5.111593	0.94339	.	.	ENSG00000078061	ENST00000377045;ENST00000290277;ENST00000377039	T;D;D	0.94687	-0.97;-3.49;-3.49	5.82	4.94	0.65067	Raf-like Ras-binding (3);	0.000000	0.85682	D	0.000000	D	0.95617	0.8575	L	0.51422	1.61	0.47819	D	0.999528	D	0.69078	0.997	D	0.67900	0.954	D	0.94962	0.8109	10	0.46703	T	0.11	.	13.4578	0.61210	0.0:0.154:0.846:0.0	.	89	P10398	ARAF_HUMAN	K	89	ENSP00000366244:E89K;ENSP00000290277:E89K;ENSP00000366238:E89K	ENSP00000290277:E89K	E	+	1	0	ARAF	47309204	1.000000	0.71417	0.980000	0.43619	0.998000	0.95712	9.291000	0.96070	1.181000	0.42912	0.600000	0.82982	GAG		0.582	ARAF-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056418.1		
ZNF630	57232	broad.mit.edu	37	X	47919258	47919258	+	Silent	SNP	T	T	C			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:47919258T>C	ENST00000409324.3	-	5	799	c.573A>G	c.(571-573)ttA>ttG	p.L191L	ZNF630_ENST00000442455.3_Silent_p.L177L|ZNF630_ENST00000276054.4_Silent_p.L67L|ZNF630-AS1_ENST00000436124.1_RNA	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	191					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.L191L(1)		endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						TATAATTTAGTAAGTCTGAAT	0.383																																					p.L177L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A531G	X						.						50.0	44.0	46.0					X																	47919258		2194	4288	6482	47804202	SO:0001819	synonymous_variant	57232	exon5			AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"""Zinc fingers, C2H2-type"", ""-"""	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.573A>G	X.37:g.47919258T>C		Somatic		Capture	Illumina HiSeq	Phase_I	47804202	NM_001190255	F8WAG4|Q5H8Z5	Silent	SNP	ENST00000409324.3	37	CCDS35237.2																																																																																				0.383	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735	
HDAC6	10013	broad.mit.edu	37	X	48673091	48673091	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:48673091C>T	ENST00000334136.5	+	12	1121	c.943C>T	c.(943-945)Cgg>Tgg	p.R315W	HDAC6_ENST00000444343.2_Missense_Mutation_p.R329W|HDAC6_ENST00000376619.2_Missense_Mutation_p.R315W|HDAC6_ENST00000413163.2_Missense_Mutation_p.R260W			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	315	Histone deacetylase 1.				aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|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)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)	p.R315W(1)		breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	GGTGGGGATGCGGGATGCTGA	0.632																																					p.R315W	Pancreas(112;205 1675 2305 8976 15959)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C943T	X						.						67.0	57.0	61.0					X																	48673091		2203	4300	6503	48558035	SO:0001583	missense	10013	exon12			AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 90"""	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.943C>T	X.37:g.48673091C>T	ENSP00000334061:p.Arg315Trp	Somatic		Capture	Illumina HiSeq	Phase_I	48558035	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	37	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	C	12.66	2.003241	0.35320	.	.	ENSG00000094631	ENST00000444343;ENST00000334136;ENST00000376619;ENST00000436813;ENST00000413163	T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48	5.05	3.05	0.35203	Histone deacetylase domain (2);	0.369011	0.26411	N	0.024530	T	0.77157	0.4089	M	0.74467	2.265	0.40128	D	0.976689	D;D;D	0.89917	1.0;0.991;1.0	P;P;P	0.59703	0.862;0.849;0.862	T	0.76955	-0.2767	10	0.62326	D	0.03	-10.9899	5.9601	0.19295	0.3864:0.4641:0.1495:0.0	.	305;260;315	B4DZN1;E7EUZ1;Q9UBN7	.;.;HDAC6_HUMAN	W	329;315;315;315;260	ENSP00000398566:R329W;ENSP00000334061:R315W;ENSP00000365804:R315W;ENSP00000398801:R260W	ENSP00000334061:R315W	R	+	1	2	HDAC6	48558035	1.000000	0.71417	1.000000	0.80357	0.059000	0.15707	2.216000	0.42871	0.915000	0.36847	-0.346000	0.07831	CGG		0.632	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044	
PRAF2	11230	broad.mit.edu	37	X	48929637	48929637	+	Missense_Mutation	SNP	C	C	T	rs199768194		TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:48929637C>T	ENST00000376390.4	-	3	511	c.428G>A	c.(427-429)cGc>cAc	p.R143H	AF196779.12_ENST00000376358.3_Missense_Mutation_p.R257H|WDR45_ENST00000553851.1_Missense_Mutation_p.R257H|PRAF2_ENST00000491199.1_5'UTR	NM_007213.1	NP_009144.1	O60831	PRAF2_HUMAN	PRA1 domain family, member 2	143					L-glutamate transport (GO:0015813)|protein transport (GO:0015031)	endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.R143H(1)		endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	8						CTTAAGGTTGCGCAGGCGCAA	0.597																																					p.R143H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G428A	X						.						98.0	69.0	79.0					X																	48929637		2203	4300	6503	48816581	SO:0001583	missense	11230	exon3			BC021213	CCDS14317.1	Xp11.23	2008-02-05	2004-11-15		ENSG00000243279	ENSG00000243279			28911	protein-coding gene	gene with protein product		300840	"""PRA1 domain family 2"""			16481131	Standard	NM_007213		Approved	JM4		O60831	OTTHUMG00000034499	ENST00000376390.4:c.428G>A	X.37:g.48929637C>T	ENSP00000365570:p.Arg143His	Somatic		Capture	Illumina HiSeq	Phase_I	48816581	NM_007213	B2RD20	Missense_Mutation	SNP	ENST00000376390.4	37	CCDS14317.1	.	.	.	.	.	.	.	.	.	.	.	19.74	3.884049	0.72410	.	.	ENSG00000243279;ENSG00000196998;ENSG00000250232	ENST00000376390;ENST00000553851;ENST00000376358	T;T;T	0.48836	0.8;0.8;0.8	3.98	3.98	0.46160	.	0.000000	0.64402	D	0.000005	T	0.53932	0.1827	M	0.85197	2.74	0.27193	N	0.960369	P;P	0.42161	0.665;0.772	B;B	0.39419	0.12;0.299	T	0.61481	-0.7054	10	0.87932	D	0	-21.5501	14.8242	0.70097	0.0:1.0:0.0:0.0	.	257;143	A6NM71;O60831	.;PRAF2_HUMAN	H	143;257;257	ENSP00000365570:R143H;ENSP00000451962:R257H;ENSP00000365536:R257H	ENSP00000365536:R257H	R	-	2	0	PRAF2;AF196779.12;WDR45	48816581	1.000000	0.71417	0.996000	0.52242	0.351000	0.29236	5.376000	0.66178	1.931000	0.55961	0.540000	0.68198	CGC		0.597	PRAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083415.2	NM_007213	
PAGE1	8712	broad.mit.edu	37	X	49455857	49455857	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:49455857G>A	ENST00000376150.3	-	4	419	c.287C>T	c.(286-288)gCa>gTa	p.A96V		NM_003785.3	NP_003776.2	O75459	PAGE1_HUMAN	P antigen family, member 1 (prostate associated)	96					cellular defense response (GO:0006968)			p.A96V(1)		endometrium(1)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	7	Ovarian(276;0.236)					CCTACCTTCTGCGGGCAGTTT	0.463																																					p.A96V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C287T	X						.						136.0	108.0	117.0					X																	49455857		2203	4300	6503	49342561	SO:0001583	missense	8712	exon4			AF058989	CCDS14327.1	Xp11.23	2009-06-17	2005-01-26	2005-01-27	ENSG00000068985	ENSG00000068985			4107	protein-coding gene	gene with protein product		300288	"""G antigen, family B, 1 (prostate associated)"""	GAGEB1		9651357, 9724777	Standard	NM_003785		Approved	PAGE-1, GAGE-9, CT16.3	uc004dom.3	O75459	OTTHUMG00000033224	ENST00000376150.3:c.287C>T	X.37:g.49455857G>A	ENSP00000365320:p.Ala96Val	Somatic		Capture	Illumina HiSeq	Phase_I	49342561	NM_003785	Q6FGM3|Q9BSS7	Missense_Mutation	SNP	ENST00000376150.3	37	CCDS14327.1	.	.	.	.	.	.	.	.	.	.	.	2.931	-0.221094	0.06061	.	.	ENSG00000068985	ENST00000376150	T	0.10477	2.87	1.47	-1.37	0.09056	.	.	.	.	.	T	0.04407	0.0121	N	0.17564	0.495	0.09310	N	1	P	0.42357	0.777	B	0.32762	0.152	T	0.31081	-0.9956	9	0.87932	D	0	.	2.3	0.04160	0.0:0.2283:0.3219:0.4498	.	96	O75459	GAGB1_HUMAN	V	96	ENSP00000365320:A96V	ENSP00000365320:A96V	A	-	2	0	PAGE1	49342561	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	0.204000	0.17335	-0.441000	0.07201	-0.814000	0.03130	GCA		0.463	PAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081210.1		
DGKK	139189	broad.mit.edu	37	X	50121098	50121098	+	RNA	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:50121098C>T	ENST00000376025.2	-	0	3168							Q5KSL6	DGKK_HUMAN	diacylglycerol kinase, kappa						blood coagulation (GO:0007596)|diacylglycerol metabolic process (GO:0046339)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			central_nervous_system(1)|endometrium(12)|kidney(4)|large_intestine(5)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Ovarian(276;0.236)					CCCCCTTACCCGATCTCTTGT	0.473																																					p.G1037R												.	.	0			c.G3109A	X						.						133.0	123.0	126.0					X																	50121098		1906	4118	6024	50137838			139189	exon22			AB183864	CCDS75980.1	Xp11.22	2006-02-08				ENSG00000274588			32395	protein-coding gene	gene with protein product		300837				16210324	Standard	NM_001013742		Approved		uc010njr.2	Q5KSL6			X.37:g.50121098C>T		Somatic		Capture	Illumina HiSeq	Phase_I	50137838	NM_001013742	B2RP91	Missense_Mutation	SNP	ENST00000376025.2	37																																																																																					0.473	DGKK-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000368187.1	NM_001013742	
HUWE1	10075	broad.mit.edu	37	X	53564590	53564590	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:53564590G>A	ENST00000342160.3	-	77	12521	c.12064C>T	c.(12064-12066)Cgt>Tgt	p.R4022C	HUWE1_ENST00000262854.6_Missense_Mutation_p.R4022C			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	4022				R -> L (in Ref. 10; AAH02602). {ECO:0000305}.	base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.R3912C(1)		NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TGGTCACGACGGACATGCACA	0.488																																					p.R4022C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C12064T	X						.						94.0	67.0	76.0					X																	53564590		2203	4300	6503	53581315	SO:0001583	missense	10075	exon78			AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.12064C>T	X.37:g.53564590G>A	ENSP00000340648:p.Arg4022Cys	Somatic		Capture	Illumina HiSeq	Phase_I	53581315	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.72|14.72	2.620313|2.620313	0.46736|0.46736	.|.	.|.	ENSG00000086758|ENSG00000086758	ENST00000427052;ENST00000426907|ENST00000342160;ENST00000262854	.|D;D	.|0.83163	.|-1.69;-1.69	5.78|5.78	5.78|5.78	0.91487|0.91487	.|HECT (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.92573|0.92573	0.7641|0.7641	M|M	0.90082|0.90082	3.085|3.085	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|P;D;D	.|0.79784	.|0.888;0.985;0.993	D|D	0.93740|0.93740	0.7049|0.7049	5|10	.|0.87932	.|D	.|0	.|.	15.9981|15.9981	0.80268|0.80268	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|844;4022;4006	.|Q5H935;Q7Z6Z7;Q7Z6Z7-2	.|.;HUWE1_HUMAN;.	L|C	3055;844|4022	.|ENSP00000340648:R4022C;ENSP00000262854:R4022C	.|ENSP00000262854:R4022C	P|R	-|-	2|1	0|0	HUWE1|HUWE1	53581315|53581315	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.460000|6.460000	0.73518|0.73518	2.580000|2.580000	0.87095|0.87095	0.600000|0.600000	0.82982|0.82982	CCG|CGT		0.488	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
HUWE1	10075	broad.mit.edu	37	X	53571567	53571567	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:53571567G>A	ENST00000342160.3	-	71	11662	c.11205C>T	c.(11203-11205)gaC>gaT	p.D3735D	HUWE1_ENST00000262854.6_Silent_p.D3735D|HUWE1_ENST00000474288.1_5'UTR			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	3735					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.D3625D(1)		NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						GGCGCGTGTCGTCCCGGAGCT	0.552																																					p.D3735D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C11205T	X						.						83.0	65.0	71.0					X																	53571567		2203	4300	6503	53588292	SO:0001819	synonymous_variant	10075	exon72			AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.11205C>T	X.37:g.53571567G>A		Somatic		Capture	Illumina HiSeq	Phase_I	53588292	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	37	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	-	6.773	0.511557	0.12944	.	.	ENSG00000086758	ENST00000427052;ENST00000426907	.	.	.	5.52	1.19	0.21007	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.1667	0.25695	0.6672:0.0:0.3328:0.0	.	.	.	.	X	2769;573	.	.	R	-	1	2	HUWE1	53588292	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.398000	0.34554	0.175000	0.19841	0.534000	0.68092	CGA		0.552	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
FAM120C	54954	broad.mit.edu	37	X	54160246	54160246	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:54160246C>A	ENST00000375180.2	-	8	1906	c.1850G>T	c.(1849-1851)aGg>aTg	p.R617M	FAM120C_ENST00000328235.4_Missense_Mutation_p.R617M	NM_017848.4	NP_060318.3	Q9NX05	F120C_HUMAN	family with sequence similarity 120C	617							poly(A) RNA binding (GO:0044822)	p.R617M(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						CATAAGACCCCTCCGGTGTCT	0.488																																					p.R617M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1850T	X						.						76.0	58.0	64.0					X																	54160246		2203	4300	6503	54176971	SO:0001583	missense	54954	exon8			AY150025	CCDS14356.1, CCDS55421.1, CCDS75987.1	Xp11.22	2011-04-13	2006-07-04	2006-07-04	ENSG00000184083	ENSG00000184083			16949	protein-coding gene	gene with protein product		300741	"""chromosome X open reading frame 17"""	CXorf17		14585507	Standard	XM_006724589		Approved	ORF34, FLJ20506	uc004dsz.4	Q9NX05	OTTHUMG00000021625	ENST00000375180.2:c.1850G>T	X.37:g.54160246C>A	ENSP00000364324:p.Arg617Met	Somatic		Capture	Illumina HiSeq	Phase_I	54176971	NM_017848	B2RMT7	Missense_Mutation	SNP	ENST00000375180.2	37	CCDS14356.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.490518	0.64074	.	.	ENSG00000184083	ENST00000375180;ENST00000328235	T;T	0.55760	0.5;0.5	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.47488	0.1448	N	0.22421	0.69	0.80722	D	1	P;P	0.48911	0.739;0.917	P;P	0.46076	0.461;0.503	T	0.53294	-0.8459	10	0.72032	D	0.01	-13.1431	17.3597	0.87346	0.0:1.0:0.0:0.0	.	617;617	F8W881;Q9NX05	.;F120C_HUMAN	M	617	ENSP00000364324:R617M;ENSP00000329896:R617M	ENSP00000329896:R617M	R	-	2	0	FAM120C	54176971	0.800000	0.28916	1.000000	0.80357	0.992000	0.81027	1.378000	0.34328	2.454000	0.82982	0.600000	0.82982	AGG		0.488	FAM120C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056795.2	NM_017848	
TRO	7216	broad.mit.edu	37	X	54949365	54949365	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:54949365G>A	ENST00000173898.7	+	3	512	c.400G>A	c.(400-402)Gct>Act	p.A134T	TRO_ENST00000420798.2_Intron|TRO_ENST00000375022.4_Missense_Mutation_p.A134T|TRO_ENST00000319167.8_Missense_Mutation_p.A134T|TRO_ENST00000484031.1_Intron|TRO_ENST00000399736.1_Intron|TRO_ENST00000375041.2_Intron	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	134					embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.A134T(2)		breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						TTCAGTCACTGCTCAGCCTAA	0.498																																					p.A134T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G400A	X						.						48.0	44.0	45.0					X																	54949365		1978	4153	6131	54966090	SO:0001583	missense	7216	exon3			U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.400G>A	X.37:g.54949365G>A	ENSP00000173898:p.Ala134Thr	Somatic		Capture	Illumina HiSeq	Phase_I	54966090	NM_016157	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Missense_Mutation	SNP	ENST00000173898.7	37	CCDS43959.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.468440	0.00169	.	.	ENSG00000067445	ENST00000411534;ENST00000430420;ENST00000442098;ENST00000173898;ENST00000319167;ENST00000375022;ENST00000440759;ENST00000449980;ENST00000416704;ENST00000427099	T;T;T;T;T;T;T;T;T;T	0.50813	0.74;0.73;0.83;4.04;3.76;3.76;0.83;0.88;0.83;0.88	3.36	-1.79	0.07932	.	.	.	.	.	T	0.19248	0.0462	N	0.03608	-0.345	0.09310	N	1	B;B	0.12013	0.001;0.005	B;B	0.04013	0.001;0.001	T	0.11567	-1.0582	9	0.48119	T	0.1	.	2.6189	0.04911	0.3581:0.0:0.2826:0.3593	.	134;134	Q96SX2;Q12816	.;TROP_HUMAN	T	90;90;134;134;134;134;134;90;134;90	ENSP00000388947:A90T;ENSP00000411717:A90T;ENSP00000404645:A134T;ENSP00000173898:A134T;ENSP00000318278:A134T;ENSP00000364162:A134T;ENSP00000406574:A134T;ENSP00000392841:A90T;ENSP00000404767:A134T;ENSP00000405311:A90T	ENSP00000173898:A134T	A	+	1	0	TRO	54966090	0.002000	0.14202	0.000000	0.03702	0.007000	0.05969	-0.944000	0.03913	-0.662000	0.05338	-1.336000	0.01259	GCT		0.498	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157	
ALAS2	212	broad.mit.edu	37	X	55047636	55047636	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:55047636G>A	ENST00000330807.5	-	5	624	c.487C>T	c.(487-489)Cgt>Tgt	p.R163C	ALAS2_ENST00000396198.3_Missense_Mutation_p.R150C|ALAS2_ENST00000335854.4_Missense_Mutation_p.R126C|ALAS2_ENST00000498636.1_5'Flank	NM_000032.4	NP_000023.2	P22557	HEM0_HUMAN	aminolevulinate, delta-, synthase 2	163					cellular iron ion homeostasis (GO:0006879)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|hemoglobin biosynthetic process (GO:0042541)|oxygen homeostasis (GO:0032364)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5-aminolevulinate synthase activity (GO:0003870)|coenzyme binding (GO:0050662)|glycine binding (GO:0016594)|pyridoxal phosphate binding (GO:0030170)	p.R163C(1)		central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)	17					Glycine(DB00145)	TTGAACACACGGTAGGTGTGA	0.473																																					p.R126C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C376T	X						.						172.0	123.0	139.0					X																	55047636		2203	4300	6503	55064361	SO:0001583	missense	212	exon4				CCDS14366.1, CCDS35303.1, CCDS43960.1	Xp11.21	2008-02-05	2008-02-04		ENSG00000158578	ENSG00000158578	2.3.1.37		397	protein-coding gene	gene with protein product	"""sideroblastic/hypochromic anemia"""	301300	"""aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia)"""	ASB		1577484	Standard	NM_000032		Approved		uc004dua.4	P22557	OTTHUMG00000021641	ENST00000330807.5:c.487C>T	X.37:g.55047636G>A	ENSP00000332369:p.Arg163Cys	Somatic		Capture	Illumina HiSeq	Phase_I	55064361	NM_001037967	A8K3F0|A8K6C4|Q13735|Q5JZF5|Q8N6H3	Missense_Mutation	SNP	ENST00000330807.5	37	CCDS14366.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.264966	0.80358	.	.	ENSG00000158578	ENST00000330807;ENST00000396198;ENST00000335854	D;D;D	0.96011	-3.88;-3.88;-3.88	4.92	4.92	0.64577	Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.054910	0.64402	D	0.000002	D	0.97971	0.9332	M	0.88377	2.95	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	0.99123	1.0850	10	0.87932	D	0	-13.3994	16.2829	0.82707	0.0:0.0:1.0:0.0	.	126;150;163	A8K6C4;Q5JZF5;P22557	.;.;HEM0_HUMAN	C	163;150;126	ENSP00000332369:R163C;ENSP00000379501:R150C;ENSP00000337131:R126C	ENSP00000332369:R163C	R	-	1	0	ALAS2	55064361	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.654000	0.83653	2.185000	0.69588	0.529000	0.55759	CGT		0.473	ALAS2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056843.3	NM_000032	
AMER1	139285	broad.mit.edu	37	X	63412872	63412872	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:63412872G>T	ENST00000330258.3	-	2	567	c.295C>A	c.(295-297)Ctg>Atg	p.L99M	AMER1_ENST00000374869.3_Missense_Mutation_p.L99M|AMER1_ENST00000403336.1_Missense_Mutation_p.L99M	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	99					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.L99M(2)									GCTTCACTCAGGCCATCGTGG	0.537																																					p.L99M												.	.	69	Whole gene deletion(67)|Substitution - Missense(2)	kidney(65)|large_intestine(3)|ovary(1)	c.C295A	X						.						115.0	84.0	95.0					X																	63412872		2203	4300	6503	63329597	SO:0001583	missense	139285	exon2			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.295C>A	X.37:g.63412872G>T	ENSP00000329117:p.Leu99Met	Somatic		Capture	Illumina HiSeq	Phase_I	63329597	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	G	13.63	2.295745	0.40594	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.33438	1.41;1.41;1.41	4.52	0.601	0.17529	.	0.191518	0.34750	N	0.003720	T	0.42494	0.1205	M	0.71036	2.16	0.19775	N	0.999957	D	0.58970	0.984	P	0.62184	0.899	T	0.25950	-1.0117	10	0.72032	D	0.01	-0.8303	3.4607	0.07532	0.4437:0.0:0.2984:0.2579	.	99	Q5JTC6	F123B_HUMAN	M	99	ENSP00000364003:L99M;ENSP00000329117:L99M;ENSP00000384722:L99M	ENSP00000329117:L99M	L	-	1	2	FAM123B	63329597	0.785000	0.28726	0.688000	0.30117	0.938000	0.57974	0.777000	0.26718	-0.022000	0.13986	0.600000	0.82982	CTG		0.537	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424	
VSIG4	11326	broad.mit.edu	37	X	65238728	65238728	+	IGR	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:65238728G>A	ENST00000374737.4	-	0	1834				MIR223_ENST00000385204.1_RNA	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4						complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.C6Y(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTCCTGCAGTGCCACGCTCCG	0.517																																					.												.	.	1	Substitution - Missense(1)	large_intestine(1)	.	X						.						43.0	36.0	38.0					X																	65238728		1568	3581	5149	65155453	SO:0001628	intergenic_variant	407008	.			AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727		X.37:g.65238728G>A		Somatic		Capture	Illumina HiSeq	Phase_I	65155453	.	Q6UXI4	RNA	SNP	ENST00000374737.4	37	CCDS14383.1																																																																																				0.517	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268	
VSIG4	11326	broad.mit.edu	37	X	65244885	65244885	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:65244885G>A	ENST00000374737.4	-	6	1030	c.922C>T	c.(922-924)Cgg>Tgg	p.R308W	VSIG4_ENST00000455586.2_Missense_Mutation_p.R308W|VSIG4_ENST00000412866.2_Missense_Mutation_p.R214W	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	308					complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.R308W(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GATGTCTTCCGACAGAGCATG	0.438																																					p.R214W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C640T	X						.						113.0	80.0	91.0					X																	65244885		2203	4300	6503	65161610	SO:0001583	missense	11326	exon5			AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.922C>T	X.37:g.65244885G>A	ENSP00000363869:p.Arg308Trp	Somatic		Capture	Illumina HiSeq	Phase_I	65161610	NM_001184831	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	37	CCDS14383.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.226|9.226	1.034602|1.034602	0.19590|0.19590	.|.	.|.	ENSG00000155659|ENSG00000155659	ENST00000374737;ENST00000455586;ENST00000412866|ENST00000427538	T;T;T|.	0.45668|.	0.89;1.01;1.64|.	4.29|4.29	2.46|2.46	0.29980|0.29980	.|.	0.243833|.	0.27787|.	N|.	0.017845|.	T|T	0.45538|0.45538	0.1347|0.1347	M|M	0.72894|0.72894	2.215|2.215	0.09310|0.09310	N|N	1|1	D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D|.	0.77004|.	0.913;0.989;0.965;0.977;0.981|.	T|T	0.38090|0.38090	-0.9677|-0.9677	10|5	0.72032|.	D|.	0.01|.	-2.6553|-2.6553	4.7459|4.7459	0.13036|0.13036	0.1158:0.0:0.6741:0.2101|0.1158:0.0:0.6741:0.2101	.|.	214;308;298;214;308|.	C9J1L3;Q9Y279-2;C9JH67;Q9Y279-3;Q9Y279|.	.;.;.;.;VSIG4_HUMAN|.	W|L	308;308;214|234	ENSP00000363869:R308W;ENSP00000411581:R308W;ENSP00000394143:R214W|.	ENSP00000363869:R308W|.	R|S	-|-	1|2	2|0	VSIG4|VSIG4	65161610|65161610	0.006000|0.006000	0.16342|0.16342	0.029000|0.029000	0.17559|0.17559	0.020000|0.020000	0.10135|0.10135	0.362000|0.362000	0.20284|0.20284	0.275000|0.275000	0.22094|0.22094	0.600000|0.600000	0.82982|0.82982	CGG|TCG		0.438	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268	
EFNB1	1947	broad.mit.edu	37	X	68058543	68058543	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:68058543G>A	ENST00000204961.4	+	2	992	c.212G>A	c.(211-213)cGg>cAg	p.R71Q		NM_004429.4	NP_004420.1	P98172	EFNB1_HUMAN	ephrin-B1	71	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|embryonic pattern specification (GO:0009880)|ephrin receptor signaling pathway (GO:0048013)|neural crest cell migration (GO:0001755)|positive regulation of T cell proliferation (GO:0042102)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ephrin receptor binding (GO:0046875)	p.R71Q(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	22						GAAGCAGGGCGGCCCTATGAG	0.567																																					p.R71Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G212A	X						.						60.0	46.0	51.0					X																	68058543		2203	4300	6503	67975268	SO:0001583	missense	1947	exon2			U09303	CCDS14391.1	Xq12	2011-03-09			ENSG00000090776	ENSG00000090776		"""Ephrins"""	3226	protein-coding gene	gene with protein product		300035	"""craniofrontonasal syndrome (craniofrontonasal dysplasia)"""	EPLG2, CFNS		7774950, 16526919	Standard	NM_004429		Approved	LERK2, Elk-L	uc004dxd.4	P98172	OTTHUMG00000021751	ENST00000204961.4:c.212G>A	X.37:g.68058543G>A	ENSP00000204961:p.Arg71Gln	Somatic		Capture	Illumina HiSeq	Phase_I	67975268	NM_004429	D3DVU0	Missense_Mutation	SNP	ENST00000204961.4	37	CCDS14391.1	.	.	.	.	.	.	.	.	.	.	G	12.29	1.893875	0.33442	.	.	ENSG00000090776	ENST00000204961	D	0.92752	-3.1	5.03	5.03	0.67393	Cupredoxin (2);	0.449209	0.22871	N	0.054633	T	0.81059	0.4744	N	0.10945	0.07	0.40305	D	0.978651	B	0.24576	0.106	B	0.19148	0.024	T	0.76305	-0.3008	10	0.22109	T	0.4	-21.7179	8.2661	0.31815	0.1066:0.0:0.8934:0.0	.	71	P98172	EFNB1_HUMAN	Q	71	ENSP00000204961:R71Q	ENSP00000204961:R71Q	R	+	2	0	EFNB1	67975268	0.984000	0.35163	1.000000	0.80357	0.945000	0.59286	2.100000	0.41777	2.333000	0.79357	0.436000	0.28706	CGG		0.567	EFNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057029.1	NM_004429	
P2RY4	5030	broad.mit.edu	37	X	69478681	69478681	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:69478681C>T	ENST00000374519.2	-	1	973	c.794G>A	c.(793-795)cGc>cAc	p.R265H		NM_002565.3	NP_002556.1	P51582	P2RY4_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 4	265					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.R265H(1)		cervix(2)|endometrium(2)|large_intestine(8)|lung(6)	18						GTAAATGGTGCGGGTGATGTG	0.567																																					p.R265H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G794A	X						.						60.0	49.0	53.0					X																	69478681		2203	4300	6503	69395406	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.794G>A	X.37:g.69478681C>T	ENSP00000363643:p.Arg265His	Somatic		Capture	Illumina HiSeq	Phase_I	69395406	NM_002565	Q4VBB7|Q4VBB8|Q502W2|Q5JT22	Missense_Mutation	SNP	ENST00000374519.2	37	CCDS14398.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.723735	0.68959	.	.	ENSG00000186912	ENST00000374519	T	0.20738	2.05	4.53	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	U	0.000000	T	0.46833	0.1413	M	0.75884	2.315	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.49399	-0.8944	10	0.54805	T	0.06	.	15.4528	0.75285	0.0:1.0:0.0:0.0	.	265	P51582	P2RY4_HUMAN	H	265	ENSP00000363643:R265H	ENSP00000363643:R265H	R	-	2	0	P2RY4	69395406	1.000000	0.71417	1.000000	0.80357	0.373000	0.29922	3.833000	0.55790	2.093000	0.63338	0.589000	0.80489	CGC		0.567	P2RY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057058.2	NM_002565	
TEX11	56159	broad.mit.edu	37	X	70072986	70072986	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:70072986G>A	ENST00000395889.2	-	8	623	c.468C>T	c.(466-468)taC>taT	p.Y156Y	TEX11_ENST00000344304.3_Silent_p.Y156Y|TEX11_ENST00000374333.2_Silent_p.Y141Y	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	156					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.Y141Y(1)		breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					TTAATTTGACGTATAATTGCT	0.398																																					p.Y156Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C468T	X						.						69.0	58.0	61.0					X																	70072986		2203	4300	6503	69989711	SO:0001819	synonymous_variant	56159	exon8			AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"""testis expressed sequence 11"""			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.468C>T	X.37:g.70072986G>A		Somatic		Capture	Illumina HiSeq	Phase_I	69989711	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Silent	SNP	ENST00000395889.2	37	CCDS35323.1																																																																																				0.398	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1		
MED12	9968	broad.mit.edu	37	X	70360552	70360552	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:70360552G>A	ENST00000374080.3	+	42	6144	c.6112G>A	c.(6112-6114)Gtc>Atc	p.V2038I	MED12_ENST00000374102.1_Missense_Mutation_p.V2037I|AL590764.1_ENST00000579622.1_RNA|MED12_ENST00000333646.6_Missense_Mutation_p.V2041I			Q93074	MED12_HUMAN	mediator complex subunit 12	2038	Gln-rich.|Interaction with CTNNB1 and GLI3.				androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.V2038I(1)		breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					TGCCCAGGGCGTCCAGGCAGG	0.552			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome						G|||	1	0.000264901	0.0	0.0	3775	,	,		11018	0.0		0.0	False		,,,				2504	0.001				p.V2038I			Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6112A	X						.						106.0	104.0	105.0					X																	70360552		2191	4289	6480	70277277	SO:0001583	missense	9968	exon42			U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.6112G>A	X.37:g.70360552G>A	ENSP00000363193:p.Val2038Ile	Somatic		Capture	Illumina HiSeq	Phase_I	70277277	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	37	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	G	9.575	1.122121	0.20877	.	.	ENSG00000184634	ENST00000333646;ENST00000374102;ENST00000374080;ENST00000430072;ENST00000439750	T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06	4.82	3.96	0.45880	.	0.218239	0.39274	N	0.001404	T	0.55289	0.1911	N	0.08118	0	0.45852	D	0.998719	B;B;B	0.14805	0.006;0.011;0.006	B;B;B	0.12837	0.003;0.008;0.003	T	0.45600	-0.9250	10	0.12103	T	0.63	-16.9129	10.7362	0.46126	0.0904:0.0:0.9096:0.0	.	1888;2037;2038	Q7Z3Z5;Q93074-3;Q93074	.;.;MED12_HUMAN	I	2041;2037;2038;1988;786	ENSP00000333125:V2041I;ENSP00000363215:V2037I;ENSP00000363193:V2038I;ENSP00000414203:V1988I;ENSP00000408388:V786I	ENSP00000333125:V2041I	V	+	1	0	MED12	70277277	1.000000	0.71417	0.986000	0.45419	0.417000	0.31264	5.163000	0.64948	1.040000	0.40099	-0.312000	0.09012	GTC		0.552	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
NLGN3	54413	broad.mit.edu	37	X	70389284	70389284	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:70389284G>A	ENST00000358741.3	+	8	2187	c.1884G>A	c.(1882-1884)gtG>gtA	p.V628V	NLGN3_ENST00000476589.1_3'UTR|NLGN3_ENST00000374051.3_Silent_p.V608V|NLGN3_ENST00000536169.1_Silent_p.V588V	NM_181303.1	NP_851820.1	Q9NZ94	NLGN3_HUMAN	neuroligin 3	628					adult behavior (GO:0030534)|axon extension (GO:0048675)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|oligodendrocyte differentiation (GO:0048709)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor-mediated endocytosis (GO:0006898)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term synaptic potentiation (GO:1900271)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|regulation of terminal button organization (GO:2000331)|rhythmic synaptic transmission (GO:0060024)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|visual learning (GO:0008542)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)	p.V608V(1)		biliary_tract(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	37	Renal(35;0.156)					AACATCTGGTGCCCCACCTAT	0.557																																					p.V588V	Esophageal Squamous(103;760 1488 16849 22250 40351)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1764A	X						.						70.0	57.0	62.0					X																	70389284		2199	4299	6498	70306009	SO:0001819	synonymous_variant	54413	exon6			AB040913	CCDS14407.1, CCDS55441.1, CCDS55442.1	Xq13.1	2008-08-01			ENSG00000196338	ENSG00000196338			14289	protein-coding gene	gene with protein product		300336				10767552, 10819331	Standard	NM_181303		Approved	HNL3, KIAA1480, ASPGX1, AUTSX1	uc004dzd.2	Q9NZ94	OTTHUMG00000021790	ENST00000358741.3:c.1884G>A	X.37:g.70389284G>A		Somatic		Capture	Illumina HiSeq	Phase_I	70306009	NM_001166660	B2RBK1|D2X2H6|D3DVV0|D3DVV1|Q86V51|Q8NCD0|Q9NZ95|Q9NZ96|Q9NZ97|Q9P248	Silent	SNP	ENST00000358741.3	37	CCDS55441.1																																																																																				0.557	NLGN3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057121.1	NM_018977	
TAF1	6872	broad.mit.edu	37	X	70683799	70683799	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:70683799C>T	ENST00000373790.4	+	38	5573	c.5522C>T	c.(5521-5523)cCg>cTg	p.P1841L	TAF1_ENST00000276072.3_Missense_Mutation_p.P1862L|TAF1_ENST00000449580.1_Missense_Mutation_p.P1875L|TAF1_ENST00000423759.1_Missense_Mutation_p.P1864L|TAF1_ENST00000461764.1_Intron	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	1841	Asp/Glu-rich (acidic tail).|Protein kinase 2.				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.P1841L(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)				CGCTCTGGGCCGAGCGTACTA	0.557																																					p.P1841L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5522T	X						.						144.0	94.0	111.0					X																	70683799		2203	4299	6502	70600524	SO:0001583	missense	6872	exon38				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.5522C>T	X.37:g.70683799C>T	ENSP00000362895:p.Pro1841Leu	Somatic		Capture	Illumina HiSeq	Phase_I	70600524	NM_138923	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	c	16.87	3.241944	0.58995	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.14893	2.97;2.47;3.03;2.97	4.88	4.0	0.46444	.	0.052468	0.85682	D	0.000000	T	0.25717	0.0626	L	0.34521	1.04	0.80722	D	1	D;D;D	0.64830	0.994;0.981;0.977	P;P;P	0.57960	0.83;0.452;0.654	T	0.01512	-1.1336	10	0.62326	D	0.03	.	13.689	0.62533	0.1553:0.8447:0.0:0.0	.	1875;1841;1862	P21675-4;P21675;P21675-2	.;TAF1_HUMAN;.	L	1841;1875;1864;1862	ENSP00000362895:P1841L;ENSP00000389000:P1875L;ENSP00000406549:P1864L;ENSP00000276072:P1862L	ENSP00000276072:P1862L	P	+	2	0	TAF1	70600524	1.000000	0.71417	0.979000	0.43373	0.964000	0.63967	7.126000	0.77201	1.013000	0.39391	0.287000	0.19450	CCG		0.557	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
NHSL2	340527	broad.mit.edu	37	X	71358706	71358706	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:71358706G>T	ENST00000373677.1	+	2	1472	c.210G>T	c.(208-210)aaG>aaT	p.K70N	NHSL2_ENST00000540800.1_Missense_Mutation_p.K436N|NHSL2_ENST00000510661.1_Missense_Mutation_p.K205N|NHSL2_ENST00000535692.1_Missense_Mutation_p.K70N			Q5HYW2	NHSL2_HUMAN	NHS-like 2	70								p.K67N(1)|p.K436N(1)		NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					TGGTTCCTAAGGAGGCTGCTA	0.522																																					p.K436N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1308T	X						.						52.0	44.0	46.0					X																	71358706		2203	4300	6503	71275431	SO:0001583	missense	340527	exon6					Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.210G>T	X.37:g.71358706G>T	ENSP00000362781:p.Lys70Asn	Somatic		Capture	Illumina HiSeq	Phase_I	71275431	NM_001013627	B2RN94	Missense_Mutation	SNP	ENST00000373677.1	37		.	.	.	.	.	.	.	.	.	.	G	13.72	2.320439	0.41096	.	.	ENSG00000204131	ENST00000540800;ENST00000373677;ENST00000510661;ENST00000535692	T;T;T;T	0.46819	1.46;0.88;0.86;0.88	5.73	3.86	0.44501	.	0.219645	0.37483	N	0.002073	T	0.47875	0.1469	L	0.47716	1.5	0.30827	N	0.737153	D;D;D	0.54047	0.964;0.964;0.964	P;P;P	0.54210	0.7;0.745;0.745	T	0.53927	-0.8369	10	0.56958	D	0.05	-15.8387	4.7676	0.13139	0.1913:0.1748:0.6338:0.0	.	436;205;70	F5H593;D6RBM4;Q5HYW2	.;.;NHSL2_HUMAN	N	436;70;205;70	ENSP00000444617:K436N;ENSP00000362781:K70N;ENSP00000424079:K205N;ENSP00000444914:K70N	ENSP00000362781:K70N	K	+	3	2	NHSL2	71275431	0.011000	0.17503	1.000000	0.80357	0.947000	0.59692	0.372000	0.20467	1.184000	0.42957	0.544000	0.68410	AAG		0.522	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627	
NHSL2	340527	broad.mit.edu	37	X	71359504	71359504	+	Silent	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:71359504G>A	ENST00000373677.1	+	2	2270	c.1008G>A	c.(1006-1008)ccG>ccA	p.P336P	NHSL2_ENST00000540800.1_Silent_p.P702P|NHSL2_ENST00000510661.1_Silent_p.P471P|NHSL2_ENST00000535692.1_Silent_p.P336P			Q5HYW2	NHSL2_HUMAN	NHS-like 2	336	Ser-rich.							p.P333P(1)|p.P702P(1)		NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					TATCATCCCCGGGAAGGCCCC	0.582																																					p.P702P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G2106A	X						.						53.0	44.0	47.0					X																	71359504		2203	4300	6503	71276229	SO:0001819	synonymous_variant	340527	exon6					Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.1008G>A	X.37:g.71359504G>A		Somatic		Capture	Illumina HiSeq	Phase_I	71276229	NM_001013627	B2RN94	Silent	SNP	ENST00000373677.1	37																																																																																					0.582	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627	
ZCCHC5	203430	broad.mit.edu	37	X	77912656	77912656	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:77912656G>A	ENST00000321110.1	-	2	1557	c.1262C>T	c.(1261-1263)cCt>cTt	p.P421L		NM_152694.2	NP_689907.1	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	421							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.P421L(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)|prostate(1)|skin(1)	37						AGCCTGCATAGGTTGGTTTTC	0.517																																					p.P421L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1262T	X						.						156.0	125.0	135.0					X																	77912656		2203	4300	6503	77799312	SO:0001583	missense	203430	exon2			AK096184	CCDS14440.1	Xq13.3	2008-02-05			ENSG00000179300	ENSG00000179300		"""Zinc fingers, CCHC domain containing"""	22997	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_152694		Approved	FLJ38865, Mar3, Mart3, ZHC5	uc004edc.1	Q8N8U3	OTTHUMG00000021892	ENST00000321110.1:c.1262C>T	X.37:g.77912656G>A	ENSP00000316794:p.Pro421Leu	Somatic		Capture	Illumina HiSeq	Phase_I	77799312	NM_152694	B2RMZ0|Q5JQE9	Missense_Mutation	SNP	ENST00000321110.1	37	CCDS14440.1	.	.	.	.	.	.	.	.	.	.	G	8.049	0.765529	0.15914	.	.	ENSG00000179300	ENST00000321110	T	0.25912	1.77	3.05	2.18	0.27775	.	.	.	.	.	T	0.17450	0.0419	L	0.40543	1.245	0.09310	N	1	P	0.43094	0.799	B	0.36092	0.217	T	0.15065	-1.0450	9	0.72032	D	0.01	.	5.2084	0.15302	0.165:0.0:0.835:0.0	.	421	Q8N8U3	ZCHC5_HUMAN	L	421	ENSP00000316794:P421L	ENSP00000316794:P421L	P	-	2	0	ZCCHC5	77799312	0.001000	0.12720	0.011000	0.14972	0.008000	0.06430	0.250000	0.18235	0.672000	0.31204	0.513000	0.50165	CCT		0.517	ZCCHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057319.1	NM_152694	
TBX22	50945	broad.mit.edu	37	X	79282236	79282236	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:79282236C>T	ENST00000373294.5	+	5	695	c.667C>T	c.(667-669)Cga>Tga	p.R223*	TBX22_ENST00000442340.1_Nonsense_Mutation_p.R103*|TBX22_ENST00000373291.1_Nonsense_Mutation_p.R103*|TBX22_ENST00000373296.3_Nonsense_Mutation_p.R223*	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	223					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R223*(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(13)|lung(38)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						GTACAAACCCCGAGTGCACGT	0.453																																					p.R223X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C667T	X	GRCh37	CD013205	TBX22	D		.						158.0	128.0	138.0					X																	79282236		2203	4300	6503	79168892	SO:0001587	stop_gained	50945	exon6			AL031000	CCDS14445.1, CCDS43975.1	Xq21.1	2011-02-11			ENSG00000122145	ENSG00000122145		"""T-boxes"""	11600	protein-coding gene	gene with protein product		300307	"""cleft palate and/or ankyloglossia"""	CPX, CLPA		11559848, 14729838	Standard	NM_001109878		Approved		uc004edj.1	Q9Y458	OTTHUMG00000021901	ENST00000373294.5:c.667C>T	X.37:g.79282236C>T	ENSP00000362390:p.Arg223*	Somatic		Capture	Illumina HiSeq	Phase_I	79168892	NM_001109878	Q5JZ06|Q96LC0|Q9HBF1	Nonsense_Mutation	SNP	ENST00000373294.5	37	CCDS14445.1	.	.	.	.	.	.	.	.	.	.	C	31	5.085176	0.94100	.	.	ENSG00000122145	ENST00000373296;ENST00000442340;ENST00000373294;ENST00000373291	.	.	.	3.88	3.02	0.34903	.	0.066379	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.6322	0.33926	0.0:0.8815:0.0:0.1185	.	.	.	.	X	223;103;223;103	.	ENSP00000362388:R103X	R	+	1	2	TBX22	79168892	0.995000	0.38212	0.989000	0.46669	0.375000	0.29983	3.192000	0.50989	0.787000	0.33731	-0.192000	0.12808	CGA		0.453	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954	
HDX	139324	broad.mit.edu	37	X	83730395	83730395	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:83730395C>T	ENST00000297977.5	-	2	122	c.11G>A	c.(10-12)cGt>cAt	p.R4H	HDX_ENST00000506585.2_Intron|HDX_ENST00000373177.2_Missense_Mutation_p.R4H	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	4						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R4H(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						AAATACAGAACGTAGATTCAT	0.269																																					p.R4H	Pancreas(53;231 1169 36156 43751 51139)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G11A	X						.						41.0	34.0	36.0					X																	83730395		2202	4295	6497	83617051	SO:0001583	missense	139324	exon3			BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"""Homeoboxes / POU class"""	26411	protein-coding gene	gene with protein product			"""chromosome X open reading frame 43"""	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.11G>A	X.37:g.83730395C>T	ENSP00000297977:p.Arg4His	Somatic		Capture	Illumina HiSeq	Phase_I	83617051	NM_001177479	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	ENST00000297977.5	37	CCDS35342.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.858607	0.91433	.	.	ENSG00000165259	ENST00000297977;ENST00000506585	T;T	0.61274	0.12;0.12	6.16	6.16	0.99307	Homeodomain-related (1);Homeobox (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.77350	0.4117	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.78247	-0.2278	10	0.87932	D	0	-10.6332	19.7181	0.96131	0.0:1.0:0.0:0.0	.	4	Q7Z353	HDX_HUMAN	H	4	ENSP00000297977:R4H;ENSP00000423670:R4H	ENSP00000297977:R4H	R	-	2	0	HDX	83617051	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.264000	0.78432	2.614000	0.88457	0.594000	0.82650	CGT		0.269	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657	
APOOL	139322	broad.mit.edu	37	X	84322132	84322132	+	Splice_Site	SNP	G	G	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:84322132G>T	ENST00000373173.2	+	6	481		c.e6-1			NM_198450.5	NP_940852.3	Q6UXV4	MIC27_HUMAN	apolipoprotein O-like							integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.?(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8						GCATTTTATAGGTTCCAAGTT	0.373																																					.												.	.	1	Unknown(1)	large_intestine(1)	.	X						.						35.0	30.0	31.0					X																	84322132		1721	3817	5538	84208788	SO:0001630	splice_region_variant	139322	.			AK130506	CCDS48138.1	Xq21.1	2007-01-17	2007-01-17	2007-01-17	ENSG00000155008	ENSG00000155008			24009	protein-coding gene	gene with protein product			"""chromosome X open reading frame 33"", ""family with sequence similarity 121A"""	CXorf33, FAM121A		12975309	Standard	NM_198450		Approved	UNQ8193, AAIR8193	uc004eem.3	Q6UXV4	OTTHUMG00000021930	ENST00000373173.2:c.395-1G>T	X.37:g.84322132G>T		Somatic		Capture	Illumina HiSeq	Phase_I	84208788	.	Q3KNU7|Q5H9D1	Splice_Site	SNP	ENST00000373173.2	37	CCDS48138.1	.	.	.	.	.	.	.	.	.	.	G	15.25	2.777165	0.49786	.	.	ENSG00000155008	ENST00000373173;ENST00000373169	.	.	.	4.64	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6807	0.51455	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	APOOL	84208788	1.000000	0.71417	0.991000	0.47740	0.827000	0.46813	4.763000	0.62257	2.137000	0.66172	0.500000	0.49745	.		0.373	APOOL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057385.2	NM_198450	Intron
TNMD	64102	broad.mit.edu	37	X	99854139	99854139	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:99854139C>T	ENST00000373031.4	+	6	921	c.704C>T	c.(703-705)gCc>gTc	p.A235V		NM_022144.2	NP_071427.2	Q9H2S6	TNMD_HUMAN	tenomodulin	235					cellular response to BMP stimulus (GO:0071773)|endothelial cell morphogenesis (GO:0001886)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|tendon cell differentiation (GO:0035990)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.A235V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(7)|skin(1)	16						ACCCGTCACGCCAGACAAGCA	0.413																																					p.A235V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C704T	X						.						67.0	52.0	57.0					X																	99854139		2203	4300	6503	99740795	SO:0001583	missense	64102	exon6			AF191770	CCDS14469.1	Xq21.33-q23	2012-10-10			ENSG00000000005	ENSG00000000005		"""BRICHOS domain containing"""	17757	protein-coding gene	gene with protein product	"""BRICHOS domain containing 4"""	300459					Standard	NM_022144		Approved	myodulin, ChM1L, tendin, TEM, BRICD4	uc004efy.4	Q9H2S6	OTTHUMG00000022001	ENST00000373031.4:c.704C>T	X.37:g.99854139C>T	ENSP00000362122:p.Ala235Val	Somatic		Capture	Illumina HiSeq	Phase_I	99740795	NM_022144	Q9HBX0|Q9UJG0	Missense_Mutation	SNP	ENST00000373031.4	37	CCDS14469.1	.	.	.	.	.	.	.	.	.	.	C	13.68	2.309531	0.40895	.	.	ENSG00000000005	ENST00000373031	T	0.31510	1.49	5.35	4.45	0.53987	.	0.798993	0.11432	N	0.564710	T	0.26159	0.0638	L	0.29908	0.895	0.36571	D	0.873012	B	0.31351	0.32	B	0.29077	0.098	T	0.24297	-1.0164	10	0.42905	T	0.14	-21.1292	15.5528	0.76167	0.0:0.8503:0.1497:0.0	.	235	Q9H2S6	TNMD_HUMAN	V	235	ENSP00000362122:A235V	ENSP00000362122:A235V	A	+	2	0	TNMD	99740795	0.952000	0.32445	0.953000	0.39169	0.934000	0.57294	2.207000	0.42788	2.226000	0.72624	0.513000	0.50165	GCC		0.413	TNMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057481.1	NM_022144	
ATP6AP1	537	broad.mit.edu	37	X	153660741	153660741	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3864-01A-01W-0995-10	TCGA-AA-3864-10A-01W-0995-10	g.chrX:153660741C>T	ENST00000369762.2	+	4	554	c.493C>T	c.(493-495)Cgg>Tgg	p.R165W	ATP6AP1_ENST00000484908.1_3'UTR	NM_001183.4	NP_001174.2	Q15904	VAS1_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 1	165					ATP hydrolysis coupled proton transport (GO:0015991)|establishment of organelle localization (GO:0051656)|pH reduction (GO:0045851)|positive regulation of bone resorption (GO:0045780)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoclast development (GO:2001206)|proton transport (GO:0015992)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuole (GO:0005773)	ATP binding (GO:0005524)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)	p.R165W(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(5)	14	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGCCACCCTGCGGGAGCTGAA	0.652																																					p.R165W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C493T	X						.						41.0	33.0	36.0					X																	153660741		2202	4300	6502	153313935	SO:0001583	missense	537	exon4			D16469	CCDS35451.1	Xq28	2010-03-10	2003-08-28	2003-08-29	ENSG00000071553	ENSG00000071553			868	protein-coding gene	gene with protein product		300197	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump), subunit 1"""	ATP6S1, ATP6IP1		8733135, 8281148	Standard	NM_001183		Approved	ORF, XAP-3, VATPS1, 16A, Ac45, XAP3, CF2	uc004flf.1	Q15904	OTTHUMG00000033291	ENST00000369762.2:c.493C>T	X.37:g.153660741C>T	ENSP00000358777:p.Arg165Trp	Somatic		Capture	Illumina HiSeq	Phase_I	153313935	NM_001183	A6ZKI4|Q8NBT4|Q9H0C7	Missense_Mutation	SNP	ENST00000369762.2	37	CCDS35451.1	.	.	.	.	.	.	.	.	.	.	C	17.17	3.322159	0.60634	.	.	ENSG00000071553	ENST00000369762;ENST00000449556	.	.	.	5.84	2.63	0.31362	.	0.727143	0.14300	N	0.328367	T	0.49423	0.1556	L	0.44542	1.39	0.09310	N	0.999993	D;D	0.67145	0.989;0.996	P;P	0.56916	0.72;0.809	T	0.40627	-0.9553	9	0.66056	D	0.02	-18.3037	12.3378	0.55077	0.5388:0.4612:0.0:0.0	.	125;165	B3KR70;Q15904	.;VAS1_HUMAN	W	165	.	ENSP00000358777:R165W	R	+	1	2	ATP6AP1	153313935	0.229000	0.23729	0.716000	0.30569	0.622000	0.37654	0.372000	0.20467	0.537000	0.28751	0.529000	0.55759	CGG		0.652	ATP6AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081639.4	NM_001183	
